From 84dfc80af18484773a03d84f7e0796b5877236a6 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 14 Sep 2026 17:51:38 -0700
Subject: [PATCH 01/11] fix: bind graph source claims to generation receipts
Refs #917; full verified graph regeneration remains tracked separately.
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pages/traits/morphology/spore_forming.html | 4 +-
pages/traits/morphology/spore_shaped.html | 4 +-
pages/traits/morphology/sporulation.html | 4 +-
pages/traits/morphology/square_shaped.html | 4 +-
.../staphylococcus_arrangement.html | 4 +-
pages/traits/morphology/star_shaped.html | 4 +-
.../morphology/streptococcus_arrangement.html | 4 +-
.../morphology/subpolar_flagellation.html | 2 +-
pages/traits/morphology/sulfur_globule.html | 4 +-
.../traits/morphology/swarming_motility.html | 4 +-
pages/traits/morphology/tailed_shaped.html | 4 +-
.../traits/morphology/tetrad_arrangement.html | 4 +-
.../traits/morphology/triangular_shaped.html | 4 +-
.../traits/morphology/twitching_motility.html | 4 +-
pages/traits/morphology/type_iv_pilus.html | 2 +-
pages/traits/morphology/vibrio_shaped.html | 4 +-
pages/traits/morphology/white_pigmented.html | 4 +-
pages/traits/morphology/yellow_pigmented.html | 4 +-
.../observation/growth_nacl_observation.html | 4 +-
.../growth_oxygen_observation.html | 4 +-
.../observation/growth_ph_observation.html | 4 +-
.../growth_temperature_observation.html | 4 +-
.../observation/nacl_delta_observation.html | 4 +-
.../traits/observation/nacl_observation.html | 4 +-
.../observation/nacl_range_observation.html | 4 +-
.../observation/optimum_nacl_observation.html | 4 +-
.../optimum_oxygen_observation.html | 4 +-
.../observation/optimum_ph_observation.html | 4 +-
.../optimum_temperature_observation.html | 4 +-
.../observation/oxygen_delta_observation.html | 4 +-
.../observation/oxygen_observation.html | 4 +-
.../observation/oxygen_range_observation.html | 4 +-
.../observation/ph_delta_observation.html | 4 +-
pages/traits/observation/ph_observation.html | 4 +-
.../observation/ph_range_observation.html | 4 +-
.../temperature_delta_observation.html | 4 +-
.../observation/temperature_observation.html | 4 +-
.../temperature_range_observation.html | 4 +-
pages/traits/other/catalase_negative.html | 2 +-
pages/traits/other/catalase_test.html | 2 +-
pages/traits/other/circular_colony.html | 2 +-
pages/traits/other/coagulase_negative.html | 2 +-
pages/traits/other/coagulase_positive.html | 2 +-
pages/traits/other/colony_morphology.html | 2 +-
pages/traits/other/colony_shape.html | 2 +-
pages/traits/other/epibiont_phenotype.html | 2 +-
pages/traits/other/filamentous_colony.html | 2 +-
.../traits/other/fried_egg_shaped_colony.html | 2 +-
pages/traits/other/generalist.html | 2 +-
pages/traits/other/hemolysis.html | 2 +-
pages/traits/other/hemolytic.html | 2 +-
pages/traits/other/indole_test.html | 2 +-
pages/traits/other/indole_test_negative.html | 2 +-
pages/traits/other/indole_test_positive.html | 2 +-
pages/traits/other/irregular_colony.html | 2 +-
pages/traits/other/methyl_red_test.html | 2 +-
.../other/methyl_red_test_negative.html | 2 +-
.../other/methyl_red_test_positive.html | 2 +-
pages/traits/other/non_hemolytic.html | 2 +-
pages/traits/other/osmotic_tolerance.html | 2 +-
pages/traits/other/oxidase_negative.html | 2 +-
pages/traits/other/oxidase_test.html | 2 +-
pages/traits/other/punctiform_colony.html | 2 +-
pages/traits/other/rhizoid_colony.html | 2 +-
pages/traits/other/specialist.html | 2 +-
pages/traits/other/urease_negative.html | 2 +-
pages/traits/other/urease_test.html | 2 +-
pages/traits/other/voges_proskauer_test.html | 2 +-
.../other/voges_proskauer_test_negative.html | 2 +-
.../other/voges_proskauer_test_positive.html | 2 +-
.../physiology/acid_phosphatase_activity.html | 2 +-
.../aerobic_anoxygenic_phototrophy.html | 2 +-
.../alanine_arylamidase_activity.html | 2 +-
.../alkaline_phosphatase_activity.html | 2 +-
.../alpha_chymotrypsin_activity.html | 2 +-
.../physiology/alpha_fucosidase_activity.html | 2 +-
.../alpha_galactosidase_activity.html | 2 +-
.../alpha_glucosidase_activity.html | 2 +-
.../alpha_mannosidase_activity.html | 2 +-
pages/traits/physiology/amylase_activity.html | 2 +-
.../physiology/antibiotic_resistance.html | 4 +-
.../arginine_arylamidase_activity.html | 2 +-
.../arginine_dihydrolase_activity.html | 2 +-
pages/traits/physiology/autotrophic.html | 4 +-
.../physiology/bacteriocin_production.html | 2 +-
.../beta_galactosidase_activity.html | 2 +-
.../physiology/beta_glucosidase_activity.html | 2 +-
.../beta_glucuronidase_activity.html | 2 +-
.../beta_n_acetylhexosaminidase_activity.html | 2 +-
pages/traits/physiology/bioluminescence.html | 4 +-
pages/traits/physiology/carboxydotrophic.html | 4 +-
.../physiology/carboxylesterase_activity.html | 2 +-
.../traits/physiology/caseinase_activity.html | 2 +-
.../traits/physiology/catalase_activity.html | 4 +-
.../physiology/chemoautolithotrophic.html | 4 +-
pages/traits/physiology/chemoautotrophic.html | 4 +-
.../traits/physiology/chemoheterotrophic.html | 4 +-
.../physiology/chemolithoautotrophic.html | 4 +-
.../physiology/chemolithoheterotrophic.html | 4 +-
.../traits/physiology/chemolithotrophic.html | 4 +-
.../physiology/chemoorganoheterotrophic.html | 4 +-
.../traits/physiology/chemoorganotrophic.html | 4 +-
pages/traits/physiology/chemotaxis.html | 4 +-
pages/traits/physiology/chemotrophic.html | 4 +-
.../traits/physiology/coagulase_activity.html | 2 +-
pages/traits/physiology/copiotrophic.html | 4 +-
.../cystine_arylamidase_activity.html | 2 +-
pages/traits/physiology/dnase_activity.html | 2 +-
pages/traits/physiology/dormancy.html | 4 +-
.../gamma_glutamyltransferase_activity.html | 2 +-
.../physiology/gelatinase_activity.html | 2 +-
...yl_glutamic_acid_arylamidase_activity.html | 2 +-
.../glycine_arylamidase_activity.html | 2 +-
pages/traits/physiology/heterotrophic.html | 4 +-
.../histidine_arylamidase_activity.html | 2 +-
pages/traits/physiology/hydrogenotrophic.html | 4 +-
.../physiology/lecithinase_activity.html | 2 +-
.../leucine_arylamidase_activity.html | 2 +-
.../leucyl_glycine_arylamidase_activity.html | 2 +-
pages/traits/physiology/lipase_activity.html | 2 +-
pages/traits/physiology/lithoautotrophic.html | 4 +-
.../traits/physiology/lithoheterotrophic.html | 4 +-
pages/traits/physiology/lithotrophic.html | 4 +-
.../lysine_decarboxylase_activity.html | 2 +-
pages/traits/physiology/magnetotaxis.html | 2 +-
pages/traits/physiology/methanotrophic.html | 4 +-
pages/traits/physiology/methylotrophic.html | 4 +-
pages/traits/physiology/mixotrophic.html | 4 +-
...endent_alcohol_dehydrogenase_activity.html | 2 +-
...hthol_as_bi_phosphohydrolase_activity.html | 2 +-
.../traits/physiology/natural_competence.html | 4 +-
.../physiology/nutrient_adaptation.html | 4 +-
pages/traits/physiology/oligotrophic.html | 4 +-
.../physiology/organoheterotrophic.html | 4 +-
pages/traits/physiology/organotrophic.html | 4 +-
.../ornithine_decarboxylase_activity.html | 2 +-
pages/traits/physiology/oxidase_activity.html | 4 +-
.../physiology/oxidative_stress_response.html | 4 +-
.../physiology/persister_cell_formation.html | 4 +-
.../phenylalanine_arylamidase_activity.html | 2 +-
pages/traits/physiology/photoautotrophic.html | 4 +-
.../traits/physiology/photoheterotrophic.html | 4 +-
.../physiology/photolithoautotrophic.html | 4 +-
.../traits/physiology/photolithotrophic.html | 4 +-
.../physiology/photoorganoheterotrophic.html | 4 +-
pages/traits/physiology/phototrophic.html | 4 +-
.../prolyl_aminopeptidase_activity.html | 2 +-
.../physiology/pyrazinamidase_activity.html | 2 +-
.../pyrrolidonyl_arylamidase_activity.html | 2 +-
pages/traits/physiology/quorum_sensing.html | 4 +-
.../serine_arylamidase_activity.html | 2 +-
.../physiology/siderophore_production.html | 2 +-
.../traits/physiology/spore_germination.html | 4 +-
pages/traits/physiology/stress_response.html | 4 +-
pages/traits/physiology/trophic_type.html | 4 +-
pages/traits/physiology/trypsin_activity.html | 2 +-
.../tyrosine_arylamidase_activity.html | 2 +-
pages/traits/physiology/urease_activity.html | 4 +-
.../valine_arylamidase_activity.html | 2 +-
.../viable_but_nonculturable_state.html | 4 +-
.../has_maximum_observed_value.html | 4 +-
.../has_minimum_observed_value.html | 4 +-
.../has_observed_spot_value.html | 4 +-
.../quantitative_property/has_value.html | 4 +-
.../has_value_comments.html | 4 +-
.../is_negative_data.html | 4 +-
.../observation_data_property.html | 4 +-
pages/traits/upper/biological_process.html | 4 +-
pages/traits/upper/chemical_entity.html | 4 +-
pages/traits/upper/enzyme.html | 4 +-
pages/traits/upper/material_entity.html | 4 +-
pages/traits/upper/microbe.html | 4 +-
pages/traits/upper/observation.html | 4 +-
pages/traits/upper/phenotype.html | 4 +-
pages/traits/upper/quality.html | 4 +-
pages/umap.html | 6 +-
scripts/build_embedding_index.py | 99 ++++++++++++-------
scripts/render_trait_pages.py | 57 +++++++++--
src/traitmech/templates/graph.html | 8 +-
src/traitmech/templates/index.html | 4 +-
src/traitmech/templates/trait.html | 4 +-
src/traitmech/templates/umap.html | 6 +-
tests/test_graph_projection_correctness.py | 87 ++++++++++++++++
600 files changed, 1287 insertions(+), 1132 deletions(-)
mode change 100644 => 100755 scripts/build_embedding_index.py
mode change 100644 => 100755 scripts/render_trait_pages.py
create mode 100644 tests/test_graph_projection_correctness.py
diff --git a/pages/graph.html b/pages/graph.html
index 34f920b97e..89f4cbd7d3 100644
--- a/pages/graph.html
+++ b/pages/graph.html
@@ -3,7 +3,7 @@
Trait graph layout (sfdp) — TraitMech
+Trait graph layout — TraitMech
TraitMech › Graph layout
- Trait graph layout (sfdp)
- Graphviz sfdp force-directed layout over
- 477 METPO trait embeddings from kg-microbe's
- 2026-04-25 deepwalk (512-D, layout k=15). The 768 visible links are
+
Trait graph layout
+ Unverified projection over
+ 477 METPO trait embeddings. Projection: Unverified projection.
+ Source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded. The 768 visible links are
reciprocal relationships in the committed top-neighbor index. Hover for a
label; click to open the trait page.
diff --git a/pages/index.html b/pages/index.html
index 7010d23df1..2df64239f6 100644
--- a/pages/index.html
+++ b/pages/index.html
@@ -125,9 +125,9 @@ Record browser
🗺️
-
+
Embedding browser
-
Interactive PaCMAP of the trait embedding space with click-through to records.
+
Interactive Unverified projection of the trait embedding space with click-through to records.
💻
diff --git a/pages/traits/ecology/animal_pathogen.html b/pages/traits/ecology/animal_pathogen.html
index 6bfe8f83eb..d528130177 100644
--- a/pages/traits/ecology/animal_pathogen.html
+++ b/pages/traits/ecology/animal_pathogen.html
@@ -366,7 +366,7 @@
kg-microbe context
METPO:1004002 [-1.564, -64.092, -0.620, -28.964, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -374,7 +374,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biofilm_formation.html b/pages/traits/ecology/biofilm_formation.html
index e80d63375d..f40c83f0db 100644
--- a/pages/traits/ecology/biofilm_formation.html
+++ b/pages/traits/ecology/biofilm_formation.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level.html b/pages/traits/ecology/biosafety_level.html
index 1cb11f5e06..79c85e3c88 100644
--- a/pages/traits/ecology/biosafety_level.html
+++ b/pages/traits/ecology/biosafety_level.html
@@ -358,7 +358,7 @@ kg-microbe context
METPO:1001101 [-2.107, -3.186, -2.412, +0.971, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -366,7 +366,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level_1.html b/pages/traits/ecology/biosafety_level_1.html
index 1e7b6343a3..e32d20e354 100644
--- a/pages/traits/ecology/biosafety_level_1.html
+++ b/pages/traits/ecology/biosafety_level_1.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1001102 [+13.390, -49.149, -21.083, +19.067, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level_2.html b/pages/traits/ecology/biosafety_level_2.html
index a87a2e14b7..47b2c30f2d 100644
--- a/pages/traits/ecology/biosafety_level_2.html
+++ b/pages/traits/ecology/biosafety_level_2.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1001103 [+47.740, -114.909, +42.074, +68.627, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level_3.html b/pages/traits/ecology/biosafety_level_3.html
index 0056fbc1bc..f8559abf93 100644
--- a/pages/traits/ecology/biosafety_level_3.html
+++ b/pages/traits/ecology/biosafety_level_3.html
@@ -258,7 +258,7 @@ kg-microbe context
METPO:1001104 [+22.599, -24.248, -48.083, +0.798, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -266,7 +266,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level_4.html b/pages/traits/ecology/biosafety_level_4.html
index cb224a4f4f..565264c2df 100644
--- a/pages/traits/ecology/biosafety_level_4.html
+++ b/pages/traits/ecology/biosafety_level_4.html
@@ -291,7 +291,7 @@ kg-microbe context
METPO:1001105 [-2.744, -3.128, -2.945, +1.660, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -299,7 +299,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/biosafety_level_5.html b/pages/traits/ecology/biosafety_level_5.html
index 24792d9e5b..4be41a58c8 100644
--- a/pages/traits/ecology/biosafety_level_5.html
+++ b/pages/traits/ecology/biosafety_level_5.html
@@ -154,7 +154,7 @@ kg-microbe context
METPO:1001106 [-1.943, -2.943, -2.758, +0.700, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -162,7 +162,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/commensalism.html b/pages/traits/ecology/commensalism.html
index 384ebc8f44..829774eaca 100644
--- a/pages/traits/ecology/commensalism.html
+++ b/pages/traits/ecology/commensalism.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/endosymbiosis.html b/pages/traits/ecology/endosymbiosis.html
index 5a0622cd86..d7812e5223 100644
--- a/pages/traits/ecology/endosymbiosis.html
+++ b/pages/traits/ecology/endosymbiosis.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/free_living.html b/pages/traits/ecology/free_living.html
index cd8326dd0c..d4117dc28c 100644
--- a/pages/traits/ecology/free_living.html
+++ b/pages/traits/ecology/free_living.html
@@ -265,7 +265,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -273,7 +273,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/gut_associated.html b/pages/traits/ecology/gut_associated.html
index e907853412..47354040c7 100644
--- a/pages/traits/ecology/gut_associated.html
+++ b/pages/traits/ecology/gut_associated.html
@@ -342,7 +342,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -350,7 +350,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/habitat_association.html b/pages/traits/ecology/habitat_association.html
index f20c2a7637..b0fdc7c50b 100644
--- a/pages/traits/ecology/habitat_association.html
+++ b/pages/traits/ecology/habitat_association.html
@@ -271,7 +271,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -279,7 +279,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/host_associated.html b/pages/traits/ecology/host_associated.html
index cb65b7b448..ae30f1b34f 100644
--- a/pages/traits/ecology/host_associated.html
+++ b/pages/traits/ecology/host_associated.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/human_pathogen.html b/pages/traits/ecology/human_pathogen.html
index 8bbc59c7a3..b340c782f9 100644
--- a/pages/traits/ecology/human_pathogen.html
+++ b/pages/traits/ecology/human_pathogen.html
@@ -324,7 +324,7 @@ kg-microbe context
METPO:1004004 [-23.400, -36.820, -39.335, +4.843, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -332,7 +332,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/mutualism.html b/pages/traits/ecology/mutualism.html
index 30571aee8a..56bd04d0a6 100644
--- a/pages/traits/ecology/mutualism.html
+++ b/pages/traits/ecology/mutualism.html
@@ -248,7 +248,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -256,7 +256,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/nitrogen_fixing_symbiosis.html b/pages/traits/ecology/nitrogen_fixing_symbiosis.html
index 9ce5cf8649..654a65bcb8 100644
--- a/pages/traits/ecology/nitrogen_fixing_symbiosis.html
+++ b/pages/traits/ecology/nitrogen_fixing_symbiosis.html
@@ -339,7 +339,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -347,7 +347,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/opportunistic_pathogen.html b/pages/traits/ecology/opportunistic_pathogen.html
index df1d20c40a..1413aabd00 100644
--- a/pages/traits/ecology/opportunistic_pathogen.html
+++ b/pages/traits/ecology/opportunistic_pathogen.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1004000 [-1.432, -2.796, -2.792, +0.353, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/parasitism.html b/pages/traits/ecology/parasitism.html
index 600d78b9e1..f14d4979bd 100644
--- a/pages/traits/ecology/parasitism.html
+++ b/pages/traits/ecology/parasitism.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/pathogenic_to_host.html b/pages/traits/ecology/pathogenic_to_host.html
index f8c19b1be3..ca8f061efa 100644
--- a/pages/traits/ecology/pathogenic_to_host.html
+++ b/pages/traits/ecology/pathogenic_to_host.html
@@ -341,7 +341,7 @@ kg-microbe context
METPO:1004000 [-1.432, -2.796, -2.792, +0.353, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -349,7 +349,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/plant_pathogen.html b/pages/traits/ecology/plant_pathogen.html
index e6971d8747..85cf9fd898 100644
--- a/pages/traits/ecology/plant_pathogen.html
+++ b/pages/traits/ecology/plant_pathogen.html
@@ -315,7 +315,7 @@ kg-microbe context
METPO:1004003 [+6.432, -2.221, -31.218, +2.228, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -323,7 +323,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/predatory_bacterium.html b/pages/traits/ecology/predatory_bacterium.html
index d83b48cfae..dc87722f5d 100644
--- a/pages/traits/ecology/predatory_bacterium.html
+++ b/pages/traits/ecology/predatory_bacterium.html
@@ -324,7 +324,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -332,7 +332,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/rhizosphere_association.html b/pages/traits/ecology/rhizosphere_association.html
index bbba82d4c6..96f7d8390d 100644
--- a/pages/traits/ecology/rhizosphere_association.html
+++ b/pages/traits/ecology/rhizosphere_association.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/saprotrophy.html b/pages/traits/ecology/saprotrophy.html
index fdcdc5002d..767e47b95e 100644
--- a/pages/traits/ecology/saprotrophy.html
+++ b/pages/traits/ecology/saprotrophy.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/soil_dwelling.html b/pages/traits/ecology/soil_dwelling.html
index ce616f5a6a..93fb27835b 100644
--- a/pages/traits/ecology/soil_dwelling.html
+++ b/pages/traits/ecology/soil_dwelling.html
@@ -358,7 +358,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -366,7 +366,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/ecology/symbiosis.html b/pages/traits/ecology/symbiosis.html
index ffbf69e645..d7a8744ffb 100644
--- a/pages/traits/ecology/symbiosis.html
+++ b/pages/traits/ecology/symbiosis.html
@@ -322,7 +322,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -330,7 +330,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/acidophilic.html b/pages/traits/environment/acidophilic.html
index ba827a9e51..f508bccb3a 100644
--- a/pages/traits/environment/acidophilic.html
+++ b/pages/traits/environment/acidophilic.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1003003 [-2.194, -1.869, -2.537, -0.747, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/acidotolerant.html b/pages/traits/environment/acidotolerant.html
index 99dc09727a..58b3370a35 100644
--- a/pages/traits/environment/acidotolerant.html
+++ b/pages/traits/environment/acidotolerant.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1003008 [-2.269, -2.440, -2.363, -0.685, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/aerobic.html b/pages/traits/environment/aerobic.html
index 8dc5e47c30..2492c1b72c 100644
--- a/pages/traits/environment/aerobic.html
+++ b/pages/traits/environment/aerobic.html
@@ -325,7 +325,7 @@ kg-microbe context
METPO:1000602 [-37.032, +29.784, -5.356, +74.090, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -333,7 +333,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/aerotolerant.html b/pages/traits/environment/aerotolerant.html
index f1a6583989..b742971518 100644
--- a/pages/traits/environment/aerotolerant.html
+++ b/pages/traits/environment/aerotolerant.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000609 [+0.004, -0.947, -1.036, -0.467, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/alkalotolerant.html b/pages/traits/environment/alkalotolerant.html
index 5694ddba6a..f9d19e156c 100644
--- a/pages/traits/environment/alkalotolerant.html
+++ b/pages/traits/environment/alkalotolerant.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1003009 [-2.574, -1.858, -2.415, -0.954, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/alkaphilic.html b/pages/traits/environment/alkaphilic.html
index a2c511b5a6..22173fd951 100644
--- a/pages/traits/environment/alkaphilic.html
+++ b/pages/traits/environment/alkaphilic.html
@@ -303,7 +303,7 @@ kg-microbe context
METPO:1003002 [-2.640, -2.180, -1.907, -0.788, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -311,7 +311,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/anaerobic.html b/pages/traits/environment/anaerobic.html
index 178f440d2f..8550cc0fb9 100644
--- a/pages/traits/environment/anaerobic.html
+++ b/pages/traits/environment/anaerobic.html
@@ -299,7 +299,7 @@ kg-microbe context
METPO:1000603 [+295.383, -195.343, -25.409, +1.165, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -307,7 +307,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/arsenic_tolerant.html b/pages/traits/environment/arsenic_tolerant.html
index 1199f287db..5e582fee13 100644
--- a/pages/traits/environment/arsenic_tolerant.html
+++ b/pages/traits/environment/arsenic_tolerant.html
@@ -371,7 +371,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -379,7 +379,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/cadmium_tolerant.html b/pages/traits/environment/cadmium_tolerant.html
index aec597a397..24676b5150 100644
--- a/pages/traits/environment/cadmium_tolerant.html
+++ b/pages/traits/environment/cadmium_tolerant.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/capnophilic.html b/pages/traits/environment/capnophilic.html
index 9e170ece28..d2255059f1 100644
--- a/pages/traits/environment/capnophilic.html
+++ b/pages/traits/environment/capnophilic.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/environment/cobalt_tolerant.html b/pages/traits/environment/cobalt_tolerant.html
index 89a6678432..cd29213f1b 100644
--- a/pages/traits/environment/cobalt_tolerant.html
+++ b/pages/traits/environment/cobalt_tolerant.html
@@ -328,7 +328,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -336,7 +336,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/copper_tolerant.html b/pages/traits/environment/copper_tolerant.html
index 0a6d702f06..24e3619aba 100644
--- a/pages/traits/environment/copper_tolerant.html
+++ b/pages/traits/environment/copper_tolerant.html
@@ -286,7 +286,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -294,7 +294,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/delta_phenotype_with_numerical_limits.html b/pages/traits/environment/delta_phenotype_with_numerical_limits.html
index 181eee26cf..4b1fd7495d 100644
--- a/pages/traits/environment/delta_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/delta_phenotype_with_numerical_limits.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000534 [-3.799, -1.882, -3.281, +0.097, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/desiccation_tolerant.html b/pages/traits/environment/desiccation_tolerant.html
index da6308ebbd..6e3899bafd 100644
--- a/pages/traits/environment/desiccation_tolerant.html
+++ b/pages/traits/environment/desiccation_tolerant.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/euryhaline.html b/pages/traits/environment/euryhaline.html
index f0739e50d5..9ad65ed553 100644
--- a/pages/traits/environment/euryhaline.html
+++ b/pages/traits/environment/euryhaline.html
@@ -349,7 +349,7 @@ kg-microbe context
METPO:1000627 [-3.209, -1.862, -0.407, -3.229, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -357,7 +357,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/extreme_hyperthermophilic.html b/pages/traits/environment/extreme_hyperthermophilic.html
index 09b9c8aa77..605c7a49d4 100644
--- a/pages/traits/environment/extreme_hyperthermophilic.html
+++ b/pages/traits/environment/extreme_hyperthermophilic.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000721 [-1.816, -2.651, -5.319, +2.332, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/extremely_halophilic.html b/pages/traits/environment/extremely_halophilic.html
index c2ef763e33..c1b769778d 100644
--- a/pages/traits/environment/extremely_halophilic.html
+++ b/pages/traits/environment/extremely_halophilic.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000628 [-5.564, -4.889, -1.753, +2.203, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultative_oxygen_preference.html b/pages/traits/environment/facultative_oxygen_preference.html
index da208ca67f..81cf094d9e 100644
--- a/pages/traits/environment/facultative_oxygen_preference.html
+++ b/pages/traits/environment/facultative_oxygen_preference.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000612 [+0.107, -1.436, -3.263, +2.339, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultative_psychrophilic.html b/pages/traits/environment/facultative_psychrophilic.html
index 25fb634179..a39ca7e446 100644
--- a/pages/traits/environment/facultative_psychrophilic.html
+++ b/pages/traits/environment/facultative_psychrophilic.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000720 [-2.148, -2.202, -4.718, +2.478, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultatively_acidophilic.html b/pages/traits/environment/facultatively_acidophilic.html
index 9f4a5ae72c..d9858cbf99 100644
--- a/pages/traits/environment/facultatively_acidophilic.html
+++ b/pages/traits/environment/facultatively_acidophilic.html
@@ -358,7 +358,7 @@ kg-microbe context
METPO:1003007 [-2.661, -2.047, -2.231, -0.786, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -366,7 +366,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultatively_aerobic.html b/pages/traits/environment/facultatively_aerobic.html
index 50abbc0c0e..209dd83133 100644
--- a/pages/traits/environment/facultatively_aerobic.html
+++ b/pages/traits/environment/facultatively_aerobic.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000608 [-151.729, -272.921, +66.702, -217.406, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultatively_alkaphilic.html b/pages/traits/environment/facultatively_alkaphilic.html
index 98a1af987d..338a6cc1c3 100644
--- a/pages/traits/environment/facultatively_alkaphilic.html
+++ b/pages/traits/environment/facultatively_alkaphilic.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1003005 [-2.320, -2.077, -2.647, -0.697, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/facultatively_anaerobic.html b/pages/traits/environment/facultatively_anaerobic.html
index 1cb62db2bc..8d0ae6a668 100644
--- a/pages/traits/environment/facultatively_anaerobic.html
+++ b/pages/traits/environment/facultatively_anaerobic.html
@@ -258,7 +258,7 @@ kg-microbe context
METPO:1000605 [-3.711, -2.702, +1.434, -2.504, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -266,7 +266,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html b/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html
index fda51cf61b..ace4fd7e48 100644
--- a/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html
@@ -328,7 +328,7 @@ kg-microbe context
METPO:1000535 [-2.537, -1.642, -2.853, +0.728, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -336,7 +336,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/haloalkaliphilic.html b/pages/traits/environment/haloalkaliphilic.html
index e4206af38c..dd1d45985a 100644
--- a/pages/traits/environment/haloalkaliphilic.html
+++ b/pages/traits/environment/haloalkaliphilic.html
@@ -315,7 +315,7 @@ kg-microbe context
METPO:1000621 [-2.095, -1.126, +0.094, -2.061, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -323,7 +323,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/halophilic.html b/pages/traits/environment/halophilic.html
index 0e0aa5b2bb..6244c6f0fa 100644
--- a/pages/traits/environment/halophilic.html
+++ b/pages/traits/environment/halophilic.html
@@ -315,7 +315,7 @@ kg-microbe context
METPO:1000620 [-1.039, -0.924, -1.635, -0.067, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -323,7 +323,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/halophily_preference.html b/pages/traits/environment/halophily_preference.html
index 6138d8c48a..5de2fbf674 100644
--- a/pages/traits/environment/halophily_preference.html
+++ b/pages/traits/environment/halophily_preference.html
@@ -368,7 +368,7 @@ kg-microbe context
METPO:1000629 [-3.748, -1.433, -0.015, -2.487, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -376,7 +376,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/halotolerant.html b/pages/traits/environment/halotolerant.html
index ae7a9c0aec..ce72adc4eb 100644
--- a/pages/traits/environment/halotolerant.html
+++ b/pages/traits/environment/halotolerant.html
@@ -315,7 +315,7 @@ kg-microbe context
METPO:1000622 [-1.440, -1.500, -3.854, +0.583, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -323,7 +323,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/hyperthermophilic.html b/pages/traits/environment/hyperthermophilic.html
index 22f58bb056..57b43f8c6d 100644
--- a/pages/traits/environment/hyperthermophilic.html
+++ b/pages/traits/environment/hyperthermophilic.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000617 [-1.374, -3.022, -1.424, +2.441, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ionizing_radiation_tolerant.html b/pages/traits/environment/ionizing_radiation_tolerant.html
index 10c65a38a7..8a728cb122 100644
--- a/pages/traits/environment/ionizing_radiation_tolerant.html
+++ b/pages/traits/environment/ionizing_radiation_tolerant.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/mercury_tolerant.html b/pages/traits/environment/mercury_tolerant.html
index 7747e869ab..97b2625345 100644
--- a/pages/traits/environment/mercury_tolerant.html
+++ b/pages/traits/environment/mercury_tolerant.html
@@ -303,7 +303,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -311,7 +311,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/mesophilic.html b/pages/traits/environment/mesophilic.html
index 47cfd7db8f..f96cfc757d 100644
--- a/pages/traits/environment/mesophilic.html
+++ b/pages/traits/environment/mesophilic.html
@@ -349,7 +349,7 @@ kg-microbe context
METPO:1000615 [+102.284, -178.453, -111.655, -113.199, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -357,7 +357,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/metal_tolerant.html b/pages/traits/environment/metal_tolerant.html
index 8a840f5472..bb2b5c96f2 100644
--- a/pages/traits/environment/metal_tolerant.html
+++ b/pages/traits/environment/metal_tolerant.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/microaerophilic.html b/pages/traits/environment/microaerophilic.html
index 0fb88e101a..ef2a7c14d7 100644
--- a/pages/traits/environment/microaerophilic.html
+++ b/pages/traits/environment/microaerophilic.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000604 [-7.958, +0.708, -1.624, -12.523, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/microaerotolerant.html b/pages/traits/environment/microaerotolerant.html
index 8ecb9b1955..f985398108 100644
--- a/pages/traits/environment/microaerotolerant.html
+++ b/pages/traits/environment/microaerotolerant.html
@@ -298,7 +298,7 @@ kg-microbe context
METPO:1000610 [-1.136, -2.135, -2.147, +0.656, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -306,7 +306,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/moderately_halophilic.html b/pages/traits/environment/moderately_halophilic.html
index 3be7c9f52f..1878a202fb 100644
--- a/pages/traits/environment/moderately_halophilic.html
+++ b/pages/traits/environment/moderately_halophilic.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000623 [-94.883, -13.167, +11.221, +70.341, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_delta.html b/pages/traits/environment/nacl_delta.html
index 8fa8a7e214..0ce8e449e3 100644
--- a/pages/traits/environment/nacl_delta.html
+++ b/pages/traits/environment/nacl_delta.html
@@ -281,7 +281,7 @@ kg-microbe context
METPO:1000335 [-3.596, -2.760, -3.043, +0.053, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -289,7 +289,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_delta_high.html b/pages/traits/environment/nacl_delta_high.html
index 6baf53ddaf..9fafb7d20d 100644
--- a/pages/traits/environment/nacl_delta_high.html
+++ b/pages/traits/environment/nacl_delta_high.html
@@ -341,7 +341,7 @@ kg-microbe context
METPO:1000482 [-0.207, -1.867, +0.267, +2.264, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -349,7 +349,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_delta_low.html b/pages/traits/environment/nacl_delta_low.html
index ec74a64a64..c61a414ae4 100644
--- a/pages/traits/environment/nacl_delta_low.html
+++ b/pages/traits/environment/nacl_delta_low.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000479 [-3.032, -4.103, -2.404, +1.560, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_delta_mid1.html b/pages/traits/environment/nacl_delta_mid1.html
index 3ab7a3151d..0736815c4d 100644
--- a/pages/traits/environment/nacl_delta_mid1.html
+++ b/pages/traits/environment/nacl_delta_mid1.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000480 [-4.436, -1.982, -1.374, -0.530, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_delta_mid2.html b/pages/traits/environment/nacl_delta_mid2.html
index 901866c336..429577e470 100644
--- a/pages/traits/environment/nacl_delta_mid2.html
+++ b/pages/traits/environment/nacl_delta_mid2.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000481 [-2.652, -0.385, +1.033, +2.032, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_optimum.html b/pages/traits/environment/nacl_optimum.html
index 90e6048246..74dbc5674d 100644
--- a/pages/traits/environment/nacl_optimum.html
+++ b/pages/traits/environment/nacl_optimum.html
@@ -383,7 +383,7 @@ kg-microbe context
METPO:1000333 [-3.125, -1.042, -1.721, +1.474, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -391,7 +391,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_optimum_high.html b/pages/traits/environment/nacl_optimum_high.html
index 0fe44f1f20..a2142de9fd 100644
--- a/pages/traits/environment/nacl_optimum_high.html
+++ b/pages/traits/environment/nacl_optimum_high.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000468 [-2.565, -2.720, +0.941, +0.988, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_optimum_low.html b/pages/traits/environment/nacl_optimum_low.html
index 2cf6365d52..4fdb01b292 100644
--- a/pages/traits/environment/nacl_optimum_low.html
+++ b/pages/traits/environment/nacl_optimum_low.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000465 [-1.310, -1.240, -3.413, +3.699, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_optimum_mid1.html b/pages/traits/environment/nacl_optimum_mid1.html
index 74f9de2803..271560306c 100644
--- a/pages/traits/environment/nacl_optimum_mid1.html
+++ b/pages/traits/environment/nacl_optimum_mid1.html
@@ -260,7 +260,7 @@ kg-microbe context
METPO:1000466 [-2.252, -1.820, +0.770, +1.144, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -268,7 +268,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_optimum_mid2.html b/pages/traits/environment/nacl_optimum_mid2.html
index 5b13c0778a..311a054962 100644
--- a/pages/traits/environment/nacl_optimum_mid2.html
+++ b/pages/traits/environment/nacl_optimum_mid2.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000467 [-0.989, -0.801, -1.139, +3.616, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_range.html b/pages/traits/environment/nacl_range.html
index d878b3115f..1fec177fd9 100644
--- a/pages/traits/environment/nacl_range.html
+++ b/pages/traits/environment/nacl_range.html
@@ -281,7 +281,7 @@ kg-microbe context
METPO:1000334 [-2.929, -1.954, -2.325, +0.965, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -289,7 +289,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_range_high.html b/pages/traits/environment/nacl_range_high.html
index 65503998f8..fc24b4195e 100644
--- a/pages/traits/environment/nacl_range_high.html
+++ b/pages/traits/environment/nacl_range_high.html
@@ -241,7 +241,7 @@ kg-microbe context
METPO:1000472 [+0.219, -2.224, +0.350, +2.763, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -249,7 +249,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_range_low.html b/pages/traits/environment/nacl_range_low.html
index 3c36b14013..8aec2288a6 100644
--- a/pages/traits/environment/nacl_range_low.html
+++ b/pages/traits/environment/nacl_range_low.html
@@ -243,7 +243,7 @@ kg-microbe context
METPO:1000469 [-3.957, -1.727, +0.312, +1.025, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -251,7 +251,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_range_mid1.html b/pages/traits/environment/nacl_range_mid1.html
index b862c7da38..0b2377dd6b 100644
--- a/pages/traits/environment/nacl_range_mid1.html
+++ b/pages/traits/environment/nacl_range_mid1.html
@@ -243,7 +243,7 @@ kg-microbe context
METPO:1000470 [-4.071, -1.891, -0.359, +0.724, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -251,7 +251,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/nacl_range_mid2.html b/pages/traits/environment/nacl_range_mid2.html
index 2b674416f9..358b9ff77a 100644
--- a/pages/traits/environment/nacl_range_mid2.html
+++ b/pages/traits/environment/nacl_range_mid2.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000471 [-2.730, -1.359, +0.847, +2.066, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/neutrophilic.html b/pages/traits/environment/neutrophilic.html
index 5697eb2c9f..2ca88cbbec 100644
--- a/pages/traits/environment/neutrophilic.html
+++ b/pages/traits/environment/neutrophilic.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1003001 [-2.302, -2.147, -2.266, -0.758, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/non_halophilic.html b/pages/traits/environment/non_halophilic.html
index d35363ac0b..f7bd6a44c8 100644
--- a/pages/traits/environment/non_halophilic.html
+++ b/pages/traits/environment/non_halophilic.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000624 [-6.997, -46.693, +70.873, -15.746, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/obligately_acidophilic.html b/pages/traits/environment/obligately_acidophilic.html
index dd37a8a76d..a1bf586657 100644
--- a/pages/traits/environment/obligately_acidophilic.html
+++ b/pages/traits/environment/obligately_acidophilic.html
@@ -341,7 +341,7 @@ kg-microbe context
METPO:1003006 [-2.557, -2.409, -2.459, -0.781, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -349,7 +349,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/obligately_aerobic.html b/pages/traits/environment/obligately_aerobic.html
index 6470f24a03..45e0da11ad 100644
--- a/pages/traits/environment/obligately_aerobic.html
+++ b/pages/traits/environment/obligately_aerobic.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000606 [-9.610, +1.401, -2.576, -1.238, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/obligately_alkaphilic.html b/pages/traits/environment/obligately_alkaphilic.html
index 3a2760a6a6..1033acde7f 100644
--- a/pages/traits/environment/obligately_alkaphilic.html
+++ b/pages/traits/environment/obligately_alkaphilic.html
@@ -343,7 +343,7 @@ kg-microbe context
METPO:1003004 [-2.837, -2.238, -1.977, -0.877, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -351,7 +351,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/obligately_anaerobic.html b/pages/traits/environment/obligately_anaerobic.html
index 6cf5ea51a5..a7ec7989e6 100644
--- a/pages/traits/environment/obligately_anaerobic.html
+++ b/pages/traits/environment/obligately_anaerobic.html
@@ -335,7 +335,7 @@ kg-microbe context
METPO:1000607 [+2.697, -7.983, -23.900, +3.915, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -343,7 +343,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/obligately_piezophilic.html b/pages/traits/environment/obligately_piezophilic.html
index 622f7b93f3..8d43ffeccc 100644
--- a/pages/traits/environment/obligately_piezophilic.html
+++ b/pages/traits/environment/obligately_piezophilic.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/optimum_phenotype_with_numerical_limits.html b/pages/traits/environment/optimum_phenotype_with_numerical_limits.html
index bebfe46f43..e9f3344674 100644
--- a/pages/traits/environment/optimum_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/optimum_phenotype_with_numerical_limits.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000536 [-3.285, -0.855, -3.233, +0.883, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/oxygen_preference.html b/pages/traits/environment/oxygen_preference.html
index c4d7afedd4..47ad42fc4d 100644
--- a/pages/traits/environment/oxygen_preference.html
+++ b/pages/traits/environment/oxygen_preference.html
@@ -338,7 +338,7 @@ kg-microbe context
METPO:1000601 [-1.145, -2.522, -2.827, -0.321, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -346,7 +346,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta.html b/pages/traits/environment/ph_delta.html
index f8f37fb49b..b81fda5c8f 100644
--- a/pages/traits/environment/ph_delta.html
+++ b/pages/traits/environment/ph_delta.html
@@ -285,7 +285,7 @@ kg-microbe context
METPO:1000232 [-1.997, -1.168, -3.290, +0.199, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -293,7 +293,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_high.html b/pages/traits/environment/ph_delta_high.html
index 5848f7cfe0..e4f95270fc 100644
--- a/pages/traits/environment/ph_delta_high.html
+++ b/pages/traits/environment/ph_delta_high.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000478 [-0.781, -1.339, -0.603, +3.022, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_low.html b/pages/traits/environment/ph_delta_low.html
index 2876135c6a..9c0a1c16b3 100644
--- a/pages/traits/environment/ph_delta_low.html
+++ b/pages/traits/environment/ph_delta_low.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000474 [-1.168, -0.624, -1.427, +0.785, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_mid1.html b/pages/traits/environment/ph_delta_mid1.html
index b64c5ffcdd..a6f88a47b2 100644
--- a/pages/traits/environment/ph_delta_mid1.html
+++ b/pages/traits/environment/ph_delta_mid1.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000475 [-0.998, -0.536, -1.733, +2.157, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_mid2.html b/pages/traits/environment/ph_delta_mid2.html
index 35813a22d4..020f391d65 100644
--- a/pages/traits/environment/ph_delta_mid2.html
+++ b/pages/traits/environment/ph_delta_mid2.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000476 [-2.192, -1.235, -2.140, +3.297, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_mid3.html b/pages/traits/environment/ph_delta_mid3.html
index 7e7ac85fa4..533638eb7d 100644
--- a/pages/traits/environment/ph_delta_mid3.html
+++ b/pages/traits/environment/ph_delta_mid3.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000477 [-3.578, -1.920, -3.431, +0.231, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_delta_very_low.html b/pages/traits/environment/ph_delta_very_low.html
index f07b85df3f..d58bc96063 100644
--- a/pages/traits/environment/ph_delta_very_low.html
+++ b/pages/traits/environment/ph_delta_very_low.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000473 [+1.107, -0.229, -3.624, +2.954, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_growth_preference.html b/pages/traits/environment/ph_growth_preference.html
index 96219f3c7a..edc1ae68f9 100644
--- a/pages/traits/environment/ph_growth_preference.html
+++ b/pages/traits/environment/ph_growth_preference.html
@@ -338,7 +338,7 @@ kg-microbe context
METPO:1003000 [-4.334, -2.942, -3.256, -1.316, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -346,7 +346,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_optimum.html b/pages/traits/environment/ph_optimum.html
index d2d52ef268..52b232d698 100644
--- a/pages/traits/environment/ph_optimum.html
+++ b/pages/traits/environment/ph_optimum.html
@@ -315,7 +315,7 @@ kg-microbe context
METPO:1000331 [-2.375, -0.997, -3.355, +0.508, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -323,7 +323,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_optimum_high.html b/pages/traits/environment/ph_optimum_high.html
index e5050e0e5e..80ce8b8c4f 100644
--- a/pages/traits/environment/ph_optimum_high.html
+++ b/pages/traits/environment/ph_optimum_high.html
@@ -296,7 +296,7 @@ kg-microbe context
METPO:1000458 [-1.238, -0.414, -3.609, +2.089, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -304,7 +304,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_optimum_low.html b/pages/traits/environment/ph_optimum_low.html
index 97685ca44d..65caf8cecb 100644
--- a/pages/traits/environment/ph_optimum_low.html
+++ b/pages/traits/environment/ph_optimum_low.html
@@ -255,7 +255,7 @@ kg-microbe context
METPO:1000455 [-1.126, -1.778, -1.235, -0.455, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -263,7 +263,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_optimum_mid1.html b/pages/traits/environment/ph_optimum_mid1.html
index f12081b77b..2c908d0914 100644
--- a/pages/traits/environment/ph_optimum_mid1.html
+++ b/pages/traits/environment/ph_optimum_mid1.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000456 [-0.020, -0.772, -0.806, +1.582, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_optimum_mid2.html b/pages/traits/environment/ph_optimum_mid2.html
index a4ceca9abc..79c08ff240 100644
--- a/pages/traits/environment/ph_optimum_mid2.html
+++ b/pages/traits/environment/ph_optimum_mid2.html
@@ -279,7 +279,7 @@ kg-microbe context
METPO:1000457 [-2.141, -1.296, -1.380, +3.241, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -287,7 +287,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_phenotype_with_numerical_limits.html b/pages/traits/environment/ph_phenotype_with_numerical_limits.html
index 22a16fe0d1..5415e79aae 100644
--- a/pages/traits/environment/ph_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/ph_phenotype_with_numerical_limits.html
@@ -362,7 +362,7 @@ kg-microbe context
METPO:1000531 [-2.393, -1.211, -4.380, +0.001, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -370,7 +370,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range.html b/pages/traits/environment/ph_range.html
index cfd4b265c3..46f1219e17 100644
--- a/pages/traits/environment/ph_range.html
+++ b/pages/traits/environment/ph_range.html
@@ -302,7 +302,7 @@ kg-microbe context
METPO:1000332 [-2.054, -2.222, -3.843, +1.421, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -310,7 +310,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_high.html b/pages/traits/environment/ph_range_high.html
index 783e2b78f2..e21969cec8 100644
--- a/pages/traits/environment/ph_range_high.html
+++ b/pages/traits/environment/ph_range_high.html
@@ -279,7 +279,7 @@ kg-microbe context
METPO:1000464 [-2.572, -2.517, -2.299, +3.236, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -287,7 +287,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_low.html b/pages/traits/environment/ph_range_low.html
index a8186abb9c..8b42c9c815 100644
--- a/pages/traits/environment/ph_range_low.html
+++ b/pages/traits/environment/ph_range_low.html
@@ -264,7 +264,7 @@ kg-microbe context
METPO:1000460 [-1.456, -1.684, -1.159, +1.360, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -272,7 +272,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_mid1.html b/pages/traits/environment/ph_range_mid1.html
index 4d2b693d33..0319f22e22 100644
--- a/pages/traits/environment/ph_range_mid1.html
+++ b/pages/traits/environment/ph_range_mid1.html
@@ -262,7 +262,7 @@ kg-microbe context
METPO:1000461 [-1.688, -1.528, -1.234, +3.477, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -270,7 +270,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_mid2.html b/pages/traits/environment/ph_range_mid2.html
index c6d23fa769..c65127fa52 100644
--- a/pages/traits/environment/ph_range_mid2.html
+++ b/pages/traits/environment/ph_range_mid2.html
@@ -281,7 +281,7 @@ kg-microbe context
METPO:1000462 [-1.204, -0.579, -2.315, +2.278, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -289,7 +289,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_mid3.html b/pages/traits/environment/ph_range_mid3.html
index 4b22725e01..aaac303bbc 100644
--- a/pages/traits/environment/ph_range_mid3.html
+++ b/pages/traits/environment/ph_range_mid3.html
@@ -281,7 +281,7 @@ kg-microbe context
METPO:1000463 [-2.494, -1.885, -1.584, +2.458, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -289,7 +289,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/ph_range_very_low.html b/pages/traits/environment/ph_range_very_low.html
index 168d70743a..c04bbaebaf 100644
--- a/pages/traits/environment/ph_range_very_low.html
+++ b/pages/traits/environment/ph_range_very_low.html
@@ -249,7 +249,7 @@ kg-microbe context
METPO:1000459 [-0.855, -1.364, -1.665, +2.241, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -257,7 +257,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/piezophilic.html b/pages/traits/environment/piezophilic.html
index a31923a10d..c893f689d2 100644
--- a/pages/traits/environment/piezophilic.html
+++ b/pages/traits/environment/piezophilic.html
@@ -301,7 +301,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -309,7 +309,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/piezotolerant.html b/pages/traits/environment/piezotolerant.html
index 09d0f89783..d8771c6a61 100644
--- a/pages/traits/environment/piezotolerant.html
+++ b/pages/traits/environment/piezotolerant.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/pressure_delta.html b/pages/traits/environment/pressure_delta.html
index 951de6adbf..7bf1fcf275 100644
--- a/pages/traits/environment/pressure_delta.html
+++ b/pages/traits/environment/pressure_delta.html
@@ -287,7 +287,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -295,7 +295,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/pressure_optimum.html b/pages/traits/environment/pressure_optimum.html
index f6e656b894..34aeba8dff 100644
--- a/pages/traits/environment/pressure_optimum.html
+++ b/pages/traits/environment/pressure_optimum.html
@@ -230,7 +230,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -238,7 +238,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/pressure_range.html b/pages/traits/environment/pressure_range.html
index 25fb00181f..df6e520d6e 100644
--- a/pages/traits/environment/pressure_range.html
+++ b/pages/traits/environment/pressure_range.html
@@ -230,7 +230,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -238,7 +238,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/psychrophilic.html b/pages/traits/environment/psychrophilic.html
index 80283e1073..0d64d85db8 100644
--- a/pages/traits/environment/psychrophilic.html
+++ b/pages/traits/environment/psychrophilic.html
@@ -298,7 +298,7 @@ kg-microbe context
METPO:1000614 [-77.153, +7.937, -20.243, -1.295, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -306,7 +306,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/psychrotolerant.html b/pages/traits/environment/psychrotolerant.html
index b758aea2eb..3d6347b0af 100644
--- a/pages/traits/environment/psychrotolerant.html
+++ b/pages/traits/environment/psychrotolerant.html
@@ -247,7 +247,7 @@ kg-microbe context
METPO:1000618 [-0.575, -4.190, -4.805, +2.930, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -255,7 +255,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/radiotolerant.html b/pages/traits/environment/radiotolerant.html
index fcf3573156..fe7a0428ec 100644
--- a/pages/traits/environment/radiotolerant.html
+++ b/pages/traits/environment/radiotolerant.html
@@ -365,7 +365,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -373,7 +373,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/salinity_phenotype_with_numerical_limits.html b/pages/traits/environment/salinity_phenotype_with_numerical_limits.html
index 37d3ea824c..6ce91925c1 100644
--- a/pages/traits/environment/salinity_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/salinity_phenotype_with_numerical_limits.html
@@ -311,7 +311,7 @@ kg-microbe context
METPO:1000532 [-3.600, -2.074, -2.363, +0.233, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -319,7 +319,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/slightly_halophilic.html b/pages/traits/environment/slightly_halophilic.html
index cdecaf76a4..a93fa933e4 100644
--- a/pages/traits/environment/slightly_halophilic.html
+++ b/pages/traits/environment/slightly_halophilic.html
@@ -264,7 +264,7 @@ kg-microbe context
METPO:1000625 [-3.580, -0.620, -1.375, -1.507, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -272,7 +272,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/stenohaline.html b/pages/traits/environment/stenohaline.html
index a87a362a44..6eb8f4de09 100644
--- a/pages/traits/environment/stenohaline.html
+++ b/pages/traits/environment/stenohaline.html
@@ -383,7 +383,7 @@ kg-microbe context
METPO:1000626 [-3.586, -1.523, +0.846, -3.582, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -391,7 +391,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/strictly_anaerobic.html b/pages/traits/environment/strictly_anaerobic.html
index f489376da8..275a4e2e67 100644
--- a/pages/traits/environment/strictly_anaerobic.html
+++ b/pages/traits/environment/strictly_anaerobic.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000611 [-2.094, -2.231, -3.010, +0.611, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta.html b/pages/traits/environment/temperature_delta.html
index 9c58a002b3..3479e29099 100644
--- a/pages/traits/environment/temperature_delta.html
+++ b/pages/traits/environment/temperature_delta.html
@@ -249,7 +249,7 @@ kg-microbe context
METPO:1000303 [-4.128, -0.585, -3.451, +0.762, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -257,7 +257,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta_high.html b/pages/traits/environment/temperature_delta_high.html
index e214a1113a..4950c0a8f9 100644
--- a/pages/traits/environment/temperature_delta_high.html
+++ b/pages/traits/environment/temperature_delta_high.html
@@ -341,7 +341,7 @@ kg-microbe context
METPO:1000487 [-0.692, +0.274, -0.785, +3.229, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -349,7 +349,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta_low.html b/pages/traits/environment/temperature_delta_low.html
index 4e39519cbf..8c94aed919 100644
--- a/pages/traits/environment/temperature_delta_low.html
+++ b/pages/traits/environment/temperature_delta_low.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000484 [+0.568, +2.604, -3.872, -0.321, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta_mid1.html b/pages/traits/environment/temperature_delta_mid1.html
index 74dc0409ea..414564aed3 100644
--- a/pages/traits/environment/temperature_delta_mid1.html
+++ b/pages/traits/environment/temperature_delta_mid1.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000485 [+0.841, -0.698, +1.716, +3.076, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta_mid2.html b/pages/traits/environment/temperature_delta_mid2.html
index a99990c643..4f0db15b4c 100644
--- a/pages/traits/environment/temperature_delta_mid2.html
+++ b/pages/traits/environment/temperature_delta_mid2.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000486 [-3.073, +0.032, -2.627, +2.668, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_delta_very_low.html b/pages/traits/environment/temperature_delta_very_low.html
index 5848494eed..77d2020577 100644
--- a/pages/traits/environment/temperature_delta_very_low.html
+++ b/pages/traits/environment/temperature_delta_very_low.html
@@ -330,7 +330,7 @@ kg-microbe context
METPO:1000483 [-4.820, -3.932, -4.489, +2.974, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -338,7 +338,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum.html b/pages/traits/environment/temperature_optimum.html
index 6917dd6401..180099cf02 100644
--- a/pages/traits/environment/temperature_optimum.html
+++ b/pages/traits/environment/temperature_optimum.html
@@ -270,7 +270,7 @@ kg-microbe context
METPO:1000304 [-3.535, +0.422, -2.014, +1.133, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -278,7 +278,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_high.html b/pages/traits/environment/temperature_optimum_high.html
index 72acbf2bb6..1c46ae6f57 100644
--- a/pages/traits/environment/temperature_optimum_high.html
+++ b/pages/traits/environment/temperature_optimum_high.html
@@ -360,7 +360,7 @@ kg-microbe context
METPO:1000447 [+1.114, +1.991, -0.944, +1.377, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -368,7 +368,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_low.html b/pages/traits/environment/temperature_optimum_low.html
index 5539a14269..ae45a3c0b8 100644
--- a/pages/traits/environment/temperature_optimum_low.html
+++ b/pages/traits/environment/temperature_optimum_low.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000442 [-5.433, -0.515, -1.647, +0.570, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_mid1.html b/pages/traits/environment/temperature_optimum_mid1.html
index b76b5053cd..0dfe9609ee 100644
--- a/pages/traits/environment/temperature_optimum_mid1.html
+++ b/pages/traits/environment/temperature_optimum_mid1.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000443 [-2.358, -0.748, +0.437, +3.286, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_mid2.html b/pages/traits/environment/temperature_optimum_mid2.html
index 40ae02ea3a..8fccd033b5 100644
--- a/pages/traits/environment/temperature_optimum_mid2.html
+++ b/pages/traits/environment/temperature_optimum_mid2.html
@@ -260,7 +260,7 @@ kg-microbe context
METPO:1000444 [-3.661, -4.062, -0.551, +2.283, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -268,7 +268,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_mid3.html b/pages/traits/environment/temperature_optimum_mid3.html
index 793bbf064d..6965af9c90 100644
--- a/pages/traits/environment/temperature_optimum_mid3.html
+++ b/pages/traits/environment/temperature_optimum_mid3.html
@@ -243,7 +243,7 @@ kg-microbe context
METPO:1000445 [-0.039, -2.246, -0.582, +1.156, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -251,7 +251,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_mid4.html b/pages/traits/environment/temperature_optimum_mid4.html
index ab75be8aab..54eed21b6c 100644
--- a/pages/traits/environment/temperature_optimum_mid4.html
+++ b/pages/traits/environment/temperature_optimum_mid4.html
@@ -311,7 +311,7 @@ kg-microbe context
METPO:1000446 [-0.375, -2.796, -0.478, +0.320, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -319,7 +319,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_optimum_very_low.html b/pages/traits/environment/temperature_optimum_very_low.html
index 26be32fe0a..b9997cea0a 100644
--- a/pages/traits/environment/temperature_optimum_very_low.html
+++ b/pages/traits/environment/temperature_optimum_very_low.html
@@ -383,7 +383,7 @@ kg-microbe context
METPO:1000441 [-4.303, -0.200, +0.305, +0.724, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -391,7 +391,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_phenotype_with_numerical_limits.html b/pages/traits/environment/temperature_phenotype_with_numerical_limits.html
index 4ce4d66499..03fa3e309e 100644
--- a/pages/traits/environment/temperature_phenotype_with_numerical_limits.html
+++ b/pages/traits/environment/temperature_phenotype_with_numerical_limits.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000533 [-3.985, -0.177, -3.580, +0.367, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_preference.html b/pages/traits/environment/temperature_preference.html
index d763cc25b4..38455e5fb6 100644
--- a/pages/traits/environment/temperature_preference.html
+++ b/pages/traits/environment/temperature_preference.html
@@ -349,7 +349,7 @@ kg-microbe context
METPO:1000613 [-1.543, -2.658, -5.268, +1.287, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -357,7 +357,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range.html b/pages/traits/environment/temperature_range.html
index 11c044ce68..d151f151d0 100644
--- a/pages/traits/environment/temperature_range.html
+++ b/pages/traits/environment/temperature_range.html
@@ -338,7 +338,7 @@ kg-microbe context
METPO:1000306 [-3.058, -0.353, -2.836, +1.133, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -346,7 +346,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_high.html b/pages/traits/environment/temperature_range_high.html
index 189df76df2..5d4cc616d2 100644
--- a/pages/traits/environment/temperature_range_high.html
+++ b/pages/traits/environment/temperature_range_high.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000454 [-0.542, -0.105, +0.004, +2.753, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_low.html b/pages/traits/environment/temperature_range_low.html
index 81cc32bca9..3ee77bb67a 100644
--- a/pages/traits/environment/temperature_range_low.html
+++ b/pages/traits/environment/temperature_range_low.html
@@ -260,7 +260,7 @@ kg-microbe context
METPO:1000449 [-2.321, -1.131, -2.283, +3.294, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -268,7 +268,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_mid1.html b/pages/traits/environment/temperature_range_mid1.html
index 17d4e2cbbb..0adc3f0ece 100644
--- a/pages/traits/environment/temperature_range_mid1.html
+++ b/pages/traits/environment/temperature_range_mid1.html
@@ -260,7 +260,7 @@ kg-microbe context
METPO:1000450 [-1.575, -0.696, -2.370, +3.825, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -268,7 +268,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_mid2.html b/pages/traits/environment/temperature_range_mid2.html
index 8faf8a1d23..c2bb7a716f 100644
--- a/pages/traits/environment/temperature_range_mid2.html
+++ b/pages/traits/environment/temperature_range_mid2.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000451 [-1.548, -0.208, -2.721, +3.019, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_mid3.html b/pages/traits/environment/temperature_range_mid3.html
index d39517122a..58662f0d2f 100644
--- a/pages/traits/environment/temperature_range_mid3.html
+++ b/pages/traits/environment/temperature_range_mid3.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000452 [-1.351, +1.368, -2.814, +2.551, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_mid4.html b/pages/traits/environment/temperature_range_mid4.html
index 6d573ef1df..f99b26da75 100644
--- a/pages/traits/environment/temperature_range_mid4.html
+++ b/pages/traits/environment/temperature_range_mid4.html
@@ -311,7 +311,7 @@ kg-microbe context
METPO:1000453 [-2.152, +0.301, -2.280, +3.386, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -319,7 +319,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/temperature_range_very_low.html b/pages/traits/environment/temperature_range_very_low.html
index a1f464985b..052a98f69d 100644
--- a/pages/traits/environment/temperature_range_very_low.html
+++ b/pages/traits/environment/temperature_range_very_low.html
@@ -360,7 +360,7 @@ kg-microbe context
METPO:1000448 [-3.031, -0.161, -1.423, +4.596, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -368,7 +368,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/thermophilic.html b/pages/traits/environment/thermophilic.html
index 0029879f58..340b9acbab 100644
--- a/pages/traits/environment/thermophilic.html
+++ b/pages/traits/environment/thermophilic.html
@@ -281,7 +281,7 @@ kg-microbe context
METPO:1000616 [+21.170, -11.999, -10.457, +4.736, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -289,7 +289,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/thermotolerant.html b/pages/traits/environment/thermotolerant.html
index a999d910bb..c3cdb2445b 100644
--- a/pages/traits/environment/thermotolerant.html
+++ b/pages/traits/environment/thermotolerant.html
@@ -264,7 +264,7 @@ kg-microbe context
METPO:1000619 [-1.721, -2.562, -3.565, +2.040, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -272,7 +272,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/uv_radiation_tolerant.html b/pages/traits/environment/uv_radiation_tolerant.html
index 56dbdc72f5..a9e07ef799 100644
--- a/pages/traits/environment/uv_radiation_tolerant.html
+++ b/pages/traits/environment/uv_radiation_tolerant.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/xerophilic.html b/pages/traits/environment/xerophilic.html
index 460c9f9eb1..b3f8ca9b5a 100644
--- a/pages/traits/environment/xerophilic.html
+++ b/pages/traits/environment/xerophilic.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/environment/zinc_tolerant.html b/pages/traits/environment/zinc_tolerant.html
index 89414c2453..cb5a8c6fe1 100644
--- a/pages/traits/environment/zinc_tolerant.html
+++ b/pages/traits/environment/zinc_tolerant.html
@@ -362,7 +362,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -370,7 +370,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/codon_usage_bias.html b/pages/traits/genomics/codon_usage_bias.html
index e20d9a20f1..875ca928e7 100644
--- a/pages/traits/genomics/codon_usage_bias.html
+++ b/pages/traits/genomics/codon_usage_bias.html
@@ -228,7 +228,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -236,7 +236,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/crispr_cas_system.html b/pages/traits/genomics/crispr_cas_system.html
index 8856d377c5..d598833b66 100644
--- a/pages/traits/genomics/crispr_cas_system.html
+++ b/pages/traits/genomics/crispr_cas_system.html
@@ -320,7 +320,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -328,7 +328,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_content.html b/pages/traits/genomics/gc_content.html
index 0d42b48d93..768da5ed3d 100644
--- a/pages/traits/genomics/gc_content.html
+++ b/pages/traits/genomics/gc_content.html
@@ -330,7 +330,7 @@ kg-microbe context
METPO:1000127 [-0.539, -1.149, -2.445, +1.588, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -338,7 +338,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_high.html b/pages/traits/genomics/gc_high.html
index 2dc02371f1..ae30a35ce7 100644
--- a/pages/traits/genomics/gc_high.html
+++ b/pages/traits/genomics/gc_high.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000432 [+0.921, +1.707, +0.625, +3.297, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_low.html b/pages/traits/genomics/gc_low.html
index b0fc6eb491..7eabda810c 100644
--- a/pages/traits/genomics/gc_low.html
+++ b/pages/traits/genomics/gc_low.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000429 [-2.626, -2.012, +2.413, +3.679, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_mid1.html b/pages/traits/genomics/gc_mid1.html
index 38c9ca3b1b..48e8c3560f 100644
--- a/pages/traits/genomics/gc_mid1.html
+++ b/pages/traits/genomics/gc_mid1.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000430 [-2.804, -2.753, -0.396, +5.171, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_mid2.html b/pages/traits/genomics/gc_mid2.html
index 2972917f1d..135fae00b0 100644
--- a/pages/traits/genomics/gc_mid2.html
+++ b/pages/traits/genomics/gc_mid2.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000431 [-0.166, -0.334, -3.408, +1.036, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/gc_skew.html b/pages/traits/genomics/gc_skew.html
index ce9e356f09..036d0d28bb 100644
--- a/pages/traits/genomics/gc_skew.html
+++ b/pages/traits/genomics/gc_skew.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/genome_size.html b/pages/traits/genomics/genome_size.html
index 8ecc9845d1..80d1d416a0 100644
--- a/pages/traits/genomics/genome_size.html
+++ b/pages/traits/genomics/genome_size.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/genome_streamlining.html b/pages/traits/genomics/genome_streamlining.html
index 2474d940e5..951a01accd 100644
--- a/pages/traits/genomics/genome_streamlining.html
+++ b/pages/traits/genomics/genome_streamlining.html
@@ -245,7 +245,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -253,7 +253,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/genomic_island.html b/pages/traits/genomics/genomic_island.html
index 6a002cf20c..ea719d569c 100644
--- a/pages/traits/genomics/genomic_island.html
+++ b/pages/traits/genomics/genomic_island.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/mobile_genetic_element.html b/pages/traits/genomics/mobile_genetic_element.html
index 81eb5bb2a3..aac835a04b 100644
--- a/pages/traits/genomics/mobile_genetic_element.html
+++ b/pages/traits/genomics/mobile_genetic_element.html
@@ -356,7 +356,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -364,7 +364,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/pangenome_openness.html b/pages/traits/genomics/pangenome_openness.html
index 0cf5440663..d110c348a1 100644
--- a/pages/traits/genomics/pangenome_openness.html
+++ b/pages/traits/genomics/pangenome_openness.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/plasmid_carriage.html b/pages/traits/genomics/plasmid_carriage.html
index 2877ab7425..be3af15978 100644
--- a/pages/traits/genomics/plasmid_carriage.html
+++ b/pages/traits/genomics/plasmid_carriage.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/ploidy.html b/pages/traits/genomics/ploidy.html
index c14ccb1434..ee18b1991b 100644
--- a/pages/traits/genomics/ploidy.html
+++ b/pages/traits/genomics/ploidy.html
@@ -246,7 +246,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -254,7 +254,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/prophage.html b/pages/traits/genomics/prophage.html
index 516f2fc40f..a6ee174e25 100644
--- a/pages/traits/genomics/prophage.html
+++ b/pages/traits/genomics/prophage.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/restriction_modification_system.html b/pages/traits/genomics/restriction_modification_system.html
index 4609470fb9..62538f2c71 100644
--- a/pages/traits/genomics/restriction_modification_system.html
+++ b/pages/traits/genomics/restriction_modification_system.html
@@ -303,7 +303,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -311,7 +311,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/rrna_operon_copy_number.html b/pages/traits/genomics/rrna_operon_copy_number.html
index 885e7e0dc4..11a58dc6a7 100644
--- a/pages/traits/genomics/rrna_operon_copy_number.html
+++ b/pages/traits/genomics/rrna_operon_copy_number.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/genomics/transposable_element.html b/pages/traits/genomics/transposable_element.html
index afeeb99312..b154aedbdf 100644
--- a/pages/traits/genomics/transposable_element.html
+++ b/pages/traits/genomics/transposable_element.html
@@ -241,7 +241,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -249,7 +249,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/accumulates.html b/pages/traits/metabolism/accumulates.html
index e5939c65f4..3ce7f52c8a 100644
--- a/pages/traits/metabolism/accumulates.html
+++ b/pages/traits/metabolism/accumulates.html
@@ -91,7 +91,7 @@ kg-microbe context
METPO:2000210 [-2.005, -0.815, -3.661, -0.676, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -99,7 +99,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/acetoclastic_methanogenesis.html b/pages/traits/metabolism/acetoclastic_methanogenesis.html
index 167b2d1d3f..81c6e74518 100644
--- a/pages/traits/metabolism/acetoclastic_methanogenesis.html
+++ b/pages/traits/metabolism/acetoclastic_methanogenesis.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/acetogenesis.html b/pages/traits/metabolism/acetogenesis.html
index 3e497374dd..600f89e86f 100644
--- a/pages/traits/metabolism/acetogenesis.html
+++ b/pages/traits/metabolism/acetogenesis.html
@@ -439,7 +439,7 @@ kg-microbe context
METPO:1000845 [-0.195, -1.369, -0.856, +1.197, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -447,7 +447,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html b/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html
index 8908597505..e93f94f50d 100644
--- a/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html
+++ b/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/aerobic_respiration.html b/pages/traits/metabolism/aerobic_respiration.html
index cd8af26bff..109dbbc3fc 100644
--- a/pages/traits/metabolism/aerobic_respiration.html
+++ b/pages/traits/metabolism/aerobic_respiration.html
@@ -295,7 +295,7 @@ kg-microbe context
METPO:1000801 [-0.171, -2.146, -1.478, +1.150, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -303,7 +303,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/anaerobic_ammonium_oxidation.html b/pages/traits/metabolism/anaerobic_ammonium_oxidation.html
index c3afe6bdaf..4ddf51b669 100644
--- a/pages/traits/metabolism/anaerobic_ammonium_oxidation.html
+++ b/pages/traits/metabolism/anaerobic_ammonium_oxidation.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/anaerobic_oxidation_of_methane.html b/pages/traits/metabolism/anaerobic_oxidation_of_methane.html
index 1f42697a5b..5ad20b1ea5 100644
--- a/pages/traits/metabolism/anaerobic_oxidation_of_methane.html
+++ b/pages/traits/metabolism/anaerobic_oxidation_of_methane.html
@@ -314,7 +314,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -322,7 +322,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/anaerobic_respiration.html b/pages/traits/metabolism/anaerobic_respiration.html
index df95c8837f..2b5dad3727 100644
--- a/pages/traits/metabolism/anaerobic_respiration.html
+++ b/pages/traits/metabolism/anaerobic_respiration.html
@@ -420,7 +420,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -428,7 +428,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/anoxygenic_photosynthesis.html b/pages/traits/metabolism/anoxygenic_photosynthesis.html
index 10ddf75d98..97a1bac5c3 100644
--- a/pages/traits/metabolism/anoxygenic_photosynthesis.html
+++ b/pages/traits/metabolism/anoxygenic_photosynthesis.html
@@ -297,7 +297,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -305,7 +305,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/aromatic_compound_degradation.html b/pages/traits/metabolism/aromatic_compound_degradation.html
index 8b2090272f..42147c1986 100644
--- a/pages/traits/metabolism/aromatic_compound_degradation.html
+++ b/pages/traits/metabolism/aromatic_compound_degradation.html
@@ -91,7 +91,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html b/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html
index ee0201aa64..df4d9913ff 100644
--- a/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html
+++ b/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html
@@ -84,7 +84,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/arsenate_respiration.html b/pages/traits/metabolism/arsenate_respiration.html
index 934af5c4f1..0bae8ee53f 100644
--- a/pages/traits/metabolism/arsenate_respiration.html
+++ b/pages/traits/metabolism/arsenate_respiration.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/arsenite_oxidation.html b/pages/traits/metabolism/arsenite_oxidation.html
index 1e1dff07f9..7866962729 100644
--- a/pages/traits/metabolism/arsenite_oxidation.html
+++ b/pages/traits/metabolism/arsenite_oxidation.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/assimilates.html b/pages/traits/metabolism/assimilates.html
index fa43d6f859..1d3a6d8303 100644
--- a/pages/traits/metabolism/assimilates.html
+++ b/pages/traits/metabolism/assimilates.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000002 [-1.321, -0.339, -2.420, -0.139, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/biopolymer_degradation.html b/pages/traits/metabolism/biopolymer_degradation.html
index 4f29991b7c..1099e5646c 100644
--- a/pages/traits/metabolism/biopolymer_degradation.html
+++ b/pages/traits/metabolism/biopolymer_degradation.html
@@ -409,7 +409,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -417,7 +417,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/builds_acid_from.html b/pages/traits/metabolism/builds_acid_from.html
index f1fdeebb0a..b50dc01e5f 100644
--- a/pages/traits/metabolism/builds_acid_from.html
+++ b/pages/traits/metabolism/builds_acid_from.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000003 [-1.238, -0.104, -2.195, -0.166, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/builds_base_from.html b/pages/traits/metabolism/builds_base_from.html
index 7c448a1b12..7a153cc7e2 100644
--- a/pages/traits/metabolism/builds_base_from.html
+++ b/pages/traits/metabolism/builds_base_from.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000004 [-1.245, -0.324, -2.328, -0.147, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/builds_gas_from.html b/pages/traits/metabolism/builds_gas_from.html
index 8d5fc0aa23..fe0fa3fac6 100644
--- a/pages/traits/metabolism/builds_gas_from.html
+++ b/pages/traits/metabolism/builds_gas_from.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000005 [-1.262, -0.471, -2.520, -0.163, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/butanediol_fermentation.html b/pages/traits/metabolism/butanediol_fermentation.html
index 38b1a0f061..50df4553e2 100644
--- a/pages/traits/metabolism/butanediol_fermentation.html
+++ b/pages/traits/metabolism/butanediol_fermentation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/butyric_acid_fermentation.html b/pages/traits/metabolism/butyric_acid_fermentation.html
index dfb2c2026c..5965ca8123 100644
--- a/pages/traits/metabolism/butyric_acid_fermentation.html
+++ b/pages/traits/metabolism/butyric_acid_fermentation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/cable_bacteria_metabolism.html b/pages/traits/metabolism/cable_bacteria_metabolism.html
index 72e1a7e6c4..fd87f53aba 100644
--- a/pages/traits/metabolism/cable_bacteria_metabolism.html
+++ b/pages/traits/metabolism/cable_bacteria_metabolism.html
@@ -446,7 +446,7 @@ kg-microbe context
METPO:1002003 [+0.053, -0.795, -1.040, -0.108, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -454,7 +454,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/calvin_benson_bassham_cycle.html b/pages/traits/metabolism/calvin_benson_bassham_cycle.html
index 541525a7b3..0c3beb0fca 100644
--- a/pages/traits/metabolism/calvin_benson_bassham_cycle.html
+++ b/pages/traits/metabolism/calvin_benson_bassham_cycle.html
@@ -390,7 +390,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -398,7 +398,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/capable_of.html b/pages/traits/metabolism/capable_of.html
index 92714ae23d..9d8442b721 100644
--- a/pages/traits/metabolism/capable_of.html
+++ b/pages/traits/metabolism/capable_of.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:2000103 [-0.096, -0.006, -0.056, -0.047, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/carbon_fixation.html b/pages/traits/metabolism/carbon_fixation.html
index 3c43a47003..6b02aeb6a3 100644
--- a/pages/traits/metabolism/carbon_fixation.html
+++ b/pages/traits/metabolism/carbon_fixation.html
@@ -439,7 +439,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -447,7 +447,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/cellulolysis.html b/pages/traits/metabolism/cellulolysis.html
index f1aac1ead1..4f9d086d1a 100644
--- a/pages/traits/metabolism/cellulolysis.html
+++ b/pages/traits/metabolism/cellulolysis.html
@@ -441,7 +441,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -449,7 +449,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/chitinolysis.html b/pages/traits/metabolism/chitinolysis.html
index 6074624e22..5eb66a9c8c 100644
--- a/pages/traits/metabolism/chitinolysis.html
+++ b/pages/traits/metabolism/chitinolysis.html
@@ -350,7 +350,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -358,7 +358,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/citrate_fermentation.html b/pages/traits/metabolism/citrate_fermentation.html
index b5f8962ef7..709ff03992 100644
--- a/pages/traits/metabolism/citrate_fermentation.html
+++ b/pages/traits/metabolism/citrate_fermentation.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/compartmentalizes.html b/pages/traits/metabolism/compartmentalizes.html
index 73893024fe..98004a9791 100644
--- a/pages/traits/metabolism/compartmentalizes.html
+++ b/pages/traits/metabolism/compartmentalizes.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000212 [-1.839, -0.962, -3.410, -0.263, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/complete_ammonia_oxidation.html b/pages/traits/metabolism/complete_ammonia_oxidation.html
index dd7349fa6d..22362f1415 100644
--- a/pages/traits/metabolism/complete_ammonia_oxidation.html
+++ b/pages/traits/metabolism/complete_ammonia_oxidation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/dark_hydrogen_oxidation.html b/pages/traits/metabolism/dark_hydrogen_oxidation.html
index de152f353c..e0c5864aea 100644
--- a/pages/traits/metabolism/dark_hydrogen_oxidation.html
+++ b/pages/traits/metabolism/dark_hydrogen_oxidation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html b/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html
index 42e404777a..a6525fec92 100644
--- a/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html
+++ b/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/degrades.html b/pages/traits/metabolism/degrades.html
index 0a9a7ff22d..20a0ac1f62 100644
--- a/pages/traits/metabolism/degrades.html
+++ b/pages/traits/metabolism/degrades.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000007 [-1.236, -0.298, -2.385, -0.099, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/denitrification.html b/pages/traits/metabolism/denitrification.html
index 7c23ca0653..e5d61a1ce5 100644
--- a/pages/traits/metabolism/denitrification.html
+++ b/pages/traits/metabolism/denitrification.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html b/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html
index c0b630ab4b..962eaa1fef 100644
--- a/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html
+++ b/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/disproportionates.html b/pages/traits/metabolism/disproportionates.html
index 81e7b684ec..f68c25b0da 100644
--- a/pages/traits/metabolism/disproportionates.html
+++ b/pages/traits/metabolism/disproportionates.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000200 [-1.290, -0.244, -2.346, -0.220, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/disproportionation.html b/pages/traits/metabolism/disproportionation.html
index b40af650e5..e7ea85a572 100644
--- a/pages/traits/metabolism/disproportionation.html
+++ b/pages/traits/metabolism/disproportionation.html
@@ -413,7 +413,7 @@ kg-microbe context
METPO:1000806 [-0.155, -1.068, -1.362, +0.081, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -421,7 +421,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dissimilatory_iron_reduction.html b/pages/traits/metabolism/dissimilatory_iron_reduction.html
index 7afecbfe62..4cd465ea7e 100644
--- a/pages/traits/metabolism/dissimilatory_iron_reduction.html
+++ b/pages/traits/metabolism/dissimilatory_iron_reduction.html
@@ -322,7 +322,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -330,7 +330,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dissimilatory_manganese_reduction.html b/pages/traits/metabolism/dissimilatory_manganese_reduction.html
index fe887d26af..a4c251a209 100644
--- a/pages/traits/metabolism/dissimilatory_manganese_reduction.html
+++ b/pages/traits/metabolism/dissimilatory_manganese_reduction.html
@@ -286,7 +286,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -294,7 +294,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dissimilatory_metal_reduction.html b/pages/traits/metabolism/dissimilatory_metal_reduction.html
index a6b2143940..cb32af97c3 100644
--- a/pages/traits/metabolism/dissimilatory_metal_reduction.html
+++ b/pages/traits/metabolism/dissimilatory_metal_reduction.html
@@ -331,7 +331,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -339,7 +339,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html b/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html
index 5ae2e6a3aa..650e268092 100644
--- a/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html
+++ b/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html
@@ -356,7 +356,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -364,7 +364,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/dissimilatory_sulfate_reduction.html b/pages/traits/metabolism/dissimilatory_sulfate_reduction.html
index b47b0db52a..9129150d47 100644
--- a/pages/traits/metabolism/dissimilatory_sulfate_reduction.html
+++ b/pages/traits/metabolism/dissimilatory_sulfate_reduction.html
@@ -396,7 +396,7 @@ kg-microbe context
METPO:1000802 [-0.426, -1.069, -1.023, +1.207, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -404,7 +404,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_accumulate.html b/pages/traits/metabolism/does_not_accumulate.html
index dc2b4179ab..0947551706 100644
--- a/pages/traits/metabolism/does_not_accumulate.html
+++ b/pages/traits/metabolism/does_not_accumulate.html
@@ -91,7 +91,7 @@ kg-microbe context
METPO:2000230 [-1.864, -0.661, -2.991, +0.368, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -99,7 +99,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_assimilate.html b/pages/traits/metabolism/does_not_assimilate.html
index 8785bb4c44..ddcfb81026 100644
--- a/pages/traits/metabolism/does_not_assimilate.html
+++ b/pages/traits/metabolism/does_not_assimilate.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000027 [-1.286, -0.307, -2.407, -0.248, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_build_acid_from.html b/pages/traits/metabolism/does_not_build_acid_from.html
index 318888d7db..aab9d91c74 100644
--- a/pages/traits/metabolism/does_not_build_acid_from.html
+++ b/pages/traits/metabolism/does_not_build_acid_from.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000028 [-1.205, -0.280, -2.303, -0.240, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_build_base_from.html b/pages/traits/metabolism/does_not_build_base_from.html
index d0fb7e783e..22e40c4199 100644
--- a/pages/traits/metabolism/does_not_build_base_from.html
+++ b/pages/traits/metabolism/does_not_build_base_from.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000029 [-1.324, -0.393, -2.396, -0.085, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_build_gas_from.html b/pages/traits/metabolism/does_not_build_gas_from.html
index cf39e53628..09bf40e4c2 100644
--- a/pages/traits/metabolism/does_not_build_gas_from.html
+++ b/pages/traits/metabolism/does_not_build_gas_from.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000030 [-1.248, -0.258, -2.248, -0.246, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_compartmentalize.html b/pages/traits/metabolism/does_not_compartmentalize.html
index 68b4536bbf..2e1f52bc57 100644
--- a/pages/traits/metabolism/does_not_compartmentalize.html
+++ b/pages/traits/metabolism/does_not_compartmentalize.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000232 [-1.896, -0.608, -2.676, +0.526, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_degrade.html b/pages/traits/metabolism/does_not_degrade.html
index ad42973db0..551d8fb2c6 100644
--- a/pages/traits/metabolism/does_not_degrade.html
+++ b/pages/traits/metabolism/does_not_degrade.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000033 [-1.371, -0.337, -2.532, -0.027, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_disproportionate.html b/pages/traits/metabolism/does_not_disproportionate.html
index 2c87a3fd00..81efcfca19 100644
--- a/pages/traits/metabolism/does_not_disproportionate.html
+++ b/pages/traits/metabolism/does_not_disproportionate.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000220 [-1.159, -0.182, -2.321, -0.260, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_export.html b/pages/traits/metabolism/does_not_export.html
index 74a9847da0..77cd7f3e5d 100644
--- a/pages/traits/metabolism/does_not_export.html
+++ b/pages/traits/metabolism/does_not_export.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000229 [-0.866, -0.718, -2.686, -0.285, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_ferment.html b/pages/traits/metabolism/does_not_ferment.html
index ae3a034665..d3708efddd 100644
--- a/pages/traits/metabolism/does_not_ferment.html
+++ b/pages/traits/metabolism/does_not_ferment.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000037 [-1.311, -0.384, -2.411, -0.128, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_hydrolyze.html b/pages/traits/metabolism/does_not_hydrolyze.html
index 4957489f25..72ad61547d 100644
--- a/pages/traits/metabolism/does_not_hydrolyze.html
+++ b/pages/traits/metabolism/does_not_hydrolyze.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000039 [-1.344, -0.234, -2.324, -0.112, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_import.html b/pages/traits/metabolism/does_not_import.html
index e2654fae75..b5deaee28e 100644
--- a/pages/traits/metabolism/does_not_import.html
+++ b/pages/traits/metabolism/does_not_import.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000228 [-0.937, -0.910, -2.615, -0.265, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_oxidize.html b/pages/traits/metabolism/does_not_oxidize.html
index eb88c4c11e..a027e75a8a 100644
--- a/pages/traits/metabolism/does_not_oxidize.html
+++ b/pages/traits/metabolism/does_not_oxidize.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000042 [-1.206, -0.564, -2.510, -0.326, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_produce.html b/pages/traits/metabolism/does_not_produce.html
index 3111a66f4f..ce1b677a1d 100644
--- a/pages/traits/metabolism/does_not_produce.html
+++ b/pages/traits/metabolism/does_not_produce.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000222 [-1.278, -0.385, -2.563, -0.283, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_reduce.html b/pages/traits/metabolism/does_not_reduce.html
index 9dea158b02..1d8cd23c4e 100644
--- a/pages/traits/metabolism/does_not_reduce.html
+++ b/pages/traits/metabolism/does_not_reduce.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000044 [-1.399, -0.317, -2.415, -0.124, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_sequester.html b/pages/traits/metabolism/does_not_sequester.html
index 7122954151..45951de425 100644
--- a/pages/traits/metabolism/does_not_sequester.html
+++ b/pages/traits/metabolism/does_not_sequester.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000231 [-1.833, -0.611, -2.662, +0.612, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_show_activity_of.html b/pages/traits/metabolism/does_not_show_activity_of.html
index c28c7144d8..045604bbc1 100644
--- a/pages/traits/metabolism/does_not_show_activity_of.html
+++ b/pages/traits/metabolism/does_not_show_activity_of.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000303 [-1.154, -1.700, -0.583, -0.926, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_transport.html b/pages/traits/metabolism/does_not_transport.html
index a7666b3572..39a1f0f03b 100644
--- a/pages/traits/metabolism/does_not_transport.html
+++ b/pages/traits/metabolism/does_not_transport.html
@@ -91,7 +91,7 @@ kg-microbe context
METPO:2000227 [-0.802, -0.930, -2.770, -0.508, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -99,7 +99,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_carbon_source.html b/pages/traits/metabolism/does_not_use_as_carbon_source.html
index e0e8d0a8c8..9e8a3e09b6 100644
--- a/pages/traits/metabolism/does_not_use_as_carbon_source.html
+++ b/pages/traits/metabolism/does_not_use_as_carbon_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000031 [-1.412, -0.334, -2.248, -0.175, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_electron_acceptor.html b/pages/traits/metabolism/does_not_use_as_electron_acceptor.html
index 0a6f331f6e..983502a81f 100644
--- a/pages/traits/metabolism/does_not_use_as_electron_acceptor.html
+++ b/pages/traits/metabolism/does_not_use_as_electron_acceptor.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000034 [-1.270, -0.393, -2.494, -0.168, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_electron_donor.html b/pages/traits/metabolism/does_not_use_as_electron_donor.html
index 76abbd3f67..93c14a7b1c 100644
--- a/pages/traits/metabolism/does_not_use_as_electron_donor.html
+++ b/pages/traits/metabolism/does_not_use_as_electron_donor.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000035 [-1.265, -0.214, -2.420, -0.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_energy_source.html b/pages/traits/metabolism/does_not_use_as_energy_source.html
index e0ce527d7c..280c722f68 100644
--- a/pages/traits/metabolism/does_not_use_as_energy_source.html
+++ b/pages/traits/metabolism/does_not_use_as_energy_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000036 [-1.315, -0.164, -2.374, -0.206, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_nitrogen_source.html b/pages/traits/metabolism/does_not_use_as_nitrogen_source.html
index 121e8c3378..18b077507c 100644
--- a/pages/traits/metabolism/does_not_use_as_nitrogen_source.html
+++ b/pages/traits/metabolism/does_not_use_as_nitrogen_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000040 [-1.154, -0.237, -2.451, -0.149, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_as_sulfur_source.html b/pages/traits/metabolism/does_not_use_as_sulfur_source.html
index adcc68f4be..b15ceec745 100644
--- a/pages/traits/metabolism/does_not_use_as_sulfur_source.html
+++ b/pages/traits/metabolism/does_not_use_as_sulfur_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000047 [-1.291, -0.204, -2.374, -0.095, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html b/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html
index 1893756b0b..9cd59c7d11 100644
--- a/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html
+++ b/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000021 [-1.263, -0.348, -2.310, -0.201, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_aerobic_growth.html b/pages/traits/metabolism/does_not_use_for_aerobic_growth.html
index 30bdf8a782..7f86d9c471 100644
--- a/pages/traits/metabolism/does_not_use_for_aerobic_growth.html
+++ b/pages/traits/metabolism/does_not_use_for_aerobic_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000022 [-1.206, -0.225, -2.389, -0.218, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html b/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html
index 26147fcbab..2f2b9763e0 100644
--- a/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html
+++ b/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000023 [-1.179, -0.262, -2.266, -0.122, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html
index 69552cfce6..14ee668b55 100644
--- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html
+++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000024 [-1.267, -0.231, -2.365, -0.145, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html
index c4bfda8de6..e03ecd8f87 100644
--- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html
+++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000025 [-1.264, -0.144, -2.450, -0.129, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html
index 226d3ecbe7..b4298c4206 100644
--- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html
+++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000026 [-1.340, -0.140, -2.462, -0.066, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_growth.html b/pages/traits/metabolism/does_not_use_for_growth.html
index 6295f9dbcb..f13eba8c98 100644
--- a/pages/traits/metabolism/does_not_use_for_growth.html
+++ b/pages/traits/metabolism/does_not_use_for_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000038 [-1.373, -0.347, -2.345, -0.259, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_for_respiration.html b/pages/traits/metabolism/does_not_use_for_respiration.html
index fab2079612..a83ba41765 100644
--- a/pages/traits/metabolism/does_not_use_for_respiration.html
+++ b/pages/traits/metabolism/does_not_use_for_respiration.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000046 [-1.171, -0.162, -2.417, -0.089, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/does_not_use_in_other_way.html b/pages/traits/metabolism/does_not_use_in_other_way.html
index 559d8ed2a9..99afcf6929 100644
--- a/pages/traits/metabolism/does_not_use_in_other_way.html
+++ b/pages/traits/metabolism/does_not_use_in_other_way.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000041 [-1.399, -0.155, -2.247, -0.135, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/electron_transfer.html b/pages/traits/metabolism/electron_transfer.html
index be05328472..a59bf13988 100644
--- a/pages/traits/metabolism/electron_transfer.html
+++ b/pages/traits/metabolism/electron_transfer.html
@@ -430,7 +430,7 @@ kg-microbe context
METPO:1000805 [-0.425, -0.393, -1.506, +0.156, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -438,7 +438,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/enzyme_activity_analyzed.html b/pages/traits/metabolism/enzyme_activity_analyzed.html
index bc8682f320..7731236d72 100644
--- a/pages/traits/metabolism/enzyme_activity_analyzed.html
+++ b/pages/traits/metabolism/enzyme_activity_analyzed.html
@@ -91,7 +91,7 @@ kg-microbe context
METPO:2000301 [-1.199, -1.757, -0.485, -1.099, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -99,7 +99,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/ethanol_fermentation.html b/pages/traits/metabolism/ethanol_fermentation.html
index 11bb52ff8f..f43e5c8f93 100644
--- a/pages/traits/metabolism/ethanol_fermentation.html
+++ b/pages/traits/metabolism/ethanol_fermentation.html
@@ -329,7 +329,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -337,7 +337,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/exports.html b/pages/traits/metabolism/exports.html
index db48f5fdd8..5af81d3e03 100644
--- a/pages/traits/metabolism/exports.html
+++ b/pages/traits/metabolism/exports.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000209 [-1.508, -0.086, -2.445, -0.073, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/fermentation.html b/pages/traits/metabolism/fermentation.html
index fe20770574..45ce48f740 100644
--- a/pages/traits/metabolism/fermentation.html
+++ b/pages/traits/metabolism/fermentation.html
@@ -445,7 +445,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -453,7 +453,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/fermentative_hydrogen_production.html b/pages/traits/metabolism/fermentative_hydrogen_production.html
index 96166de4c7..579e19c1d5 100644
--- a/pages/traits/metabolism/fermentative_hydrogen_production.html
+++ b/pages/traits/metabolism/fermentative_hydrogen_production.html
@@ -269,7 +269,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -277,7 +277,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/ferments.html b/pages/traits/metabolism/ferments.html
index 401f926e62..42bfb2d3ae 100644
--- a/pages/traits/metabolism/ferments.html
+++ b/pages/traits/metabolism/ferments.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000011 [-1.137, -0.154, -2.250, -0.147, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_growth_nacl_observation.html b/pages/traits/metabolism/has_growth_nacl_observation.html
index 9699f6f5c5..0d79e7509c 100644
--- a/pages/traits/metabolism/has_growth_nacl_observation.html
+++ b/pages/traits/metabolism/has_growth_nacl_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000508 [+0.015, -0.081, +0.019, -0.018, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_growth_oxygen_observation.html b/pages/traits/metabolism/has_growth_oxygen_observation.html
index f888ca15f6..2ef0573739 100644
--- a/pages/traits/metabolism/has_growth_oxygen_observation.html
+++ b/pages/traits/metabolism/has_growth_oxygen_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000514 [+0.098, -0.086, +0.038, +0.073, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_growth_ph_observation.html b/pages/traits/metabolism/has_growth_ph_observation.html
index 14cd144f58..7f58c53a7a 100644
--- a/pages/traits/metabolism/has_growth_ph_observation.html
+++ b/pages/traits/metabolism/has_growth_ph_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000502 [+0.036, +0.084, +0.103, +0.076, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_growth_temperature_observation.html b/pages/traits/metabolism/has_growth_temperature_observation.html
index 93d67b03af..c4822cd7be 100644
--- a/pages/traits/metabolism/has_growth_temperature_observation.html
+++ b/pages/traits/metabolism/has_growth_temperature_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000054 [-0.079, -0.077, -0.022, -0.008, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_nacl_delta_observation.html b/pages/traits/metabolism/has_nacl_delta_observation.html
index 7ef2f9195d..81d36d6e2a 100644
--- a/pages/traits/metabolism/has_nacl_delta_observation.html
+++ b/pages/traits/metabolism/has_nacl_delta_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000510 [+0.104, +0.078, +0.108, +0.063, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_nacl_observation.html b/pages/traits/metabolism/has_nacl_observation.html
index 06aca826f3..85ac163e34 100644
--- a/pages/traits/metabolism/has_nacl_observation.html
+++ b/pages/traits/metabolism/has_nacl_observation.html
@@ -95,7 +95,7 @@ kg-microbe context
METPO:2000506 [+0.093, -0.023, -0.063, +0.040, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -103,7 +103,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_observation.html b/pages/traits/metabolism/has_observation.html
index 4171deca27..7721d256bc 100644
--- a/pages/traits/metabolism/has_observation.html
+++ b/pages/traits/metabolism/has_observation.html
@@ -84,7 +84,7 @@ kg-microbe context
METPO:2000511 [-0.072, -0.027, +0.027, +0.075, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -92,7 +92,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_optimum_nacl_observation.html b/pages/traits/metabolism/has_optimum_nacl_observation.html
index a344a58c47..b686089094 100644
--- a/pages/traits/metabolism/has_optimum_nacl_observation.html
+++ b/pages/traits/metabolism/has_optimum_nacl_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000507 [-0.083, +0.042, +0.104, +0.012, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_optimum_oxygen_observation.html b/pages/traits/metabolism/has_optimum_oxygen_observation.html
index cdc25121ea..4f45dc3525 100644
--- a/pages/traits/metabolism/has_optimum_oxygen_observation.html
+++ b/pages/traits/metabolism/has_optimum_oxygen_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000513 [+0.084, +0.077, -0.016, -0.000, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_optimum_ph_observation.html b/pages/traits/metabolism/has_optimum_ph_observation.html
index d8f1a3d460..86a7f99c9d 100644
--- a/pages/traits/metabolism/has_optimum_ph_observation.html
+++ b/pages/traits/metabolism/has_optimum_ph_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000501 [+0.022, +0.084, -0.038, -0.059, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_optimum_temperature_observation.html b/pages/traits/metabolism/has_optimum_temperature_observation.html
index 188a1a7263..55d2b02a2b 100644
--- a/pages/traits/metabolism/has_optimum_temperature_observation.html
+++ b/pages/traits/metabolism/has_optimum_temperature_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000053 [-0.086, -0.074, +0.082, -0.093, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_oxygen_delta_observation.html b/pages/traits/metabolism/has_oxygen_delta_observation.html
index f30bb345d0..01dca0d5a0 100644
--- a/pages/traits/metabolism/has_oxygen_delta_observation.html
+++ b/pages/traits/metabolism/has_oxygen_delta_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000516 [-0.097, +0.084, -0.075, -0.027, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_oxygen_observation.html b/pages/traits/metabolism/has_oxygen_observation.html
index 2e90e4e634..cca1100788 100644
--- a/pages/traits/metabolism/has_oxygen_observation.html
+++ b/pages/traits/metabolism/has_oxygen_observation.html
@@ -95,7 +95,7 @@ kg-microbe context
METPO:2000512 [+0.090, +0.046, +0.005, -0.089, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -103,7 +103,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_ph_delta_observation.html b/pages/traits/metabolism/has_ph_delta_observation.html
index 8ee3e2a4a5..75c088ce1f 100644
--- a/pages/traits/metabolism/has_ph_delta_observation.html
+++ b/pages/traits/metabolism/has_ph_delta_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000504 [-0.024, +0.031, -0.041, -0.020, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_ph_observation.html b/pages/traits/metabolism/has_ph_observation.html
index d2cd7f236c..c5d91d591f 100644
--- a/pages/traits/metabolism/has_ph_observation.html
+++ b/pages/traits/metabolism/has_ph_observation.html
@@ -95,7 +95,7 @@ kg-microbe context
METPO:2000239 [-0.061, +0.077, -0.071, +0.026, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -103,7 +103,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_phenotype.html b/pages/traits/metabolism/has_phenotype.html
index d66fa286dd..da8313e833 100644
--- a/pages/traits/metabolism/has_phenotype.html
+++ b/pages/traits/metabolism/has_phenotype.html
@@ -85,7 +85,7 @@ kg-microbe context
METPO:2000102 [-0.520, -1.796, -1.085, +0.793, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -93,7 +93,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_quality.html b/pages/traits/metabolism/has_quality.html
index 41b75119e2..22b414167b 100644
--- a/pages/traits/metabolism/has_quality.html
+++ b/pages/traits/metabolism/has_quality.html
@@ -85,7 +85,7 @@ kg-microbe context
METPO:2000101 [-0.759, -1.885, -0.724, +0.560, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -93,7 +93,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_range_nacl_observation.html b/pages/traits/metabolism/has_range_nacl_observation.html
index 13a0dcdd48..35e782fb1a 100644
--- a/pages/traits/metabolism/has_range_nacl_observation.html
+++ b/pages/traits/metabolism/has_range_nacl_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000509 [-0.060, -0.035, +0.101, +0.031, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_range_oxygen_observation.html b/pages/traits/metabolism/has_range_oxygen_observation.html
index a722a2dd43..d91ff2ce02 100644
--- a/pages/traits/metabolism/has_range_oxygen_observation.html
+++ b/pages/traits/metabolism/has_range_oxygen_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000515 [-0.032, +0.032, -0.020, -0.053, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_range_ph_observation.html b/pages/traits/metabolism/has_range_ph_observation.html
index 24de0ede22..8bef59b89e 100644
--- a/pages/traits/metabolism/has_range_ph_observation.html
+++ b/pages/traits/metabolism/has_range_ph_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000503 [+0.046, -0.047, +0.053, +0.056, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_range_temperature_observation.html b/pages/traits/metabolism/has_range_temperature_observation.html
index c20a5f3667..796e8bcd82 100644
--- a/pages/traits/metabolism/has_range_temperature_observation.html
+++ b/pages/traits/metabolism/has_range_temperature_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000055 [+0.074, +0.056, -0.073, -0.054, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_temperature_delta_observation.html b/pages/traits/metabolism/has_temperature_delta_observation.html
index c636bb33e4..5363b61530 100644
--- a/pages/traits/metabolism/has_temperature_delta_observation.html
+++ b/pages/traits/metabolism/has_temperature_delta_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000056 [+0.099, -0.056, +0.003, +0.031, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/has_temperature_observation.html b/pages/traits/metabolism/has_temperature_observation.html
index 61eaef4d77..67a7751aa3 100644
--- a/pages/traits/metabolism/has_temperature_observation.html
+++ b/pages/traits/metabolism/has_temperature_observation.html
@@ -95,7 +95,7 @@ kg-microbe context
METPO:2000052 [-0.077, -0.027, +0.041, +0.010, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -103,7 +103,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/homoacetogenesis.html b/pages/traits/metabolism/homoacetogenesis.html
index ef751ee885..dc317a1f10 100644
--- a/pages/traits/metabolism/homoacetogenesis.html
+++ b/pages/traits/metabolism/homoacetogenesis.html
@@ -532,7 +532,7 @@ kg-microbe context
METPO:1000846 [-0.148, -0.934, -1.245, +0.063, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -540,7 +540,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/hydrocarbon_degradation.html b/pages/traits/metabolism/hydrocarbon_degradation.html
index b9d795861f..2f51957c2a 100644
--- a/pages/traits/metabolism/hydrocarbon_degradation.html
+++ b/pages/traits/metabolism/hydrocarbon_degradation.html
@@ -98,7 +98,7 @@ Cross-references
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html b/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html
index b44131bf00..ed28ff39fd 100644
--- a/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html
+++ b/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/hydrolyzes.html b/pages/traits/metabolism/hydrolyzes.html
index 9df8505d59..4522576c8c 100644
--- a/pages/traits/metabolism/hydrolyzes.html
+++ b/pages/traits/metabolism/hydrolyzes.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000013 [-1.446, -0.206, -2.474, +0.001, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/imports.html b/pages/traits/metabolism/imports.html
index 1665da9da6..0e63e6f317 100644
--- a/pages/traits/metabolism/imports.html
+++ b/pages/traits/metabolism/imports.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000208 [-1.353, -0.126, -2.494, -0.028, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/iron_oxidation.html b/pages/traits/metabolism/iron_oxidation.html
index 77f13b0105..bbbd0e4ff4 100644
--- a/pages/traits/metabolism/iron_oxidation.html
+++ b/pages/traits/metabolism/iron_oxidation.html
@@ -363,7 +363,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -371,7 +371,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/is_not_required_for_growth.html b/pages/traits/metabolism/is_not_required_for_growth.html
index d8c0c3c839..2105829e43 100644
--- a/pages/traits/metabolism/is_not_required_for_growth.html
+++ b/pages/traits/metabolism/is_not_required_for_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000045 [-1.197, -0.313, -2.507, -0.156, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/lactic_acid_fermentation.html b/pages/traits/metabolism/lactic_acid_fermentation.html
index b41a5b66fe..e0643a8b64 100644
--- a/pages/traits/metabolism/lactic_acid_fermentation.html
+++ b/pages/traits/metabolism/lactic_acid_fermentation.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/lignin_degradation.html b/pages/traits/metabolism/lignin_degradation.html
index b5e0664c3c..8e414b9884 100644
--- a/pages/traits/metabolism/lignin_degradation.html
+++ b/pages/traits/metabolism/lignin_degradation.html
@@ -382,7 +382,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -390,7 +390,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/lipolysis.html b/pages/traits/metabolism/lipolysis.html
index af7141f638..ef01386e66 100644
--- a/pages/traits/metabolism/lipolysis.html
+++ b/pages/traits/metabolism/lipolysis.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/manganese_oxidation.html b/pages/traits/metabolism/manganese_oxidation.html
index 9f68550cb4..43714dbfe2 100644
--- a/pages/traits/metabolism/manganese_oxidation.html
+++ b/pages/traits/metabolism/manganese_oxidation.html
@@ -337,7 +337,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -345,7 +345,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/metabolism.html b/pages/traits/metabolism/metabolism.html
index d69cc64ec7..c73b08d7fa 100644
--- a/pages/traits/metabolism/metabolism.html
+++ b/pages/traits/metabolism/metabolism.html
@@ -441,7 +441,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -449,7 +449,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/methanogenesis.html b/pages/traits/metabolism/methanogenesis.html
index 45887d473c..2e587d3266 100644
--- a/pages/traits/metabolism/methanogenesis.html
+++ b/pages/traits/metabolism/methanogenesis.html
@@ -425,7 +425,7 @@ kg-microbe context
METPO:1000844 [+2.183, -3.599, -0.641, +0.610, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -433,7 +433,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/methanol_oxidation.html b/pages/traits/metabolism/methanol_oxidation.html
index 8fb2071027..e9d5630857 100644
--- a/pages/traits/metabolism/methanol_oxidation.html
+++ b/pages/traits/metabolism/methanol_oxidation.html
@@ -89,7 +89,7 @@ Cross-references
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/methyl_based_methanogenesis.html b/pages/traits/metabolism/methyl_based_methanogenesis.html
index 4dfcdf779e..073d0def7a 100644
--- a/pages/traits/metabolism/methyl_based_methanogenesis.html
+++ b/pages/traits/metabolism/methyl_based_methanogenesis.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/mixed_acid_fermentation.html b/pages/traits/metabolism/mixed_acid_fermentation.html
index 6f8db47dbf..9054a5b076 100644
--- a/pages/traits/metabolism/mixed_acid_fermentation.html
+++ b/pages/traits/metabolism/mixed_acid_fermentation.html
@@ -396,7 +396,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -404,7 +404,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/nitrate_reduction.html b/pages/traits/metabolism/nitrate_reduction.html
index 884beeac23..01a4fb245d 100644
--- a/pages/traits/metabolism/nitrate_reduction.html
+++ b/pages/traits/metabolism/nitrate_reduction.html
@@ -91,7 +91,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/nitrate_respiration.html b/pages/traits/metabolism/nitrate_respiration.html
index 62dfbe4afd..4c8bfa2de4 100644
--- a/pages/traits/metabolism/nitrate_respiration.html
+++ b/pages/traits/metabolism/nitrate_respiration.html
@@ -95,7 +95,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/nitrification.html b/pages/traits/metabolism/nitrification.html
index f9d5694c4d..9852ce6fb9 100644
--- a/pages/traits/metabolism/nitrification.html
+++ b/pages/traits/metabolism/nitrification.html
@@ -82,7 +82,7 @@ Children (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/nitrite_respiration.html b/pages/traits/metabolism/nitrite_respiration.html
index 2648268a33..349b24e827 100644
--- a/pages/traits/metabolism/nitrite_respiration.html
+++ b/pages/traits/metabolism/nitrite_respiration.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/nitrogen_fixation.html b/pages/traits/metabolism/nitrogen_fixation.html
index 8a12e5556e..35b8530db1 100644
--- a/pages/traits/metabolism/nitrogen_fixation.html
+++ b/pages/traits/metabolism/nitrogen_fixation.html
@@ -344,7 +344,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -352,7 +352,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/nitrogen_respiration.html b/pages/traits/metabolism/nitrogen_respiration.html
index f35e612bfc..9a31c2803c 100644
--- a/pages/traits/metabolism/nitrogen_respiration.html
+++ b/pages/traits/metabolism/nitrogen_respiration.html
@@ -95,7 +95,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/organism_interacts_with_chemical.html b/pages/traits/metabolism/organism_interacts_with_chemical.html
index 821a2f4ec3..507583ceab 100644
--- a/pages/traits/metabolism/organism_interacts_with_chemical.html
+++ b/pages/traits/metabolism/organism_interacts_with_chemical.html
@@ -194,7 +194,7 @@ kg-microbe context
METPO:2000001 [-2.274, -0.169, -3.849, -0.731, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -202,7 +202,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/oxidative_phosphorylation.html b/pages/traits/metabolism/oxidative_phosphorylation.html
index ad44b2ca0c..5d6fa01cd7 100644
--- a/pages/traits/metabolism/oxidative_phosphorylation.html
+++ b/pages/traits/metabolism/oxidative_phosphorylation.html
@@ -412,7 +412,7 @@ kg-microbe context
METPO:1000803 [-1.060, -0.950, -1.248, -0.351, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -420,7 +420,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/oxidizes.html b/pages/traits/metabolism/oxidizes.html
index 3dbcd58397..4df188a3e1 100644
--- a/pages/traits/metabolism/oxidizes.html
+++ b/pages/traits/metabolism/oxidizes.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000016 [-1.419, -0.244, -2.446, -0.185, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/oxygenic_photosynthesis.html b/pages/traits/metabolism/oxygenic_photosynthesis.html
index d9593abf25..ec235c55ec 100644
--- a/pages/traits/metabolism/oxygenic_photosynthesis.html
+++ b/pages/traits/metabolism/oxygenic_photosynthesis.html
@@ -371,7 +371,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -379,7 +379,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/pectin_degradation.html b/pages/traits/metabolism/pectin_degradation.html
index e39a384f6f..775b52de2b 100644
--- a/pages/traits/metabolism/pectin_degradation.html
+++ b/pages/traits/metabolism/pectin_degradation.html
@@ -95,7 +95,7 @@ Cross-references
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/photoferrotrophy.html b/pages/traits/metabolism/photoferrotrophy.html
index e2c7e339c2..2b592c9fce 100644
--- a/pages/traits/metabolism/photoferrotrophy.html
+++ b/pages/traits/metabolism/photoferrotrophy.html
@@ -253,7 +253,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/photosynthesis.html b/pages/traits/metabolism/photosynthesis.html
index 490a54eb08..e222d16dd4 100644
--- a/pages/traits/metabolism/photosynthesis.html
+++ b/pages/traits/metabolism/photosynthesis.html
@@ -363,7 +363,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -371,7 +371,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/phototrophy.html b/pages/traits/metabolism/phototrophy.html
index 7f907d5079..fbe7201575 100644
--- a/pages/traits/metabolism/phototrophy.html
+++ b/pages/traits/metabolism/phototrophy.html
@@ -348,7 +348,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -356,7 +356,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/produces.html b/pages/traits/metabolism/produces.html
index 3be9b7d9c8..8c9c35b39d 100644
--- a/pages/traits/metabolism/produces.html
+++ b/pages/traits/metabolism/produces.html
@@ -87,7 +87,7 @@ kg-microbe context
METPO:2000202 [-1.210, -0.273, -2.355, -0.086, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -95,7 +95,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/propionic_acid_fermentation.html b/pages/traits/metabolism/propionic_acid_fermentation.html
index ce755b0a53..9e8d31768d 100644
--- a/pages/traits/metabolism/propionic_acid_fermentation.html
+++ b/pages/traits/metabolism/propionic_acid_fermentation.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/proteolysis.html b/pages/traits/metabolism/proteolysis.html
index 8c0681cd49..027f6968e4 100644
--- a/pages/traits/metabolism/proteolysis.html
+++ b/pages/traits/metabolism/proteolysis.html
@@ -305,7 +305,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -313,7 +313,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/proteorhodopsin_phototrophy.html b/pages/traits/metabolism/proteorhodopsin_phototrophy.html
index 27c334bbf8..2f3d85fa96 100644
--- a/pages/traits/metabolism/proteorhodopsin_phototrophy.html
+++ b/pages/traits/metabolism/proteorhodopsin_phototrophy.html
@@ -286,7 +286,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -294,7 +294,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/reduces.html b/pages/traits/metabolism/reduces.html
index f0f35519f1..850352892a 100644
--- a/pages/traits/metabolism/reduces.html
+++ b/pages/traits/metabolism/reduces.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000017 [-1.152, -0.339, -2.249, -0.170, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/reductive_tca_cycle.html b/pages/traits/metabolism/reductive_tca_cycle.html
index 879a04aea4..89b90741a9 100644
--- a/pages/traits/metabolism/reductive_tca_cycle.html
+++ b/pages/traits/metabolism/reductive_tca_cycle.html
@@ -357,7 +357,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -365,7 +365,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/requires_for_growth.html b/pages/traits/metabolism/requires_for_growth.html
index b67e47de93..e4d736386b 100644
--- a/pages/traits/metabolism/requires_for_growth.html
+++ b/pages/traits/metabolism/requires_for_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000018 [-1.197, -0.079, -2.218, -0.073, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/respiration.html b/pages/traits/metabolism/respiration.html
index a65183322f..f60ea9abb7 100644
--- a/pages/traits/metabolism/respiration.html
+++ b/pages/traits/metabolism/respiration.html
@@ -384,7 +384,7 @@ kg-microbe context
METPO:1000800 [-0.241, -1.847, -1.014, +1.020, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -392,7 +392,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/respiration_of_sulfur_compounds.html b/pages/traits/metabolism/respiration_of_sulfur_compounds.html
index bb94e377aa..608ac5f298 100644
--- a/pages/traits/metabolism/respiration_of_sulfur_compounds.html
+++ b/pages/traits/metabolism/respiration_of_sulfur_compounds.html
@@ -95,7 +95,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/sequesters.html b/pages/traits/metabolism/sequesters.html
index eadee083cd..6a8685dc46 100644
--- a/pages/traits/metabolism/sequesters.html
+++ b/pages/traits/metabolism/sequesters.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000211 [-1.868, -0.826, -3.392, -0.381, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/shows_activity_of.html b/pages/traits/metabolism/shows_activity_of.html
index 56341bf16d..0dc5fcb848 100644
--- a/pages/traits/metabolism/shows_activity_of.html
+++ b/pages/traits/metabolism/shows_activity_of.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000302 [-1.251, -1.767, -0.586, -0.834, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/starch_degradation.html b/pages/traits/metabolism/starch_degradation.html
index ebca2d7860..b588d47bfb 100644
--- a/pages/traits/metabolism/starch_degradation.html
+++ b/pages/traits/metabolism/starch_degradation.html
@@ -280,7 +280,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -288,7 +288,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/substrate_level_phosphorylation.html b/pages/traits/metabolism/substrate_level_phosphorylation.html
index 826166bf9f..6566b4a559 100644
--- a/pages/traits/metabolism/substrate_level_phosphorylation.html
+++ b/pages/traits/metabolism/substrate_level_phosphorylation.html
@@ -362,7 +362,7 @@ kg-microbe context
METPO:1000804 [+0.098, -0.513, -1.357, -0.315, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -370,7 +370,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/sulfur_oxidation.html b/pages/traits/metabolism/sulfur_oxidation.html
index 330c714bbc..ac210aae67 100644
--- a/pages/traits/metabolism/sulfur_oxidation.html
+++ b/pages/traits/metabolism/sulfur_oxidation.html
@@ -380,7 +380,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -388,7 +388,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/sulfur_respiration.html b/pages/traits/metabolism/sulfur_respiration.html
index a5f68d02ef..eb1e456f80 100644
--- a/pages/traits/metabolism/sulfur_respiration.html
+++ b/pages/traits/metabolism/sulfur_respiration.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/syntrophy.html b/pages/traits/metabolism/syntrophy.html
index 79f2255941..fb936cdb68 100644
--- a/pages/traits/metabolism/syntrophy.html
+++ b/pages/traits/metabolism/syntrophy.html
@@ -430,7 +430,7 @@ kg-microbe context
METPO:1002006 [-0.312, -0.639, -1.585, +0.222, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -438,7 +438,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/thiosulfate_respiration.html b/pages/traits/metabolism/thiosulfate_respiration.html
index 260a7b3107..6753e928fd 100644
--- a/pages/traits/metabolism/thiosulfate_respiration.html
+++ b/pages/traits/metabolism/thiosulfate_respiration.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/metabolism/three_hydroxypropionate_bicycle.html b/pages/traits/metabolism/three_hydroxypropionate_bicycle.html
index f44d390c26..c99dc95a04 100644
--- a/pages/traits/metabolism/three_hydroxypropionate_bicycle.html
+++ b/pages/traits/metabolism/three_hydroxypropionate_bicycle.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html b/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html
index 35799b77c4..fd1c396322 100644
--- a/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html
+++ b/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html
@@ -436,7 +436,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -444,7 +444,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/transports.html b/pages/traits/metabolism/transports.html
index 94e52c9745..6f39269c9d 100644
--- a/pages/traits/metabolism/transports.html
+++ b/pages/traits/metabolism/transports.html
@@ -91,7 +91,7 @@ kg-microbe context
METPO:2000207 [-1.261, -0.133, -2.951, -0.069, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -99,7 +99,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_carbon_source.html b/pages/traits/metabolism/uses_as_carbon_source.html
index 4f41090844..af99b2fd3d 100644
--- a/pages/traits/metabolism/uses_as_carbon_source.html
+++ b/pages/traits/metabolism/uses_as_carbon_source.html
@@ -96,7 +96,7 @@ kg-microbe context
METPO:2000006 [-1.211, -0.216, -2.379, -0.057, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -104,7 +104,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_electron_acceptor.html b/pages/traits/metabolism/uses_as_electron_acceptor.html
index cf363aa00b..bff4c9b13e 100644
--- a/pages/traits/metabolism/uses_as_electron_acceptor.html
+++ b/pages/traits/metabolism/uses_as_electron_acceptor.html
@@ -96,7 +96,7 @@ kg-microbe context
METPO:2000008 [-1.185, -0.120, -2.348, -0.244, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -104,7 +104,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_electron_donor.html b/pages/traits/metabolism/uses_as_electron_donor.html
index 424b9cecbd..e8af6197a7 100644
--- a/pages/traits/metabolism/uses_as_electron_donor.html
+++ b/pages/traits/metabolism/uses_as_electron_donor.html
@@ -96,7 +96,7 @@ kg-microbe context
METPO:2000009 [-1.438, -0.144, -2.282, -0.128, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -104,7 +104,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_energy_source.html b/pages/traits/metabolism/uses_as_energy_source.html
index 28122971b8..d0157c5ba9 100644
--- a/pages/traits/metabolism/uses_as_energy_source.html
+++ b/pages/traits/metabolism/uses_as_energy_source.html
@@ -96,7 +96,7 @@ kg-microbe context
METPO:2000010 [-1.190, -0.217, -2.451, -0.286, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -104,7 +104,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_nitrogen_source.html b/pages/traits/metabolism/uses_as_nitrogen_source.html
index 46906db450..86fddb19f5 100644
--- a/pages/traits/metabolism/uses_as_nitrogen_source.html
+++ b/pages/traits/metabolism/uses_as_nitrogen_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000014 [-1.099, -0.147, -2.183, -0.040, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_as_sulfur_source.html b/pages/traits/metabolism/uses_as_sulfur_source.html
index 265eb7f762..f227c40ffd 100644
--- a/pages/traits/metabolism/uses_as_sulfur_source.html
+++ b/pages/traits/metabolism/uses_as_sulfur_source.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000020 [-1.201, -0.193, -2.383, -0.149, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_aerobic_catabolization.html b/pages/traits/metabolism/uses_for_aerobic_catabolization.html
index 0a2db37c9f..d2b7fe74d9 100644
--- a/pages/traits/metabolism/uses_for_aerobic_catabolization.html
+++ b/pages/traits/metabolism/uses_for_aerobic_catabolization.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000032 [-1.321, -0.211, -2.272, -0.219, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_aerobic_growth.html b/pages/traits/metabolism/uses_for_aerobic_growth.html
index 0b169874d4..405ee0c32c 100644
--- a/pages/traits/metabolism/uses_for_aerobic_growth.html
+++ b/pages/traits/metabolism/uses_for_aerobic_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000043 [-1.276, -0.277, -2.261, -0.058, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_anaerobic_catabolization.html b/pages/traits/metabolism/uses_for_anaerobic_catabolization.html
index 477c8cfb87..86accbb4c9 100644
--- a/pages/traits/metabolism/uses_for_anaerobic_catabolization.html
+++ b/pages/traits/metabolism/uses_for_anaerobic_catabolization.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000048 [-1.167, -0.251, -2.436, -0.107, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth.html b/pages/traits/metabolism/uses_for_anaerobic_growth.html
index d4d0de0517..a9ec4f2825 100644
--- a/pages/traits/metabolism/uses_for_anaerobic_growth.html
+++ b/pages/traits/metabolism/uses_for_anaerobic_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000049 [-1.232, -0.238, -2.354, -0.293, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html b/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html
index 80b5ea5c6d..566c9b1046 100644
--- a/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html
+++ b/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000050 [-1.332, -0.290, -2.317, -0.177, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html b/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html
index c2eb3085ac..88395c8a51 100644
--- a/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html
+++ b/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000051 [-1.056, -0.269, -2.485, -0.197, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_growth.html b/pages/traits/metabolism/uses_for_growth.html
index bbc89f5aad..e57e73aed5 100644
--- a/pages/traits/metabolism/uses_for_growth.html
+++ b/pages/traits/metabolism/uses_for_growth.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000012 [-1.291, -0.327, -2.398, -0.174, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_for_respiration.html b/pages/traits/metabolism/uses_for_respiration.html
index 3f1c6272aa..7b281ac3ca 100644
--- a/pages/traits/metabolism/uses_for_respiration.html
+++ b/pages/traits/metabolism/uses_for_respiration.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000019 [-1.331, -0.120, -2.402, -0.082, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/uses_in_other_way.html b/pages/traits/metabolism/uses_in_other_way.html
index e61a2e6322..e0f7d72bc4 100644
--- a/pages/traits/metabolism/uses_in_other_way.html
+++ b/pages/traits/metabolism/uses_in_other_way.html
@@ -89,7 +89,7 @@ kg-microbe context
METPO:2000015 [-1.208, -0.160, -2.469, -0.205, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -97,7 +97,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/wood_ljungdahl_pathway.html b/pages/traits/metabolism/wood_ljungdahl_pathway.html
index 4e30400eb4..665de5333f 100644
--- a/pages/traits/metabolism/wood_ljungdahl_pathway.html
+++ b/pages/traits/metabolism/wood_ljungdahl_pathway.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/metabolism/xylan_degradation.html b/pages/traits/metabolism/xylan_degradation.html
index 89ca87dc89..eb84de7d5d 100644
--- a/pages/traits/metabolism/xylan_degradation.html
+++ b/pages/traits/metabolism/xylan_degradation.html
@@ -301,7 +301,7 @@ kg-microbe context
METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -309,7 +309,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/akinete.html b/pages/traits/morphology/akinete.html
index 578d790be5..3b10358b79 100644
--- a/pages/traits/morphology/akinete.html
+++ b/pages/traits/morphology/akinete.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/amphitrichous.html b/pages/traits/morphology/amphitrichous.html
index 3631f624d9..1375c61e1f 100644
--- a/pages/traits/morphology/amphitrichous.html
+++ b/pages/traits/morphology/amphitrichous.html
@@ -264,7 +264,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -272,7 +272,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/axially_filamented.html b/pages/traits/morphology/axially_filamented.html
index f1374358bd..7c852070a2 100644
--- a/pages/traits/morphology/axially_filamented.html
+++ b/pages/traits/morphology/axially_filamented.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000705 [-1.207, -3.411, -0.763, +0.835, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/bacillus_shaped.html b/pages/traits/morphology/bacillus_shaped.html
index 666ac52830..8f1e5eecaa 100644
--- a/pages/traits/morphology/bacillus_shaped.html
+++ b/pages/traits/morphology/bacillus_shaped.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000667 [-93.971, +37.913, +150.959, -201.986, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/black_pigmented.html b/pages/traits/morphology/black_pigmented.html
index 2f1f3a6b18..a4377c68fe 100644
--- a/pages/traits/morphology/black_pigmented.html
+++ b/pages/traits/morphology/black_pigmented.html
@@ -324,7 +324,7 @@ kg-microbe context
METPO:1003022 [-1.598, -1.748, -2.126, +1.386, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -332,7 +332,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/branched_shaped.html b/pages/traits/morphology/branched_shaped.html
index f81c813985..98f242ec67 100644
--- a/pages/traits/morphology/branched_shaped.html
+++ b/pages/traits/morphology/branched_shaped.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1000687 [-3.113, -4.524, -0.722, -1.425, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/brown_pigmented.html b/pages/traits/morphology/brown_pigmented.html
index bbf57b4817..5adbcb5e93 100644
--- a/pages/traits/morphology/brown_pigmented.html
+++ b/pages/traits/morphology/brown_pigmented.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1003023 [-2.125, -1.589, -1.615, +1.116, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/capsule.html b/pages/traits/morphology/capsule.html
index e2b5cb595e..d458b48851 100644
--- a/pages/traits/morphology/capsule.html
+++ b/pages/traits/morphology/capsule.html
@@ -265,7 +265,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -273,7 +273,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/carboxysome.html b/pages/traits/morphology/carboxysome.html
index 695a969dcd..c95bdacff3 100644
--- a/pages/traits/morphology/carboxysome.html
+++ b/pages/traits/morphology/carboxysome.html
@@ -344,7 +344,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -352,7 +352,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/carotenoid_pigmentation.html b/pages/traits/morphology/carotenoid_pigmentation.html
index 4946b799fb..7a02d6e45f 100644
--- a/pages/traits/morphology/carotenoid_pigmentation.html
+++ b/pages/traits/morphology/carotenoid_pigmentation.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1003031 [-2.345, -1.877, -1.987, -1.228, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_length.html b/pages/traits/morphology/cell_length.html
index 8217e58523..3650401866 100644
--- a/pages/traits/morphology/cell_length.html
+++ b/pages/traits/morphology/cell_length.html
@@ -330,7 +330,7 @@ kg-microbe context
METPO:1000881 [-1.413, -1.159, -3.315, +0.964, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -338,7 +338,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_length_large.html b/pages/traits/morphology/cell_length_large.html
index a4fce3461b..407c58eb85 100644
--- a/pages/traits/morphology/cell_length_large.html
+++ b/pages/traits/morphology/cell_length_large.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000886 [-0.375, -2.130, -2.643, +3.325, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_length_medium.html b/pages/traits/morphology/cell_length_medium.html
index 7ae8cf4a01..9698699cad 100644
--- a/pages/traits/morphology/cell_length_medium.html
+++ b/pages/traits/morphology/cell_length_medium.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000885 [-0.546, -0.957, -2.038, +2.464, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_length_small.html b/pages/traits/morphology/cell_length_small.html
index 0866ceed9c..b2c332841a 100644
--- a/pages/traits/morphology/cell_length_small.html
+++ b/pages/traits/morphology/cell_length_small.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000884 [-1.814, -0.837, -3.570, +2.198, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_length_very_small.html b/pages/traits/morphology/cell_length_very_small.html
index 04ca7e59a0..e3deb701d2 100644
--- a/pages/traits/morphology/cell_length_very_small.html
+++ b/pages/traits/morphology/cell_length_very_small.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000883 [-1.058, -2.584, -0.836, +2.454, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_shape.html b/pages/traits/morphology/cell_shape.html
index 40a7224a0f..10b734558c 100644
--- a/pages/traits/morphology/cell_shape.html
+++ b/pages/traits/morphology/cell_shape.html
@@ -401,7 +401,7 @@ kg-microbe context
METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -409,7 +409,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_width.html b/pages/traits/morphology/cell_width.html
index ad201633b9..f45c46c846 100644
--- a/pages/traits/morphology/cell_width.html
+++ b/pages/traits/morphology/cell_width.html
@@ -262,7 +262,7 @@ kg-microbe context
METPO:1000882 [-1.477, -0.754, -1.899, +0.480, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -270,7 +270,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_width_large.html b/pages/traits/morphology/cell_width_large.html
index fd651fc021..6f4c5ef751 100644
--- a/pages/traits/morphology/cell_width_large.html
+++ b/pages/traits/morphology/cell_width_large.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000890 [+0.641, -3.918, -1.937, +4.002, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_width_medium.html b/pages/traits/morphology/cell_width_medium.html
index cf26aadf74..ee8fbd4669 100644
--- a/pages/traits/morphology/cell_width_medium.html
+++ b/pages/traits/morphology/cell_width_medium.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000889 [-1.494, -2.132, -3.757, +2.828, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_width_small.html b/pages/traits/morphology/cell_width_small.html
index cabf86b773..4284e5a714 100644
--- a/pages/traits/morphology/cell_width_small.html
+++ b/pages/traits/morphology/cell_width_small.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000888 [-1.239, +0.787, -0.502, +4.802, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cell_width_very_small.html b/pages/traits/morphology/cell_width_very_small.html
index e88bc07239..4110ed3fc0 100644
--- a/pages/traits/morphology/cell_width_very_small.html
+++ b/pages/traits/morphology/cell_width_very_small.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000887 [-0.349, -0.753, -1.789, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/coccobacillus_shaped.html b/pages/traits/morphology/coccobacillus_shaped.html
index 5a163abab0..75f689c4a3 100644
--- a/pages/traits/morphology/coccobacillus_shaped.html
+++ b/pages/traits/morphology/coccobacillus_shaped.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000688 [-20.154, -47.811, +18.193, -1.988, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/coccus_shaped.html b/pages/traits/morphology/coccus_shaped.html
index 152b040068..76557ee5a0 100644
--- a/pages/traits/morphology/coccus_shaped.html
+++ b/pages/traits/morphology/coccus_shaped.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000668 [+298.218, -515.508, -75.836, -35.326, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/cream_pigmented.html b/pages/traits/morphology/cream_pigmented.html
index 917a848d38..7f8af9c53a 100644
--- a/pages/traits/morphology/cream_pigmented.html
+++ b/pages/traits/morphology/cream_pigmented.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1003024 [-1.327, -0.484, -1.054, -1.119, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/crescent_shaped.html b/pages/traits/morphology/crescent_shaped.html
index 54cb8ace09..d9127e2b6c 100644
--- a/pages/traits/morphology/crescent_shaped.html
+++ b/pages/traits/morphology/crescent_shaped.html
@@ -303,7 +303,7 @@ kg-microbe context
METPO:1000669 [-4.617, -3.346, -2.304, +0.470, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -311,7 +311,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/curved_shaped.html b/pages/traits/morphology/curved_shaped.html
index 3880cb94dc..72e1b91243 100644
--- a/pages/traits/morphology/curved_shaped.html
+++ b/pages/traits/morphology/curved_shaped.html
@@ -258,7 +258,7 @@ kg-microbe context
METPO:1000670 [-1.017, -1.801, -3.696, +0.440, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -266,7 +266,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/diplococcus_shaped.html b/pages/traits/morphology/diplococcus_shaped.html
index 2fb9d7e074..c6f845fcba 100644
--- a/pages/traits/morphology/diplococcus_shaped.html
+++ b/pages/traits/morphology/diplococcus_shaped.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1000671 [-3.757, -1.830, -2.403, -0.453, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/disc_shaped.html b/pages/traits/morphology/disc_shaped.html
index b7c412b4a4..f9502b5685 100644
--- a/pages/traits/morphology/disc_shaped.html
+++ b/pages/traits/morphology/disc_shaped.html
@@ -205,7 +205,7 @@ kg-microbe context
METPO:1000689 [-0.014, -3.804, -1.044, +0.754, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -213,7 +213,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/dumbbell_shaped.html b/pages/traits/morphology/dumbbell_shaped.html
index db827fa27f..bf342ad4db 100644
--- a/pages/traits/morphology/dumbbell_shaped.html
+++ b/pages/traits/morphology/dumbbell_shaped.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000672 [-3.439, -2.809, -2.204, +0.668, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/ellipsoidal.html b/pages/traits/morphology/ellipsoidal.html
index 7c8eb6de41..c74f31187f 100644
--- a/pages/traits/morphology/ellipsoidal.html
+++ b/pages/traits/morphology/ellipsoidal.html
@@ -362,7 +362,7 @@ kg-microbe context
METPO:1000673 [-1.999, -1.383, -2.615, +0.176, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -370,7 +370,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/filament_shaped.html b/pages/traits/morphology/filament_shaped.html
index 8e724bc296..61865ec4e8 100644
--- a/pages/traits/morphology/filament_shaped.html
+++ b/pages/traits/morphology/filament_shaped.html
@@ -328,7 +328,7 @@ kg-microbe context
METPO:1000674 [+1.704, -8.992, +4.797, -2.737, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -336,7 +336,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/flagellar_arrangement.html b/pages/traits/morphology/flagellar_arrangement.html
index d0d43f0f6e..d92ac9c7db 100644
--- a/pages/traits/morphology/flagellar_arrangement.html
+++ b/pages/traits/morphology/flagellar_arrangement.html
@@ -279,7 +279,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -287,7 +287,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/flagellated.html b/pages/traits/morphology/flagellated.html
index d2f742ff9b..9920573f7f 100644
--- a/pages/traits/morphology/flagellated.html
+++ b/pages/traits/morphology/flagellated.html
@@ -380,7 +380,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -388,7 +388,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/flask_shaped.html b/pages/traits/morphology/flask_shaped.html
index 433b02d898..63ae192b64 100644
--- a/pages/traits/morphology/flask_shaped.html
+++ b/pages/traits/morphology/flask_shaped.html
@@ -241,7 +241,7 @@ kg-microbe context
METPO:1000675 [-2.136, -1.080, +0.747, -1.495, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -249,7 +249,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/fusiform_shaped.html b/pages/traits/morphology/fusiform_shaped.html
index 5951eb51b1..703937eb4f 100644
--- a/pages/traits/morphology/fusiform_shaped.html
+++ b/pages/traits/morphology/fusiform_shaped.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000690 [-2.797, -1.128, -4.645, -0.791, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gas_vesicle.html b/pages/traits/morphology/gas_vesicle.html
index f11134d4cd..55a1dd8858 100644
--- a/pages/traits/morphology/gas_vesicle.html
+++ b/pages/traits/morphology/gas_vesicle.html
@@ -378,7 +378,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -386,7 +386,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gliding.html b/pages/traits/morphology/gliding.html
index 3687d84d67..565573595a 100644
--- a/pages/traits/morphology/gliding.html
+++ b/pages/traits/morphology/gliding.html
@@ -328,7 +328,7 @@ kg-microbe context
METPO:1000706 [-1.115, +0.741, -2.784, -0.615, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -336,7 +336,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gram_negative.html b/pages/traits/morphology/gram_negative.html
index 51d9ee101c..80b3600dbf 100644
--- a/pages/traits/morphology/gram_negative.html
+++ b/pages/traits/morphology/gram_negative.html
@@ -326,7 +326,7 @@ kg-microbe context
METPO:1000699 [+365.243, +263.306, -35.927, -345.448, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -334,7 +334,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gram_positive.html b/pages/traits/morphology/gram_positive.html
index 97c6ccadd5..96eff384d6 100644
--- a/pages/traits/morphology/gram_positive.html
+++ b/pages/traits/morphology/gram_positive.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1000698 [+104.737, -799.711, +133.158, -97.829, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gram_stain.html b/pages/traits/morphology/gram_stain.html
index ae9431f271..a3e1210dd6 100644
--- a/pages/traits/morphology/gram_stain.html
+++ b/pages/traits/morphology/gram_stain.html
@@ -271,7 +271,7 @@ kg-microbe context
METPO:1000697 [-2.552, -2.118, -3.376, -0.738, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -279,7 +279,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/gram_variable.html b/pages/traits/morphology/gram_variable.html
index e022fc1db9..9e28e8e055 100644
--- a/pages/traits/morphology/gram_variable.html
+++ b/pages/traits/morphology/gram_variable.html
@@ -256,7 +256,7 @@ kg-microbe context
METPO:1000700 [-3.645, -2.566, -2.886, -0.695, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -264,7 +264,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/green_pigmented.html b/pages/traits/morphology/green_pigmented.html
index dcde9a5f02..508832f672 100644
--- a/pages/traits/morphology/green_pigmented.html
+++ b/pages/traits/morphology/green_pigmented.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1003025 [-0.292, -0.545, -1.390, +0.056, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/helical_shaped.html b/pages/traits/morphology/helical_shaped.html
index fc42c3e35c..08549f96d2 100644
--- a/pages/traits/morphology/helical_shaped.html
+++ b/pages/traits/morphology/helical_shaped.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000676 [-1.491, -3.251, -3.052, +1.582, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/heterocyst.html b/pages/traits/morphology/heterocyst.html
index 949778341f..bf29d7f4a5 100644
--- a/pages/traits/morphology/heterocyst.html
+++ b/pages/traits/morphology/heterocyst.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/holdfast.html b/pages/traits/morphology/holdfast.html
index 54c101b0a8..6269afd672 100644
--- a/pages/traits/morphology/holdfast.html
+++ b/pages/traits/morphology/holdfast.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/intracellular_inclusion.html b/pages/traits/morphology/intracellular_inclusion.html
index fcb3fd1444..f4bb2d1412 100644
--- a/pages/traits/morphology/intracellular_inclusion.html
+++ b/pages/traits/morphology/intracellular_inclusion.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/irregular_shaped.html b/pages/traits/morphology/irregular_shaped.html
index fc034cb111..e2fd4c00f7 100644
--- a/pages/traits/morphology/irregular_shaped.html
+++ b/pages/traits/morphology/irregular_shaped.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000691 [-4.712, -0.924, -1.303, -1.253, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/lateral_flagellation.html b/pages/traits/morphology/lateral_flagellation.html
index ae6bc2fd67..218fd3ed53 100644
--- a/pages/traits/morphology/lateral_flagellation.html
+++ b/pages/traits/morphology/lateral_flagellation.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/lophotrichous.html b/pages/traits/morphology/lophotrichous.html
index 7e00200195..957e6dc95a 100644
--- a/pages/traits/morphology/lophotrichous.html
+++ b/pages/traits/morphology/lophotrichous.html
@@ -247,7 +247,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -255,7 +255,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/magnetosome.html b/pages/traits/morphology/magnetosome.html
index df4dfba4d1..3968837a4b 100644
--- a/pages/traits/morphology/magnetosome.html
+++ b/pages/traits/morphology/magnetosome.html
@@ -386,7 +386,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -394,7 +394,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/monotrichous.html b/pages/traits/morphology/monotrichous.html
index 2a3b81de35..a4939f19f3 100644
--- a/pages/traits/morphology/monotrichous.html
+++ b/pages/traits/morphology/monotrichous.html
@@ -247,7 +247,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -255,7 +255,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/motile.html b/pages/traits/morphology/motile.html
index 46de2d6cab..fbe8d9aac8 100644
--- a/pages/traits/morphology/motile.html
+++ b/pages/traits/morphology/motile.html
@@ -507,7 +507,7 @@ kg-microbe context
METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -515,7 +515,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/motility.html b/pages/traits/morphology/motility.html
index d488319642..612109ec2f 100644
--- a/pages/traits/morphology/motility.html
+++ b/pages/traits/morphology/motility.html
@@ -318,7 +318,7 @@ kg-microbe context
METPO:1000701 [-1.722, -3.036, -3.705, +0.093, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -326,7 +326,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/mycelial_growth.html b/pages/traits/morphology/mycelial_growth.html
index 923d375123..7ca747a8b9 100644
--- a/pages/traits/morphology/mycelial_growth.html
+++ b/pages/traits/morphology/mycelial_growth.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/non_motile.html b/pages/traits/morphology/non_motile.html
index 5c89f30806..fa54529f4c 100644
--- a/pages/traits/morphology/non_motile.html
+++ b/pages/traits/morphology/non_motile.html
@@ -275,7 +275,7 @@ kg-microbe context
METPO:1000703 [+135.175, -208.275, +67.323, -38.317, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -283,7 +283,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/non_spore_forming.html b/pages/traits/morphology/non_spore_forming.html
index e02ab7efee..85b09c7157 100644
--- a/pages/traits/morphology/non_spore_forming.html
+++ b/pages/traits/morphology/non_spore_forming.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000872 [+88.853, -240.826, -35.218, -139.525, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/orange_pigmented.html b/pages/traits/morphology/orange_pigmented.html
index 3fafb0a6b0..304ed18ce6 100644
--- a/pages/traits/morphology/orange_pigmented.html
+++ b/pages/traits/morphology/orange_pigmented.html
@@ -324,7 +324,7 @@ kg-microbe context
METPO:1003026 [-1.743, -2.814, -1.192, -0.288, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -332,7 +332,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/oval_shaped.html b/pages/traits/morphology/oval_shaped.html
index 1cead82fc4..5ade174121 100644
--- a/pages/traits/morphology/oval_shaped.html
+++ b/pages/traits/morphology/oval_shaped.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1000678 [-12.940, -17.188, -48.453, +20.919, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/ovoid_shaped.html b/pages/traits/morphology/ovoid_shaped.html
index dfdef9867c..6db10f96b0 100644
--- a/pages/traits/morphology/ovoid_shaped.html
+++ b/pages/traits/morphology/ovoid_shaped.html
@@ -373,7 +373,7 @@ kg-microbe context
METPO:1000677 [+1.410, -5.519, -0.585, +0.196, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -381,7 +381,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/peritrichous.html b/pages/traits/morphology/peritrichous.html
index e9524750c7..1708e7539f 100644
--- a/pages/traits/morphology/peritrichous.html
+++ b/pages/traits/morphology/peritrichous.html
@@ -247,7 +247,7 @@ kg-microbe context
METPO:1000704 [-2.371, -2.707, -4.290, +4.186, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -255,7 +255,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/pigmentation.html b/pages/traits/morphology/pigmentation.html
index c59768779e..d3229b60ab 100644
--- a/pages/traits/morphology/pigmentation.html
+++ b/pages/traits/morphology/pigmentation.html
@@ -342,7 +342,7 @@ kg-microbe context
METPO:1003021 [-2.062, -1.921, -1.630, -0.024, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -350,7 +350,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/pink_pigmented.html b/pages/traits/morphology/pink_pigmented.html
index dcdb29e989..3721d10f30 100644
--- a/pages/traits/morphology/pink_pigmented.html
+++ b/pages/traits/morphology/pink_pigmented.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1003027 [-4.184, -3.258, -1.095, +0.518, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/pleomorphic_shaped.html b/pages/traits/morphology/pleomorphic_shaped.html
index 7a1b470954..546408dae1 100644
--- a/pages/traits/morphology/pleomorphic_shaped.html
+++ b/pages/traits/morphology/pleomorphic_shaped.html
@@ -277,7 +277,7 @@ kg-microbe context
METPO:1000679 [-2.951, -6.268, -2.114, +1.959, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -285,7 +285,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/polar_flagellation.html b/pages/traits/morphology/polar_flagellation.html
index a3dc3f71b4..12c5df7f52 100644
--- a/pages/traits/morphology/polar_flagellation.html
+++ b/pages/traits/morphology/polar_flagellation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/polyhydroxyalkanoate_granule.html b/pages/traits/morphology/polyhydroxyalkanoate_granule.html
index b1659d4c34..716e3a93a3 100644
--- a/pages/traits/morphology/polyhydroxyalkanoate_granule.html
+++ b/pages/traits/morphology/polyhydroxyalkanoate_granule.html
@@ -416,7 +416,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -424,7 +424,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/polyphosphate_granule.html b/pages/traits/morphology/polyphosphate_granule.html
index d1028fbfe2..16442039c9 100644
--- a/pages/traits/morphology/polyphosphate_granule.html
+++ b/pages/traits/morphology/polyphosphate_granule.html
@@ -271,7 +271,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -279,7 +279,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/polytrichous_flagellation.html b/pages/traits/morphology/polytrichous_flagellation.html
index 37be39330a..d99fa350d8 100644
--- a/pages/traits/morphology/polytrichous_flagellation.html
+++ b/pages/traits/morphology/polytrichous_flagellation.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/prosthecate.html b/pages/traits/morphology/prosthecate.html
index 47263f5714..fc80d52d9a 100644
--- a/pages/traits/morphology/prosthecate.html
+++ b/pages/traits/morphology/prosthecate.html
@@ -258,7 +258,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -266,7 +266,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/red_pigmented.html b/pages/traits/morphology/red_pigmented.html
index accc69cef1..34a79aa998 100644
--- a/pages/traits/morphology/red_pigmented.html
+++ b/pages/traits/morphology/red_pigmented.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1003028 [-0.620, -1.473, -2.633, -0.182, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/ring_shaped.html b/pages/traits/morphology/ring_shaped.html
index 7f0a864dfb..02de96a793 100644
--- a/pages/traits/morphology/ring_shaped.html
+++ b/pages/traits/morphology/ring_shaped.html
@@ -284,7 +284,7 @@ kg-microbe context
METPO:1000680 [-3.059, -2.534, -2.544, -0.510, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -292,7 +292,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/rod_shaped.html b/pages/traits/morphology/rod_shaped.html
index 9c4c9a7723..47c9891df1 100644
--- a/pages/traits/morphology/rod_shaped.html
+++ b/pages/traits/morphology/rod_shaped.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1000681 [+3.060, +7.761, -10.358, +10.121, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/s_layer.html b/pages/traits/morphology/s_layer.html
index 06fcb44e99..b19b88eafd 100644
--- a/pages/traits/morphology/s_layer.html
+++ b/pages/traits/morphology/s_layer.html
@@ -171,7 +171,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -179,7 +179,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/sarcina_arrangement.html b/pages/traits/morphology/sarcina_arrangement.html
index 653c7a2512..da1403891d 100644
--- a/pages/traits/morphology/sarcina_arrangement.html
+++ b/pages/traits/morphology/sarcina_arrangement.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/sphere_shaped.html b/pages/traits/morphology/sphere_shaped.html
index 78d25e182f..8ee5da45f0 100644
--- a/pages/traits/morphology/sphere_shaped.html
+++ b/pages/traits/morphology/sphere_shaped.html
@@ -292,7 +292,7 @@ kg-microbe context
METPO:1000683 [-4.221, -1.488, -1.716, +1.200, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -300,7 +300,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/spindle_shaped.html b/pages/traits/morphology/spindle_shaped.html
index e1e9a0c272..ca0cfdcee8 100644
--- a/pages/traits/morphology/spindle_shaped.html
+++ b/pages/traits/morphology/spindle_shaped.html
@@ -205,7 +205,7 @@ kg-microbe context
METPO:1000692 [-4.209, -2.313, -2.964, -1.593, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -213,7 +213,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/spiral_shaped.html b/pages/traits/morphology/spiral_shaped.html
index 6912003b2b..bbd1d90553 100644
--- a/pages/traits/morphology/spiral_shaped.html
+++ b/pages/traits/morphology/spiral_shaped.html
@@ -294,7 +294,7 @@ kg-microbe context
METPO:1000684 [+2.081, -74.961, -2.345, -78.220, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -302,7 +302,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/spirochete_shaped.html b/pages/traits/morphology/spirochete_shaped.html
index 76eb1f5145..af03b343c2 100644
--- a/pages/traits/morphology/spirochete_shaped.html
+++ b/pages/traits/morphology/spirochete_shaped.html
@@ -307,7 +307,7 @@ kg-microbe context
METPO:1000693 [-5.437, -1.510, -3.065, -0.024, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -315,7 +315,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/spore_forming.html b/pages/traits/morphology/spore_forming.html
index 7ba6e69dc5..486a01f9dc 100644
--- a/pages/traits/morphology/spore_forming.html
+++ b/pages/traits/morphology/spore_forming.html
@@ -407,7 +407,7 @@ kg-microbe context
METPO:1000871 [+10.788, -112.336, +60.034, -6.588, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -415,7 +415,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/spore_shaped.html b/pages/traits/morphology/spore_shaped.html
index 4deca4afd9..371da00432 100644
--- a/pages/traits/morphology/spore_shaped.html
+++ b/pages/traits/morphology/spore_shaped.html
@@ -456,7 +456,7 @@ kg-microbe context
METPO:1000682 [-1.729, -2.644, -1.494, +0.751, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -464,7 +464,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/sporulation.html b/pages/traits/morphology/sporulation.html
index a3ce8ef48d..0ffa5c0c56 100644
--- a/pages/traits/morphology/sporulation.html
+++ b/pages/traits/morphology/sporulation.html
@@ -486,7 +486,7 @@ kg-microbe context
METPO:1000870 [-1.554, -2.668, -2.202, -0.616, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -494,7 +494,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/square_shaped.html b/pages/traits/morphology/square_shaped.html
index 02279a5821..ad0ba8de3b 100644
--- a/pages/traits/morphology/square_shaped.html
+++ b/pages/traits/morphology/square_shaped.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000694 [-3.745, -0.587, -2.659, +0.960, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/staphylococcus_arrangement.html b/pages/traits/morphology/staphylococcus_arrangement.html
index 9918236df1..5c4d2fa86f 100644
--- a/pages/traits/morphology/staphylococcus_arrangement.html
+++ b/pages/traits/morphology/staphylococcus_arrangement.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/star_shaped.html b/pages/traits/morphology/star_shaped.html
index 7e19f86798..265268e021 100644
--- a/pages/traits/morphology/star_shaped.html
+++ b/pages/traits/morphology/star_shaped.html
@@ -286,7 +286,7 @@ kg-microbe context
METPO:1000685 [-3.843, -0.979, -3.288, -0.575, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -294,7 +294,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/streptococcus_arrangement.html b/pages/traits/morphology/streptococcus_arrangement.html
index afb1b38276..79f50f914d 100644
--- a/pages/traits/morphology/streptococcus_arrangement.html
+++ b/pages/traits/morphology/streptococcus_arrangement.html
@@ -273,7 +273,7 @@ kg-microbe context
METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -281,7 +281,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/subpolar_flagellation.html b/pages/traits/morphology/subpolar_flagellation.html
index 1ed5faccea..38878409c6 100644
--- a/pages/traits/morphology/subpolar_flagellation.html
+++ b/pages/traits/morphology/subpolar_flagellation.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/sulfur_globule.html b/pages/traits/morphology/sulfur_globule.html
index 02c0ddab7e..f07c97a478 100644
--- a/pages/traits/morphology/sulfur_globule.html
+++ b/pages/traits/morphology/sulfur_globule.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/swarming_motility.html b/pages/traits/morphology/swarming_motility.html
index 192733621f..07200fb8db 100644
--- a/pages/traits/morphology/swarming_motility.html
+++ b/pages/traits/morphology/swarming_motility.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/tailed_shaped.html b/pages/traits/morphology/tailed_shaped.html
index f455f4ed9d..856b673cd9 100644
--- a/pages/traits/morphology/tailed_shaped.html
+++ b/pages/traits/morphology/tailed_shaped.html
@@ -337,7 +337,7 @@ kg-microbe context
METPO:1000695 [-2.811, -5.750, -3.599, -1.498, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -345,7 +345,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/tetrad_arrangement.html b/pages/traits/morphology/tetrad_arrangement.html
index db7f4be916..91062722d5 100644
--- a/pages/traits/morphology/tetrad_arrangement.html
+++ b/pages/traits/morphology/tetrad_arrangement.html
@@ -222,7 +222,7 @@ kg-microbe context
METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -230,7 +230,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/triangular_shaped.html b/pages/traits/morphology/triangular_shaped.html
index 2bb10d9402..e067053fe5 100644
--- a/pages/traits/morphology/triangular_shaped.html
+++ b/pages/traits/morphology/triangular_shaped.html
@@ -239,7 +239,7 @@ kg-microbe context
METPO:1000696 [-3.450, -2.250, -3.710, +1.379, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -247,7 +247,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/twitching_motility.html b/pages/traits/morphology/twitching_motility.html
index 2a8b2aa203..66a91de338 100644
--- a/pages/traits/morphology/twitching_motility.html
+++ b/pages/traits/morphology/twitching_motility.html
@@ -337,7 +337,7 @@ kg-microbe context
METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -345,7 +345,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/type_iv_pilus.html b/pages/traits/morphology/type_iv_pilus.html
index 845c097677..5a5ec346cc 100644
--- a/pages/traits/morphology/type_iv_pilus.html
+++ b/pages/traits/morphology/type_iv_pilus.html
@@ -91,7 +91,7 @@ Cross-references
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/morphology/vibrio_shaped.html b/pages/traits/morphology/vibrio_shaped.html
index f413884999..853db0ce33 100644
--- a/pages/traits/morphology/vibrio_shaped.html
+++ b/pages/traits/morphology/vibrio_shaped.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1000686 [-5.914, -107.472, -126.065, -23.277, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/white_pigmented.html b/pages/traits/morphology/white_pigmented.html
index 0cee8f9c0a..d19ad55509 100644
--- a/pages/traits/morphology/white_pigmented.html
+++ b/pages/traits/morphology/white_pigmented.html
@@ -290,7 +290,7 @@ kg-microbe context
METPO:1003029 [-3.308, -1.196, -0.658, -0.965, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -298,7 +298,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/morphology/yellow_pigmented.html b/pages/traits/morphology/yellow_pigmented.html
index f24eaf7134..ef261654c8 100644
--- a/pages/traits/morphology/yellow_pigmented.html
+++ b/pages/traits/morphology/yellow_pigmented.html
@@ -341,7 +341,7 @@ kg-microbe context
METPO:1003030 [-3.392, -1.132, -2.360, -0.296, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -349,7 +349,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/growth_nacl_observation.html b/pages/traits/observation/growth_nacl_observation.html
index 2505f8c5c0..aaeb21d46f 100644
--- a/pages/traits/observation/growth_nacl_observation.html
+++ b/pages/traits/observation/growth_nacl_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001007 [-0.011, +0.049, +0.018, +0.028, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/growth_oxygen_observation.html b/pages/traits/observation/growth_oxygen_observation.html
index 03e5237de7..282f8105ce 100644
--- a/pages/traits/observation/growth_oxygen_observation.html
+++ b/pages/traits/observation/growth_oxygen_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001017 [+0.047, +0.021, -0.060, +0.053, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/growth_ph_observation.html b/pages/traits/observation/growth_ph_observation.html
index d412b7674d..b18bb97dd9 100644
--- a/pages/traits/observation/growth_ph_observation.html
+++ b/pages/traits/observation/growth_ph_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001012 [-0.057, -0.036, +0.067, -0.097, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/growth_temperature_observation.html b/pages/traits/observation/growth_temperature_observation.html
index 36b070f603..1813bf684e 100644
--- a/pages/traits/observation/growth_temperature_observation.html
+++ b/pages/traits/observation/growth_temperature_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001002 [-0.071, +0.010, -0.051, +0.079, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/nacl_delta_observation.html b/pages/traits/observation/nacl_delta_observation.html
index ba0ccb0b40..9b2be7c695 100644
--- a/pages/traits/observation/nacl_delta_observation.html
+++ b/pages/traits/observation/nacl_delta_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001008 [+0.012, +0.090, -0.102, +0.057, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/nacl_observation.html b/pages/traits/observation/nacl_observation.html
index 9ea493ae38..7e926097b2 100644
--- a/pages/traits/observation/nacl_observation.html
+++ b/pages/traits/observation/nacl_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001022 [-0.020, +0.028, +0.103, -0.032, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/nacl_range_observation.html b/pages/traits/observation/nacl_range_observation.html
index 7271714a2f..f51b087790 100644
--- a/pages/traits/observation/nacl_range_observation.html
+++ b/pages/traits/observation/nacl_range_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001009 [+0.038, +0.034, -0.004, -0.016, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/optimum_nacl_observation.html b/pages/traits/observation/optimum_nacl_observation.html
index 1ecedff26a..7bba5144ca 100644
--- a/pages/traits/observation/optimum_nacl_observation.html
+++ b/pages/traits/observation/optimum_nacl_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001010 [-0.000, -0.014, -0.034, +0.033, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/optimum_oxygen_observation.html b/pages/traits/observation/optimum_oxygen_observation.html
index c329a6ea9a..2fe636721d 100644
--- a/pages/traits/observation/optimum_oxygen_observation.html
+++ b/pages/traits/observation/optimum_oxygen_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001016 [-0.008, -0.004, -0.101, +0.036, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/optimum_ph_observation.html b/pages/traits/observation/optimum_ph_observation.html
index 731c0ac434..8767ac40ce 100644
--- a/pages/traits/observation/optimum_ph_observation.html
+++ b/pages/traits/observation/optimum_ph_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001013 [-0.043, -0.086, +0.078, +0.095, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/optimum_temperature_observation.html b/pages/traits/observation/optimum_temperature_observation.html
index 5b47657010..c12ee1e322 100644
--- a/pages/traits/observation/optimum_temperature_observation.html
+++ b/pages/traits/observation/optimum_temperature_observation.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:1001001 [+0.006, -0.057, +0.034, -0.042, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/oxygen_delta_observation.html b/pages/traits/observation/oxygen_delta_observation.html
index 3b60855f0d..3c60b45eef 100644
--- a/pages/traits/observation/oxygen_delta_observation.html
+++ b/pages/traits/observation/oxygen_delta_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001019 [+0.020, -0.067, -0.058, -0.096, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/oxygen_observation.html b/pages/traits/observation/oxygen_observation.html
index 0a34dbaa19..0863732091 100644
--- a/pages/traits/observation/oxygen_observation.html
+++ b/pages/traits/observation/oxygen_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001020 [-0.037, +0.082, -0.027, -0.036, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/oxygen_range_observation.html b/pages/traits/observation/oxygen_range_observation.html
index f25fd9ce51..a09a3a5616 100644
--- a/pages/traits/observation/oxygen_range_observation.html
+++ b/pages/traits/observation/oxygen_range_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001018 [-0.108, -0.063, -0.077, -0.054, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/ph_delta_observation.html b/pages/traits/observation/ph_delta_observation.html
index 69071ae32b..d6228d267b 100644
--- a/pages/traits/observation/ph_delta_observation.html
+++ b/pages/traits/observation/ph_delta_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001014 [-0.039, +0.044, +0.003, -0.059, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/ph_observation.html b/pages/traits/observation/ph_observation.html
index 09ef88c369..e82796eee4 100644
--- a/pages/traits/observation/ph_observation.html
+++ b/pages/traits/observation/ph_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001023 [-0.057, +0.033, +0.080, -0.066, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/ph_range_observation.html b/pages/traits/observation/ph_range_observation.html
index c62d55f209..678a8f4286 100644
--- a/pages/traits/observation/ph_range_observation.html
+++ b/pages/traits/observation/ph_range_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001015 [+0.081, -0.048, +0.008, +0.081, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/temperature_delta_observation.html b/pages/traits/observation/temperature_delta_observation.html
index 5f87198471..ab4709fc8a 100644
--- a/pages/traits/observation/temperature_delta_observation.html
+++ b/pages/traits/observation/temperature_delta_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001004 [+0.079, -0.028, +0.092, -0.040, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/temperature_observation.html b/pages/traits/observation/temperature_observation.html
index 31d5c3c021..c79a88d899 100644
--- a/pages/traits/observation/temperature_observation.html
+++ b/pages/traits/observation/temperature_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001021 [+0.090, -0.056, +0.002, +0.091, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/observation/temperature_range_observation.html b/pages/traits/observation/temperature_range_observation.html
index 8391015fed..b42f309c90 100644
--- a/pages/traits/observation/temperature_range_observation.html
+++ b/pages/traits/observation/temperature_range_observation.html
@@ -78,7 +78,7 @@ kg-microbe context
METPO:1001003 [-0.085, -0.018, +0.035, -0.081, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -86,7 +86,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/other/catalase_negative.html b/pages/traits/other/catalase_negative.html
index 18587d1d7b..d20b533585 100644
--- a/pages/traits/other/catalase_negative.html
+++ b/pages/traits/other/catalase_negative.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/catalase_test.html b/pages/traits/other/catalase_test.html
index aaebd519b5..f820ca26e4 100644
--- a/pages/traits/other/catalase_test.html
+++ b/pages/traits/other/catalase_test.html
@@ -93,7 +93,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/circular_colony.html b/pages/traits/other/circular_colony.html
index 45d3ce2619..27908931b7 100644
--- a/pages/traits/other/circular_colony.html
+++ b/pages/traits/other/circular_colony.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/coagulase_negative.html b/pages/traits/other/coagulase_negative.html
index 3b30113135..3b21b3e5a9 100644
--- a/pages/traits/other/coagulase_negative.html
+++ b/pages/traits/other/coagulase_negative.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/coagulase_positive.html b/pages/traits/other/coagulase_positive.html
index 06462cfc5f..9500d4c646 100644
--- a/pages/traits/other/coagulase_positive.html
+++ b/pages/traits/other/coagulase_positive.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/colony_morphology.html b/pages/traits/other/colony_morphology.html
index b307b3b207..cc1659f580 100644
--- a/pages/traits/other/colony_morphology.html
+++ b/pages/traits/other/colony_morphology.html
@@ -82,7 +82,7 @@ Children (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/colony_shape.html b/pages/traits/other/colony_shape.html
index 6a88db7030..fd10262aff 100644
--- a/pages/traits/other/colony_shape.html
+++ b/pages/traits/other/colony_shape.html
@@ -92,7 +92,7 @@ Children (6)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/epibiont_phenotype.html b/pages/traits/other/epibiont_phenotype.html
index 900c465838..06e64fdd84 100644
--- a/pages/traits/other/epibiont_phenotype.html
+++ b/pages/traits/other/epibiont_phenotype.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/filamentous_colony.html b/pages/traits/other/filamentous_colony.html
index f5b2b50dde..3a8e56c1ac 100644
--- a/pages/traits/other/filamentous_colony.html
+++ b/pages/traits/other/filamentous_colony.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/fried_egg_shaped_colony.html b/pages/traits/other/fried_egg_shaped_colony.html
index 838fd0f845..01bf13eaa7 100644
--- a/pages/traits/other/fried_egg_shaped_colony.html
+++ b/pages/traits/other/fried_egg_shaped_colony.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/generalist.html b/pages/traits/other/generalist.html
index 48ea74fe93..eafcac457c 100644
--- a/pages/traits/other/generalist.html
+++ b/pages/traits/other/generalist.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/hemolysis.html b/pages/traits/other/hemolysis.html
index fe16c85f9b..90de87cfe2 100644
--- a/pages/traits/other/hemolysis.html
+++ b/pages/traits/other/hemolysis.html
@@ -91,7 +91,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/hemolytic.html b/pages/traits/other/hemolytic.html
index 1d295e1350..b0f1b8fb75 100644
--- a/pages/traits/other/hemolytic.html
+++ b/pages/traits/other/hemolytic.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/indole_test.html b/pages/traits/other/indole_test.html
index b4d8d0b4ae..b1e2ead5b7 100644
--- a/pages/traits/other/indole_test.html
+++ b/pages/traits/other/indole_test.html
@@ -84,7 +84,7 @@ Children (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/indole_test_negative.html b/pages/traits/other/indole_test_negative.html
index 7c8366c61a..909d861124 100644
--- a/pages/traits/other/indole_test_negative.html
+++ b/pages/traits/other/indole_test_negative.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/indole_test_positive.html b/pages/traits/other/indole_test_positive.html
index 75968d5e5c..224e5be3c3 100644
--- a/pages/traits/other/indole_test_positive.html
+++ b/pages/traits/other/indole_test_positive.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/irregular_colony.html b/pages/traits/other/irregular_colony.html
index 5c02f119c8..82debc1f03 100644
--- a/pages/traits/other/irregular_colony.html
+++ b/pages/traits/other/irregular_colony.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/methyl_red_test.html b/pages/traits/other/methyl_red_test.html
index d1c47cfc1f..c70bc5009a 100644
--- a/pages/traits/other/methyl_red_test.html
+++ b/pages/traits/other/methyl_red_test.html
@@ -84,7 +84,7 @@ Children (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/methyl_red_test_negative.html b/pages/traits/other/methyl_red_test_negative.html
index 0107444b66..5a7d1871c5 100644
--- a/pages/traits/other/methyl_red_test_negative.html
+++ b/pages/traits/other/methyl_red_test_negative.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/methyl_red_test_positive.html b/pages/traits/other/methyl_red_test_positive.html
index 3f20b4be5e..17697c7020 100644
--- a/pages/traits/other/methyl_red_test_positive.html
+++ b/pages/traits/other/methyl_red_test_positive.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/non_hemolytic.html b/pages/traits/other/non_hemolytic.html
index 1bcddd5040..fcdfda0c26 100644
--- a/pages/traits/other/non_hemolytic.html
+++ b/pages/traits/other/non_hemolytic.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/osmotic_tolerance.html b/pages/traits/other/osmotic_tolerance.html
index d6024a4ca3..cdfbf9ee19 100644
--- a/pages/traits/other/osmotic_tolerance.html
+++ b/pages/traits/other/osmotic_tolerance.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/oxidase_negative.html b/pages/traits/other/oxidase_negative.html
index 6d984b6208..95ae004e60 100644
--- a/pages/traits/other/oxidase_negative.html
+++ b/pages/traits/other/oxidase_negative.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/oxidase_test.html b/pages/traits/other/oxidase_test.html
index f99e39b109..aa1d401abe 100644
--- a/pages/traits/other/oxidase_test.html
+++ b/pages/traits/other/oxidase_test.html
@@ -93,7 +93,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/punctiform_colony.html b/pages/traits/other/punctiform_colony.html
index 0a7a056185..ca48906473 100644
--- a/pages/traits/other/punctiform_colony.html
+++ b/pages/traits/other/punctiform_colony.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/rhizoid_colony.html b/pages/traits/other/rhizoid_colony.html
index e8db3b590b..b68d0a99e3 100644
--- a/pages/traits/other/rhizoid_colony.html
+++ b/pages/traits/other/rhizoid_colony.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/specialist.html b/pages/traits/other/specialist.html
index 4ef4075e7d..97326aeb66 100644
--- a/pages/traits/other/specialist.html
+++ b/pages/traits/other/specialist.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/urease_negative.html b/pages/traits/other/urease_negative.html
index 71f07bf7a7..b60b5d75d8 100644
--- a/pages/traits/other/urease_negative.html
+++ b/pages/traits/other/urease_negative.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/urease_test.html b/pages/traits/other/urease_test.html
index 890e09d1a2..a3858d9a68 100644
--- a/pages/traits/other/urease_test.html
+++ b/pages/traits/other/urease_test.html
@@ -93,7 +93,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/voges_proskauer_test.html b/pages/traits/other/voges_proskauer_test.html
index 1ddef988dd..4658325b7a 100644
--- a/pages/traits/other/voges_proskauer_test.html
+++ b/pages/traits/other/voges_proskauer_test.html
@@ -84,7 +84,7 @@ Children (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/voges_proskauer_test_negative.html b/pages/traits/other/voges_proskauer_test_negative.html
index e9a61516a0..9d2b680253 100644
--- a/pages/traits/other/voges_proskauer_test_negative.html
+++ b/pages/traits/other/voges_proskauer_test_negative.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/other/voges_proskauer_test_positive.html b/pages/traits/other/voges_proskauer_test_positive.html
index ac1c91ee1e..2fea6bafcf 100644
--- a/pages/traits/other/voges_proskauer_test_positive.html
+++ b/pages/traits/other/voges_proskauer_test_positive.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/acid_phosphatase_activity.html b/pages/traits/physiology/acid_phosphatase_activity.html
index ed6cbd33a3..71286bf90a 100644
--- a/pages/traits/physiology/acid_phosphatase_activity.html
+++ b/pages/traits/physiology/acid_phosphatase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html b/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html
index 8c99b203f7..94d30363c4 100644
--- a/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html
+++ b/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html
@@ -225,7 +225,7 @@ Synonyms (4)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alanine_arylamidase_activity.html b/pages/traits/physiology/alanine_arylamidase_activity.html
index a2691c9f2e..c7d53fa2e4 100644
--- a/pages/traits/physiology/alanine_arylamidase_activity.html
+++ b/pages/traits/physiology/alanine_arylamidase_activity.html
@@ -86,7 +86,7 @@ Synonyms (3)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alkaline_phosphatase_activity.html b/pages/traits/physiology/alkaline_phosphatase_activity.html
index fcaac6a049..8e3a2a1eac 100644
--- a/pages/traits/physiology/alkaline_phosphatase_activity.html
+++ b/pages/traits/physiology/alkaline_phosphatase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alpha_chymotrypsin_activity.html b/pages/traits/physiology/alpha_chymotrypsin_activity.html
index 975a142f13..2ef4fddbb4 100644
--- a/pages/traits/physiology/alpha_chymotrypsin_activity.html
+++ b/pages/traits/physiology/alpha_chymotrypsin_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alpha_fucosidase_activity.html b/pages/traits/physiology/alpha_fucosidase_activity.html
index 9a3afd3e40..ec45dad0a8 100644
--- a/pages/traits/physiology/alpha_fucosidase_activity.html
+++ b/pages/traits/physiology/alpha_fucosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alpha_galactosidase_activity.html b/pages/traits/physiology/alpha_galactosidase_activity.html
index 237621a197..a28abad623 100644
--- a/pages/traits/physiology/alpha_galactosidase_activity.html
+++ b/pages/traits/physiology/alpha_galactosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alpha_glucosidase_activity.html b/pages/traits/physiology/alpha_glucosidase_activity.html
index 06f60a8825..95ed7e4b2f 100644
--- a/pages/traits/physiology/alpha_glucosidase_activity.html
+++ b/pages/traits/physiology/alpha_glucosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/alpha_mannosidase_activity.html b/pages/traits/physiology/alpha_mannosidase_activity.html
index d284a541a0..e36df86b45 100644
--- a/pages/traits/physiology/alpha_mannosidase_activity.html
+++ b/pages/traits/physiology/alpha_mannosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/amylase_activity.html b/pages/traits/physiology/amylase_activity.html
index 87517fcb25..3a1fec3b2b 100644
--- a/pages/traits/physiology/amylase_activity.html
+++ b/pages/traits/physiology/amylase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/antibiotic_resistance.html b/pages/traits/physiology/antibiotic_resistance.html
index 24ea784364..b42f1d63b0 100644
--- a/pages/traits/physiology/antibiotic_resistance.html
+++ b/pages/traits/physiology/antibiotic_resistance.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/arginine_arylamidase_activity.html b/pages/traits/physiology/arginine_arylamidase_activity.html
index f6db14f6d0..710fcffa9e 100644
--- a/pages/traits/physiology/arginine_arylamidase_activity.html
+++ b/pages/traits/physiology/arginine_arylamidase_activity.html
@@ -90,7 +90,7 @@ Synonyms (5)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/arginine_dihydrolase_activity.html b/pages/traits/physiology/arginine_dihydrolase_activity.html
index 950d191a8b..4367282721 100644
--- a/pages/traits/physiology/arginine_dihydrolase_activity.html
+++ b/pages/traits/physiology/arginine_dihydrolase_activity.html
@@ -88,7 +88,7 @@ Synonyms (4)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/autotrophic.html b/pages/traits/physiology/autotrophic.html
index 6ad21290b2..cb6bf5186f 100644
--- a/pages/traits/physiology/autotrophic.html
+++ b/pages/traits/physiology/autotrophic.html
@@ -477,7 +477,7 @@ kg-microbe context
METPO:1000632 [-2.568, +0.105, -3.476, -0.957, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -485,7 +485,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/bacteriocin_production.html b/pages/traits/physiology/bacteriocin_production.html
index 821e92ef74..f2936149cb 100644
--- a/pages/traits/physiology/bacteriocin_production.html
+++ b/pages/traits/physiology/bacteriocin_production.html
@@ -80,7 +80,7 @@ Cross-references
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/beta_galactosidase_activity.html b/pages/traits/physiology/beta_galactosidase_activity.html
index 6efe3a6335..505b14afa4 100644
--- a/pages/traits/physiology/beta_galactosidase_activity.html
+++ b/pages/traits/physiology/beta_galactosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/beta_glucosidase_activity.html b/pages/traits/physiology/beta_glucosidase_activity.html
index cedbdca25c..e11f84ad87 100644
--- a/pages/traits/physiology/beta_glucosidase_activity.html
+++ b/pages/traits/physiology/beta_glucosidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/beta_glucuronidase_activity.html b/pages/traits/physiology/beta_glucuronidase_activity.html
index 79ea088d3b..0304f6a85f 100644
--- a/pages/traits/physiology/beta_glucuronidase_activity.html
+++ b/pages/traits/physiology/beta_glucuronidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html b/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html
index 67b33a335a..bf55c198d4 100644
--- a/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html
+++ b/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html
@@ -88,7 +88,7 @@ Synonyms (4)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/bioluminescence.html b/pages/traits/physiology/bioluminescence.html
index eb771f9b5c..6614ce037e 100644
--- a/pages/traits/physiology/bioluminescence.html
+++ b/pages/traits/physiology/bioluminescence.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/carboxydotrophic.html b/pages/traits/physiology/carboxydotrophic.html
index fe32f97ab9..176b949c21 100644
--- a/pages/traits/physiology/carboxydotrophic.html
+++ b/pages/traits/physiology/carboxydotrophic.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000633 [-2.124, -2.915, -5.468, -0.095, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/carboxylesterase_activity.html b/pages/traits/physiology/carboxylesterase_activity.html
index ed43e42a5b..4950ae5976 100644
--- a/pages/traits/physiology/carboxylesterase_activity.html
+++ b/pages/traits/physiology/carboxylesterase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/caseinase_activity.html b/pages/traits/physiology/caseinase_activity.html
index 124fd3321d..1d7079dd32 100644
--- a/pages/traits/physiology/caseinase_activity.html
+++ b/pages/traits/physiology/caseinase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/catalase_activity.html b/pages/traits/physiology/catalase_activity.html
index acfcb9f500..73e5b4bf1d 100644
--- a/pages/traits/physiology/catalase_activity.html
+++ b/pages/traits/physiology/catalase_activity.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemoautolithotrophic.html b/pages/traits/physiology/chemoautolithotrophic.html
index c94215cb4e..add07f5f1a 100644
--- a/pages/traits/physiology/chemoautolithotrophic.html
+++ b/pages/traits/physiology/chemoautolithotrophic.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000634 [-0.916, -0.754, -3.630, +1.094, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemoautotrophic.html b/pages/traits/physiology/chemoautotrophic.html
index 41efacbe5a..3791ffbcdb 100644
--- a/pages/traits/physiology/chemoautotrophic.html
+++ b/pages/traits/physiology/chemoautotrophic.html
@@ -456,7 +456,7 @@ kg-microbe context
METPO:1000635 [-0.624, -3.507, -4.293, +0.160, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -464,7 +464,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemoheterotrophic.html b/pages/traits/physiology/chemoheterotrophic.html
index 68fa09fffd..12775cb21d 100644
--- a/pages/traits/physiology/chemoheterotrophic.html
+++ b/pages/traits/physiology/chemoheterotrophic.html
@@ -424,7 +424,7 @@ kg-microbe context
METPO:1000636 [-2.849, -3.249, -2.560, +0.024, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -432,7 +432,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemolithoautotrophic.html b/pages/traits/physiology/chemolithoautotrophic.html
index 0938f5be0f..bc609ce91e 100644
--- a/pages/traits/physiology/chemolithoautotrophic.html
+++ b/pages/traits/physiology/chemolithoautotrophic.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1000637 [-1.631, -1.052, -4.107, +0.857, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemolithoheterotrophic.html b/pages/traits/physiology/chemolithoheterotrophic.html
index ca9a2fa5ed..a217c7f4af 100644
--- a/pages/traits/physiology/chemolithoheterotrophic.html
+++ b/pages/traits/physiology/chemolithoheterotrophic.html
@@ -456,7 +456,7 @@ kg-microbe context
METPO:1000638 [-3.114, -0.723, -4.275, +1.898, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -464,7 +464,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemolithotrophic.html b/pages/traits/physiology/chemolithotrophic.html
index 160ad8369d..d00c89c17b 100644
--- a/pages/traits/physiology/chemolithotrophic.html
+++ b/pages/traits/physiology/chemolithotrophic.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1000639 [-0.145, -1.567, -3.045, -0.245, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemoorganoheterotrophic.html b/pages/traits/physiology/chemoorganoheterotrophic.html
index 4e2be08d0e..8153be5599 100644
--- a/pages/traits/physiology/chemoorganoheterotrophic.html
+++ b/pages/traits/physiology/chemoorganoheterotrophic.html
@@ -456,7 +456,7 @@ kg-microbe context
METPO:1000640 [-0.994, -2.623, -3.294, +0.737, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -464,7 +464,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemoorganotrophic.html b/pages/traits/physiology/chemoorganotrophic.html
index 0c2250dbf1..f5ab438ee8 100644
--- a/pages/traits/physiology/chemoorganotrophic.html
+++ b/pages/traits/physiology/chemoorganotrophic.html
@@ -473,7 +473,7 @@ kg-microbe context
METPO:1000663 [-0.780, -1.684, -2.585, +1.757, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -481,7 +481,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemotaxis.html b/pages/traits/physiology/chemotaxis.html
index 7e771891b5..9dfd8be062 100644
--- a/pages/traits/physiology/chemotaxis.html
+++ b/pages/traits/physiology/chemotaxis.html
@@ -363,7 +363,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -371,7 +371,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/chemotrophic.html b/pages/traits/physiology/chemotrophic.html
index 072a387d1e..0e32ecc8cd 100644
--- a/pages/traits/physiology/chemotrophic.html
+++ b/pages/traits/physiology/chemotrophic.html
@@ -407,7 +407,7 @@ kg-microbe context
METPO:1000641 [-1.746, -0.197, -4.063, +1.592, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -415,7 +415,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/coagulase_activity.html b/pages/traits/physiology/coagulase_activity.html
index 223b05f0b5..a01a8ac435 100644
--- a/pages/traits/physiology/coagulase_activity.html
+++ b/pages/traits/physiology/coagulase_activity.html
@@ -95,7 +95,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/copiotrophic.html b/pages/traits/physiology/copiotrophic.html
index eecc9b65ce..657187735c 100644
--- a/pages/traits/physiology/copiotrophic.html
+++ b/pages/traits/physiology/copiotrophic.html
@@ -330,7 +330,7 @@ kg-microbe context
METPO:1000642 [-0.599, -2.377, -5.129, +0.987, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -338,7 +338,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/cystine_arylamidase_activity.html b/pages/traits/physiology/cystine_arylamidase_activity.html
index 6266b37ba9..24d409d9b3 100644
--- a/pages/traits/physiology/cystine_arylamidase_activity.html
+++ b/pages/traits/physiology/cystine_arylamidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/dnase_activity.html b/pages/traits/physiology/dnase_activity.html
index 513327fbce..6a05186a9e 100644
--- a/pages/traits/physiology/dnase_activity.html
+++ b/pages/traits/physiology/dnase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/dormancy.html b/pages/traits/physiology/dormancy.html
index 2e5f9ad793..449dfa34d3 100644
--- a/pages/traits/physiology/dormancy.html
+++ b/pages/traits/physiology/dormancy.html
@@ -331,7 +331,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -339,7 +339,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/gamma_glutamyltransferase_activity.html b/pages/traits/physiology/gamma_glutamyltransferase_activity.html
index fb1b1faa42..0f039a1dd9 100644
--- a/pages/traits/physiology/gamma_glutamyltransferase_activity.html
+++ b/pages/traits/physiology/gamma_glutamyltransferase_activity.html
@@ -86,7 +86,7 @@ Synonyms (3)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/gelatinase_activity.html b/pages/traits/physiology/gelatinase_activity.html
index 6bfc9998f5..a15a3e58f9 100644
--- a/pages/traits/physiology/gelatinase_activity.html
+++ b/pages/traits/physiology/gelatinase_activity.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html b/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html
index f775d90f50..19cba68afb 100644
--- a/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html
+++ b/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/glycine_arylamidase_activity.html b/pages/traits/physiology/glycine_arylamidase_activity.html
index 6f1b841582..0b81811459 100644
--- a/pages/traits/physiology/glycine_arylamidase_activity.html
+++ b/pages/traits/physiology/glycine_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/heterotrophic.html b/pages/traits/physiology/heterotrophic.html
index e36eae4def..0f26142678 100644
--- a/pages/traits/physiology/heterotrophic.html
+++ b/pages/traits/physiology/heterotrophic.html
@@ -392,7 +392,7 @@ kg-microbe context
METPO:1000644 [-2.157, -7.477, -8.079, -1.768, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -400,7 +400,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/histidine_arylamidase_activity.html b/pages/traits/physiology/histidine_arylamidase_activity.html
index c9dd291bc3..fc91ac94d3 100644
--- a/pages/traits/physiology/histidine_arylamidase_activity.html
+++ b/pages/traits/physiology/histidine_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/hydrogenotrophic.html b/pages/traits/physiology/hydrogenotrophic.html
index 3e29e3a853..61943d103b 100644
--- a/pages/traits/physiology/hydrogenotrophic.html
+++ b/pages/traits/physiology/hydrogenotrophic.html
@@ -379,7 +379,7 @@ kg-microbe context
METPO:1000646 [-2.114, -2.957, -5.142, +0.724, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -387,7 +387,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/lecithinase_activity.html b/pages/traits/physiology/lecithinase_activity.html
index 3c0714862a..ff355fefc2 100644
--- a/pages/traits/physiology/lecithinase_activity.html
+++ b/pages/traits/physiology/lecithinase_activity.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/leucine_arylamidase_activity.html b/pages/traits/physiology/leucine_arylamidase_activity.html
index 55f6bfdee9..1776bd2ef4 100644
--- a/pages/traits/physiology/leucine_arylamidase_activity.html
+++ b/pages/traits/physiology/leucine_arylamidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html b/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html
index 91ea5b481c..b7f0785576 100644
--- a/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html
+++ b/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/lipase_activity.html b/pages/traits/physiology/lipase_activity.html
index be2a2134b9..7b72661dab 100644
--- a/pages/traits/physiology/lipase_activity.html
+++ b/pages/traits/physiology/lipase_activity.html
@@ -84,7 +84,7 @@ Synonyms (2)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/lithoautotrophic.html b/pages/traits/physiology/lithoautotrophic.html
index d04cafc00b..951942d0c5 100644
--- a/pages/traits/physiology/lithoautotrophic.html
+++ b/pages/traits/physiology/lithoautotrophic.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000647 [-1.104, -2.675, -4.383, +0.615, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/lithoheterotrophic.html b/pages/traits/physiology/lithoheterotrophic.html
index 36957ad677..5b08530bf2 100644
--- a/pages/traits/physiology/lithoheterotrophic.html
+++ b/pages/traits/physiology/lithoheterotrophic.html
@@ -473,7 +473,7 @@ kg-microbe context
METPO:1000648 [-0.997, -3.520, -5.312, -0.246, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -481,7 +481,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/lithotrophic.html b/pages/traits/physiology/lithotrophic.html
index 975f9ea2a3..173ef0ed45 100644
--- a/pages/traits/physiology/lithotrophic.html
+++ b/pages/traits/physiology/lithotrophic.html
@@ -475,7 +475,7 @@ kg-microbe context
METPO:1000649 [-3.967, -1.575, -4.683, +0.255, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -483,7 +483,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/lysine_decarboxylase_activity.html b/pages/traits/physiology/lysine_decarboxylase_activity.html
index 4dcaa01cd2..9569adf621 100644
--- a/pages/traits/physiology/lysine_decarboxylase_activity.html
+++ b/pages/traits/physiology/lysine_decarboxylase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/magnetotaxis.html b/pages/traits/physiology/magnetotaxis.html
index 25eb7eb31b..a69aa69fad 100644
--- a/pages/traits/physiology/magnetotaxis.html
+++ b/pages/traits/physiology/magnetotaxis.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/methanotrophic.html b/pages/traits/physiology/methanotrophic.html
index e18b740d60..c8f718a49c 100644
--- a/pages/traits/physiology/methanotrophic.html
+++ b/pages/traits/physiology/methanotrophic.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000650 [-1.873, -2.718, -3.631, -1.154, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/methylotrophic.html b/pages/traits/physiology/methylotrophic.html
index 1d62e1f336..babe9d6673 100644
--- a/pages/traits/physiology/methylotrophic.html
+++ b/pages/traits/physiology/methylotrophic.html
@@ -477,7 +477,7 @@ kg-microbe context
METPO:1000651 [-1.480, -2.354, -1.736, -0.358, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -485,7 +485,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/mixotrophic.html b/pages/traits/physiology/mixotrophic.html
index 5761af4520..bcf8ddcda4 100644
--- a/pages/traits/physiology/mixotrophic.html
+++ b/pages/traits/physiology/mixotrophic.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000652 [-1.472, -3.019, -4.301, +1.004, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html b/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html
index a234374410..c69614f028 100644
--- a/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html
+++ b/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html
@@ -86,7 +86,7 @@ Synonyms (3)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html b/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html
index 3d55194d52..5634599f83 100644
--- a/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html
+++ b/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/natural_competence.html b/pages/traits/physiology/natural_competence.html
index 365e9d063c..125469cbc7 100644
--- a/pages/traits/physiology/natural_competence.html
+++ b/pages/traits/physiology/natural_competence.html
@@ -354,7 +354,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -362,7 +362,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/nutrient_adaptation.html b/pages/traits/physiology/nutrient_adaptation.html
index 3a45c18305..2ed5e5ed76 100644
--- a/pages/traits/physiology/nutrient_adaptation.html
+++ b/pages/traits/physiology/nutrient_adaptation.html
@@ -258,7 +258,7 @@ kg-microbe context
METPO:1000731 [-0.684, -2.860, -4.946, +1.094, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -266,7 +266,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/oligotrophic.html b/pages/traits/physiology/oligotrophic.html
index 6fa750a8dd..3219c7ac5d 100644
--- a/pages/traits/physiology/oligotrophic.html
+++ b/pages/traits/physiology/oligotrophic.html
@@ -309,7 +309,7 @@ kg-microbe context
METPO:1000654 [-0.416, -2.511, -4.279, +1.100, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -317,7 +317,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/organoheterotrophic.html b/pages/traits/physiology/organoheterotrophic.html
index 899514f356..d2356685ab 100644
--- a/pages/traits/physiology/organoheterotrophic.html
+++ b/pages/traits/physiology/organoheterotrophic.html
@@ -388,7 +388,7 @@ kg-microbe context
METPO:1000664 [-0.481, -1.211, -3.077, -0.947, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -396,7 +396,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/organotrophic.html b/pages/traits/physiology/organotrophic.html
index fbd9fe3740..4b2973f988 100644
--- a/pages/traits/physiology/organotrophic.html
+++ b/pages/traits/physiology/organotrophic.html
@@ -373,7 +373,7 @@ kg-microbe context
METPO:1000655 [+0.165, -1.239, -2.986, +1.908, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -381,7 +381,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/ornithine_decarboxylase_activity.html b/pages/traits/physiology/ornithine_decarboxylase_activity.html
index 2a3ecdf10b..8b973c006a 100644
--- a/pages/traits/physiology/ornithine_decarboxylase_activity.html
+++ b/pages/traits/physiology/ornithine_decarboxylase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/oxidase_activity.html b/pages/traits/physiology/oxidase_activity.html
index 0f11b4d31e..1b61a5ef84 100644
--- a/pages/traits/physiology/oxidase_activity.html
+++ b/pages/traits/physiology/oxidase_activity.html
@@ -337,7 +337,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -345,7 +345,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/oxidative_stress_response.html b/pages/traits/physiology/oxidative_stress_response.html
index bee638fbab..c5f7a2a014 100644
--- a/pages/traits/physiology/oxidative_stress_response.html
+++ b/pages/traits/physiology/oxidative_stress_response.html
@@ -243,7 +243,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -251,7 +251,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/persister_cell_formation.html b/pages/traits/physiology/persister_cell_formation.html
index 780a1644e1..5c02d4c97e 100644
--- a/pages/traits/physiology/persister_cell_formation.html
+++ b/pages/traits/physiology/persister_cell_formation.html
@@ -343,7 +343,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -351,7 +351,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/phenylalanine_arylamidase_activity.html b/pages/traits/physiology/phenylalanine_arylamidase_activity.html
index fbc669a5b9..145d7dc5e2 100644
--- a/pages/traits/physiology/phenylalanine_arylamidase_activity.html
+++ b/pages/traits/physiology/phenylalanine_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/photoautotrophic.html b/pages/traits/physiology/photoautotrophic.html
index 7c6fc0f88e..df3578f3f9 100644
--- a/pages/traits/physiology/photoautotrophic.html
+++ b/pages/traits/physiology/photoautotrophic.html
@@ -432,7 +432,7 @@ kg-microbe context
METPO:1000656 [-1.879, -5.853, -1.491, +0.710, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -440,7 +440,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/photoheterotrophic.html b/pages/traits/physiology/photoheterotrophic.html
index c4ae7a0e26..e70ec0eba0 100644
--- a/pages/traits/physiology/photoheterotrophic.html
+++ b/pages/traits/physiology/photoheterotrophic.html
@@ -433,7 +433,7 @@ kg-microbe context
METPO:1000657 [-0.306, -3.156, -1.761, +2.105, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -441,7 +441,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/photolithoautotrophic.html b/pages/traits/physiology/photolithoautotrophic.html
index e3e7c7ae5b..5ab769e42e 100644
--- a/pages/traits/physiology/photolithoautotrophic.html
+++ b/pages/traits/physiology/photolithoautotrophic.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000665 [-2.042, -2.782, -5.220, +0.946, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/photolithotrophic.html b/pages/traits/physiology/photolithotrophic.html
index 4cc58575e7..022ca12e00 100644
--- a/pages/traits/physiology/photolithotrophic.html
+++ b/pages/traits/physiology/photolithotrophic.html
@@ -422,7 +422,7 @@ kg-microbe context
METPO:1000658 [-1.986, -2.827, -4.047, -0.222, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -430,7 +430,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/photoorganoheterotrophic.html b/pages/traits/physiology/photoorganoheterotrophic.html
index 56d85f4017..5efc8b5b0c 100644
--- a/pages/traits/physiology/photoorganoheterotrophic.html
+++ b/pages/traits/physiology/photoorganoheterotrophic.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1000659 [-2.409, -2.535, -5.408, -0.103, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/phototrophic.html b/pages/traits/physiology/phototrophic.html
index 970209e14f..4b326ea83f 100644
--- a/pages/traits/physiology/phototrophic.html
+++ b/pages/traits/physiology/phototrophic.html
@@ -390,7 +390,7 @@ kg-microbe context
METPO:1000660 [-2.096, -3.602, -1.726, +2.700, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -398,7 +398,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/prolyl_aminopeptidase_activity.html b/pages/traits/physiology/prolyl_aminopeptidase_activity.html
index 43decfe84f..f5b6492c80 100644
--- a/pages/traits/physiology/prolyl_aminopeptidase_activity.html
+++ b/pages/traits/physiology/prolyl_aminopeptidase_activity.html
@@ -88,7 +88,7 @@ Synonyms (4)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/pyrazinamidase_activity.html b/pages/traits/physiology/pyrazinamidase_activity.html
index 684de9e77e..423bd12124 100644
--- a/pages/traits/physiology/pyrazinamidase_activity.html
+++ b/pages/traits/physiology/pyrazinamidase_activity.html
@@ -88,7 +88,7 @@ Synonyms (4)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html b/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html
index 5eeeb8552b..c227bac8ea 100644
--- a/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html
+++ b/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/quorum_sensing.html b/pages/traits/physiology/quorum_sensing.html
index 90c2e464b9..4a5fd67d0e 100644
--- a/pages/traits/physiology/quorum_sensing.html
+++ b/pages/traits/physiology/quorum_sensing.html
@@ -328,7 +328,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -336,7 +336,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/serine_arylamidase_activity.html b/pages/traits/physiology/serine_arylamidase_activity.html
index 60eaa33c6c..40d0baa983 100644
--- a/pages/traits/physiology/serine_arylamidase_activity.html
+++ b/pages/traits/physiology/serine_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/siderophore_production.html b/pages/traits/physiology/siderophore_production.html
index d70bb537dd..0aa305e137 100644
--- a/pages/traits/physiology/siderophore_production.html
+++ b/pages/traits/physiology/siderophore_production.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/spore_germination.html b/pages/traits/physiology/spore_germination.html
index 01297c5766..fe51aa6bdb 100644
--- a/pages/traits/physiology/spore_germination.html
+++ b/pages/traits/physiology/spore_germination.html
@@ -227,7 +227,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -235,7 +235,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/stress_response.html b/pages/traits/physiology/stress_response.html
index 87c2a0feff..911e54aea1 100644
--- a/pages/traits/physiology/stress_response.html
+++ b/pages/traits/physiology/stress_response.html
@@ -346,7 +346,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -354,7 +354,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/trophic_type.html b/pages/traits/physiology/trophic_type.html
index cc3abc34d6..8ebe2fee5f 100644
--- a/pages/traits/physiology/trophic_type.html
+++ b/pages/traits/physiology/trophic_type.html
@@ -408,7 +408,7 @@ kg-microbe context
METPO:1000631 [-1.491, -2.608, -4.371, +0.721, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -416,7 +416,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/trypsin_activity.html b/pages/traits/physiology/trypsin_activity.html
index e5ed9f0ae3..19ba92d7b1 100644
--- a/pages/traits/physiology/trypsin_activity.html
+++ b/pages/traits/physiology/trypsin_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/tyrosine_arylamidase_activity.html b/pages/traits/physiology/tyrosine_arylamidase_activity.html
index ed750f15cf..37cb4f9085 100644
--- a/pages/traits/physiology/tyrosine_arylamidase_activity.html
+++ b/pages/traits/physiology/tyrosine_arylamidase_activity.html
@@ -82,7 +82,7 @@ Synonyms (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/urease_activity.html b/pages/traits/physiology/urease_activity.html
index 0cb05666de..7c2578b5ec 100644
--- a/pages/traits/physiology/urease_activity.html
+++ b/pages/traits/physiology/urease_activity.html
@@ -405,7 +405,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -413,7 +413,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/physiology/valine_arylamidase_activity.html b/pages/traits/physiology/valine_arylamidase_activity.html
index 1fc1c4eb19..56cad7c335 100644
--- a/pages/traits/physiology/valine_arylamidase_activity.html
+++ b/pages/traits/physiology/valine_arylamidase_activity.html
@@ -73,7 +73,7 @@ Parent traits (1)
kg-microbe context
No kg-microbe node embedding for this METPO class
- in the 2026-04-25 deepwalk. Most unmatched terms are
+ in the Legacy graph artifact; source provenance not recorded deepwalk. Most unmatched terms are
DatatypeProperties (e.g. METPO:has_*_value) that the
graph encodes as edge attributes, not entity nodes.
diff --git a/pages/traits/physiology/viable_but_nonculturable_state.html b/pages/traits/physiology/viable_but_nonculturable_state.html
index f0a1e3cc60..6f8f0abe54 100644
--- a/pages/traits/physiology/viable_but_nonculturable_state.html
+++ b/pages/traits/physiology/viable_but_nonculturable_state.html
@@ -337,7 +337,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -345,7 +345,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/has_maximum_observed_value.html b/pages/traits/quantitative_property/has_maximum_observed_value.html
index 6099d0c34e..0d8fd9e933 100644
--- a/pages/traits/quantitative_property/has_maximum_observed_value.html
+++ b/pages/traits/quantitative_property/has_maximum_observed_value.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000060 [+0.021, -0.024, +0.067, -0.021, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/has_minimum_observed_value.html b/pages/traits/quantitative_property/has_minimum_observed_value.html
index 0a908ebea8..e970a24523 100644
--- a/pages/traits/quantitative_property/has_minimum_observed_value.html
+++ b/pages/traits/quantitative_property/has_minimum_observed_value.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000059 [+0.064, -0.085, -0.018, -0.087, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/has_observed_spot_value.html b/pages/traits/quantitative_property/has_observed_spot_value.html
index 3be04f1b77..d165ff15ee 100644
--- a/pages/traits/quantitative_property/has_observed_spot_value.html
+++ b/pages/traits/quantitative_property/has_observed_spot_value.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000058 [-0.096, -0.065, -0.002, -0.079, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/has_value.html b/pages/traits/quantitative_property/has_value.html
index 68d8324111..bd8f30c5d6 100644
--- a/pages/traits/quantitative_property/has_value.html
+++ b/pages/traits/quantitative_property/has_value.html
@@ -71,7 +71,7 @@ kg-microbe context
METPO:2000071 [-0.023, -0.016, -0.102, +0.094, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -79,7 +79,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/has_value_comments.html b/pages/traits/quantitative_property/has_value_comments.html
index bfc1742948..8dcc9d9ef1 100644
--- a/pages/traits/quantitative_property/has_value_comments.html
+++ b/pages/traits/quantitative_property/has_value_comments.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000061 [-0.054, +0.017, +0.025, -0.032, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/is_negative_data.html b/pages/traits/quantitative_property/is_negative_data.html
index 25513337c5..74b04edb19 100644
--- a/pages/traits/quantitative_property/is_negative_data.html
+++ b/pages/traits/quantitative_property/is_negative_data.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:2000062 [+0.056, -0.103, -0.000, +0.056, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/quantitative_property/observation_data_property.html b/pages/traits/quantitative_property/observation_data_property.html
index 295f061907..32a40dcd3b 100644
--- a/pages/traits/quantitative_property/observation_data_property.html
+++ b/pages/traits/quantitative_property/observation_data_property.html
@@ -86,7 +86,7 @@ kg-microbe context
METPO:2000063 [-0.033, -0.105, +0.028, +0.087, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -94,7 +94,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/biological_process.html b/pages/traits/upper/biological_process.html
index 9cb3597d4e..920191d929 100644
--- a/pages/traits/upper/biological_process.html
+++ b/pages/traits/upper/biological_process.html
@@ -248,7 +248,7 @@ kg-microbe context
METPO:1000630 [-0.906, -0.897, -0.035, -0.552, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -256,7 +256,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/chemical_entity.html b/pages/traits/upper/chemical_entity.html
index 099059def4..9017be97ee 100644
--- a/pages/traits/upper/chemical_entity.html
+++ b/pages/traits/upper/chemical_entity.html
@@ -87,7 +87,7 @@ kg-microbe context
METPO:1000526 [+0.357, -0.541, +0.061, +0.848, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -95,7 +95,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/enzyme.html b/pages/traits/upper/enzyme.html
index 47e51f0d7a..8e21bd2aaf 100644
--- a/pages/traits/upper/enzyme.html
+++ b/pages/traits/upper/enzyme.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:1000527 [+0.167, -0.909, -0.249, +1.095, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/material_entity.html b/pages/traits/upper/material_entity.html
index 179f4519a0..58d7321122 100644
--- a/pages/traits/upper/material_entity.html
+++ b/pages/traits/upper/material_entity.html
@@ -166,7 +166,7 @@ kg-microbe context
METPO:1000186 [+0.971, -0.795, +0.103, +1.493, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -174,7 +174,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/microbe.html b/pages/traits/upper/microbe.html
index d5e4fee7ba..30d6296724 100644
--- a/pages/traits/upper/microbe.html
+++ b/pages/traits/upper/microbe.html
@@ -80,7 +80,7 @@ kg-microbe context
METPO:1000525 [+0.029, -0.773, +0.243, +1.218, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -88,7 +88,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/observation.html b/pages/traits/upper/observation.html
index 29f432d074..607cbb2cd9 100644
--- a/pages/traits/upper/observation.html
+++ b/pages/traits/upper/observation.html
@@ -302,7 +302,7 @@ kg-microbe context
METPO:1001000 [-0.035, -0.074, +0.047, +0.096, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -310,7 +310,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/phenotype.html b/pages/traits/upper/phenotype.html
index f8221dd676..2903d31cd2 100644
--- a/pages/traits/upper/phenotype.html
+++ b/pages/traits/upper/phenotype.html
@@ -406,7 +406,7 @@ kg-microbe context
METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -414,7 +414,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/traits/upper/quality.html b/pages/traits/upper/quality.html
index 6ea2ef5693..b57e3e4484 100644
--- a/pages/traits/upper/quality.html
+++ b/pages/traits/upper/quality.html
@@ -193,7 +193,7 @@ kg-microbe context
METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).
+
Stored kg-microbe graph vector (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
@@ -201,7 +201,7 @@ kg-microbe context
Nearest neighbors in embedding space
Top-8 cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded).
diff --git a/pages/umap.html b/pages/umap.html
index d0acdfda3a..73f01d8855 100644
--- a/pages/umap.html
+++ b/pages/umap.html
@@ -23,8 +23,8 @@
TraitMech › Embedding space
Trait embedding space
- PaCMAP projection of 477 METPO trait
- embeddings from kg-microbe's 2026-04-25 deepwalk (512-D, n_neighbors=15).
+
Unverified projection of 477 METPO trait
+ embeddings. Source: Legacy graph artifact; source provenance not recorded; dimensions: unrecorded.
Hover for label, click to open the trait page.
@@ -45,7 +45,7 @@ Trait embedding space
diff --git a/scripts/build_embedding_index.py b/scripts/build_embedding_index.py
old mode 100644
new mode 100755
index 6934897c74..b9fcf91cbe
--- a/scripts/build_embedding_index.py
+++ b/scripts/build_embedding_index.py
@@ -2,17 +2,12 @@
"""Vendor a slim trait subset of kg-microbe's deepwalk embeddings + build a
METPO CURIE ↔ kg-microbe-node match table.
-Source priority
----------------
-1. ``../CommunityMech/CommunityMech/data/embeddings/DeepWalkSkipGramEnsmallen_degreenorm_embedding_512_v2_2026-04-25_*.tsv.gz``
- (5.7 GB, 512-D, latest; carries 380 METPO CURIEs DIRECTLY plus the legacy
- pre-METPO trait nodes for backward compatibility).
-2. Fallback to the 2024-09-25 200-D file if the 2026-04-25 one isn't present.
-
-The 2026-04-25 file is the first kg-microbe-derived embedding that ingests
-METPO. Direct CURIE lookup (METPO:1000602 → that row's 512 floats) is the
-primary match path; the alias-table + label-match fallback covers METPO
-classes whose CURIEs the embedding doesn't have but whose label does.
+Source selection
+----------------
+Explicit ``--src`` or ``KG_MICROBE_EMBEDDINGS`` takes precedence, then a local
+v3 2026-06-26 artifact, then the configured/sibling CommunityMech artifact.
+A missing selected source fails; legacy releases require an explicit path.
+No source/reducer provenance is inferred for old point arrays.
Bridge
------
@@ -40,6 +35,9 @@
import argparse
import csv
import gzip
+import hashlib
+import json
+import os
import re
import sys
from pathlib import Path
@@ -48,16 +46,21 @@
# Newest available kg-microbe-derived deepwalk: 512-D, 2026-06-26 (v3),
# includes METPO CURIEs directly. Source-of-truth for direct-METPO matching.
-DEFAULT_KGM_DEEPWALK = (
- REPO_ROOT.parent / "CommunityMech" / "CommunityMech" / "data" / "embeddings"
- / "DeepWalkSkipGramEnsmallen_degreenorm_embedding_512_v3_2026-06-26_12_55_27.tsv.gz"
-)
-# Fallback: 2024-09-25 200-D file (pre-METPO; only useful for legacy-prefix
-# trait nodes like `cell_shape:bacillus`).
-FALLBACK_KGM_DEEPWALK = (
- REPO_ROOT.parent / "kg-microbe-projects" / "taxa_media"
- / "DeepWalkSkipGramEnsmallen_degreenorm_embedding_200_1_wouniprot__2024-09-25_03_07_47.tsv.gz"
-)
+EMBEDDINGS_FILENAME = "DeepWalkSkipGramEnsmallen_degreenorm_embedding_512_v3_2026-06-26_12_55_27.tsv.gz"
+
+
+def default_deepwalk() -> Path:
+ override = os.environ.get("KG_MICROBE_EMBEDDINGS")
+ if override:
+ return Path(override).expanduser()
+ local = REPO_ROOT / "data" / "embeddings" / EMBEDDINGS_FILENAME
+ if local.is_file():
+ return local
+ community = Path(os.environ.get("COMMUNITYMECH_ROOT") or REPO_ROOT.parent / "CommunityMech")
+ return community / "data" / "embeddings" / EMBEDDINGS_FILENAME
+
+
+DEFAULT_KGM_DEEPWALK = default_deepwalk()
DEFAULT_KGM_ALIASES = (
REPO_ROOT.parent / "kg-microbe" / "mappings" / "canonical" / "metpo_alias_mappings.tsv"
)
@@ -143,8 +146,8 @@ def load_metpo_records(traits_dir: Path) -> list[tuple[str, str, list[str], str,
for path in sorted(traits_dir.rglob("*.yaml")):
try:
doc = yaml.safe_load(path.read_text())
- except Exception:
- continue
+ except (OSError, yaml.YAMLError) as error:
+ raise ValueError(f"Unable to read trait record: {path}") from error
if not isinstance(doc, dict):
continue
curie = (doc.get("identifier") or "").strip()
@@ -319,8 +322,8 @@ def compute_umap_and_neighbors(
return [], {}
elif method == "pacmap":
try:
- import pacmap # noqa: F401
- from sklearn.preprocessing import normalize # noqa: F401
+ import pacmap
+ from sklearn.preprocessing import normalize
except ImportError as e:
print(f" PaCMAP / scikit-learn not available: {e}; skipping projection",
file=sys.stderr)
@@ -328,7 +331,7 @@ def compute_umap_and_neighbors(
elif method == "sfdp":
try:
sys.path.insert(0, str(Path(__file__).resolve().parent))
- from sfdp_layout import sfdp_layout # noqa: F401
+ from sfdp_layout import sfdp_layout
except ImportError as e:
print(f" sfdp_layout / scikit-learn not available: {e}; skipping projection",
file=sys.stderr)
@@ -393,6 +396,7 @@ def compute_umap_and_neighbors(
"label": lbl,
"category": cat,
"match_method": match_by_curie[curie]["match_method"],
+ "kgm_nodes": match_by_curie[curie]["kgm_nodes"].split(";"),
"umap_x": float(coords[i, 0]),
"umap_y": float(coords[i, 1]),
})
@@ -402,6 +406,8 @@ def compute_umap_and_neighbors(
"label": record_by_curie[curies[j]][0],
"category": record_by_curie[curies[j]][2],
"similarity": float(sim[i, j]),
+ "match_method": match_by_curie[curies[j]]["match_method"],
+ "kgm_nodes": match_by_curie[curies[j]]["kgm_nodes"].split(";"),
}
for j in top_idx[i]
]
@@ -414,11 +420,36 @@ def compute_umap_and_neighbors(
def write_json(path: Path, payload) -> None:
- import json
path.parent.mkdir(parents=True, exist_ok=True)
path.write_text(json.dumps(payload, indent=2))
+
+def file_sha256(path: Path) -> str:
+ with path.open("rb") as stream:
+ return hashlib.file_digest(stream, "sha256").hexdigest()
+
+
+def write_projection_metadata(path: Path, source: Path, vectors, method: str,
+ match_table: Path, neighbors: Path) -> None:
+ """Bind newly generated outputs to the source actually selected by this run."""
+ dims = {len(vector) for vector in vectors.values()}
+ if len(dims) != 1:
+ raise ValueError("Graph vectors must have one nonempty dimension")
+ write_json(path.with_suffix(".metadata.json"), {
+ "schema_version": 1,
+ "embedding_family": "kg_microbe_deepwalk",
+ "source": {"filename": source.name, "sha256": file_sha256(source)},
+ "input_dimensions": next(iter(dims)),
+ "projection": {"method": method, "random_state": 42,
+ "normalization": "l2" if method in {"pacmap", "sfdp"} else "none"},
+ "match_table_sha256": file_sha256(match_table),
+ "outputs": {path.name: file_sha256(path), neighbors.name: file_sha256(neighbors)},
+ "coverage": {"projected": len(json.loads(path.read_text())),
+ "neighbor_records": len(json.loads(neighbors.read_text()))},
+ })
+
+
def main() -> int:
ap = argparse.ArgumentParser()
ap.add_argument("--src", type=Path, default=DEFAULT_KGM_DEEPWALK,
@@ -436,13 +467,9 @@ def main() -> int:
args = ap.parse_args()
src = args.src
- if not src.exists():
- if FALLBACK_KGM_DEEPWALK.exists():
- print(f" Primary embedding missing ({src}); using fallback {FALLBACK_KGM_DEEPWALK.name}")
- src = FALLBACK_KGM_DEEPWALK
- else:
- print(f"deepwalk source missing: {src}", file=sys.stderr)
- return 2
+ if not src.is_file():
+ print(f"Selected deepwalk source missing: {src}; pass --src for another release", file=sys.stderr)
+ return 2
print(f"[1/4] Vendoring slim deepwalk subset → {args.out_deepwalk}")
print(f" source: {src.name}")
@@ -474,8 +501,12 @@ def main() -> int:
umap_points, nn_map = compute_umap_and_neighbors(
metpo_records, rows, vectors, method=args.method
)
+ if not umap_points:
+ print("Projection produced no points; outputs were not published", file=sys.stderr)
+ return 2
write_json(args.umap_out, umap_points)
write_json(OUT_NN_JSON, nn_map)
+ write_projection_metadata(args.umap_out, src, vectors, args.method, args.out_match, OUT_NN_JSON)
print(f" {len(umap_points)} UMAP points → {args.umap_out.name}")
nn_with_data = sum(1 for v in nn_map.values() if v)
print(f" {nn_with_data} traits with ≥1 nearest neighbor → {OUT_NN_JSON.name}")
diff --git a/scripts/render_trait_pages.py b/scripts/render_trait_pages.py
old mode 100644
new mode 100755
index 8fa98749f7..dc65411d0d
--- a/scripts/render_trait_pages.py
+++ b/scripts/render_trait_pages.py
@@ -24,6 +24,8 @@
import argparse
import csv
import gzip
+import hashlib
+import json
import re
import shutil
import sys
@@ -33,7 +35,6 @@
import yaml
from jinja2 import Environment, FileSystemLoader, select_autoescape
-
from research_trait import is_pipeline_report
from trait_causal_graph import causal_graphs_for_template
@@ -49,7 +50,38 @@
NN_JSON = EMBED_DIR / "trait_nearest_neighbors.json"
DIM_PREVIEW = 4 # number of dims to show inline next to each kg-microbe node
-EMBEDDING_RELEASE = "2026-04-25"
+def load_projection_receipt(path: Path) -> dict:
+ """Display only metadata bound to the current map and neighbor bytes.
+
+ Old arrays have no generation receipt. Their current defaults are not
+ evidence about the algorithm, source release or dimension used before.
+ """
+ legacy = {"label": "Unverified projection", "method": "unknown",
+ "source": "Legacy graph artifact; source provenance not recorded",
+ "dimensions": "unrecorded", "verified": False}
+ try:
+ receipt = json.loads(path.with_suffix(".metadata.json").read_text())
+ source = receipt["source"]
+ dimensions = receipt["input_dimensions"]
+ method = receipt["projection"]["method"]
+ if (receipt["schema_version"] != 1 or method not in {"pacmap", "umap", "sfdp"}
+ or type(dimensions) is not int or dimensions < 1
+ or not isinstance(source["filename"], str) or not source["filename"]
+ or not re.fullmatch(r"[0-9a-f]{64}", source["sha256"])):
+ return legacy
+ # Include neighbor integrity so a newer neighbor run cannot silently
+ # borrow an older map's source claim on every trait page.
+ for output in (path, path.parent / "trait_nearest_neighbors.json"):
+ with output.open("rb") as stream:
+ digest = hashlib.file_digest(stream, "sha256").hexdigest()
+ if receipt["outputs"].get(output.name) != digest:
+ return legacy
+ return {"label": {"pacmap": "PaCMAP", "umap": "UMAP", "sfdp": "sfdp layout"}[method],
+ "method": method, "source": source["filename"],
+ "source_sha256": source["sha256"], "dimensions": dimensions, "verified": True}
+ except (OSError, ValueError, KeyError, TypeError, AttributeError):
+ return legacy
+
# Provider precedence for the deep-research lookup.
#
@@ -122,8 +154,8 @@ def load_traits() -> list[tuple[Path, dict]]:
for path in sorted(TRAITS_DIR.rglob("*.yaml")):
try:
doc = yaml.safe_load(path.read_text())
- except Exception:
- continue
+ except (OSError, yaml.YAMLError) as error:
+ raise ValueError(f"Unable to read trait record: {path}") from error
if isinstance(doc, dict):
out.append((path, doc))
return out
@@ -256,10 +288,10 @@ def load_node_dim_preview(needed_nodes: set[str]) -> dict[str, str]:
sid = parts[0]
if sid in needed_nodes:
dims = parts[1:1 + DIM_PREVIEW]
- if dims and dims[0] in ("0", "0.0", ""):
- # Header / index column? skip.
- if all(d.isdigit() for d in dims if d):
- continue
+ # Header / index column? skip.
+ if (dims and dims[0] in ("0", "0.0", "")
+ and all(d.isdigit() for d in dims if d)):
+ continue
preview = ", ".join(f"{float(d):+.3f}" for d in dims if d)
out[sid] = f"[{preview}, …]"
return out
@@ -370,6 +402,7 @@ def render_pages(args: argparse.Namespace) -> int:
metpo_version = load_metpo_version(RAW_OWL)
traits = load_traits()
match_table = load_match_table()
+ embedding_receipt = load_projection_receipt(UMAP_JSON)
# One value for every page in the run, derived from the data (#228).
corpus_stamp = corpus_timestamp(traits)
@@ -484,7 +517,8 @@ def render_pages(args: argparse.Namespace) -> int:
research_blob_url=(
f"{GH_BLOB_BASE}/{research_rel}" if research_rel else ""
),
- embedding_release=EMBEDDING_RELEASE,
+ embedding_release=embedding_receipt["source"],
+ embedding_dimensions=embedding_receipt["dimensions"],
metpo_version=metpo_version,
yaml_path=yaml_rel,
yaml_blob_url=f"{GH_BLOB_BASE}/{yaml_rel}",
@@ -534,6 +568,7 @@ def render_pages(args: argparse.Namespace) -> int:
title="Trait embedding space",
root="",
data_url="data/trait_umap.json",
+ projection=embedding_receipt,
href_by_id=_json.dumps({p["id"]: page_path.get(p["id"], "") for p in umap_points}),
n_points=len(umap_points),
metpo_version=metpo_version,
@@ -554,9 +589,10 @@ def render_pages(args: argparse.Namespace) -> int:
nn_by_curie, {point["id"] for point in graph_points}
)
graph_html = env.get_template("graph.html").render(
- title="Trait graph layout (sfdp)",
+ title="Trait graph layout",
root="",
data_url="data/trait_graph.json",
+ projection=load_projection_receipt(GRAPH_JSON),
href_by_id=_json.dumps({p["id"]: page_path.get(p["id"], "") for p in graph_points}),
graph_edges=_json.dumps(graph_edges),
n_points=len(graph_points),
@@ -578,6 +614,7 @@ def render_pages(args: argparse.Namespace) -> int:
embedded_count = sum(1 for v in match_table.values() if v["n_kgm_nodes"] > 0)
landing = env.get_template("index.html").render(
title="Microbial trait knowledge base",
+ projection_label=embedding_receipt["label"],
root="",
total_traits=len(traits),
embedded_count=embedded_count,
diff --git a/src/traitmech/templates/graph.html b/src/traitmech/templates/graph.html
index 67f1245f93..5811a39745 100644
--- a/src/traitmech/templates/graph.html
+++ b/src/traitmech/templates/graph.html
@@ -2,10 +2,10 @@
{% block content %}
TraitMech › Graph layout
- Trait graph layout (sfdp)
- Graphviz sfdp force-directed layout over
- {{ n_points }} METPO trait embeddings from kg-microbe's
- 2026-04-25 deepwalk (512-D, layout k=15). The {{ n_edges }} visible links are
+
Trait graph layout
+ {{ projection.label }} over
+ {{ n_points }} METPO trait embeddings. Projection: {{ projection.label }}.
+ Source: {{ projection.source }}; dimensions: {{ projection.dimensions }}. The {{ n_edges }} visible links are
reciprocal relationships in the committed top-neighbor index. Hover for a
label; click to open the trait page.
diff --git a/src/traitmech/templates/index.html b/src/traitmech/templates/index.html
index ffb21d0d6b..c0feaf13f2 100644
--- a/src/traitmech/templates/index.html
+++ b/src/traitmech/templates/index.html
@@ -125,9 +125,9 @@ Record browser
🗺️
-
+
Embedding browser
-
Interactive PaCMAP of the trait embedding space with click-through to records.
+
Interactive {{ projection_label }} of the trait embedding space with click-through to records.
💻
diff --git a/src/traitmech/templates/trait.html b/src/traitmech/templates/trait.html
index 0d8eaf3c04..db5c77be78 100644
--- a/src/traitmech/templates/trait.html
+++ b/src/traitmech/templates/trait.html
@@ -210,7 +210,7 @@
kg-microbe context
{{ node }}{% if node in node_dim_preview %} {{ node_dim_preview[node] }} {% endif %}
{% endfor %}
-
512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe ({{ embedding_release }}).
+
Stored kg-microbe graph vector (source: {{ embedding_release }}; dimensions: {{ embedding_dimensions }}).
{% else %}
No kg-microbe node embedding for this METPO class
in the {{ embedding_release }} deepwalk. Most unmatched terms are
@@ -223,7 +223,7 @@
kg-microbe context
Nearest neighbors in embedding space
Top-{{ nearest_neighbors|length }} cosine-similar METPO traits
- from the 2026-04-25 deepwalk (512-D).
+ from the stored graph vectors (source: {{ embedding_release }}; dimensions: {{ embedding_dimensions }}).
{% for nn in nearest_neighbors %}
diff --git a/src/traitmech/templates/umap.html b/src/traitmech/templates/umap.html
index 37d88f4b22..5e1f6623f4 100644
--- a/src/traitmech/templates/umap.html
+++ b/src/traitmech/templates/umap.html
@@ -3,8 +3,8 @@
TraitMech › Embedding space
Trait embedding space
- PaCMAP projection of {{ n_points }} METPO trait
- embeddings from kg-microbe's 2026-04-25 deepwalk (512-D, n_neighbors=15).
+
{{ projection.label }} of {{ n_points }} METPO trait
+ embeddings. Source: {{ projection.source }}; dimensions: {{ projection.dimensions }}.
Hover for label, click to open the trait page.
@@ -25,7 +25,7 @@ Trait embedding space
diff --git a/tests/test_graph_projection_correctness.py b/tests/test_graph_projection_correctness.py
new file mode 100644
index 0000000000..069dcb780b
--- /dev/null
+++ b/tests/test_graph_projection_correctness.py
@@ -0,0 +1,87 @@
+"""Selected graph sources and published receipts must be literal, not guessed."""
+import importlib.util
+import json
+import sys
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def builder():
+ path = Path(__file__).resolve().parents[1] / "scripts/build_embedding_index.py"
+ spec = importlib.util.spec_from_file_location("graph_builder_under_test", path)
+ module = importlib.util.module_from_spec(spec)
+ spec.loader.exec_module(module)
+ return module
+
+
+def test_explicit_missing_source_fails_without_fallback(builder, tmp_path, monkeypatch):
+ monkeypatch.setattr(sys, "argv", ["builder", "--src", str(tmp_path / "typo.gz"),
+ "--out-deepwalk", str(tmp_path / "out.gz")])
+ assert builder.main() == 2
+ assert not (tmp_path / "out.gz").exists()
+
+
+def test_configured_source_is_selected_even_if_missing(builder, tmp_path, monkeypatch):
+ missing = tmp_path / "selected.gz"
+ monkeypatch.setenv("KG_MICROBE_EMBEDDINGS", str(missing))
+ assert builder.default_deepwalk() == missing
+
+
+def test_current_local_and_configured_sibling_layout(builder, tmp_path, monkeypatch):
+ monkeypatch.delenv("KG_MICROBE_EMBEDDINGS", raising=False)
+ monkeypatch.setattr(builder, "REPO_ROOT", tmp_path / "TraitMech")
+ sibling = tmp_path / "CommunityMech"
+ monkeypatch.setenv("COMMUNITYMECH_ROOT", str(sibling))
+ assert builder.default_deepwalk() == sibling / "data/embeddings" / builder.EMBEDDINGS_FILENAME
+ local = builder.REPO_ROOT / "data/embeddings" / builder.EMBEDDINGS_FILENAME
+ local.parent.mkdir(parents=True)
+ local.write_bytes(b"source")
+ assert builder.default_deepwalk() == local
+
+
+def test_receipt_uses_actual_source_dimensions_and_output_digests(builder, tmp_path):
+ source = tmp_path / "explicit_legacy_graph.tsv.gz"
+ source.write_bytes(b"a caller-selected legacy artifact")
+ output = tmp_path / "map.json"
+ output.write_text('[{"id":"METPO:1"}]')
+ neighbors = tmp_path / "neighbors.json"
+ neighbors.write_text('{"METPO:1":[]}')
+ matches = tmp_path / "matches.tsv"
+ matches.write_text("match_method\nparent_proxy\n")
+ builder.write_projection_metadata(output, source, {"METPO:1": [1.] * 200}, "umap", matches, neighbors)
+ metadata = json.loads(output.with_suffix(".metadata.json").read_text())
+ assert metadata["source"] == {"filename": source.name, "sha256": builder.file_sha256(source)}
+ assert metadata["input_dimensions"] == 200
+ assert metadata["projection"]["method"] == "umap"
+ assert metadata["outputs"][output.name] == builder.file_sha256(output)
+ assert metadata["outputs"][neighbors.name] == builder.file_sha256(neighbors)
+
+
+def test_renderer_checks_receipt_and_labels_legacy_without_guessing(builder, tmp_path, monkeypatch):
+ import hashlib
+ path = Path(__file__).resolve().parents[1] / "scripts/render_trait_pages.py"
+ monkeypatch.syspath_prepend(str(path.parent))
+ spec = importlib.util.spec_from_file_location("graph_renderer_under_test", path)
+ renderer = importlib.util.module_from_spec(spec)
+ spec.loader.exec_module(renderer)
+ projection = tmp_path / "map.json"
+ projection.write_text("[]")
+ neighbors = tmp_path / "trait_nearest_neighbors.json"
+ neighbors.write_text("{}")
+ assert renderer.load_projection_receipt(projection)["verified"] is False
+ receipt = {"schema_version": 1, "input_dimensions": 200,
+ "source": {"filename": "actual_legacy_source.gz", "sha256": "a" * 64},
+ "projection": {"method": "umap"},
+ "outputs": {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in (projection, neighbors)}}
+ projection.with_suffix(".metadata.json").write_text(json.dumps(receipt))
+ result = renderer.load_projection_receipt(projection)
+ assert result["label"] == "UMAP"
+ assert result["dimensions"] == 200
+ assert result["source"] == "actual_legacy_source.gz"
+ assert result["verified"] is True
+ neighbors.write_text('{"changed": []}')
+ assert renderer.load_projection_receipt(projection)["verified"] is False
+ projection.with_suffix(".metadata.json").write_text("broken")
+ assert renderer.load_projection_receipt(projection)["label"] == "Unverified projection"
From e278671dd99a5f2e261dc16e6132c25207ec5b2c Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 14 Sep 2026 18:07:41 -0700
Subject: [PATCH 02/11] feat: export versioned semantic text for shared fleet
maps
---
docs/TEXT_MAP_INPUTS.md | 19 +++
justfile | 4 +
scripts/text_map_inputs.py | 7 +
src/traitmech/text_map_inputs.py | 215 +++++++++++++++++++++++++++++++
tests/test_text_map_inputs.py | 106 +++++++++++++++
5 files changed, 351 insertions(+)
create mode 100644 docs/TEXT_MAP_INPUTS.md
create mode 100755 scripts/text_map_inputs.py
create mode 100644 src/traitmech/text_map_inputs.py
create mode 100644 tests/test_text_map_inputs.py
diff --git a/docs/TEXT_MAP_INPUTS.md b/docs/TEXT_MAP_INPUTS.md
new file mode 100644
index 0000000000..6a98d00fff
--- /dev/null
+++ b/docs/TEXT_MAP_INPUTS.md
@@ -0,0 +1,19 @@
+# Common semantic text map inputs
+
+Includes all canonical trait YAML records. Stable record identifiers link to
+the exact existing category/stem page. Text includes label, definition, semantic
+category, synonyms, resolved parent labels and named canonical taxa. Citation,
+history, mapping status, ontology identifiers and curation discussions are
+excluded; graph structure and graph-source vectors remain a separate view.
+Parent labels come from the full corpus, so canary selection cannot alter text.
+
+Export with `just text-map-inputs --output data/text_map/inputs.jsonl`. Without `--output`, the command validates a preview. `--record` (repeatable repository-relative YAML path) and `--limit` explicitly select canary subsets; ordinary exports cover every eligible record.
+
+Each JSONL row has exactly `identifier`, `label`, `category`, `page`, `source_path`, `text`, `text_sha256`, and `adapter_version`. The text digest is SHA-256 over the exact UTF-8 text. Input order and text are deterministic; duplicate IDs and unreadable records fail. This adapter makes no model call. Common model/projection generation and publication require the fleet pipeline and full-input checks.
+
+Changing provenance-only fields leaves semantic text unchanged. Editing a selected semantic field changes its digest. This text view supplements the existing graph view; it does not alter graph aggregation or its scientific interpretation.
+
+The `page` field is relative to the directory containing the published map
+folder: from `text-map/index.html`, the shared renderer uses `../` plus `page`.
+This repository publishes the bundle at `pages/text-map/`, so record links omit
+the deployment wrapper `pages/` and resolve to its sibling record directories.
diff --git a/justfile b/justfile
index e6d0eaa59e..48074829ea 100644
--- a/justfile
+++ b/justfile
@@ -1191,3 +1191,7 @@ report-label-drift:
gen-discussions-data: (_require-claw "kg_microbe_discussions")
PYTHONPATH={{claw_src}} uv run python \
-m kg_microbe_discussions --config conf/discussions_config.yaml --output app/discussions
+
+# Full canonical semantic text by default; --record/--limit are explicit canaries.
+text-map-inputs *args:
+ uv run python scripts/text_map_inputs.py {{args}}
diff --git a/scripts/text_map_inputs.py b/scripts/text_map_inputs.py
new file mode 100755
index 0000000000..4c1fe69ff9
--- /dev/null
+++ b/scripts/text_map_inputs.py
@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+"""Export versioned semantic YAML text for the common fleet map."""
+
+from traitmech.text_map_inputs import main
+
+if __name__ == "__main__":
+ raise SystemExit(main())
diff --git a/src/traitmech/text_map_inputs.py b/src/traitmech/text_map_inputs.py
new file mode 100644
index 0000000000..175fed6633
--- /dev/null
+++ b/src/traitmech/text_map_inputs.py
@@ -0,0 +1,215 @@
+"""Versioned semantic YAML text for the common fleet map; no model calls.
+
+Includes all canonical trait YAML records. Stable record identifiers link to
+the exact existing category/stem page. Text includes label, definition, semantic
+category, synonyms, resolved parent labels and named canonical taxa. Citation,
+history, mapping status, ontology identifiers and curation discussions are
+excluded; graph structure and graph-source vectors remain a separate view.
+Parent labels come from the full corpus, so canary selection cannot alter text.
+"""
+from __future__ import annotations
+
+import argparse
+import hashlib
+import json
+import os
+import sys
+import tempfile
+from collections.abc import Iterator
+from contextlib import nullcontext
+from pathlib import Path
+from urllib.parse import quote
+
+import yaml
+
+REPO_ROOT = Path(__file__).resolve().parents[2]
+ADAPTER_VERSION = "traitmech-semantic-v1"
+RECORD_ROOTS = ('data/traits',)
+
+
+def clean(value: object) -> str:
+ return " ".join(str(value).split()) if value is not None else ""
+
+
+def enum_text(value: object) -> str:
+ return clean(value).lower().replace("_", " ")
+
+
+def label_of(value: object) -> str:
+ if isinstance(value, str):
+ return clean(value)
+ if not isinstance(value, dict):
+ return ""
+ return clean(value.get("preferred_term") or value.get("label") or value.get("name")
+ or (value.get("term") or {}).get("label"))
+
+
+def add(lines: list[str], label: str, value: object) -> None:
+ text = clean(value)
+ if text:
+ lines.append(f"{label}: {text}")
+
+
+def _load(path: Path) -> dict:
+ with path.open(encoding="utf-8") as stream:
+ # Both possible loaders are safe and never construct Python objects.
+ record = yaml.load(stream, Loader=getattr(yaml, "CSafeLoader", yaml.SafeLoader))
+ if not isinstance(record, dict):
+ raise TypeError(f"record is not a YAML mapping: {path}")
+ return record
+
+
+def _discover(directory: Path) -> Iterator[Path]:
+ with os.scandir(directory) as entries:
+ for entry in entries:
+ if entry.is_symlink():
+ raise ValueError(f"symlink in corpus: {entry.path}")
+ if entry.is_dir(follow_symlinks=False):
+ yield from _discover(Path(entry.path))
+ elif entry.name.endswith(".yaml") and entry.is_file(follow_symlinks=False):
+ yield Path(entry.path)
+
+
+def _record_path(root: Path, relative: str) -> Path:
+ path = Path(relative)
+ if path.is_absolute() or ".." in path.parts or path.suffix != ".yaml":
+ raise ValueError(f"not a repository-relative corpus YAML path: {relative}")
+ source = root / path
+ if not any(source.is_relative_to(root / directory) for directory in RECORD_ROOTS):
+ raise ValueError(f"record leaves the corpus: {relative}")
+ if any((root / Path(*path.parts[:length])).is_symlink() for length in range(1, len(path.parts) + 1)):
+ raise ValueError(f"symlink in corpus path: {relative}")
+ if not source.is_file():
+ raise ValueError(f"missing corpus record: {relative}")
+ return source
+
+
+
+def include_record(record: dict) -> bool:
+ return True
+
+
+def build_context(paths: list[Path]) -> dict:
+ context = {}
+ for path in sorted(paths):
+ record = _load(path)
+ identifier = record.get("identifier")
+ if identifier in context:
+ raise ValueError(f"duplicate trait identifier: {identifier}")
+ context[identifier] = clean(record.get("label"))
+ return context
+
+
+def record_details(record: dict, path: Path) -> tuple[str, str, str, str]:
+ return (record.get("identifier"), clean(record.get("label")),
+ clean(record.get("trait_category")) or "UNKNOWN",
+ "traits/" + quote(path.parent.name, safe="-._") + "/" + quote(path.stem, safe="-._") + ".html")
+
+
+def semantic_text(record: dict, context: dict | None = None) -> str:
+ context = context or {}
+ lines = []
+ add(lines, "name", record.get("label"))
+ add(lines, "definition", record.get("definition"))
+ add(lines, "trait category", enum_text(record.get("trait_category")))
+ add(lines, "synonyms", "; ".join(sorted({clean(item.get("synonym_text"))
+ for item in record.get("synonyms") or []} - {""})))
+ for label in sorted({context.get(parent, "") for parent in record.get("parent_traits") or []} - {""}):
+ add(lines, "broader trait", label)
+ for example in record.get("canonical_examples") or []:
+ add(lines, "example taxon", example.get("taxon_label"))
+ return "\n".join(lines) + "\n"
+
+
+
+def iter_inputs(root: Path = REPO_ROOT, *, records: list[str] | None = None,
+ limit: int | None = None) -> Iterator[dict]:
+ root = root.resolve()
+ if limit is not None and limit < 1:
+ raise ValueError("limit must be a positive integer")
+ paths = []
+ for directory in RECORD_ROOTS:
+ corpus = root / directory
+ if not corpus.is_dir() or any((root / Path(*Path(directory).parts[:length])).is_symlink()
+ for length in range(1, len(Path(directory).parts) + 1)):
+ raise ValueError(f"missing real corpus directory: {corpus}")
+ paths.extend(_discover(corpus))
+ context = build_context(paths)
+ selected = [_record_path(root, relative) for relative in records] if records else paths
+ if len(set(selected)) != len(selected):
+ raise ValueError("duplicate selected record path")
+ selected = sorted(selected)
+ identifiers = set()
+ count = 0
+ for path in selected:
+ record = _load(path)
+ if not include_record(record):
+ continue
+ identifier, label, category, page = record_details(record, path)
+ if not all(isinstance(value, str) and value.strip() for value in (identifier, label, category, page)):
+ raise ValueError(f"missing record identity, label, category or page: {path}")
+ if identifier in identifiers:
+ raise ValueError(f"duplicate record identifier: {identifier}")
+ identifiers.add(identifier)
+ text = semantic_text(record, context)
+ yield {"identifier": identifier, "label": label, "category": category, "page": page,
+ "source_path": path.relative_to(root).as_posix(), "text": text,
+ "text_sha256": hashlib.sha256(text.encode("utf-8")).hexdigest(),
+ "adapter_version": ADAPTER_VERSION}
+ count += 1
+ if limit is not None and count >= limit:
+ break
+
+
+def export_inputs(root: Path, output: Path | None, *, records: list[str] | None = None,
+ limit: int | None = None) -> dict:
+ destination = output.resolve() if output is not None else None
+ if destination is not None and destination.suffix != ".jsonl":
+ raise ValueError("output must have a .jsonl suffix")
+ temporary = None
+ digest = hashlib.sha256()
+ count = 0
+ try:
+ if destination is not None:
+ destination.parent.mkdir(parents=True, exist_ok=True)
+ with (tempfile.NamedTemporaryFile(mode="wb", prefix=".text-map-", dir=destination.parent,
+ delete=False) if destination is not None else nullcontext()) as handle:
+ if handle is not None:
+ temporary = Path(handle.name)
+ for record in iter_inputs(root, records=records, limit=limit):
+ data = (json.dumps(record, sort_keys=True, ensure_ascii=False) + "\n").encode("utf-8")
+ digest.update(data)
+ count += 1
+ if handle is not None:
+ handle.write(data)
+ if not count:
+ raise ValueError("selection contains no eligible corpus records")
+ if temporary is not None:
+ temporary.replace(destination)
+ return {"mode": "export" if destination else "preview",
+ "scope": "subset" if records or limit is not None else "full",
+ "records": count, "adapter_version": ADAPTER_VERSION,
+ "jsonl_sha256": digest.hexdigest(), "output": str(destination) if destination else None}
+ finally:
+ if temporary is not None:
+ temporary.unlink(missing_ok=True)
+
+
+def main(argv: list[str] | None = None) -> int:
+ parser = argparse.ArgumentParser(description=__doc__)
+ parser.add_argument("--root", type=Path, default=REPO_ROOT)
+ parser.add_argument("--output", type=Path, help="write JSONL atomically; otherwise validate a preview")
+ parser.add_argument("--record", action="append", help="repeat a repo-relative path for an explicit canary")
+ parser.add_argument("--limit", type=int, help="explicit canary limit; normal exports cover the full corpus")
+ args = parser.parse_args(argv)
+ try:
+ result = export_inputs(args.root, args.output, records=args.record, limit=args.limit)
+ except (OSError, ValueError, TypeError, yaml.YAMLError) as error:
+ print(f"text-map inputs refused: {error}", file=sys.stderr)
+ return 2
+ print(json.dumps(result, sort_keys=True))
+ return 0
+
+
+if __name__ == "__main__":
+ raise SystemExit(main())
diff --git a/tests/test_text_map_inputs.py b/tests/test_text_map_inputs.py
new file mode 100644
index 0000000000..1bb7535042
--- /dev/null
+++ b/tests/test_text_map_inputs.py
@@ -0,0 +1,106 @@
+"""Semantic adapter behavior, corpus boundaries, identity and atomic refusal."""
+import copy
+import hashlib
+import json
+from pathlib import Path
+
+import pytest
+import yaml
+
+from traitmech import text_map_inputs as adapter
+
+SOURCE = 'data/traits/ecology/example.yaml'
+RECORD = {'identifier': 'METPO:000001', 'label': 'Example trait', 'trait_category': 'ECOLOGY', 'definition': 'A biological adaptation', 'parent_traits': ['METPO:parent']}
+LABEL_FIELD = 'label'
+PAGE = 'traits/ecology/example.html'
+
+
+def fixture_tree(root):
+ for directory in adapter.RECORD_ROOTS:
+ (root / directory).mkdir(parents=True, exist_ok=True)
+ path = root / SOURCE
+ path.parent.mkdir(parents=True, exist_ok=True)
+ path.write_text(yaml.safe_dump(RECORD))
+ if adapter.ADAPTER_VERSION.startswith("traitmech-"):
+ parent = path.with_name("parent.yaml")
+ parent.write_text(yaml.safe_dump({"identifier": "METPO:parent", "label": "Resolved parent", "trait_category": "ECOLOGY"}))
+ return path
+
+
+def test_exact_contract_and_semantic_digest_ignores_provenance(tmp_path):
+ path = fixture_tree(tmp_path)
+ row = next(adapter.iter_inputs(tmp_path, records=[SOURCE]))
+ assert set(row) == {"identifier", "label", "category", "page", "source_path", "text", "text_sha256", "adapter_version"}
+ assert row["page"] == PAGE
+ assert row["source_path"] == SOURCE
+ assert row["text_sha256"] == hashlib.sha256(row["text"].encode("utf-8")).hexdigest()
+ assert "REJECTED_SENTINEL" not in row["text"]
+ record = copy.deepcopy(RECORD)
+ record.update({"curation_history": [{"notes": "PRIVATE_PROVENANCE_SENTINEL"}],
+ "references": [{"reference": "PMID:999999"}],
+ "evidence": [{"snippet": "PRIVATE_PROVENANCE_SENTINEL"}],
+ "notes": "PRIVATE_PROVENANCE_SENTINEL"})
+ path.write_text(yaml.safe_dump(record))
+ unchanged = next(adapter.iter_inputs(tmp_path, records=[SOURCE]))
+ assert unchanged["text_sha256"] == row["text_sha256"]
+ assert "PRIVATE_PROVENANCE_SENTINEL" not in unchanged["text"]
+ record[LABEL_FIELD] = "A different biological entity"
+ path.write_text(yaml.safe_dump(record))
+ changed = next(adapter.iter_inputs(tmp_path, records=[SOURCE]))
+ assert changed["text_sha256"] != row["text_sha256"]
+
+
+def test_canary_and_full_keep_identical_semantics(tmp_path):
+ fixture_tree(tmp_path)
+ full = list(adapter.iter_inputs(tmp_path))
+ subset = list(adapter.iter_inputs(tmp_path, records=[SOURCE]))
+ assert subset[0] == next(row for row in full if row["source_path"] == SOURCE)
+ if adapter.ADAPTER_VERSION.startswith("traitmech-"):
+ assert "Resolved parent" in subset[0]["text"]
+ assert "METPO:parent" not in subset[0]["text"]
+ result = adapter.export_inputs(tmp_path, tmp_path / "records.jsonl", limit=1)
+ assert result["records"] == 1 and result["scope"] == "subset"
+ result = adapter.export_inputs(tmp_path, None)
+ assert result["records"] == len(full) and result["scope"] == "full"
+
+
+def test_atomic_failure_preserves_previous_output(tmp_path):
+ path = fixture_tree(tmp_path)
+ output = tmp_path / "records.jsonl"
+ output.write_text("previous output")
+ broken = path.with_name("zz_broken.yaml")
+ broken.write_text("not: [valid YAML")
+ with pytest.raises(yaml.YAMLError):
+ adapter.export_inputs(tmp_path, output)
+ assert output.read_text() == "previous output"
+ assert not list(tmp_path.glob(".text-map-*"))
+
+
+def test_selection_cannot_escape_or_repeat(tmp_path):
+ fixture_tree(tmp_path)
+ for selection in (["../outside.yaml"], [SOURCE, SOURCE]):
+ with pytest.raises(ValueError):
+ list(adapter.iter_inputs(tmp_path, records=selection))
+ with pytest.raises(ValueError, match="positive"):
+ list(adapter.iter_inputs(tmp_path, limit=0))
+
+
+def test_symlinked_yaml_is_refused(tmp_path):
+ path = fixture_tree(tmp_path)
+ alias = path.with_name("alias.yaml")
+ alias.symlink_to(path)
+ with pytest.raises(ValueError, match="symlink"):
+ list(adapter.iter_inputs(tmp_path))
+
+
+
+def test_export_round_trip_and_map_sibling_route(tmp_path):
+ from urllib.parse import urljoin
+
+ fixture_tree(tmp_path)
+ output = tmp_path / "output.jsonl"
+ receipt = adapter.export_inputs(tmp_path, output, records=[SOURCE])
+ row = json.loads(output.read_text())
+ assert receipt["jsonl_sha256"] == hashlib.sha256(output.read_bytes()).hexdigest()
+ assert Path(row["source_path"]).suffix == ".yaml"
+ assert urljoin("https://example.test/deployment/text-map/index.html", "../" + row["page"]) == "https://example.test/deployment/" + PAGE
From e59c6a32ac92b5a9f907f307776d879b0566fa64 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 14 Sep 2026 18:52:52 -0700
Subject: [PATCH 03/11] feat: add verified BGE map and source-bound graph
generation
---
conf/text_map.yaml | 2 +
data/text_map/current.json | 1 +
.../index.html | 41 ++
.../manifest.json | 1 +
.../points.json | 1 +
docs/GRAPH_PROVENANCE.md | 24 +
justfile | 2 +-
scripts/build_embedding_index.py | 591 +++++++++------
scripts/embedding_pipeline.py | 685 ++++++++++++++++++
scripts/render_trait_pages.py | 43 +-
scripts/sfdp_layout.py | 58 +-
src/traitmech/graph_embedding_receipts.py | 497 +++++++++++++
src/traitmech/templates/index.html | 7 +
src/traitmech/text_map_site.py | 90 +++
tests/test_graph_projection_correctness.py | 44 +-
tests/test_graph_receipt_proxies.py | 48 ++
tests/test_graph_receipt_publication.py | 78 ++
tests/test_graph_sfdp_receipt.py | 24 +
tests/test_text_map_recipe.py | 43 ++
tests/test_text_map_site.py | 206 ++++++
20 files changed, 2217 insertions(+), 269 deletions(-)
create mode 100644 conf/text_map.yaml
create mode 100644 data/text_map/current.json
create mode 100644 data/text_map/d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242/index.html
create mode 100644 data/text_map/d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242/manifest.json
create mode 100644 data/text_map/d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242/points.json
create mode 100644 docs/GRAPH_PROVENANCE.md
create mode 100644 scripts/embedding_pipeline.py
create mode 100644 src/traitmech/graph_embedding_receipts.py
create mode 100644 src/traitmech/text_map_site.py
create mode 100644 tests/test_graph_receipt_proxies.py
create mode 100644 tests/test_graph_receipt_publication.py
create mode 100644 tests/test_graph_sfdp_receipt.py
create mode 100644 tests/test_text_map_recipe.py
create mode 100644 tests/test_text_map_site.py
diff --git a/conf/text_map.yaml b/conf/text_map.yaml
new file mode 100644
index 0000000000..6038da6fd3
--- /dev/null
+++ b/conf/text_map.yaml
@@ -0,0 +1,2 @@
+# Shared BGE/PaCMAP map, checked against all current trait YAML.
+enabled: true
diff --git a/data/text_map/current.json b/data/text_map/current.json
new file mode 100644
index 0000000000..a38428d135
--- /dev/null
+++ b/data/text_map/current.json
@@ -0,0 +1 @@
+{"bundle":"d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242","manifest_sha256":"bb0739839147f116bb97c890948d8c5055bf3703fbec11478dba06fadeba406d"}
diff --git a/data/text_map/d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242/index.html b/data/text_map/d35a09079951043ef34efe99ffbb19a269377143e2bb50750942d2c24199a242/index.html
new file mode 100644
index 0000000000..5645e997fb
--- /dev/null
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+
+traitmech semantic text map
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+
+Map provenance and coverage
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+
\ No newline at end of file
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new file mode 100644
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new file mode 100644
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shaped","page":"traits/morphology/irregular_shaped.html","source_path":"data/traits/morphology/irregular_shaped.yaml","text_sha256":"908748baf4daa5a78a663952160eeb015459167fb0d93c068ea0a24a1f6db8ed","x":-3.919032096862793,"y":10.989350318908691},{"adapter_version":"traitmech-semantic-v1","category":"PHYSIOLOGY","identifier":"METPO:1000655","label":"organotrophic","page":"traits/physiology/organotrophic.html","source_path":"data/traits/physiology/organotrophic.yaml","text_sha256":"24a7b48b94619324754559de0cb27397cdfb39aff440c67c8c57eda2d654bce2","x":2.793717384338379,"y":-4.510611057281494},{"adapter_version":"traitmech-semantic-v1","category":"METABOLISM","identifier":"traitmech:000132","label":"dark oxidation of sulfur compounds","page":"traits/metabolism/dark_oxidation_of_sulfur_compounds.html","source_path":"data/traits/metabolism/dark_oxidation_of_sulfur_compounds.yaml","text_sha256":"3755a3038791f25434762ff233ca89a48e2c843ef716ca16c8400567e4685787","x":6.929476261138916,"y":-5.519293308258057},{"adapter_version":"traitmech-semantic-v1","category":"PHYSIOLOGY","identifier":"traitmech:000168","label":"phenylalanine arylamidase activity","page":"traits/physiology/phenylalanine_arylamidase_activity.html","source_path":"data/traits/physiology/phenylalanine_arylamidase_activity.yaml","text_sha256":"5ac88adc2e00ddc3df673ffdc7677ea7a308b208ffb9026a960a36495de5ebba","x":9.459418296813965,"y":9.54367733001709},{"adapter_version":"traitmech-semantic-v1","category":"PHYSIOLOGY","identifier":"METPO:1000665","label":"photolithoautotrophic","page":"traits/physiology/photolithoautotrophic.html","source_path":"data/traits/physiology/photolithoautotrophic.yaml","text_sha256":"fbdd4815aaaedf31c960f23c401a1c0187d00fd05e128e05b58f86dcc1ad4f70","x":2.810964345932007,"y":-4.789657115936279},{"adapter_version":"traitmech-semantic-v1","category":"METABOLISM","identifier":"METPO:2000029","label":"does not build base from","page":"traits/metabolism/does_not_build_base_from.html","source_path":"data/traits/metabolism/does_not_build_base_from.yaml","text_sha256":"da4346c63a684c70cd9ffd20fbdb5f3d3663d0a5262e30d6693c0c1f0eea86b0","x":11.589187622070312,"y":-4.754922866821289},{"adapter_version":"traitmech-semantic-v1","category":"MORPHOLOGY","identifier":"traitmech:000117","label":"streptococcus arrangement","page":"traits/morphology/streptococcus_arrangement.html","source_path":"data/traits/morphology/streptococcus_arrangement.yaml","text_sha256":"5aefc051bfe76bbe8ce3ebcaf2c527b85ec3696fa16d55e63a10c4d6ff7c2310","x":0.2125472128391266,"y":10.687810897827148},{"adapter_version":"traitmech-semantic-v1","category":"QUANTITATIVE_PROPERTY","identifier":"METPO:2000061","label":"has value comments","page":"traits/quantitative_property/has_value_comments.html","source_path":"data/traits/quantitative_property/has_value_comments.yaml","text_sha256":"6dd2c58a38970a0d45ff4537cca02af3fdf9bf4c30aa1ff0ef9c3a836b75b673","x":-2.097883939743042,"y":-19.022369384765625},{"adapter_version":"traitmech-semantic-v1","category":"PHYSIOLOGY","identifier":"traitmech:000172","label":"serine arylamidase activity","page":"traits/physiology/serine_arylamidase_activity.html","source_path":"data/traits/physiology/serine_arylamidase_activity.yaml","text_sha256":"05c5faaf8e27c1a78dec0fbf7963d31fdbeab9215dbaa293eb6a1f0a1bee2f34","x":9.399986267089844,"y":9.536328315734863},{"adapter_version":"traitmech-semantic-v1","category":"UPPER","identifier":"METPO:1001000","label":"observation","page":"traits/upper/observation.html","source_path":"data/traits/upper/observation.yaml","text_sha256":"2f88455dd0ddbf1fdae347d0d83407f609ad34ef975b461551f0b31520d35593","x":-2.248331308364868,"y":-19.360464096069336},{"adapter_version":"traitmech-semantic-v1","category":"ENVIRONMENT","identifier":"traitmech:000010","label":"desiccation tolerant","page":"traits/environment/desiccation_tolerant.html","source_path":"data/traits/environment/desiccation_tolerant.yaml","text_sha256":"49f59b35521c44eb67cdeaa64cf015c3cb41cea072b3fd87dcacd0b57612c0dc","x":-12.050228118896484,"y":-2.49018931388855},{"adapter_version":"traitmech-semantic-v1","category":"PHYSIOLOGY","identifier":"METPO:1000641","label":"chemotrophic","page":"traits/physiology/chemotrophic.html","source_path":"data/traits/physiology/chemotrophic.yaml","text_sha256":"515c5dec6dfced8bc56ce751eca4b4c86830fa7251bdd660c1d1022012902575","x":2.466118812561035,"y":-4.605922698974609},{"adapter_version":"traitmech-semantic-v1","category":"OTHER","identifier":"METPO:1007082","label":"urease test","page":"traits/other/urease_test.html","source_path":"data/traits/other/urease_test.yaml","text_sha256":"ecdfd108daf07e2e2d248b12a8735312964f15f7f869c18dbe09aaf29f48e4cf","x":4.960689067840576,"y":9.14401626586914},{"adapter_version":"traitmech-semantic-v1","category":"MORPHOLOGY","identifier":"METPO:1000705","label":"axially filamented","page":"traits/morphology/axially_filamented.html","source_path":"data/traits/morphology/axially_filamented.yaml","text_sha256":"3c40553fc10a569f4003dfdf4ab20130bc397d722721d3fcf6e818904d760562","x":0.7900215983390808,"y":11.54912281036377},{"adapter_version":"traitmech-semantic-v1","category":"METABOLISM","identifier":"traitmech:000025","label":"dicarboxylate/4-hydroxybutyrate cycle","page":"traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html","source_path":"data/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.yaml","text_sha256":"86cee7f5a0cfdb041242dda43580e94b2329bd0893e5d5436e49c939bbe6423b","x":4.565250396728516,"y":-4.236157417297363},{"adapter_version":"traitmech-semantic-v1","category":"ENVIRONMENT","identifier":"METPO:1000480","label":"NaCl delta mid1","page":"traits/environment/nacl_delta_mid1.html","source_path":"data/traits/environment/nacl_delta_mid1.yaml","text_sha256":"290500d764083805d9390641d33b19e6eee896c5177ada23d4262df5a81d1f13","x":-15.485164642333984,"y":-3.631303310394287},{"adapter_version":"traitmech-semantic-v1","category":"OTHER","identifier":"METPO:1007067","label":"punctiform colony","page":"traits/other/punctiform_colony.html","source_path":"data/traits/other/punctiform_colony.yaml","text_sha256":"b14eea90e086723dc3f802cf43bcf68be5018847143fdfaaf7ae85539ebdf4e5","x":-0.45687904953956604,"y":9.892577171325684},{"adapter_version":"traitmech-semantic-v1","category":"METABOLISM","identifier":"METPO:2000024","label":"does not use for anaerobic growth","page":"traits/metabolism/does_not_use_for_anaerobic_growth.html","source_path":"data/traits/metabolism/does_not_use_for_anaerobic_growth.yaml","text_sha256":"17523e77645dbdba8e6e0f78ac5af56b256ca9c0468f8c66ec757814df0ea0b0","x":11.32761001586914,"y":-6.054926872253418},{"adapter_version":"traitmech-semantic-v1","category":"METABOLISM","identifier":"traitmech:000032","label":"manganese oxidation","page":"traits/metabolism/manganese_oxidation.html","source_path":"data/traits/metabolism/manganese_oxidation.yaml","text_sha256":"09b78b72d6f891b6ba34b664984411b18811c75990421bbee49458128fb8b281","x":6.832780361175537,"y":-5.162868022918701}]
diff --git a/docs/GRAPH_PROVENANCE.md b/docs/GRAPH_PROVENANCE.md
new file mode 100644
index 0000000000..c971242c64
--- /dev/null
+++ b/docs/GRAPH_PROVENANCE.md
@@ -0,0 +1,24 @@
+# TraitMech trait graph provenance
+
+Graph maps retain their KG-Microbe DeepWalk features and domain matching policies. The fleet's common BGE text map is a separate view. This work follows #917.
+
+Run `python scripts/build_embedding_index.py --src /path/to/source.tsv.gz --kgm-aliases /path/to/metpo_alias_mappings.tsv --method pacmap`. For the retained graph layout add `--method sfdp --umap-out data/embeddings/trait_graph.json`. `--method umap` is an explicit alternative.
+
+The slim source, match TSV, selected projection and nearest-neighbor JSON are staged together. Their destinations (`--out-deepwalk`, `--out-match`, `--umap-out`, `--out-neighbors`) must be distinct siblings, so the projection's `.metadata.json` can validate the complete generation. Default names are `deepwalk_traits.tsv.gz`, `metpo_to_kgm_node.tsv`, `trait_umap.json`, and `trait_nearest_neighbors.json` under `data/embeddings`.
+
+The source scan retains only direct/parent CURIEs and record/alias label candidates. Every trait has a projected or omitted ledger entry. Parent-proxy source IDs, mean weights, exact normalized reducer matrix and cosine nearest-neighbor matrix are recorded separately. Generating the alternate projection from identical inputs preserves the shared artifact bytes; both receipts must validate afterward.
+
+New generation reads the selected TSV or TSV.gz stream directly and hashes the exact bytes while parsing. Old basename/size/mtime pickle caches are ignored, including when `force_reload` is false. The scan is streaming and retains only required node vectors; the full source file is still read once per generation. Do not infer source identity by hashing a different file beside old coordinates.
+
+Schema-v2 receipts bind the full corpus, matching/omission ledger, ordered reducer matrix, actual algorithm/normalization/settings and installed backend versions to checksums of every output. PaCMAP records fitted pair counts. The sfdp backend, where available, records the symmetric union-kNN construction, DOT checksum, Graphviz version and command arguments. Failed generation leaves previous outputs unchanged; publication rolls back ordinary write failures. A process kill can leave a `.graph-recovery-*` directory for recovery and is not claimed to be an atomic website deployment.
+
+Validate a completed generation with:
+
+```python
+from pathlib import Path
+from traitmech.graph_embedding_receipts import load_receipt
+
+receipt = load_receipt(Path("path/to/projection.metadata.json"))
+```
+
+This verifies all sibling artifacts declared by the receipt. It is not a tool for attaching newly guessed provenance to legacy arrays. Full published artifacts must be regenerated from reviewed current inputs before the graph correction is considered complete.
diff --git a/justfile b/justfile
index 48074829ea..062fb08b4a 100644
--- a/justfile
+++ b/justfile
@@ -1194,4 +1194,4 @@ gen-discussions-data: (_require-claw "kg_microbe_discussions")
# Full canonical semantic text by default; --record/--limit are explicit canaries.
text-map-inputs *args:
- uv run python scripts/text_map_inputs.py {{args}}
+ uv run python scripts/text_map_inputs.py "$@"
diff --git a/scripts/build_embedding_index.py b/scripts/build_embedding_index.py
index b9fcf91cbe..3841091f3b 100755
--- a/scripts/build_embedding_index.py
+++ b/scripts/build_embedding_index.py
@@ -30,6 +30,7 @@
just build-embeddings # uses defaults
python3 scripts/build_embedding_index.py --src
"""
+
from __future__ import annotations
import argparse
@@ -40,13 +41,25 @@
import os
import re
import sys
+import tempfile
from pathlib import Path
+from traitmech.graph_embedding_receipts import (
+ GraphSource,
+ corpus_receipt,
+ make_receipt,
+ matrix_receipt,
+ projection_receipt,
+ publish_artifacts,
+)
+
REPO_ROOT = Path(__file__).resolve().parent.parent
# Newest available kg-microbe-derived deepwalk: 512-D, 2026-06-26 (v3),
# includes METPO CURIEs directly. Source-of-truth for direct-METPO matching.
-EMBEDDINGS_FILENAME = "DeepWalkSkipGramEnsmallen_degreenorm_embedding_512_v3_2026-06-26_12_55_27.tsv.gz"
+EMBEDDINGS_FILENAME = (
+ "DeepWalkSkipGramEnsmallen_degreenorm_embedding_512_v3_2026-06-26_12_55_27.tsv.gz"
+)
def default_deepwalk() -> Path:
@@ -70,14 +83,30 @@ def default_deepwalk() -> Path:
# kept for older embeddings but not present in the 2026-04-25 file.
_TRAIT_PREFIXES: tuple[str, ...] = (
"METPO:", # primary anchor in 2026-04-25 file
- "cell_shape:", "cell_length:", "cell_width:",
- "gram_stain:", "motility:",
- "gc:", "NaCl_opt:", "NaCl_range:", "NaCl_delta:",
- "pH_opt:", "pH_range:", "pH_delta:",
- "temp_opt:", "temp_range:", "temp_delta:", "temperature:",
- "oxygen:", "trophic_type:", "salinity:",
- "pathogen:", "pigment:", "production:",
- "carbon_substrates:", "isolation_source:",
+ "cell_shape:",
+ "cell_length:",
+ "cell_width:",
+ "gram_stain:",
+ "motility:",
+ "gc:",
+ "NaCl_opt:",
+ "NaCl_range:",
+ "NaCl_delta:",
+ "pH_opt:",
+ "pH_range:",
+ "pH_delta:",
+ "temp_opt:",
+ "temp_range:",
+ "temp_delta:",
+ "temperature:",
+ "oxygen:",
+ "trophic_type:",
+ "salinity:",
+ "pathogen:",
+ "pigment:",
+ "production:",
+ "carbon_substrates:",
+ "isolation_source:",
"assay:",
"BSL:",
"PATO:",
@@ -100,25 +129,26 @@ def _normalise(s: str) -> str:
return s.strip("_")
-def vendor_slim_deepwalk(src: Path, dst: Path) -> tuple[int, set[str]]:
- """Copy only trait-relevant rows from ``src`` to ``dst`` (gzipped TSV).
- Returns (n_rows, set of kg-microbe node ids carried)."""
+def vendor_slim_deepwalk(src: Path, dst: Path, *, node_filter=None, return_receipt=False):
+ """Parse source bytes and retain only requested trait/proxy candidates."""
+ source = GraphSource(
+ src,
+ _TRAIT_PREFIXES,
+ node_filter=node_filter,
+ filter_name="trait-record-parent-alias-label-candidates-v1" if node_filter else None,
+ )
dst.parent.mkdir(parents=True, exist_ok=True)
- n_rows = 0
- nodes: set[str] = set()
- with gzip.open(src, "rt", encoding="utf-8") as fin, \
- gzip.open(dst, "wt", encoding="utf-8") as fout:
- # Pass-through header.
- header = fin.readline()
- fout.write(header)
- for line in fin:
- tab = line.find("\t")
- sid = line[:tab] if tab > 0 else line.strip()
- if sid.startswith(_TRAIT_PREFIXES):
- fout.write(line)
- n_rows += 1
- nodes.add(sid)
- return n_rows, nodes
+ nodes = set()
+ with dst.open("wb") as raw, gzip.GzipFile(fileobj=raw, mode="wb", mtime=0) as output:
+ for node, vector in source:
+ if not nodes:
+ output.write(
+ ("node_id\t" + "\t".join(f"d{i}" for i in range(len(vector))) + "\n").encode()
+ )
+ output.write((node + "\t" + "\t".join(repr(value) for value in vector) + "\n").encode())
+ nodes.add(node)
+ result = (len(nodes), nodes)
+ return (*result, source.receipt) if return_receipt else result
def load_alias_table(path: Path) -> dict[str, str]:
@@ -140,26 +170,33 @@ def load_alias_table(path: Path) -> dict[str, str]:
def load_metpo_records(traits_dir: Path) -> list[tuple[str, str, list[str], str, list[str]]]:
"""Return list of (curie, label, synonyms, category_dir, parents) tuples for
every seeded TraitRecord. ``parents`` is the record's ``parent_traits`` CURIE
- list (used by the parent-proxy match tier). Skips files that fail to parse."""
+ list (used by the parent-proxy match tier). Invalid records fail generation."""
import yaml # lazy import; only this script needs it
+
out: list[tuple[str, str, list[str], str, list[str]]] = []
+ seen = set()
for path in sorted(traits_dir.rglob("*.yaml")):
try:
doc = yaml.safe_load(path.read_text())
except (OSError, yaml.YAMLError) as error:
raise ValueError(f"Unable to read trait record: {path}") from error
if not isinstance(doc, dict):
- continue
+ raise TypeError(f"Trait record is not a mapping: {path}")
curie = (doc.get("identifier") or "").strip()
label = (doc.get("label") or "").strip()
if not curie:
- continue
+ raise ValueError(f"Trait record has no identifier: {path}")
+ if curie in seen:
+ raise ValueError(f"Duplicate trait identifier: {curie}")
+ seen.add(curie)
synonyms = []
- for s in (doc.get("synonyms") or []):
+ for s in doc.get("synonyms") or []:
txt = (s.get("synonym_text") or "").strip()
if txt:
synonyms.append(txt)
- parents = [p.strip() for p in (doc.get("parent_traits") or []) if isinstance(p, str) and p.strip()]
+ parents = [
+ p.strip() for p in (doc.get("parent_traits") or []) if isinstance(p, str) and p.strip()
+ ]
category_dir = path.parent.name
out.append((curie, label, synonyms, category_dir, parents))
return out
@@ -171,20 +208,18 @@ def build_match_table(
alias_table: dict[str, str],
) -> list[dict[str, str]]:
"""Match each record to ≥0 kg-microbe trait nodes via, in order:
- 1. direct_metpo — the record's own CURIE is in the deepwalk.
- 2. alias_table — reverse alias lookup (METPO → known label → node).
- 3. label_match — normalised label / synonym matches a node value-form.
- 4. parent_proxy — for records whose own CURIE is absent (synthetic
- ``traitmech:`` traits, or METPO classes minted after the deepwalk
- run), walk ``parent_traits`` transitively to the nearest ancestor
- whose CURIE *is* in the deepwalk and borrow its embedding. The trait
- is positioned with its semantic parent rather than dropped entirely.
+ 1. direct_metpo — the record's own CURIE is in the deepwalk.
+ 2. alias_table — reverse alias lookup (METPO → known label → node).
+ 3. label_match — normalised label / synonym matches a node value-form.
+ 4. parent_proxy — for records whose own CURIE is absent (synthetic
+ ``traitmech:`` traits, or METPO classes minted after the deepwalk
+ run), walk ``parent_traits`` transitively to the nearest ancestor
+ whose CURIE *is* in the deepwalk and borrow its embedding. The trait
+ is positioned with its semantic parent rather than dropped entirely.
"""
# Parent map for the proxy tier: curie -> list of parent curies (may chain
# traitmech: -> traitmech: -> METPO:).
- parent_map: dict[str, list[str]] = {
- curie: parents for curie, _, _, _, parents in metpo_records
- }
+ parent_map: dict[str, list[str]] = {curie: parents for curie, _, _, _, parents in metpo_records}
def resolve_parent_proxy(curie: str) -> str | None:
"""BFS up the parent chain to the first ancestor CURIE in the deepwalk."""
@@ -199,6 +234,7 @@ def resolve_parent_proxy(curie: str) -> str | None:
return p
queue.extend(parent_map.get(p, []))
return None
+
# Build reverse alias index: METPO CURIE -> set of acceptable normalised labels
metpo_to_norm_labels: dict[str, set[str]] = {}
for norm, curie in alias_table.items():
@@ -252,14 +288,16 @@ def resolve_parent_proxy(curie: str) -> str | None:
candidates.add(proxy)
method = "parent_proxy"
- rows.append({
- "metpo_curie": curie,
- "label": label,
- "category": category,
- "match_method": method or "no_match",
- "kgm_nodes": ";".join(sorted(candidates)),
- "n_kgm_nodes": str(len(candidates)),
- })
+ rows.append(
+ {
+ "metpo_curie": curie,
+ "label": label,
+ "category": category,
+ "match_method": method or "no_match",
+ "kgm_nodes": ";".join(sorted(candidates)),
+ "n_kgm_nodes": str(len(candidates)),
+ }
+ )
return rows
@@ -293,130 +331,157 @@ def load_embedding_vectors(slim_deepwalk: Path) -> dict[str, list[float]]:
def compute_umap_and_neighbors(
- metpo_records: list[tuple[str, str, list[str], str]],
- match_rows: list[dict[str, str]],
- vectors: dict[str, list[float]],
- method: str = "pacmap",
-) -> tuple[list[dict], dict[str, list[dict]]]:
- """Project the matched-record embeddings to 2-D and compute k nearest
- neighbors per record. Returns (umap_points, nn_per_curie).
-
- ``method`` selects the 2-D reducer: ``"pacmap"`` (default; PCA-init,
- fixed seed, L2-normalised rows to mirror cosine geometry), ``"umap"``
- (legacy UMAP path), or ``"sfdp"`` (Graphviz force-directed layout of a
- mutual-kNN graph over the embeddings). The output JSON keys
- (umap_x / umap_y) are unchanged regardless of reducer.
-
- Records without an embedding are NOT in the UMAP output (they have no
- coordinates) but still appear in nn_per_curie as []."""
- try:
- import numpy as np
- except ImportError as e:
- print(f" numpy not available: {e}; skipping projection", file=sys.stderr)
- return [], {}
- if method == "umap":
- try:
- import umap as _umap
- except ImportError as e:
- print(f" UMAP not available: {e}; skipping projection", file=sys.stderr)
- return [], {}
- elif method == "pacmap":
- try:
- import pacmap
- from sklearn.preprocessing import normalize
- except ImportError as e:
- print(f" PaCMAP / scikit-learn not available: {e}; skipping projection",
- file=sys.stderr)
- return [], {}
- elif method == "sfdp":
- try:
- sys.path.insert(0, str(Path(__file__).resolve().parent))
- from sfdp_layout import sfdp_layout
- except ImportError as e:
- print(f" sfdp_layout / scikit-learn not available: {e}; skipping projection",
- file=sys.stderr)
- return [], {}
- else:
- print(f" Unknown reducer method {method!r}; skipping projection", file=sys.stderr)
- return [], {}
-
- # Index match table by curie
- match_by_curie = {r["metpo_curie"]: r for r in match_rows}
- record_by_curie = {c: (lbl, syn, cat) for c, lbl, syn, cat, _par in metpo_records}
-
- # Build matrix: take ANY matched node's vector for each METPO record;
- # when multiple nodes match, average them.
- curies: list[str] = []
- matrix: list[list[float]] = []
- for r in match_rows:
- nodes = [n.strip() for n in r["kgm_nodes"].split(";") if n.strip()]
- vecs = [vectors[n] for n in nodes if n in vectors]
- if not vecs:
- continue
- n = len(vecs[0])
- avg = [sum(v[i] for v in vecs) / len(vecs) for i in range(n)]
- curies.append(r["metpo_curie"])
- matrix.append(avg)
-
+ metpo_records, match_rows, vectors, method="pacmap", *, receipt_details=None
+):
+ """Keep the matched/proxy graph construction; receipt the actual reducer inputs."""
+ import numpy as np
+ from sklearn import config_context
+ from sklearn.neighbors import NearestNeighbors
+ from sklearn.preprocessing import normalize
+
+ match_by_curie = {row["metpo_curie"]: row for row in match_rows}
+ record_by_curie = {
+ curie: (label, synonyms, category) for curie, label, synonyms, category, _ in metpo_records
+ }
+ curies, matrix, ledger = [], [], []
+ for row in match_rows:
+ curie = row["metpo_curie"]
+ if curie not in record_by_curie:
+ raise ValueError(f"Matched trait is outside the corpus: {curie}")
+ nodes = [node.strip() for node in row["kgm_nodes"].split(";") if node.strip()]
+ found = [node for node in nodes if node in vectors]
+ ledger.append(
+ {
+ "identifier": curie,
+ "source_nodes": found,
+ "missing_nodes": [node for node in nodes if node not in vectors],
+ "status": "projected" if found else "no_vectors",
+ "match_method": row["match_method"],
+ "aggregation_method": "mean",
+ "weight_per_source": 1 / len(found) if found else 0,
+ }
+ )
+ if found:
+ matrix.append(np.mean([vectors[node] for node in found], axis=0))
+ curies.append(curie)
if len(matrix) < 5:
- print(f" Only {len(matrix)} matched embeddings — projection skipped", file=sys.stderr)
- return [], {}
-
- arr = np.array(matrix, dtype=float)
- if method == "umap":
- print(f" Running UMAP on {arr.shape[0]} × {arr.shape[1]} matrix")
- reducer = _umap.UMAP(
- n_components=2, n_neighbors=min(15, len(matrix) - 1), random_state=42
+ raise ValueError(
+ f"Only {len(matrix)} matched embeddings; trait projection requires at least five"
+ )
+ arr = np.asarray(matrix, dtype=np.float64)
+ if method == "pacmap":
+ import pacmap
+
+ parameters = {
+ "n_components": 2,
+ "random_state": 42,
+ "n_neighbors": None,
+ "MN_ratio": 0.5,
+ "FP_ratio": 2.0,
+ "distance": "euclidean",
+ "lr": 1.0,
+ "num_iters": (100, 100, 250),
+ "apply_pca": True,
+ "knn_backend": "faiss",
+ }
+ actual = normalize(arr.astype("float32"))
+ vectors_receipt = matrix_receipt(actual, curies)
+ reducer = pacmap.PaCMAP(**parameters)
+ coords = reducer.fit_transform(actual, init="pca")
+ projection = projection_receipt(
+ method, parameters, reducer=reducer, normalization="l2", initialization="pca"
)
+ elif method == "umap":
+ import umap
+
+ parameters = {
+ "n_components": 2,
+ "n_neighbors": min(15, len(matrix) - 1),
+ "random_state": 42,
+ "metric": "euclidean",
+ }
+ vectors_receipt = matrix_receipt(arr, curies, dtype="float64-le")
+ reducer = umap.UMAP(**parameters)
coords = reducer.fit_transform(arr)
+ projection = projection_receipt(method, parameters, reducer=reducer, normalization="none")
elif method == "sfdp":
- print(f" Running sfdp force-directed layout on {arr.shape[0]} × {arr.shape[1]} matrix")
- coords = sfdp_layout(arr, k=15, seed=42)
- else: # pacmap (default)
- from sklearn.preprocessing import normalize
- print(f" Running PaCMAP on {arr.shape[0]} × {arr.shape[1]} matrix")
- X = normalize(arr.astype("float32"))
- coords = pacmap.PaCMAP(n_components=2, random_state=42).fit_transform(X, init="pca")
-
- # Cosine-style nearest neighbors via L2 normalisation + dot product.
- norms = np.linalg.norm(arr, axis=1, keepdims=True)
- norms[norms == 0] = 1.0
- normed = arr / norms
- sim = normed @ normed.T
- np.fill_diagonal(sim, -1.0)
- k = min(UMAP_NEAREST_K, len(matrix) - 1)
- top_idx = np.argsort(-sim, axis=1)[:, :k]
-
- umap_points: list[dict] = []
- nn_map: dict[str, list[dict]] = {}
+ sys.path.insert(0, str(Path(__file__).resolve().parent))
+ from sfdp_layout import sfdp_layout
+
+ coords, graph = sfdp_layout(arr, k=15, seed=42, return_receipt=True, record_ids=curies)
+ vectors_receipt = graph.pop("matrix")
+ projection = projection_receipt(
+ method, {"k": 15, "seed": 42}, normalization="l2", graph=graph
+ )
+ else:
+ raise ValueError(f"Unknown trait projection: {method}")
+ if np.asarray(coords).shape != (len(curies), 2) or not np.isfinite(coords).all():
+ raise ValueError(
+ "Trait projection did not return finite coordinates for every selected record"
+ )
+ # Chunked exact cosine neighbors avoid an all-pairs matrix, including for
+ # future corpus growth. Self is excluded explicitly even among proxy ties.
+ normed = normalize(arr)
+ nearest_matrix = matrix_receipt(normed, curies, dtype="float64-le")
+ k = min(UMAP_NEAREST_K, len(curies) - 1)
+ with config_context(working_memory=64):
+ distances, indices = (
+ NearestNeighbors(n_neighbors=k + 1, metric="cosine", algorithm="brute")
+ .fit(normed)
+ .kneighbors(normed)
+ )
+ ledger_by_curie = {row["identifier"]: row for row in ledger}
+ points, neighbors = [], {}
for i, curie in enumerate(curies):
- lbl, _, cat = record_by_curie.get(curie, ("", [], "OTHER"))
- umap_points.append({
- "id": curie,
- "label": lbl,
- "category": cat,
- "match_method": match_by_curie[curie]["match_method"],
- "kgm_nodes": match_by_curie[curie]["kgm_nodes"].split(";"),
- "umap_x": float(coords[i, 0]),
- "umap_y": float(coords[i, 1]),
- })
- nn_map[curie] = [
+ label, _, category = record_by_curie[curie]
+ points.append(
{
- "id": curies[j],
- "label": record_by_curie[curies[j]][0],
- "category": record_by_curie[curies[j]][2],
- "similarity": float(sim[i, j]),
- "match_method": match_by_curie[curies[j]]["match_method"],
- "kgm_nodes": match_by_curie[curies[j]]["kgm_nodes"].split(";"),
+ "id": curie,
+ "label": label,
+ "category": category,
+ "match_method": match_by_curie[curie]["match_method"],
+ "kgm_nodes": ledger_by_curie[curie]["source_nodes"],
+ "umap_x": float(coords[i, 0]),
+ "umap_y": float(coords[i, 1]),
}
- for j in top_idx[i]
- ]
-
- # Records without embeddings still get an entry (empty list) so the renderer
- # can distinguish "no embedding" from "no neighbors found".
- for curie, _, _, _, _ in metpo_records:
- nn_map.setdefault(curie, [])
- return umap_points, nn_map
+ )
+ neighbors[curie] = []
+ for distance, j in zip(distances[i], indices[i], strict=True):
+ if j == i:
+ continue
+ other = curies[j]
+ neighbors[curie].append(
+ {
+ "id": other,
+ "label": record_by_curie[other][0],
+ "category": record_by_curie[other][2],
+ "similarity": float(1 - distance),
+ "match_method": match_by_curie[other]["match_method"],
+ "kgm_nodes": [
+ node
+ for node in match_by_curie[other]["kgm_nodes"].split(";")
+ if node in vectors
+ ],
+ }
+ )
+ if len(neighbors[curie]) == k:
+ break
+ for curie in record_by_curie:
+ neighbors.setdefault(curie, [])
+ if receipt_details is not None:
+ receipt_details.update(
+ matrix=vectors_receipt,
+ projection=projection,
+ ledger=ledger,
+ nearest_neighbors={
+ "metric": "cosine",
+ "k": k,
+ "implementation": "sklearn.neighbors.NearestNeighbors",
+ "working_memory_mib": 64,
+ "matrix": nearest_matrix,
+ },
+ )
+ return points, neighbors
def write_json(path: Path, payload) -> None:
@@ -424,92 +489,150 @@ def write_json(path: Path, payload) -> None:
path.write_text(json.dumps(payload, indent=2))
-
def file_sha256(path: Path) -> str:
with path.open("rb") as stream:
return hashlib.file_digest(stream, "sha256").hexdigest()
-def write_projection_metadata(path: Path, source: Path, vectors, method: str,
- match_table: Path, neighbors: Path) -> None:
- """Bind newly generated outputs to the source actually selected by this run."""
- dims = {len(vector) for vector in vectors.values()}
- if len(dims) != 1:
- raise ValueError("Graph vectors must have one nonempty dimension")
- write_json(path.with_suffix(".metadata.json"), {
- "schema_version": 1,
- "embedding_family": "kg_microbe_deepwalk",
- "source": {"filename": source.name, "sha256": file_sha256(source)},
- "input_dimensions": next(iter(dims)),
- "projection": {"method": method, "random_state": 42,
- "normalization": "l2" if method in {"pacmap", "sfdp"} else "none"},
- "match_table_sha256": file_sha256(match_table),
- "outputs": {path.name: file_sha256(path), neighbors.name: file_sha256(neighbors)},
- "coverage": {"projected": len(json.loads(path.read_text())),
- "neighbor_records": len(json.loads(neighbors.read_text()))},
- })
+def write_projection_metadata(
+ path: Path,
+ source=None,
+ vectors=None,
+ method=None,
+ match_table=None,
+ neighbors=None,
+ *,
+ generation_receipt=None,
+ staged=None,
+):
+ """Output-only source labels cannot establish provenance; stage a real generation."""
+ if generation_receipt is None or staged is None:
+ raise ValueError(
+ "Output-only provenance is unsupported; regenerate from the actual graph source"
+ )
+ return publish_artifacts(staged, path.with_suffix(".metadata.json"), generation_receipt)
def main() -> int:
ap = argparse.ArgumentParser()
- ap.add_argument("--src", type=Path, default=DEFAULT_KGM_DEEPWALK,
- help="path to the source deepwalk .tsv.gz")
+ ap.add_argument(
+ "--src", type=Path, default=DEFAULT_KGM_DEEPWALK, help="path to the source deepwalk .tsv.gz"
+ )
ap.add_argument("--kgm-aliases", type=Path, default=DEFAULT_KGM_ALIASES)
ap.add_argument("--out-deepwalk", type=Path, default=OUT_DEEPWALK)
ap.add_argument("--out-match", type=Path, default=OUT_MATCH)
- ap.add_argument("--umap-out", type=Path, default=OUT_UMAP_JSON,
- help="output path for the 2-D projection JSON "
- "(default: data/embeddings/trait_umap.json). Use a "
- "separate path (e.g. trait_graph.json) for --method sfdp "
- "so the pacmap default output is not overwritten.")
- ap.add_argument("--method", choices=["pacmap", "umap", "sfdp"], default="pacmap",
- help="2-D reducer for the trait projection (default: pacmap)")
+ ap.add_argument(
+ "--umap-out",
+ type=Path,
+ default=OUT_UMAP_JSON,
+ help="output path for the 2-D projection JSON "
+ "(default: data/embeddings/trait_umap.json). Use a "
+ "separate path (e.g. trait_graph.json) for --method sfdp "
+ "so the pacmap default output is not overwritten.",
+ )
+ ap.add_argument(
+ "--method",
+ choices=["pacmap", "umap", "sfdp"],
+ default="pacmap",
+ help="2-D reducer for the trait projection (default: pacmap)",
+ )
+ ap.add_argument(
+ "--out-neighbors",
+ type=Path,
+ default=OUT_NN_JSON,
+ help="Neighbor JSON destination; all graph outputs must share one directory",
+ )
args = ap.parse_args()
src = args.src
if not src.is_file():
- print(f"Selected deepwalk source missing: {src}; pass --src for another release", file=sys.stderr)
+ print(
+ f"Selected deepwalk source missing: {src}; pass --src for another release",
+ file=sys.stderr,
+ )
return 2
- print(f"[1/4] Vendoring slim deepwalk subset → {args.out_deepwalk}")
- print(f" source: {src.name}")
- n_rows, nodes = vendor_slim_deepwalk(src, args.out_deepwalk)
- metpo_count = sum(1 for n in nodes if n.startswith("METPO:"))
- print(f" {n_rows} trait-relevant rows carried; {len(nodes)} unique node ids "
- f"(METPO:* = {metpo_count})")
-
- print(f"[2/4] Loading metpo alias table → {args.kgm_aliases}")
+ destinations = [args.out_deepwalk, args.out_match, args.umap_out, args.out_neighbors]
+ if len({path.parent.resolve() for path in destinations}) != 1:
+ ap.error("graph outputs must share one directory for complete receipt validation")
+ if len({path.name for path in destinations}) != len(destinations):
+ ap.error("graph output filenames must be distinct")
+
+ corpus_paths = sorted(TRAITS_DIR.rglob("*.yaml"))
+ corpus = corpus_receipt(corpus_paths, TRAITS_DIR)
+ records = load_metpo_records(TRAITS_DIR)
+ alias_receipt = {
+ "filename": args.kgm_aliases.name,
+ "sha256": file_sha256(args.kgm_aliases) if args.kgm_aliases.is_file() else None,
+ }
aliases = load_alias_table(args.kgm_aliases)
- print(f" {len(aliases)} alias rows loaded")
-
- print(f"[3/4] Building METPO ↔ kg-microbe match table → {args.out_match}")
- metpo_records = load_metpo_records(TRAITS_DIR)
- rows = build_match_table(metpo_records, nodes, aliases)
- write_match_table(rows, args.out_match)
-
- matched = sum(1 for r in rows if int(r["n_kgm_nodes"]) > 0)
- print(f" {len(rows)} TraitRecords; {matched} matched ≥1 kg-microbe node "
- f"({matched / max(len(rows), 1) * 100:.1f}% coverage)")
- by_method: dict[str, int] = {}
- for r in rows:
- by_method[r["match_method"]] = by_method.get(r["match_method"], 0) + 1
- for m, n in sorted(by_method.items(), key=lambda x: -x[1]):
- print(f" {m:<15} {n}")
-
- print(f"[4/4] 2-D projection ({args.method}) + nearest neighbors")
- vectors = load_embedding_vectors(args.out_deepwalk)
- umap_points, nn_map = compute_umap_and_neighbors(
- metpo_records, rows, vectors, method=args.method
+ curies = {row[0] for row in records}
+ direct_candidates = curies | {parent for row in records for parent in row[4]}
+ labels = {
+ _normalise(label) for _, label, synonyms, _, _ in records for label in [label, *synonyms]
+ }
+ labels.update(norm for norm, curie in aliases.items() if curie in curies)
+ labels.discard("")
+
+ def candidate(node):
+ return (
+ node in direct_candidates
+ or _normalise(node) in labels
+ or _normalise(node.split(":", 1)[-1]) in labels
+ )
+
+ args.umap_out.parent.mkdir(parents=True, exist_ok=True)
+ with tempfile.TemporaryDirectory(prefix=".trait-graph-", dir=args.umap_out.parent) as temporary:
+ stage = Path(temporary)
+ slim, match_path = stage / args.out_deepwalk.name, stage / args.out_match.name
+ _, nodes, source_receipt = vendor_slim_deepwalk(
+ src, slim, node_filter=candidate, return_receipt=True
+ )
+ matches = build_match_table(records, nodes, aliases)
+ write_match_table(matches, match_path)
+ vectors = load_embedding_vectors(slim)
+ details = {}
+ points, neighbors = compute_umap_and_neighbors(
+ records, matches, vectors, method=args.method, receipt_details=details
+ )
+ staged_map, staged_neighbors = stage / args.umap_out.name, stage / args.out_neighbors.name
+ write_json(staged_map, points)
+ write_json(staged_neighbors, neighbors)
+ receipt = make_receipt(
+ source=source_receipt,
+ corpus=corpus,
+ ledger=details["ledger"],
+ matrix=details["matrix"],
+ projection=details["projection"],
+ coverage={
+ "eligible": len(records),
+ "projected": len(points),
+ "omitted": len(records) - len(points),
+ "neighbor_records": len(neighbors),
+ },
+ auxiliary={"aliases": alias_receipt},
+ )
+ receipt["nearest_neighbors"] = details["nearest_neighbors"]
+ if corpus_receipt(sorted(TRAITS_DIR.rglob("*.yaml")), TRAITS_DIR) != corpus:
+ raise ValueError("Trait corpus changed during graph generation")
+ if (file_sha256(args.kgm_aliases) if args.kgm_aliases.is_file() else None) != alias_receipt[
+ "sha256"
+ ]:
+ raise ValueError("Alias table changed during graph generation")
+ write_projection_metadata(
+ args.umap_out,
+ generation_receipt=receipt,
+ staged={
+ args.out_deepwalk: slim,
+ args.out_match: match_path,
+ args.umap_out: staged_map,
+ args.out_neighbors: staged_neighbors,
+ },
+ )
+ print(
+ f"{len(points)} verified {args.method} points and {len(neighbors)} neighbor records published"
)
- if not umap_points:
- print("Projection produced no points; outputs were not published", file=sys.stderr)
- return 2
- write_json(args.umap_out, umap_points)
- write_json(OUT_NN_JSON, nn_map)
- write_projection_metadata(args.umap_out, src, vectors, args.method, args.out_match, OUT_NN_JSON)
- print(f" {len(umap_points)} UMAP points → {args.umap_out.name}")
- nn_with_data = sum(1 for v in nn_map.values() if v)
- print(f" {nn_with_data} traits with ≥1 nearest neighbor → {OUT_NN_JSON.name}")
+
return 0
diff --git a/scripts/embedding_pipeline.py b/scripts/embedding_pipeline.py
new file mode 100644
index 0000000000..1a97ec400d
--- /dev/null
+++ b/scripts/embedding_pipeline.py
@@ -0,0 +1,685 @@
+#!/usr/bin/env python3
+"""Build provenance-bound semantic-text maps from a Mech's JSONL adapter.
+
+Inspection and verification use the standard library. Model inference and
+projection are explicit operations with separately installed dependencies.
+"""
+from __future__ import annotations
+
+import argparse
+import contextlib
+import datetime as dt
+import hashlib
+import heapq
+import importlib.metadata
+import json
+import math
+import os
+import re
+import shutil
+import sqlite3
+import struct
+import sys
+import tempfile
+from pathlib import Path
+from urllib.parse import unquote, urlsplit
+
+FORMAT_VERSION = 1
+MODEL = "BAAI/bge-large-en-v1.5"
+MODEL_REVISION = "d4aa6901d3a41ba39fb536a557fa166f842b0e09"
+MODEL_DIMENSION = 1024
+MAX_SEQ_LENGTH = 512
+REQUIRED_FIELDS = (
+ "identifier", "label", "category", "page", "source_path", "text",
+ "text_sha256", "adapter_version",
+)
+
+
+class ContractError(ValueError):
+ """Malformed input or an unverified artifact; never a successful map."""
+
+
+def canonical(value: object) -> bytes:
+ return json.dumps(value, sort_keys=True, separators=(",", ":"),
+ ensure_ascii=False, allow_nan=False).encode("utf-8")
+
+
+def digest_file(path: Path) -> str:
+ digest = hashlib.sha256()
+ with path.open("rb") as stream:
+ for chunk in iter(lambda: stream.read(1024 * 1024), b""):
+ digest.update(chunk)
+ return digest.hexdigest()
+
+
+def framed_update(digest, *values: str) -> None:
+ for value in values:
+ encoded = value.encode("utf-8")
+ digest.update(struct.pack(">Q", len(encoded)))
+ digest.update(encoded)
+
+
+def local_link(value: str) -> bool:
+ if not isinstance(value, str) or not value.strip():
+ return False
+ parsed = urlsplit(value)
+ decoded = unquote(parsed.path)
+ return bool(value) and not (
+ parsed.scheme or parsed.netloc or decoded.startswith("/")
+ or "\\" in decoded or ".." in decoded.split("/")
+ or any(ord(char) < 32 for char in unquote(value))
+ )
+
+
+def records(path: Path, *, raw_digest=None):
+ """Read one adapter record at a time; no YAML or biological policy here."""
+ with path.open("rb") as stream:
+ for number, line in enumerate(stream, 1):
+ if raw_digest is not None:
+ raw_digest.update(line)
+ try:
+ record = json.loads(line.decode("utf-8"))
+ except (ValueError, UnicodeError) as exc:
+ raise ContractError(f"invalid JSONL record at line {number}") from exc
+ if not isinstance(record, dict) or any(
+ not isinstance(record.get(key), str) or not record[key].strip()
+ for key in REQUIRED_FIELDS
+ ):
+ raise ContractError(f"line {number}: required fields must be nonempty strings")
+ if not local_link(record["page"]) or not local_link(record["source_path"]):
+ raise ContractError(f"line {number}: page and source paths must be local")
+ if record["text_sha256"] != hashlib.sha256(record["text"].encode()).hexdigest():
+ raise ContractError(f"line {number}: text checksum mismatch")
+ yield record
+
+
+def inspect_inputs(path: Path) -> dict:
+ """Validate full ordered inputs, using disk for duplicate detection."""
+ content = hashlib.sha256()
+ display = hashlib.sha256()
+ raw = hashlib.sha256()
+ counts: dict[str, int] = {}
+ versions: set[str] = set()
+ count = 0
+ with tempfile.TemporaryDirectory(prefix="embedding-inputs-") as tmp:
+ with sqlite3.connect(str(Path(tmp) / "ids.sqlite")) as db:
+ db.execute("CREATE TABLE ids (id TEXT PRIMARY KEY)")
+ for record in records(path, raw_digest=raw):
+ try:
+ db.execute("INSERT INTO ids VALUES (?)", (record["identifier"],))
+ except sqlite3.IntegrityError as exc:
+ raise ContractError(f"duplicate identifier: {record['identifier']}") from exc
+ framed_update(content, record["identifier"], record["text"])
+ framed_update(display, canonical(record).decode())
+ counts[record["category"]] = counts.get(record["category"], 0) + 1
+ versions.add(record["adapter_version"])
+ count += 1
+ if not count:
+ raise ContractError("adapter input contains no records")
+ if len(versions) != 1:
+ raise ContractError("adapter versions must agree within one input")
+ if digest_file(path) != raw.hexdigest():
+ raise ContractError("adapter input changed while inspecting; rerun")
+ return {"count": count, "corpus_sha256": content.hexdigest(),
+ "records_sha256": display.hexdigest(), "input_sha256": raw.hexdigest(),
+ "categories": counts, "adapter_version": versions.pop()}
+
+
+def encoder_profile(*, library_versions: dict | None = None, device: str = "cpu") -> dict:
+ return {"format_version": FORMAT_VERSION, "model": MODEL,
+ "revision": MODEL_REVISION, "dimension": MODEL_DIMENSION,
+ "normalized": True, "dtype": "float32-le", "max_seq_length": MAX_SEQ_LENGTH,
+ "pooling": "sentence-transformers-model", "truncation": "tail",
+ "inference_device": device, "weight_dtype": "torch.float32",
+ "query_instruction": None, "library_versions": library_versions or {}}
+
+
+def validate_profile(profile: dict) -> None:
+ if not isinstance(profile, dict) or not re.fullmatch(
+ r"[0-9a-f]{40}", str(profile.get("revision", ""))
+ ):
+ raise ContractError("encoder profile must identify an immutable model revision")
+ if (type(profile.get("format_version")) is not int
+ or profile["format_version"] != FORMAT_VERSION
+ or not isinstance(profile.get("model"), str) or not profile["model"]
+ or type(profile.get("dimension")) is not int or profile["dimension"] < 2
+ or profile.get("normalized") is not True or profile.get("dtype") != "float32-le"
+ or type(profile.get("max_seq_length")) is not int
+ or profile["max_seq_length"] < 1
+ or profile.get("pooling") != "sentence-transformers-model"
+ or profile.get("truncation") != "tail"
+ or not re.fullmatch(r"cpu|mps(?::\d+)?|cuda(?::\d+)?",
+ str(profile.get("inference_device", "")))
+ or profile.get("weight_dtype") != "torch.float32"
+ or "query_instruction" not in profile or profile["query_instruction"] is not None):
+ raise ContractError("invalid encoder profile")
+ validate_versions(profile.get("library_versions"), "encoder")
+ canonical(profile)
+
+
+def validate_versions(value, context: str) -> None:
+ if (not isinstance(value, dict) or not value
+ or any(not isinstance(name, str) or not name.strip()
+ or not isinstance(version, str) or not version.strip()
+ for name, version in value.items())):
+ raise ContractError(f"{context} requires recorded software versions")
+
+
+def profile_id(profile: dict) -> str:
+ validate_profile(profile)
+ return hashlib.sha256(canonical(profile)).hexdigest()
+
+
+def vector_bytes(vector, dimension: int) -> bytes:
+ values = [float(value) for value in vector]
+ if len(values) != dimension or not all(math.isfinite(value) for value in values):
+ raise ContractError("vector dimension or finiteness check failed")
+ norm = math.sqrt(sum(value * value for value in values))
+ if not 0.999 <= norm <= 1.001:
+ raise ContractError("embedding vector must have unit norm")
+ return struct.pack("<" + "f" * dimension, *values)
+
+
+def unpack_vector(blob: bytes, dimension: int):
+ if len(blob) != dimension * 4:
+ raise ContractError("cached vector byte length does not match its dimension")
+ values = struct.unpack("<" + "f" * dimension, blob)
+ vector_bytes(values, dimension)
+ return values
+
+
+@contextlib.contextmanager
+def cache_connection(path: Path, *, writable: bool = False):
+ if writable:
+ path.parent.mkdir(parents=True, exist_ok=True)
+ connection = sqlite3.connect(path, timeout=30)
+ connection.execute("PRAGMA synchronous=FULL")
+ connection.execute("CREATE TABLE IF NOT EXISTS profiles (id TEXT PRIMARY KEY, json TEXT)")
+ connection.execute("""CREATE TABLE IF NOT EXISTS vectors (
+ profile TEXT, identifier TEXT, text_sha256 TEXT, vector BLOB, vector_sha256 TEXT,
+ PRIMARY KEY (profile, identifier, text_sha256))""")
+ else:
+ connection = sqlite3.connect(path.resolve().as_uri() + "?mode=ro", uri=True)
+ try:
+ yield connection
+ finally:
+ connection.close()
+
+
+def cached_vector(db, key: str, record: dict, dimension: int):
+ row = db.execute(
+ "SELECT vector, vector_sha256 FROM vectors "
+ "WHERE profile=? AND identifier=? AND text_sha256=?",
+ (key, record["identifier"], record["text_sha256"]),
+ ).fetchone()
+ if row is None:
+ return None
+ blob, checksum = row
+ if hashlib.sha256(blob).hexdigest() != checksum:
+ raise ContractError("cached vector checksum mismatch")
+ unpack_vector(blob, dimension)
+ return blob
+
+
+def populate_cache(input_path: Path, cache_path: Path, profile: dict, encoder,
+ *, batch_size: int = 64) -> dict:
+ """Reuse exact records and atomically commit each verified encoded batch."""
+ if batch_size < 1:
+ raise ContractError("batch size must be positive")
+ identity = inspect_inputs(input_path)
+ key = profile_id(profile)
+ encoded_count = reused = 0
+ pending = []
+ with cache_connection(cache_path, writable=True) as db:
+ previous = db.execute("SELECT json FROM profiles WHERE id=?", (key,)).fetchone()
+ if previous is not None and previous[0] != canonical(profile).decode():
+ raise ContractError("cache profile metadata is inconsistent with its identity")
+
+ def save_batch():
+ nonlocal encoded_count
+ vectors = encoder([record["text"] for record in pending])
+ if len(vectors) != len(pending):
+ raise ContractError("encoder returned the wrong number of vectors")
+ # Validate the WHOLE batch before starting its transaction.
+ blobs = [vector_bytes(vector, profile["dimension"]) for vector in vectors]
+ with db:
+ db.execute("INSERT OR IGNORE INTO profiles VALUES (?, ?)",
+ (key, canonical(profile).decode()))
+ for record, blob in zip(pending, blobs, strict=True):
+ db.execute("INSERT OR REPLACE INTO vectors VALUES (?, ?, ?, ?, ?)",
+ (key, record["identifier"], record["text_sha256"], blob,
+ hashlib.sha256(blob).hexdigest()))
+ encoded_count += len(pending)
+ pending.clear()
+
+ for record in records(input_path):
+ if cached_vector(db, key, record, profile["dimension"]) is not None:
+ reused += 1
+ else:
+ pending.append(record)
+ if len(pending) == batch_size:
+ save_batch()
+ if pending:
+ save_batch()
+ if digest_file(input_path) != identity["input_sha256"]:
+ raise ContractError("adapter input changed while embedding; rerun")
+ return {**identity, "profile_id": key, "encoded": encoded_count, "reused": reused}
+
+
+def versions(names: tuple[str, ...]) -> dict[str, str]:
+ return {name: importlib.metadata.version(name) for name in names}
+
+
+def local_encoder(device: str | None = None):
+ from sentence_transformers import SentenceTransformer
+
+ model = SentenceTransformer(MODEL, revision=MODEL_REVISION,
+ trust_remote_code=False, device=device)
+ model.max_seq_length = MAX_SEQ_LENGTH
+ model.tokenizer.truncation_side = "right"
+ profile = encoder_profile(library_versions=versions(
+ ("sentence-transformers", "transformers", "tokenizers", "torch", "numpy")
+ ), device=str(model.device))
+ if str(next(model.parameters()).dtype) != profile["weight_dtype"]:
+ raise ContractError("model weights must use the declared float32 precision")
+ if model.get_sentence_embedding_dimension() != MODEL_DIMENSION:
+ raise ContractError("model returned an unexpected embedding dimension")
+
+ def encode(texts):
+ return model.encode(texts, batch_size=len(texts), normalize_embeddings=True,
+ convert_to_numpy=True, show_progress_bar=False)
+
+ return profile, encode
+
+
+def select_records(input_path: Path, maximum: int, seed: int) -> list[dict]:
+ if maximum < 3:
+ raise ContractError("map selection maximum must be at least three")
+ # Bottom-k hashes are deterministic, bounded and independent of input order.
+ def ranked():
+ for record in records(input_path):
+ key = hashlib.sha256(canonical([seed, record["identifier"]])).digest()
+ yield key, record["identifier"], record
+ return [record for _, _, record in heapq.nsmallest(maximum, ranked())]
+
+
+def atomic_json(path: Path, value: dict) -> None:
+ path.parent.mkdir(parents=True, exist_ok=True)
+ descriptor, filename = tempfile.mkstemp(prefix="." + path.name + ".", dir=path.parent)
+ temporary = Path(filename)
+ try:
+ with os.fdopen(descriptor, "wb") as stream:
+ stream.write(canonical(value) + b"\n")
+ stream.flush()
+ os.fsync(stream.fileno())
+ os.replace(temporary, path)
+ finally:
+ temporary.unlink(missing_ok=True)
+
+
+def build_map(input_path: Path, cache_path: Path, output: Path, profile: dict,
+ *, maximum: int = 50000, seed: int = 42, neighbors: int = 15,
+ projector=None, projection_versions: dict | None = None,
+ title: str = "Semantic text map") -> dict:
+ import numpy as np
+
+ inputs = inspect_inputs(input_path)
+ key = profile_id(profile)
+ selected = select_records(input_path, maximum, seed)
+ if len(selected) < 3:
+ raise ContractError("PaCMAP map requires at least three input records")
+ if neighbors < 1:
+ raise ContractError("neighbors must be positive")
+ neighbor_count = min(neighbors, len(selected) - 1)
+ matrix = np.empty((len(selected), profile["dimension"]), dtype=" dict:
+ if bundle.is_symlink() or (bundle / "manifest.json").is_symlink():
+ raise ContractError("bundle and manifest must not be symbolic links")
+ manifest = json.loads((bundle / "manifest.json").read_text())
+ if not isinstance(manifest, dict) or manifest.get("format_version") != FORMAT_VERSION:
+ raise ContractError("unsupported map bundle format")
+ if (manifest.get("representation") != "semantic-text"
+ or any(not isinstance(manifest.get(name), dict) for name in
+ ("encoder", "inputs", "files", "coverage", "projection", "source_vectors"))):
+ raise ContractError("invalid map bundle metadata")
+ if manifest.get("encoder_profile_sha256") != profile_id(manifest["encoder"]):
+ raise ContractError("encoder profile checksum mismatch")
+ expected = {"points.json", "index.html"}
+ if set(manifest.get("files", {})) != expected:
+ raise ContractError("bundle must contain exactly the required artifact checksums")
+ for filename, checksum in manifest["files"].items():
+ path = bundle / filename
+ if path.is_symlink() or digest_file(path) != checksum:
+ raise ContractError(f"artifact checksum mismatch: {filename}")
+ if input_path is not None and inspect_inputs(input_path) != manifest["inputs"]:
+ raise ContractError("map is stale relative to current adapter input")
+ points = json.loads((bundle / "points.json").read_text())
+ if not isinstance(points, list) or len(points) < 3:
+ raise ContractError("map points must contain at least three records")
+ coverage = manifest["coverage"]
+ projection = manifest["projection"]
+ if (projection.get("method") != "pacmap" or projection.get("dimensions") != 2
+ or type(projection.get("seed")) is not int
+ or type(projection.get("neighbors")) is not int
+ or not 1 <= projection["neighbors"] < len(points)
+ or type(projection.get("requested_neighbors")) is not int
+ or projection["requested_neighbors"] < 1
+ or projection.get("initialization") != "pca"
+ or projection.get("MN_ratio") != 0.5 or projection.get("FP_ratio") != 2.0
+ or projection.get("distance") != "euclidean"
+ or projection.get("learning_rate") != 1.0
+ or projection.get("iterations") != [100, 100, 250]
+ or projection.get("apply_pca") is not True
+ or projection.get("knn_backend") != "faiss"):
+ raise ContractError("invalid PaCMAP projection metadata")
+ validate_versions(projection.get("library_versions"), "projection")
+ if projection.get("implementation") == "pacmap.PaCMAP":
+ pairs = projection.get("effective_pairs")
+ if (not isinstance(pairs, dict)
+ or any(type(pairs.get(name)) is not int or not 0 <= pairs[name] < len(points)
+ for name in ("neighbors", "mid_near", "further"))
+ or pairs["neighbors"] != projection["neighbors"] or pairs["further"] < 1):
+ raise ContractError("invalid effective PaCMAP pair counts")
+ elif projection.get("implementation") != "injected-projector":
+ raise ContractError("unidentified projection implementation")
+ if (not isinstance(points, list) or len(points) < 3
+ or any(type(coverage.get(name)) is not int for name in
+ ("displayed", "eligible", "total", "omitted", "maximum"))
+ or not 3 <= len(points) <= coverage["maximum"]
+ or coverage["omitted"] < 0
+ or coverage.get("selection") != "bottom-k-sha256(seed,identifier)"):
+ raise ContractError("invalid map selection coverage")
+ source_vectors = manifest["source_vectors"]
+ if (source_vectors.get("shape") != [len(points), manifest["encoder"]["dimension"]]
+ or source_vectors.get("dtype") != "float32-le"
+ or source_vectors.get("order") != "points.json"
+ or source_vectors.get("storage") != "local-profile-bound-cache"
+ or not re.fullmatch(r"[0-9a-f]{64}", str(source_vectors.get("sha256", "")))):
+ raise ContractError("invalid source vector receipt")
+ for row in points:
+ if (not isinstance(row, dict)
+ or any(not isinstance(row.get(name), str) or not row[name].strip()
+ for name in REQUIRED_FIELDS if name != "text")
+ or not local_link(row["page"]) or not local_link(row["source_path"])
+ or not re.fullmatch(r"[0-9a-f]{64}", row["text_sha256"])
+ or not all(type(row.get(name)) in (int, float) and math.isfinite(row[name])
+ for name in ("x", "y"))):
+ raise ContractError("invalid map coordinate or record metadata")
+ if (coverage["displayed"] != len(points)
+ or coverage["total"] != manifest["inputs"]["count"]
+ or coverage["eligible"] != coverage["total"]
+ or coverage["omitted"] != coverage["total"] - len(points)
+ or len({row["identifier"] for row in points}) != len(points)):
+ raise ContractError("map coverage or identifiers are inconsistent")
+ if input_path is not None:
+ selected = select_records(input_path, coverage["maximum"], projection["seed"])
+ expected = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"}
+ for row in selected]
+ observed = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"}
+ for row in points]
+ if observed != expected:
+ raise ContractError("map records differ from the declared input selection")
+ if cache_path is not None:
+ digest = hashlib.sha256()
+ with cache_connection(cache_path) as db:
+ profile_row = db.execute("SELECT json FROM profiles WHERE id=?",
+ (manifest["encoder_profile_sha256"],)).fetchone()
+ if profile_row is None or profile_row[0] != canonical(manifest["encoder"]).decode():
+ raise ContractError("cache does not contain the exact encoder profile")
+ for row in points:
+ blob = cached_vector(db, manifest["encoder_profile_sha256"], row,
+ manifest["encoder"]["dimension"])
+ if blob is None:
+ raise ContractError("source vector is missing from the verified cache")
+ digest.update(blob)
+ if digest.hexdigest() != source_vectors["sha256"]:
+ raise ContractError("map source vector receipt differs from the cache")
+ return manifest
+
+
+def current_bundle(output: Path) -> Path:
+ pointer = json.loads((output / "current.json").read_text())
+ if not re.fullmatch(r"[0-9a-f]{64}", str(pointer.get("bundle", ""))):
+ raise ContractError("invalid current bundle identifier")
+ bundle = output / pointer["bundle"]
+ if bundle.is_symlink() or digest_file(bundle / "manifest.json") != pointer["manifest_sha256"]:
+ raise ContractError("active manifest checksum mismatch")
+ return bundle
+
+
+def stage_map(output: Path, published_dir: Path, *, input_path: Path,
+ expected_bundle: str | None = None) -> dict:
+ """Stage a verified map into a site build, restoring old files on exceptions.
+
+ The caller owns the repository/build lock. The site's later deployment is
+ its publication boundary; the two directory renames are not a live-server
+ transaction. An interrupted machine may leave a named recovery directory.
+ Policy-checking callers pass the generation name they approved at preflight;
+ both the selection and its content identity must still match before writes.
+ """
+ source = current_bundle(output)
+ if expected_bundle is not None and source.name != expected_bundle:
+ raise ContractError("map generation changed after site preflight")
+ manifest = validate_bundle(source, input_path=input_path)
+ if hashlib.sha256(canonical(manifest)).hexdigest() != source.name:
+ raise ContractError("map manifest differs from its immutable generation identity")
+ if manifest["projection"]["implementation"] != "pacmap.PaCMAP":
+ raise ContractError("site publication requires the actual PaCMAP implementation")
+ if (published_dir.is_symlink()
+ or (published_dir.exists() and not published_dir.is_dir())
+ or source.resolve().is_relative_to(published_dir.resolve())
+ or published_dir.resolve().is_relative_to(output.resolve())
+ or input_path.resolve().is_relative_to(published_dir.resolve())):
+ raise ContractError("unsafe map staging destination")
+ published_dir.parent.mkdir(parents=True, exist_ok=True)
+ temporary = Path(tempfile.mkdtemp(prefix=".text-map-stage-", dir=published_dir.parent))
+ backup = None
+ try:
+ for name in ("index.html", "points.json", "manifest.json"):
+ shutil.copyfile(source / name, temporary / name)
+ copied = validate_bundle(temporary, input_path=input_path)
+ if copied != manifest:
+ raise ContractError("map source changed during site staging")
+ if published_dir.exists():
+ backup = Path(tempfile.mkdtemp(prefix=".text-map-recovery-", dir=published_dir.parent))
+ backup.rmdir()
+ os.rename(published_dir, backup)
+ try:
+ os.rename(temporary, published_dir)
+ except BaseException:
+ if backup is not None:
+ os.rename(backup, published_dir)
+ raise
+ if backup is not None:
+ shutil.rmtree(backup)
+ return manifest
+ finally:
+ if temporary.exists():
+ shutil.rmtree(temporary)
+
+
+def render_html(title: str, points: list[dict], total: int) -> str:
+ import html
+
+ payload = canonical(points).decode().replace("<", "\\u003c").replace("&", "\\u0026")
+ # The site adapter publishes this directory at text-map/. Record pages are
+ # relative to the site root, one level above this self-contained page.
+ return f'''
+{html.escape(title)}
+
+{html.escape(title)} Showing {len(points):,} of {total:,} input records.
+PaCMAP positions summarize similarity between record descriptions.
+Find a record
+Select a point to open its record.
+
+Map provenance and coverage
+
+'''
+
+
+def main(argv=None) -> int:
+ parser = argparse.ArgumentParser(description=__doc__)
+ sub = parser.add_subparsers(dest="command", required=True)
+ inspect_parser = sub.add_parser("inspect")
+ inspect_parser.add_argument("--input", type=Path, required=True)
+ embed_parser = sub.add_parser("embed")
+ embed_parser.add_argument("--input", type=Path, required=True)
+ embed_parser.add_argument("--cache", type=Path, required=True)
+ embed_parser.add_argument("--profile-output", type=Path, required=True)
+ embed_parser.add_argument("--batch-size", type=int, default=64)
+ embed_parser.add_argument("--device", choices=("cpu", "mps", "cuda"))
+ project_parser = sub.add_parser("project")
+ for name in ("input", "cache", "profile", "output"):
+ project_parser.add_argument("--" + name, type=Path, required=True)
+ project_parser.add_argument("--max-points", type=int, default=50000)
+ project_parser.add_argument("--seed", type=int, default=42)
+ project_parser.add_argument("--neighbors", type=int, default=15)
+ project_parser.add_argument("--title", default="Semantic text map")
+ check_parser = sub.add_parser("check")
+ check_parser.add_argument("--output", type=Path, required=True)
+ check_parser.add_argument("--input", type=Path)
+ check_parser.add_argument("--cache", type=Path)
+ stage_parser = sub.add_parser("stage")
+ stage_parser.add_argument("--output", type=Path, required=True)
+ stage_parser.add_argument("--input", type=Path, required=True)
+ stage_parser.add_argument("--published-dir", type=Path, required=True)
+ stage_parser.add_argument("--expected-bundle")
+ args = parser.parse_args(argv)
+ try:
+ if args.command == "inspect":
+ result = inspect_inputs(args.input)
+ elif args.command == "embed":
+ inspect_inputs(args.input) # fail before loading model weights
+ profile, encoder = local_encoder(args.device)
+ result = populate_cache(args.input, args.cache, profile, encoder,
+ batch_size=args.batch_size)
+ atomic_json(args.profile_output, profile)
+ elif args.command == "project":
+ profile = json.loads(args.profile.read_text())
+ result = build_map(args.input, args.cache, args.output, profile,
+ maximum=args.max_points, seed=args.seed,
+ neighbors=args.neighbors, title=args.title)
+ elif args.command == "check":
+ result = validate_bundle(current_bundle(args.output), input_path=args.input,
+ cache_path=args.cache)
+ else:
+ result = stage_map(args.output, args.published_dir, input_path=args.input,
+ expected_bundle=args.expected_bundle)
+ print(json.dumps(result, indent=2, allow_nan=False))
+ return 0
+ except (ContractError, OSError, ValueError, KeyError, sqlite3.Error,
+ importlib.metadata.PackageNotFoundError) as exc:
+ print(f"embedding-pipeline: {exc}", file=sys.stderr)
+ return 1
+
+
+if __name__ == "__main__":
+ raise SystemExit(main())
diff --git a/scripts/render_trait_pages.py b/scripts/render_trait_pages.py
index dc65411d0d..d14979e5ff 100755
--- a/scripts/render_trait_pages.py
+++ b/scripts/render_trait_pages.py
@@ -29,6 +29,7 @@
import re
import shutil
import sys
+import tempfile
from collections import defaultdict
from datetime import datetime, timezone
from pathlib import Path
@@ -37,6 +38,7 @@
from jinja2 import Environment, FileSystemLoader, select_autoescape
from research_trait import is_pipeline_report
from trait_causal_graph import causal_graphs_for_template
+from traitmech.text_map_site import prepare_text_map
REPO_ROOT = Path(__file__).resolve().parent.parent
TRAITS_DIR = REPO_ROOT / "data" / "traits"
@@ -64,18 +66,30 @@ def load_projection_receipt(path: Path) -> dict:
source = receipt["source"]
dimensions = receipt["input_dimensions"]
method = receipt["projection"]["method"]
- if (receipt["schema_version"] != 1 or method not in {"pacmap", "umap", "sfdp"}
+ if (receipt["schema_version"] not in {1, 2} or method not in {"pacmap", "umap", "sfdp"}
or type(dimensions) is not int or dimensions < 1
or not isinstance(source["filename"], str) or not source["filename"]
or not re.fullmatch(r"[0-9a-f]{64}", source["sha256"])):
return legacy
- # Include neighbor integrity so a newer neighbor run cannot silently
- # borrow an older map's source claim on every trait page.
- for output in (path, path.parent / "trait_nearest_neighbors.json"):
- with output.open("rb") as stream:
- digest = hashlib.file_digest(stream, "sha256").hexdigest()
- if receipt["outputs"].get(output.name) != digest:
+ if receipt["schema_version"] == 2:
+ from traitmech.graph_embedding_receipts import validate_receipt
+
+ outputs = receipt["outputs"]
+ required = {path.name, "trait_nearest_neighbors.json", "deepwalk_traits.tsv.gz",
+ "metpo_to_kgm_node.tsv"}
+ if (not isinstance(outputs, dict) or not required.issubset(outputs)
+ or any(not isinstance(name, str) or Path(name).name != name
+ or name in {".", ".."} for name in outputs)):
return legacy
+ validate_receipt(receipt, {name: path.parent / name for name in outputs})
+ else:
+ # The older receipt binds the projection and nearest neighbors.
+ # Its metadata must not be borrowed by a later neighbor run.
+ for output in (path, path.parent / "trait_nearest_neighbors.json"):
+ with output.open("rb") as stream:
+ digest = hashlib.file_digest(stream, "sha256").hexdigest()
+ if receipt["outputs"].get(output.name) != digest:
+ return legacy
return {"label": {"pacmap": "PaCMAP", "umap": "UMAP", "sfdp": "sfdp layout"}[method],
"method": method, "source": source["filename"],
"source_sha256": source["sha256"], "dimensions": dimensions, "verified": True}
@@ -386,6 +400,18 @@ def research_answer(text: str) -> list[str]:
def render_pages(args: argparse.Namespace) -> int:
+ # Finish full-input/policy validation and artifact staging before --clean
+ # can remove any existing pages. The temporary copy survives pointer swaps.
+ with prepare_text_map(REPO_ROOT) as ready:
+ if ready is None or args.dry_run:
+ return _render_pages(args)
+ with tempfile.TemporaryDirectory(prefix="traitmech-site-map-") as directory:
+ staging = Path(directory)
+ ready.stage(staging)
+ return _render_pages(args, staged_text_map=staging / "text-map")
+
+
+def _render_pages(args: argparse.Namespace, *, staged_text_map: Path | None = None) -> int:
# Output root is a parameter, not the module constant, so the staleness gate
# can render into a temp dir and diff (#230). Checking must never dirty the
# tree — that is half of what #214 was about — and this function wipes and
@@ -415,6 +441,8 @@ def render_pages(args: argparse.Namespace) -> int:
shutil.rmtree(pages_dir)
pages_dir.mkdir(parents=True, exist_ok=True)
+ if staged_text_map is not None:
+ shutil.copytree(staged_text_map, pages_dir / "text-map", dirs_exist_ok=True)
(pages_dir / "category").mkdir(exist_ok=True)
(pages_dir / "assets").mkdir(exist_ok=True)
shutil.copyfile(TEMPLATES_DIR / "style.css", pages_dir / "assets" / "style.css")
@@ -614,6 +642,7 @@ def render_pages(args: argparse.Namespace) -> int:
embedded_count = sum(1 for v in match_table.values() if v["n_kgm_nodes"] > 0)
landing = env.get_template("index.html").render(
title="Microbial trait knowledge base",
+ text_map_enabled=staged_text_map is not None,
projection_label=embedding_receipt["label"],
root="",
total_traits=len(traits),
diff --git a/scripts/sfdp_layout.py b/scripts/sfdp_layout.py
index 9ed2c158b3..f7f650a8ab 100644
--- a/scripts/sfdp_layout.py
+++ b/scripts/sfdp_layout.py
@@ -1,39 +1,83 @@
-"""Force-directed 2D layout of a mutual-kNN graph over embeddings, via Graphviz sfdp.
+"""Force-directed 2D layout of a symmetric union-kNN graph over embeddings, via Graphviz sfdp.
Self-contained: scikit-learn (kNN) + the `sfdp` binary (Graphviz). No pygraphviz/
pydot needed. Deterministic-ish via -Gstart=. Rows are L2-normalized so the
Euclidean kNN mirrors the cosine metric used elsewhere. Output row order == input.
"""
+
+import hashlib
import subprocess
+
import numpy as np
-from sklearn.preprocessing import normalize
from sklearn.neighbors import kneighbors_graph
+from sklearn.preprocessing import normalize
+
+from traitmech.graph_embedding_receipts import matrix_receipt
-def sfdp_layout(matrix, k=15, seed=42, sfdp_bin="sfdp"):
+def sfdp_layout(matrix, k=15, seed=42, sfdp_bin="sfdp", *, return_receipt=False, record_ids=None):
"""Return an (n, 2) float32 array of 2D coordinates for the rows of `matrix`."""
matrix = normalize(np.asarray(matrix, dtype="float32"))
n = matrix.shape[0]
if n == 0:
return np.zeros((0, 2), dtype="float32")
+ requested_k = k
k = min(k, max(1, n - 1))
A = kneighbors_graph(matrix, n_neighbors=k, mode="connectivity")
A = A.maximum(A.T) # symmetric union-kNN graph
coo = A.tocoo()
- edges = {(min(i, j), max(i, j)) for i, j in zip(coo.row.tolist(), coo.col.tolist()) if i != j}
- dot = "\n".join(["graph G {"] + [f"{i};" for i in range(n)]
- + [f"{i}--{j};" for i, j in edges] + ["}"])
+ edges = {
+ (min(i, j), max(i, j))
+ for i, j in zip(coo.row.tolist(), coo.col.tolist(), strict=True)
+ if i != j
+ }
+ dot = "\n".join(
+ ["graph G {"]
+ + [f"{i};" for i in range(n)]
+ + [f"{i}--{j};" for i, j in sorted(edges)]
+ + ["}"]
+ )
out = subprocess.run(
[sfdp_bin, "-Tplain", f"-Gstart={seed}", "-Goverlap=prism", "-Gsmoothing=triangle"],
- input=dot, capture_output=True, text=True, timeout=900,
+ input=dot,
+ capture_output=True,
+ text=True,
+ timeout=900,
+ check=False,
)
if out.returncode != 0:
raise RuntimeError(f"sfdp failed (is graphviz installed?): {out.stderr[:300]}")
xy = np.zeros((n, 2), dtype="float32")
+ seen = set()
for ln in out.stdout.splitlines():
if ln.startswith("node "):
p = ln.split()
idx = int(p[1])
+ if idx in seen or not 0 <= idx < n:
+ raise ValueError("sfdp returned an invalid or repeated node")
+ seen.add(idx)
xy[idx, 0] = float(p[2])
xy[idx, 1] = float(p[3])
+ if len(seen) != n or not np.isfinite(xy).all():
+ raise ValueError("sfdp did not return finite coordinates for every node")
+ if return_receipt:
+ version = subprocess.run(
+ [sfdp_bin, "-V"], capture_output=True, text=True, check=True
+ ).stderr.strip()
+ if not version:
+ raise ValueError("sfdp did not identify its Graphviz version")
+ graph = {
+ "construction": "symmetric_union_knn",
+ "metric": "euclidean",
+ "requested_k": requested_k,
+ "effective_k": k,
+ "edges": len(edges),
+ "dot_sha256": hashlib.sha256(dot.encode()).hexdigest(),
+ "graphviz_version": version,
+ "arguments": ["-Tplain", f"-Gstart={seed}", "-Goverlap=prism", "-Gsmoothing=triangle"],
+ "matrix": matrix_receipt(
+ matrix, record_ids if record_ids is not None else [str(i) for i in range(n)]
+ ),
+ }
+ return xy, graph
return xy
diff --git a/src/traitmech/graph_embedding_receipts.py b/src/traitmech/graph_embedding_receipts.py
new file mode 100644
index 0000000000..9fe0553a5c
--- /dev/null
+++ b/src/traitmech/graph_embedding_receipts.py
@@ -0,0 +1,497 @@
+"""Source-bound receipts for graph maps. Standard library; no legacy cache loading.
+
+Consumers own matching, aggregation and projection. Verified generation reads
+the source stream directly and stages new outputs; historical arrays cannot
+acquire provenance by passing an old cache to this module.
+"""
+
+from __future__ import annotations
+
+import gzip
+import hashlib
+import importlib.metadata
+import io
+import json
+import math
+import os
+import re
+import shutil
+import struct
+import tempfile
+from pathlib import Path
+
+SCHEMA_VERSION = 2
+
+
+def canonical(value: object) -> bytes:
+ return json.dumps(
+ value, sort_keys=True, separators=(",", ":"), ensure_ascii=False, allow_nan=False
+ ).encode("utf-8")
+
+
+def file_sha256(path: Path) -> str:
+ with Path(path).open("rb") as stream:
+ return hashlib.file_digest(stream, "sha256").hexdigest()
+
+
+def _frame(digest, value: str) -> None:
+ payload = value.encode("utf-8")
+ digest.update(struct.pack(">Q", len(payload)))
+ digest.update(payload)
+
+
+class _HashingReader(io.RawIOBase):
+ def __init__(self, stream):
+ self.stream = stream
+ self.digest = hashlib.sha256()
+ self.count = 0
+
+ def readable(self):
+ return True
+
+ def readinto(self, buffer):
+ data = self.stream.read(len(buffer))
+ buffer[: len(data)] = data
+ self.digest.update(data)
+ self.count += len(data)
+ return len(data)
+
+
+class GraphSource:
+ """Read selected node vectors while hashing the exact source bytes consumed.
+
+ Exhaust the iterator before using ``receipt``. Empty selection is recorded;
+ malformed selected rows, repeated IDs, inconsistent dimensions and nonfinite
+ values are errors. No basename/mtime cache or pickle is consulted.
+ """
+
+ def __init__(self, path: Path, prefixes, *, node_ids=None, node_filter=None, filter_name=None):
+ self.path = Path(path)
+ self.prefixes = tuple(sorted({p.rstrip(":") for p in prefixes}))
+ self.node_ids = None if node_ids is None else frozenset(node_ids)
+ if (node_filter is None) != (filter_name is None):
+ raise ValueError("a graph node filter requires an explicit policy name")
+ self.node_filter = node_filter
+ self.filter_name = filter_name
+ self.receipt = None
+ self._started = False
+
+ def __iter__(self):
+ if self._started:
+ raise ValueError("graph source reader is single-use")
+ self._started = True
+ seen = set()
+ dimension = None
+ lines = 0
+ with self.path.open("rb") as raw:
+ before = os.fstat(raw.fileno())
+ meter = _HashingReader(raw)
+ binary = (
+ gzip.GzipFile(fileobj=meter, mode="rb")
+ if self.path.suffix == ".gz"
+ else io.BufferedReader(meter)
+ )
+ with io.TextIOWrapper(binary, encoding="utf-8") as stream:
+ for line in stream:
+ lines += 1
+ node, separator, rest = line.rstrip("\r\n").partition("\t")
+ if not any(node.startswith(prefix + ":") for prefix in self.prefixes):
+ continue
+ if self.node_ids is not None and node not in self.node_ids:
+ continue
+ if self.node_filter is not None and not self.node_filter(node):
+ continue
+ if node in seen:
+ raise ValueError(f"duplicate selected graph node: {node}")
+ if not separator:
+ raise ValueError(f"missing vector for selected graph node: {node}")
+ try:
+ vector = [float(value) for value in rest.split("\t")]
+ except ValueError as error:
+ raise ValueError(f"malformed graph vector for {node}") from error
+ if (
+ len(vector) < 2
+ or not all(math.isfinite(v) for v in vector)
+ or not any(vector)
+ ):
+ raise ValueError(f"invalid graph vector for {node}")
+ if dimension is None:
+ dimension = len(vector)
+ if len(vector) != dimension:
+ raise ValueError(f"inconsistent graph vector dimension for {node}")
+ seen.add(node)
+ yield node, vector
+ after = os.fstat(raw.fileno())
+ if (before.st_dev, before.st_ino, before.st_size, before.st_mtime_ns) != (
+ after.st_dev,
+ after.st_ino,
+ after.st_size,
+ after.st_mtime_ns,
+ ) or meter.count != before.st_size:
+ raise ValueError("graph source changed or was not completely consumed")
+ self.receipt = {
+ "filename": self.path.name,
+ "sha256": meter.digest.hexdigest(),
+ "bytes": meter.count,
+ "physical_lines": lines,
+ "parser": "graph-tsv-numeric-v1",
+ "prefixes": list(self.prefixes),
+ "selection": "prefixes" if self.node_ids is None else "explicit-node-ids",
+ "filter_policy": self.filter_name,
+ "requested_node_ids_sha256": None
+ if self.node_ids is None
+ else hashlib.sha256(canonical(sorted(self.node_ids))).hexdigest(),
+ "selected_nodes": len(seen),
+ "dimensions": dimension,
+ "selected_node_ids_sha256": hashlib.sha256(canonical(sorted(seen))).hexdigest(),
+ "lineage": "parsed-source-bytes",
+ }
+
+
+def corpus_receipt(paths, root: Path) -> dict:
+ root = Path(root).resolve()
+ digest = hashlib.sha256()
+ entries = []
+ for path in sorted(Path(p) for p in paths):
+ if path.is_symlink():
+ raise ValueError(f"corpus symlink refused: {path}")
+ relative = path.resolve().relative_to(root).as_posix()
+ checksum = file_sha256(path)
+ _frame(digest, relative)
+ _frame(digest, checksum)
+ entries.append({"path": relative, "sha256": checksum})
+ if not entries or len({e["path"] for e in entries}) != len(entries):
+ raise ValueError("corpus must contain unique input files")
+ return {"count": len(entries), "sha256": digest.hexdigest(), "files": entries}
+
+
+def matrix_receipt(rows, identifiers, *, dtype="float32-le") -> dict:
+ formats = {"float32-le": "f", "float64-le": "d"}
+ if dtype not in formats:
+ raise ValueError("unsupported graph vector storage dtype")
+ ids = list(identifiers)
+ if len(set(ids)) != len(ids):
+ raise ValueError("duplicate projected record identity")
+ digest = hashlib.sha256()
+ dimension = None
+ count = 0
+ for identifier, row in zip(ids, rows, strict=True):
+ count += 1
+ if not isinstance(identifier, str) or not identifier:
+ raise ValueError("projected record identity must be nonempty")
+ values = [float(v) for v in row]
+ if len(values) < 2 or not all(math.isfinite(v) for v in values) or not any(values):
+ raise ValueError("projected vectors must be finite and nonzero")
+ dimension = len(values) if dimension is None else dimension
+ if len(values) != dimension:
+ raise ValueError("projected vectors have inconsistent dimensions")
+ digest.update(struct.pack("<" + formats[dtype] * dimension, *values))
+ if count < 1:
+ raise ValueError("projection requires at least one graph vector")
+ return {
+ "sha256": digest.hexdigest(),
+ "shape": [count, dimension],
+ "dtype": dtype,
+ "row_ids": ids,
+ "row_ids_sha256": hashlib.sha256(canonical(ids)).hexdigest(),
+ }
+
+
+def software_versions(*names) -> dict:
+ return {name: importlib.metadata.version(name) for name in names}
+
+
+def projection_receipt(
+ method, parameters, *, normalization, initialization=None, reducer=None, graph=None
+) -> dict:
+ if method not in {"pacmap", "umap", "sfdp"}:
+ raise ValueError(f"unknown projection method: {method}")
+ result = {
+ "method": method,
+ "parameters": parameters,
+ "normalization": normalization,
+ "initialization": initialization,
+ }
+ if method == "pacmap":
+ result.update(
+ implementation="pacmap.PaCMAP",
+ effective_pairs={
+ "neighbors": int(reducer.n_neighbors),
+ "mid_near": int(reducer.n_MN),
+ "further": int(reducer.n_FP),
+ },
+ library_versions=software_versions(
+ "pacmap", "numpy", "numba", "scikit-learn", "faiss-cpu"
+ ),
+ )
+ elif method == "umap":
+ result.update(
+ implementation="umap.UMAP",
+ effective_neighbors=int(reducer._n_neighbors),
+ library_versions=software_versions("umap-learn", "numpy", "numba", "scikit-learn"),
+ )
+ else:
+ if not graph:
+ raise ValueError("sfdp requires actual graph/backend provenance")
+ result.update(
+ implementation="graphviz.sfdp",
+ graph=graph,
+ library_versions=software_versions("numpy", "scikit-learn"),
+ )
+ canonical(result)
+ return result
+
+
+def make_receipt(*, source, corpus, ledger, matrix, projection, coverage, auxiliary=None):
+ if not source or source.get("lineage") != "parsed-source-bytes":
+ raise ValueError("graph provenance requires a freshly parsed source receipt")
+ if (
+ coverage.get("projected") != matrix["shape"][0]
+ or coverage.get("eligible", 0) < coverage["projected"]
+ ):
+ raise ValueError("graph coverage is inconsistent with projected vectors")
+ result = {
+ "schema_version": SCHEMA_VERSION,
+ "embedding_family": "kg_microbe_deepwalk",
+ "source": source,
+ "corpus": corpus,
+ "auxiliary_inputs": auxiliary or {},
+ "matching": {"sha256": hashlib.sha256(canonical(ledger)).hexdigest(), "rows": ledger},
+ "matrix": matrix,
+ "input_dimensions": matrix["shape"][1],
+ "projection": projection,
+ "coverage": coverage,
+ }
+ _validate_core(result)
+ return result
+
+
+def _validate_core(receipt):
+ def checksum(value):
+ return isinstance(value, str) and re.fullmatch(r"[0-9a-f]{64}", value)
+
+ source, matrix = receipt["source"], receipt["matrix"]
+ corpus, matching, projection = receipt["corpus"], receipt["matching"], receipt["projection"]
+ if (
+ receipt.get("schema_version") != SCHEMA_VERSION
+ or receipt.get("embedding_family") != "kg_microbe_deepwalk"
+ or source.get("lineage") != "parsed-source-bytes"
+ or not checksum(source.get("sha256"))
+ or type(source.get("bytes")) is not int
+ or source["bytes"] < 1
+ or not isinstance(source.get("filename"), str)
+ or not source["filename"]
+ or not checksum(corpus.get("sha256"))
+ or type(corpus.get("count")) is not int
+ or corpus["count"] < 1
+ or corpus.get("count") != len(corpus.get("files", []))
+ ):
+ raise ValueError("invalid graph source or corpus receipt")
+ corpus_digest = hashlib.sha256()
+ corpus_paths = []
+ for entry in corpus["files"]:
+ name = entry.get("path")
+ if (
+ not isinstance(name, str)
+ or not name
+ or Path(name).is_absolute()
+ or ".." in Path(name).parts
+ or not checksum(entry.get("sha256"))
+ ):
+ raise ValueError("invalid graph corpus input identity")
+ corpus_paths.append(name)
+ _frame(corpus_digest, name)
+ _frame(corpus_digest, entry["sha256"])
+ if len(set(corpus_paths)) != len(corpus_paths) or corpus_digest.hexdigest() != corpus["sha256"]:
+ raise ValueError("graph corpus ledger checksum mismatch")
+ shape = matrix.get("shape")
+ ids = matrix.get("row_ids")
+ if (
+ not isinstance(shape, list)
+ or len(shape) != 2
+ or any(type(size) is not int for size in shape)
+ or shape[0] < 1
+ or shape[1] < 2
+ or not isinstance(ids, list)
+ or len(ids) != shape[0]
+ or any(not isinstance(identifier, str) or not identifier for identifier in ids)
+ or len(set(ids)) != len(ids)
+ or not checksum(matrix.get("sha256"))
+ or matrix.get("dtype") not in {"float32-le", "float64-le"}
+ or hashlib.sha256(canonical(ids)).hexdigest() != matrix.get("row_ids_sha256")
+ or receipt.get("input_dimensions") != shape[1]
+ ):
+ raise ValueError("invalid ordered graph matrix receipt")
+ rows = matching.get("rows")
+ if (
+ not isinstance(rows, list)
+ or hashlib.sha256(canonical(rows)).hexdigest() != matching.get("sha256")
+ or any(
+ not isinstance(row, dict)
+ or not isinstance(row.get("identifier"), str)
+ or not row["identifier"]
+ or not isinstance(row.get("source_nodes"), list)
+ or any(not isinstance(node, str) or not node for node in row["source_nodes"])
+ or not isinstance(row.get("status"), str)
+ or (row["status"] == "projected" and not row["source_nodes"])
+ for row in rows
+ )
+ or len({row["identifier"] for row in rows}) != len(rows)
+ or {row["identifier"] for row in rows if row["status"] == "projected"} != set(ids)
+ ):
+ raise ValueError("invalid graph matching ledger")
+ coverage = receipt["coverage"]
+ if (
+ type(coverage.get("projected")) is not int
+ or coverage["projected"] != shape[0]
+ or type(coverage.get("eligible")) is not int
+ or coverage["eligible"] < shape[0]
+ or coverage["eligible"] != len(rows)
+ or projection.get("method") not in {"pacmap", "umap", "sfdp"}
+ or not isinstance(projection.get("parameters"), dict)
+ or projection.get("normalization") not in {"l2", "none"}
+ or not isinstance(projection.get("library_versions"), dict)
+ or not projection["library_versions"]
+ or any(
+ not isinstance(version, str) or not version
+ for version in projection["library_versions"].values()
+ )
+ ):
+ raise ValueError("invalid graph coverage or reducer provenance")
+ method = projection["method"]
+ if method == "pacmap":
+ pairs = projection.get("effective_pairs", {})
+ if (
+ projection.get("implementation") != "pacmap.PaCMAP"
+ or set(pairs) != {"neighbors", "mid_near", "further"}
+ or any(type(count) is not int or count < 0 for count in pairs.values())
+ or pairs["neighbors"] < 1
+ or pairs["further"] < 1
+ ):
+ raise ValueError("invalid effective PaCMAP reducer provenance")
+ elif method == "umap":
+ if (
+ projection.get("implementation") != "umap.UMAP"
+ or type(projection.get("effective_neighbors")) is not int
+ or projection["effective_neighbors"] < 1
+ ):
+ raise ValueError("invalid effective UMAP reducer provenance")
+ else:
+ graph = projection.get("graph", {})
+ if (
+ projection.get("implementation") != "graphviz.sfdp"
+ or graph.get("construction") != "symmetric_union_knn"
+ or not checksum(graph.get("dot_sha256"))
+ or not graph.get("graphviz_version")
+ or not graph.get("arguments")
+ or type(graph.get("effective_k")) is not int
+ or graph["effective_k"] < 1
+ or type(graph.get("edges")) is not int
+ or graph["edges"] < 1
+ ):
+ raise ValueError("invalid actual sfdp graph provenance")
+ canonical(receipt)
+
+
+def validate_receipt(receipt, files: dict[str, Path]) -> None:
+ if receipt.get("schema_version") != SCHEMA_VERSION:
+ raise ValueError("unsupported graph receipt schema")
+ _validate_core(receipt)
+ if receipt["source"].get("lineage") != "parsed-source-bytes":
+ raise ValueError("unverified graph source lineage")
+ if set(receipt.get("outputs", {})) != set(files):
+ raise ValueError("graph output set differs from the receipt")
+ if (
+ hashlib.sha256(canonical(receipt["matching"]["rows"])).hexdigest()
+ != receipt["matching"]["sha256"]
+ ):
+ raise ValueError("graph matching receipt checksum mismatch")
+ for name, path in files.items():
+ if Path(path).is_symlink() or file_sha256(path) != receipt["outputs"][name]:
+ raise ValueError(f"graph output checksum mismatch: {name}")
+
+
+def load_receipt(path: Path) -> dict:
+ path = Path(path)
+ if path.is_symlink():
+ raise ValueError("symlinked graph receipt refused")
+ receipt = json.loads(path.read_text())
+ names = receipt.get("outputs", {})
+ if (
+ not isinstance(names, dict)
+ or not names
+ or any(not isinstance(name, str) or not name or Path(name).name != name for name in names)
+ ):
+ raise ValueError("graph receipt outputs must name sibling artifacts")
+ validate_receipt(receipt, {name: path.parent / name for name in names})
+ return receipt
+
+
+def publish_artifacts(staged: dict[Path, Path], receipt_path: Path, receipt: dict) -> dict:
+ """Promote generated files and their receipt, restoring originals on errors.
+
+ Caller owns the repository lock. Receipts are promoted last. A process kill
+ may leave a recovery directory; retain it instead of claiming atomic live
+ serving. All artifacts must have distinct basenames for unambiguous checks.
+ """
+ receipt_path = Path(receipt_path)
+ destinations = [Path(path) for path in staged]
+ if (
+ not destinations
+ or receipt_path.is_symlink()
+ or len({p.name for p in destinations}) != len(destinations)
+ or any(p.parent.resolve() != receipt_path.parent.resolve() for p in destinations)
+ or receipt_path.resolve() in {path.resolve() for path in destinations}
+ or any(p.is_symlink() for p in destinations)
+ ):
+ raise ValueError("graph artifacts must have distinct, non-symlinked sibling destinations")
+ metadata = {
+ **receipt,
+ "outputs": {target.name: file_sha256(origin) for target, origin in staged.items()},
+ }
+ validate_receipt(metadata, {target.name: origin for target, origin in staged.items()})
+ receipt_path.parent.mkdir(parents=True, exist_ok=True)
+ recovery = Path(tempfile.mkdtemp(prefix=".graph-recovery-", dir=receipt_path.parent))
+ changes = []
+ success = False
+ try:
+ receipt_stage = recovery / "new-receipt.json"
+ receipt_stage.write_bytes(canonical(metadata) + b"\n")
+ for index, (target, origin) in enumerate([*staged.items(), (receipt_path, receipt_stage)]):
+ target = Path(target)
+ target.parent.mkdir(parents=True, exist_ok=True)
+ backup = recovery / f"previous-{index}"
+ existed = target.exists()
+ if existed:
+ shutil.copyfile(target, backup)
+ changes.append((target, backup if existed else None))
+ # Stage in each destination filesystem before atomic replacement.
+ fd, temporary_name = tempfile.mkstemp(prefix=".graph-publish-", dir=target.parent)
+ os.close(fd)
+ temporary = Path(temporary_name)
+ try:
+ shutil.copyfile(origin, temporary)
+ expected = (
+ file_sha256(receipt_stage)
+ if target == receipt_path
+ else metadata["outputs"][target.name]
+ )
+ if file_sha256(temporary) != expected:
+ raise ValueError(
+ f"staged graph artifact changed during publication: {target.name}"
+ )
+ os.replace(temporary, target)
+ finally:
+ temporary.unlink(missing_ok=True)
+ success = True
+ except BaseException:
+ for target, backup in reversed(changes):
+ if backup is None:
+ target.unlink(missing_ok=True)
+ else:
+ os.replace(backup, target)
+ raise
+ finally:
+ if success or not any(recovery.glob("previous-*")):
+ shutil.rmtree(recovery)
+ return metadata
diff --git a/src/traitmech/templates/index.html b/src/traitmech/templates/index.html
index c0feaf13f2..9f4f6239c0 100644
--- a/src/traitmech/templates/index.html
+++ b/src/traitmech/templates/index.html
@@ -117,6 +117,13 @@ TraitMech
+ {% if text_map_enabled %}
+
+ Semantic text map
+
+ Traits grouped by their biological descriptions, using the fleet's pinned BGE text model and PaCMAP.
+
+ {% endif %}
🔎
diff --git a/src/traitmech/text_map_site.py b/src/traitmech/text_map_site.py
new file mode 100644
index 0000000000..4a85523c3a
--- /dev/null
+++ b/src/traitmech/text_map_site.py
@@ -0,0 +1,90 @@
+"""Prepare a configured common text map before a site build can change files.
+
+All artifact validation and atomic publication belong to CLAW's shared runtime.
+This adapter only supplies fresh full-corpus semantic inputs and site policy.
+"""
+
+from __future__ import annotations
+
+import importlib.util
+import tempfile
+from collections.abc import Iterator
+from contextlib import contextmanager
+from dataclasses import dataclass
+from pathlib import Path
+from types import ModuleType
+
+import yaml
+
+from traitmech.text_map_inputs import export_inputs
+
+
+@dataclass
+class PreparedTextMap:
+ pipeline: ModuleType
+ source: Path
+ inputs: Path
+ expected_bundle: str
+
+ def stage(self, site: Path) -> None:
+ self.pipeline.stage_map(
+ self.source,
+ site / "text-map",
+ input_path=self.inputs,
+ expected_bundle=self.expected_bundle,
+ )
+
+
+def load_pipeline(root: Path) -> ModuleType:
+ path = root / "scripts" / "embedding_pipeline.py"
+ if not path.is_file() or path.is_symlink():
+ raise ValueError("enabled text map requires the CLAW-governed scripts/embedding_pipeline.py")
+ spec = importlib.util.spec_from_file_location("traitmech_embedding_pipeline", path)
+ if spec is None or spec.loader is None:
+ raise ValueError("cannot load the CLAW embedding pipeline")
+ module = importlib.util.module_from_spec(spec)
+ spec.loader.exec_module(module)
+ if not callable(getattr(module, "stage_map", None)):
+ raise ValueError("CLAW embedding pipeline does not provide validated map staging")
+ return module
+
+
+@contextmanager
+def prepare_text_map(root: Path) -> Iterator[PreparedTextMap | None]:
+ config = root / "conf" / "text_map.yaml"
+ if config.is_symlink():
+ raise ValueError("text map configuration must not be a symlink")
+ if not config.is_file():
+ raise ValueError("text map enablement requires conf/text_map.yaml")
+ settings = yaml.safe_load(config.read_text(encoding="utf-8"))
+ if (
+ not isinstance(settings, dict)
+ or set(settings) != {"enabled"}
+ or type(settings["enabled"]) is not bool
+ ):
+ raise ValueError("text map configuration must contain only an explicit enabled boolean")
+ if not settings["enabled"]:
+ yield None
+ return
+ source = root / "data" / "text_map"
+ if source.is_symlink() or not (source / "current.json").is_file():
+ raise ValueError("enabled text map requires data/text_map/current.json")
+ pipeline = load_pipeline(root)
+ with tempfile.TemporaryDirectory(prefix="traitmech-text-map-") as directory:
+ inputs = Path(directory) / "inputs.jsonl"
+ receipt = export_inputs(root, inputs)
+ if receipt["scope"] != "full":
+ raise ValueError("site publication requires fresh full-corpus inputs")
+ bundle = pipeline.current_bundle(source)
+ manifest = pipeline.validate_bundle(bundle, input_path=inputs)
+ if manifest["projection"]["implementation"] != "pacmap.PaCMAP":
+ raise ValueError("site publication requires the actual PaCMAP implementation")
+ profile = manifest["encoder"]
+ if (
+ profile["model"] != pipeline.MODEL
+ or profile["revision"] != pipeline.MODEL_REVISION
+ or profile["dimension"] != pipeline.MODEL_DIMENSION
+ or profile["max_seq_length"] != pipeline.MAX_SEQ_LENGTH
+ ):
+ raise ValueError("common semantic map requires the pinned fleet BGE encoder profile")
+ yield PreparedTextMap(pipeline, source, inputs, bundle.name)
diff --git a/tests/test_graph_projection_correctness.py b/tests/test_graph_projection_correctness.py
index 069dcb780b..ee84ae5e67 100644
--- a/tests/test_graph_projection_correctness.py
+++ b/tests/test_graph_projection_correctness.py
@@ -1,4 +1,5 @@
"""Selected graph sources and published receipts must be literal, not guessed."""
+
import importlib.util
import json
import sys
@@ -17,8 +18,11 @@ def builder():
def test_explicit_missing_source_fails_without_fallback(builder, tmp_path, monkeypatch):
- monkeypatch.setattr(sys, "argv", ["builder", "--src", str(tmp_path / "typo.gz"),
- "--out-deepwalk", str(tmp_path / "out.gz")])
+ monkeypatch.setattr(
+ sys,
+ "argv",
+ ["builder", "--src", str(tmp_path / "typo.gz"), "--out-deepwalk", str(tmp_path / "out.gz")],
+ )
assert builder.main() == 2
assert not (tmp_path / "out.gz").exists()
@@ -41,26 +45,21 @@ def test_current_local_and_configured_sibling_layout(builder, tmp_path, monkeypa
assert builder.default_deepwalk() == local
-def test_receipt_uses_actual_source_dimensions_and_output_digests(builder, tmp_path):
- source = tmp_path / "explicit_legacy_graph.tsv.gz"
- source.write_bytes(b"a caller-selected legacy artifact")
- output = tmp_path / "map.json"
- output.write_text('[{"id":"METPO:1"}]')
- neighbors = tmp_path / "neighbors.json"
- neighbors.write_text('{"METPO:1":[]}')
- matches = tmp_path / "matches.tsv"
- matches.write_text("match_method\nparent_proxy\n")
- builder.write_projection_metadata(output, source, {"METPO:1": [1.] * 200}, "umap", matches, neighbors)
- metadata = json.loads(output.with_suffix(".metadata.json").read_text())
- assert metadata["source"] == {"filename": source.name, "sha256": builder.file_sha256(source)}
- assert metadata["input_dimensions"] == 200
- assert metadata["projection"]["method"] == "umap"
- assert metadata["outputs"][output.name] == builder.file_sha256(output)
- assert metadata["outputs"][neighbors.name] == builder.file_sha256(neighbors)
+def test_output_only_metadata_cannot_bless_old_coordinates(builder, tmp_path):
+ with pytest.raises(ValueError, match="Output-only provenance"):
+ builder.write_projection_metadata(
+ tmp_path / "old-map.json",
+ tmp_path / "new-source.gz",
+ {"METPO:1": [1.0] * 200},
+ "pacmap",
+ tmp_path / "matches.tsv",
+ tmp_path / "neighbors.json",
+ )
def test_renderer_checks_receipt_and_labels_legacy_without_guessing(builder, tmp_path, monkeypatch):
import hashlib
+
path = Path(__file__).resolve().parents[1] / "scripts/render_trait_pages.py"
monkeypatch.syspath_prepend(str(path.parent))
spec = importlib.util.spec_from_file_location("graph_renderer_under_test", path)
@@ -71,10 +70,15 @@ def test_renderer_checks_receipt_and_labels_legacy_without_guessing(builder, tmp
neighbors = tmp_path / "trait_nearest_neighbors.json"
neighbors.write_text("{}")
assert renderer.load_projection_receipt(projection)["verified"] is False
- receipt = {"schema_version": 1, "input_dimensions": 200,
+ receipt = {
+ "schema_version": 1,
+ "input_dimensions": 200,
"source": {"filename": "actual_legacy_source.gz", "sha256": "a" * 64},
"projection": {"method": "umap"},
- "outputs": {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in (projection, neighbors)}}
+ "outputs": {
+ p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in (projection, neighbors)
+ },
+ }
projection.with_suffix(".metadata.json").write_text(json.dumps(receipt))
result = renderer.load_projection_receipt(projection)
assert result["label"] == "UMAP"
diff --git a/tests/test_graph_receipt_proxies.py b/tests/test_graph_receipt_proxies.py
new file mode 100644
index 0000000000..9d026e897a
--- /dev/null
+++ b/tests/test_graph_receipt_proxies.py
@@ -0,0 +1,48 @@
+"""Omitted records cannot shift the per-point graph node provenance."""
+
+import sys
+import types
+
+import numpy as np
+
+from scripts.build_embedding_index import compute_umap_and_neighbors
+
+
+def test_missing_first_trait_does_not_shift_proxy_or_point_source_nodes(monkeypatch):
+ class Reducer:
+ def __init__(self, **kwargs):
+ self.n_neighbors, self.n_MN, self.n_FP = 1, 0, 1
+
+ def fit_transform(self, values, **kwargs):
+ return values[:, :2]
+
+ monkeypatch.setitem(sys.modules, "pacmap", types.SimpleNamespace(PaCMAP=Reducer))
+ records = [("METPO:missing", "Missing", [], "fixture", [])]
+ records.extend((f"METPO:{i}", f"Trait {i}", [], "fixture", []) for i in range(6))
+ records.append(("METPO:proxy", "Proxy", [], "fixture", ["METPO:1"]))
+ matches = [
+ {
+ "metpo_curie": curie,
+ "kgm_nodes": ""
+ if curie == "METPO:missing"
+ else "METPO:1"
+ if curie == "METPO:proxy"
+ else curie,
+ "match_method": "parent_proxy" if curie == "METPO:proxy" else "direct_metpo",
+ }
+ for curie, *_ in records
+ ]
+ vectors = {f"METPO:{i}": np.array([i + 1, 2, 3.0]) for i in range(6)}
+ details = {}
+ points, neighbors = compute_umap_and_neighbors(
+ records, matches, vectors, receipt_details=details
+ )
+ by_id = {row["id"]: row for row in points}
+ assert by_id["METPO:0"]["kgm_nodes"] == ["METPO:0"]
+ assert by_id["METPO:proxy"]["kgm_nodes"] == ["METPO:1"]
+ assert by_id["METPO:proxy"]["match_method"] == "parent_proxy"
+ assert neighbors["METPO:missing"] == []
+ assert len(details["ledger"]) == 8 and len(points) == 7
+ assert details["ledger"][0]["status"] == "no_vectors"
+ for curie, rows in neighbors.items():
+ assert all(row["id"] != curie for row in rows)
diff --git a/tests/test_graph_receipt_publication.py b/tests/test_graph_receipt_publication.py
new file mode 100644
index 0000000000..cb4ebfe88b
--- /dev/null
+++ b/tests/test_graph_receipt_publication.py
@@ -0,0 +1,78 @@
+"""The rendered source claim covers the whole graph output generation."""
+from __future__ import annotations
+
+import gzip
+import importlib.util
+import json
+from pathlib import Path
+
+import pytest
+from traitmech import graph_embedding_receipts as receipts
+
+
+@pytest.fixture
+def renderer(monkeypatch):
+ script = Path(__file__).resolve().parents[1] / "scripts/render_trait_pages.py"
+ monkeypatch.syspath_prepend(str(script.parent))
+ spec = importlib.util.spec_from_file_location("trait_receipt_renderer_review", script)
+ module = importlib.util.module_from_spec(spec)
+ spec.loader.exec_module(module)
+ return module
+
+
+@pytest.fixture
+def generation(tmp_path):
+ raw = tmp_path / "graph.tsv.gz"
+ raw.write_bytes(gzip.compress(b"node\td1\td2\nMETPO:1\t1\t0\nMETPO:2\t0\t1\nMETPO:3\t1\t1\n", mtime=0))
+ reader = receipts.GraphSource(raw, ["METPO"])
+ vectors = dict(reader)
+ corpus = tmp_path / "trait.yaml"
+ corpus.write_text("identifier: METPO:1\nlabel: fixture\n")
+ metadata = receipts.make_receipt(
+ source=reader.receipt, corpus=receipts.corpus_receipt([corpus], tmp_path),
+ ledger=[{"identifier": identifier, "source_nodes": [identifier], "status": "projected"}
+ for identifier in vectors],
+ matrix=receipts.matrix_receipt(vectors.values(), vectors),
+ projection={"method": "pacmap", "parameters": {"n_components": 2},
+ "normalization": "none", "initialization": "pca",
+ "implementation": "pacmap.PaCMAP", "library_versions": {"fixture": "1"},
+ "effective_pairs": {"neighbors": 1, "mid_near": 0, "further": 1}},
+ coverage={"eligible": 3, "projected": 3},
+ )
+ staged = tmp_path / "staged"
+ staged.mkdir()
+ contents = {"deepwalk_traits.tsv.gz": raw.read_bytes(),
+ "metpo_to_kgm_node.tsv": b"metpo_id\tkgm_node\nMETPO:1\tMETPO:1\n",
+ "trait_umap.json": b'[{"id":"METPO:1","x":0,"y":0}]',
+ "trait_nearest_neighbors.json": b'{"METPO:1": []}'}
+ for name, value in contents.items():
+ (staged / name).write_bytes(value)
+ projection = tmp_path / "trait_umap.json"
+ receipts.publish_artifacts({tmp_path / name: staged / name for name in contents},
+ projection.with_suffix(".metadata.json"), metadata)
+ return projection, contents
+
+
+def test_renderer_accepts_complete_current_graph_receipt(renderer, generation):
+ projection, _ = generation
+ result = renderer.load_projection_receipt(projection)
+ assert result["verified"] is True
+ assert result["label"] == "PaCMAP" and result["source"] == "graph.tsv.gz"
+ assert result["dimensions"] == 2
+
+
+@pytest.mark.parametrize("name", ["deepwalk_traits.tsv.gz", "metpo_to_kgm_node.tsv",
+ "trait_umap.json", "trait_nearest_neighbors.json"])
+def test_changed_generation_member_cannot_borrow_old_source_claim(renderer, generation, name):
+ projection, _ = generation
+ (projection.parent / name).write_bytes(b"a later generation")
+ assert renderer.load_projection_receipt(projection)["verified"] is False
+
+
+def test_receipt_cannot_omit_a_required_generation_member(renderer, generation):
+ projection, _ = generation
+ sidecar = projection.with_suffix(".metadata.json")
+ metadata = json.loads(sidecar.read_text())
+ metadata["outputs"].pop("metpo_to_kgm_node.tsv")
+ sidecar.write_text(json.dumps(metadata))
+ assert renderer.load_projection_receipt(projection)["verified"] is False
diff --git a/tests/test_graph_sfdp_receipt.py b/tests/test_graph_sfdp_receipt.py
new file mode 100644
index 0000000000..a44e90c308
--- /dev/null
+++ b/tests/test_graph_sfdp_receipt.py
@@ -0,0 +1,24 @@
+"""Graphviz must return one finite coordinate per actual projected row."""
+
+import shutil
+
+import numpy as np
+import pytest
+
+from scripts.sfdp_layout import sfdp_layout
+
+
+@pytest.mark.skipif(
+ shutil.which("sfdp") is None, reason="Graphviz sfdp is an optional graph backend"
+)
+def test_real_sfdp_returns_all_rows_and_actual_graph_receipt():
+ matrix = np.random.default_rng(42).normal(size=(12, 5))
+ points, graph = sfdp_layout(
+ matrix, k=3, return_receipt=True, record_ids=[f"row:{i}" for i in range(12)]
+ )
+ assert points.shape == (12, 2) and np.isfinite(points).all()
+ assert graph["construction"] == "symmetric_union_knn"
+ assert graph["effective_k"] == 3 and graph["edges"] > 0
+ assert "graphviz" in graph["graphviz_version"].lower()
+ assert graph["matrix"]["shape"] == [12, 5]
+ assert graph["matrix"]["row_ids"][0] == "row:0"
diff --git a/tests/test_text_map_recipe.py b/tests/test_text_map_recipe.py
new file mode 100644
index 0000000000..43c10782dd
--- /dev/null
+++ b/tests/test_text_map_recipe.py
@@ -0,0 +1,43 @@
+"""Exercise the actual just recipe without resolving dependencies or running a model."""
+
+from __future__ import annotations
+
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+REPO = Path(__file__).resolve().parents[1]
+
+
+@pytest.mark.skipif(shutil.which("just") is None, reason="the just developer tool is required")
+def test_recipe_preserves_quoted_path_arguments(tmp_path):
+ tools = tmp_path / "tools"
+ tools.mkdir()
+ receipt = tmp_path / "argv.json"
+ uv = tools / "uv"
+ uv.write_text(
+ "#!/usr/bin/env python3\n"
+ "import json, os, sys\n"
+ "with open(os.environ['TEXT_MAP_ARGV_RECEIPT'], 'w') as output:\n"
+ " json.dump(sys.argv[1:], output)\n"
+ )
+ uv.chmod(0o755)
+ args = [
+ "--output",
+ str(tmp_path / "output folder" / "inputs.jsonl"),
+ "--record",
+ "data/example/a record.yaml",
+ "--limit",
+ "3",
+ ]
+ env = dict(
+ os.environ, PATH=str(tools) + os.pathsep + os.environ["PATH"], TEXT_MAP_ARGV_RECEIPT=str(receipt)
+ )
+ subprocess.run(
+ ["just", "text-map-inputs", *args], cwd=REPO, env=env, check=True, capture_output=True, text=True
+ )
+ assert json.loads(receipt.read_text()) == ["run", "python", "scripts/text_map_inputs.py", *args]
diff --git a/tests/test_text_map_site.py b/tests/test_text_map_site.py
new file mode 100644
index 0000000000..166e720d10
--- /dev/null
+++ b/tests/test_text_map_site.py
@@ -0,0 +1,206 @@
+"""Publication requires an explicit switch and current validated full inputs."""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from types import SimpleNamespace
+
+import pytest
+from jinja2 import Environment, FileSystemLoader
+
+from traitmech import text_map_site as site
+
+
+def configure(root: Path, value="false"):
+ config = root / "conf" / "text_map.yaml"
+ config.parent.mkdir(parents=True, exist_ok=True)
+ config.write_text(f"enabled: {value}\n")
+
+
+def fake_pipeline():
+ calls = []
+ profile = {
+ "model": "BAAI/bge-large-en-v1.5",
+ "revision": "d4aa6901d3a41ba39fb536a557fa166f842b0e09",
+ "dimension": 1024,
+ "max_seq_length": 512,
+ }
+ manifest = {"encoder": profile, "projection": {"implementation": "pacmap.PaCMAP"}}
+
+ def validate(bundle, *, input_path):
+ assert json.loads(input_path.read_text()) == {"test": "fresh full inputs"}
+ calls.append(("validate", bundle, input_path))
+ return manifest
+
+ def stage(output, published_dir, *, input_path, expected_bundle):
+ assert json.loads(input_path.read_text()) == {"test": "fresh full inputs"}
+ calls.append(("stage", output, published_dir, expected_bundle))
+ return manifest
+
+ pipeline = SimpleNamespace(
+ MODEL=profile["model"],
+ MODEL_REVISION=profile["revision"],
+ MODEL_DIMENSION=1024,
+ MAX_SEQ_LENGTH=512,
+ current_bundle=lambda output: output / ("a" * 64),
+ validate_bundle=validate,
+ stage_map=stage,
+ )
+ return pipeline, calls, manifest
+
+
+def enable_fixture(root, monkeypatch):
+ configure(root, "true")
+ source = root / "data" / "text_map"
+ source.mkdir(parents=True)
+ (source / "current.json").write_text("{}")
+ pipeline, calls, manifest = fake_pipeline()
+ monkeypatch.setattr(site, "load_pipeline", lambda _root: pipeline)
+
+ def export(actual_root, output, **kwargs):
+ assert actual_root == root
+ assert not kwargs, "publication cannot request a canary or limited input set"
+ output.write_text(json.dumps({"test": "fresh full inputs"}))
+ return {"scope": "full"}
+
+ monkeypatch.setattr(site, "export_inputs", export)
+ return pipeline, calls, manifest
+
+
+def test_disabled_map_requires_no_runtime_or_artifact(tmp_path, monkeypatch):
+ configure(tmp_path)
+ monkeypatch.setattr(site, "load_pipeline", lambda _root: pytest.fail("disabled map loaded runtime"))
+ with site.prepare_text_map(tmp_path) as ready:
+ assert ready is None
+
+
+def test_enabled_map_missing_bundle_fails(tmp_path):
+ configure(tmp_path, "true")
+ with pytest.raises(ValueError, match="current.json"), site.prepare_text_map(tmp_path):
+ pass
+
+
+def test_enabled_map_missing_shared_runtime_fails(tmp_path):
+ configure(tmp_path, "true")
+ source = tmp_path / "data" / "text_map"
+ source.mkdir(parents=True)
+ (source / "current.json").write_text("{}")
+ with pytest.raises(ValueError, match="CLAW-governed"), site.prepare_text_map(tmp_path):
+ pass
+
+
+@pytest.mark.parametrize("value", ["1", "'true'", "null", "[]"])
+def test_enablement_requires_an_actual_boolean(tmp_path, value):
+ configure(tmp_path, value)
+ with pytest.raises(ValueError, match="enabled boolean"), site.prepare_text_map(tmp_path):
+ pass
+
+
+def test_enabled_map_uses_fresh_full_inputs_and_canonical_stage(tmp_path, monkeypatch):
+ _, calls, _ = enable_fixture(tmp_path, monkeypatch)
+ with site.prepare_text_map(tmp_path) as ready:
+ inputs = ready.inputs
+ ready.stage(tmp_path / "published")
+ assert calls[-1] == (
+ "stage",
+ tmp_path / "data" / "text_map",
+ tmp_path / "published" / "text-map",
+ "a" * 64,
+ )
+ assert not inputs.exists()
+ assert calls[0][0] == "validate"
+
+
+def test_legacy_encoder_cannot_be_published_as_the_common_space(tmp_path, monkeypatch):
+ _, _, manifest = enable_fixture(tmp_path, monkeypatch)
+ manifest["encoder"] = {"model": "MiniLM", "revision": "0" * 40, "dimension": 384}
+ with pytest.raises(ValueError, match="pinned fleet BGE"), site.prepare_text_map(tmp_path):
+ pass
+
+
+def test_injected_projector_cannot_reach_the_site_build(tmp_path, monkeypatch):
+ _, _, manifest = enable_fixture(tmp_path, monkeypatch)
+ manifest["projection"]["implementation"] = "injected-projector"
+ with pytest.raises(ValueError, match="actual PaCMAP"), site.prepare_text_map(tmp_path):
+ pass
+
+
+def test_subset_receipt_cannot_reach_publication(tmp_path, monkeypatch):
+ enable_fixture(tmp_path, monkeypatch)
+ monkeypatch.setattr(site, "export_inputs", lambda _root, _output: {"scope": "subset"})
+ with pytest.raises(ValueError, match="full-corpus"), site.prepare_text_map(tmp_path):
+ pass
+
+
+def test_navigation_is_conditional_and_retains_specialty_maps():
+ templates = Path(__file__).resolve().parents[1] / "src" / "traitmech" / "templates"
+ env = Environment(loader=FileSystemLoader(str(templates)))
+ template = env.get_template("index.html")
+ context = {"root": "", "category_counts": {}, "projection_label": "PaCMAP"}
+ disabled = template.render(text_map_enabled=False, **context)
+ enabled = template.render(text_map_enabled=True, **context)
+ assert "Explore shared BGE map" not in disabled
+ assert 'href="text-map/"' in enabled
+ assert 'href="umap.html"' in enabled and 'href="graph.html"' in enabled
+
+
+def test_invalid_map_preflight_preserves_existing_pages_before_clean(tmp_path, monkeypatch):
+ monkeypatch.syspath_prepend(str(Path(__file__).resolve().parents[1] / "scripts"))
+ import render_trait_pages as render
+
+ configure(tmp_path, "true")
+ published = tmp_path / "published"
+ published.mkdir()
+ old = published / "index.html"
+ old.write_text("existing published site")
+ monkeypatch.setattr(render, "REPO_ROOT", tmp_path)
+ with pytest.raises(ValueError, match="current.json"):
+ render.render_pages(SimpleNamespace(out=published, clean=True, dry_run=False))
+ assert old.read_text() == "existing published site"
+
+
+def test_staging_failure_precedes_renderer_mutation(tmp_path, monkeypatch):
+ monkeypatch.syspath_prepend(str(Path(__file__).resolve().parents[1] / "scripts"))
+ import render_trait_pages as render
+
+ pipeline, _, _ = enable_fixture(tmp_path, monkeypatch)
+ def refuse(*args, **kwargs):
+ raise ValueError("generation changed")
+ monkeypatch.setattr(pipeline, "stage_map", refuse)
+ monkeypatch.setattr(render, "REPO_ROOT", tmp_path)
+ monkeypatch.setattr(render, "_render_pages", lambda *a, **kw: pytest.fail("renderer wrote too early"))
+ with pytest.raises(ValueError, match="generation changed"):
+ render.render_pages(SimpleNamespace(out=tmp_path / "pages", clean=True, dry_run=False))
+ assert not (tmp_path / "pages").exists()
+
+
+def test_pointer_change_does_not_replace_the_preflight_generation(tmp_path, monkeypatch):
+ pipeline, _, _ = enable_fixture(tmp_path, monkeypatch)
+ published = tmp_path / "published" / "text-map"
+ published.mkdir(parents=True)
+ old = published / "index.html"
+ old.write_text("previously published map")
+ seen = []
+
+ def checked_stage(output, published_dir, *, input_path, expected_bundle):
+ seen.append(expected_bundle)
+ if pipeline.current_bundle(output).name != expected_bundle:
+ raise ValueError("current map differs from preflight generation")
+ (published_dir / "index.html").write_text("replacement map")
+
+ monkeypatch.setattr(pipeline, "stage_map", checked_stage)
+ with site.prepare_text_map(tmp_path) as ready:
+ monkeypatch.setattr(pipeline, "current_bundle", lambda output: output / ("b" * 64))
+ with pytest.raises(ValueError, match="preflight generation"):
+ ready.stage(tmp_path / "published")
+ assert seen == ["a" * 64]
+ assert old.read_text() == "previously published map"
+
+
+def test_common_map_rejects_an_alternate_window_with_other_bge_fields_valid(tmp_path, monkeypatch):
+ _, calls, manifest = enable_fixture(tmp_path, monkeypatch)
+ manifest["encoder"]["max_seq_length"] = 256
+ with pytest.raises(ValueError, match="pinned fleet BGE"), site.prepare_text_map(tmp_path):
+ pytest.fail("different input window was approved as the common BGE map")
+ assert not any(call[0] == "stage" for call in calls)
From 090b1bba7d48cd4103ef2dd9c8de89c651db54c1 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 14 Sep 2026 18:53:16 -0700
Subject: [PATCH 04/11] chore: pin governed embedding runtime to CLAW dbac7dd
---
conf/embedding-runtime/README.md | 47 ++
conf/embedding-runtime/pyproject.toml | 17 +
conf/embedding-runtime/uv.lock | 915 ++++++++++++++++++++++
scripts/.vendored_canon_ref | 2 +-
scripts/embedding_pipeline.py | 495 ++++++++----
src/traitmech/graph_embedding_receipts.py | 23 +-
6 files changed, 1323 insertions(+), 176 deletions(-)
create mode 100644 conf/embedding-runtime/README.md
create mode 100644 conf/embedding-runtime/pyproject.toml
create mode 100644 conf/embedding-runtime/uv.lock
diff --git a/conf/embedding-runtime/README.md b/conf/embedding-runtime/README.md
new file mode 100644
index 0000000000..b5c9f2af25
--- /dev/null
+++ b/conf/embedding-runtime/README.md
@@ -0,0 +1,47 @@
+# Optional text-map runtime
+
+This governed Python 3.13 environment is for explicit local embedding and
+PaCMAP builds. Normal tests, record validation and Pages rendering do not
+install it. The lock pins numerical/model dependencies independently of a
+Mech's curation environment; the encoder and map receipts record actual
+installed library versions as well.
+
+From a Mech repository root, export current semantic input with its domain
+adapter, inspect it, and then explicitly run inference and projection:
+
+```bash
+uv run python scripts/text_map_inputs.py --output workspace/text-map-inputs.jsonl
+uv run python scripts/embedding_pipeline.py inspect --input workspace/text-map-inputs.jsonl
+uv run --locked --project conf/embedding-runtime python scripts/embedding_pipeline.py embed --input workspace/text-map-inputs.jsonl --cache workspace/text-map-vectors.sqlite --profile-output workspace/text-map-profile.json --device cpu
+uv run --locked --project conf/embedding-runtime python scripts/embedding_pipeline.py project --input workspace/text-map-inputs.jsonl --cache workspace/text-map-vectors.sqlite --profile workspace/text-map-profile.json --output data/text_map
+uv run python scripts/embedding_pipeline.py check --output data/text_map --input workspace/text-map-inputs.jsonl --cache workspace/text-map-vectors.sqlite
+```
+
+Run one small explicit `--limit` adapter canary first, with separate output and
+cache paths. Verify its vector count, finite coordinates, source receipt,
+rendered page and repeat-run cache reuse before a full build. A canary is not a
+complete-corpus artifact and cannot satisfy an enabled site's full-input check.
+
+The default display limit is 50,000 records selected deterministically. All
+input records must have a verified cache entry; the map reports omitted display
+records. No all-pairs similarity matrix is allocated.
+
+Model weights are downloaded only by the explicit `embed` command. A cached
+model can be used with `HF_HUB_OFFLINE=1 TRANSFORMERS_OFFLINE=1`. There are no
+provider API calls. Old unpinned vector caches are not assigned this profile.
+
+The existing site renderer stages a validated bundle at `text-map/` only after
+the repository enables it in `conf/text_map.yaml`. Its normal Python environment
+runs this verification without importing Torch, NumPy or PaCMAP. The build must
+fail if an enabled map is absent, stale or invalid. Preflight checks the exact
+BGE model/revision, 1024 dimensions and the fleet's 512-token window. The staging
+call passes the approved generation name through `expected_bundle`, rejecting
+a different pointer or altered generation before changing site files.
+Site deployment remains the
+publication boundary. A machine interruption during directory staging may
+leave `.text-map-recovery-*` beside the destination; preserve it for recovery.
+
+The runtime has been exercised on macOS Apple Silicon. Platform-specific model
+wheels may constrain where heavy builds run; the standard-library verifier is
+independent of those wheels. Cross-platform reproducibility is not implied by
+the lock or a fixed random seed.
diff --git a/conf/embedding-runtime/pyproject.toml b/conf/embedding-runtime/pyproject.toml
new file mode 100644
index 0000000000..6805290760
--- /dev/null
+++ b/conf/embedding-runtime/pyproject.toml
@@ -0,0 +1,17 @@
+[project]
+name = "mech-embedding-runtime"
+version = "1.0.0"
+requires-python = ">=3.13,<3.14"
+dependencies = [
+ "sentence-transformers==6.0.0",
+ "transformers==5.17.0",
+ "torch==2.14.0",
+ "pacmap==0.9.1",
+ "numpy==2.3.5",
+ "numba==0.63.1",
+ "scikit-learn==1.8.0",
+ "PyYAML==6.0.3",
+]
+
+[tool.uv]
+package = false
diff --git a/conf/embedding-runtime/uv.lock b/conf/embedding-runtime/uv.lock
new file mode 100644
index 0000000000..1e355a2923
--- /dev/null
+++ b/conf/embedding-runtime/uv.lock
@@ -0,0 +1,915 @@
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diff --git a/scripts/.vendored_canon_ref b/scripts/.vendored_canon_ref
index c6a87246d8..6aa11e9567 100644
--- a/scripts/.vendored_canon_ref
+++ b/scripts/.vendored_canon_ref
@@ -1 +1 @@
-c8b8f89ecf29574d7e24f6c65cfd925aefbdd007
+dbac7ddc8f1351493b90c6dc8850319769fdf620
diff --git a/scripts/embedding_pipeline.py b/scripts/embedding_pipeline.py
index 1a97ec400d..de15231f1d 100644
--- a/scripts/embedding_pipeline.py
+++ b/scripts/embedding_pipeline.py
@@ -4,6 +4,7 @@
Inspection and verification use the standard library. Model inference and
projection are explicit operations with separately installed dependencies.
"""
+
from __future__ import annotations
import argparse
@@ -30,8 +31,14 @@
MODEL_DIMENSION = 1024
MAX_SEQ_LENGTH = 512
REQUIRED_FIELDS = (
- "identifier", "label", "category", "page", "source_path", "text",
- "text_sha256", "adapter_version",
+ "identifier",
+ "label",
+ "category",
+ "page",
+ "source_path",
+ "text",
+ "text_sha256",
+ "adapter_version",
)
@@ -40,8 +47,9 @@ class ContractError(ValueError):
def canonical(value: object) -> bytes:
- return json.dumps(value, sort_keys=True, separators=(",", ":"),
- ensure_ascii=False, allow_nan=False).encode("utf-8")
+ return json.dumps(
+ value, sort_keys=True, separators=(",", ":"), ensure_ascii=False, allow_nan=False
+ ).encode("utf-8")
def digest_file(path: Path) -> str:
@@ -65,8 +73,11 @@ def local_link(value: str) -> bool:
parsed = urlsplit(value)
decoded = unquote(parsed.path)
return bool(value) and not (
- parsed.scheme or parsed.netloc or decoded.startswith("/")
- or "\\" in decoded or ".." in decoded.split("/")
+ parsed.scheme
+ or parsed.netloc
+ or decoded.startswith("/")
+ or "\\" in decoded
+ or ".." in decoded.split("/")
or any(ord(char) < 32 for char in unquote(value))
)
@@ -101,37 +112,53 @@ def inspect_inputs(path: Path) -> dict:
counts: dict[str, int] = {}
versions: set[str] = set()
count = 0
- with tempfile.TemporaryDirectory(prefix="embedding-inputs-") as tmp:
- with sqlite3.connect(str(Path(tmp) / "ids.sqlite")) as db:
- db.execute("CREATE TABLE ids (id TEXT PRIMARY KEY)")
- for record in records(path, raw_digest=raw):
- try:
- db.execute("INSERT INTO ids VALUES (?)", (record["identifier"],))
- except sqlite3.IntegrityError as exc:
- raise ContractError(f"duplicate identifier: {record['identifier']}") from exc
- framed_update(content, record["identifier"], record["text"])
- framed_update(display, canonical(record).decode())
- counts[record["category"]] = counts.get(record["category"], 0) + 1
- versions.add(record["adapter_version"])
- count += 1
+ with (
+ tempfile.TemporaryDirectory(prefix="embedding-inputs-") as tmp,
+ sqlite3.connect(str(Path(tmp) / "ids.sqlite")) as db,
+ ):
+ db.execute("CREATE TABLE ids (id TEXT PRIMARY KEY)")
+ for record in records(path, raw_digest=raw):
+ try:
+ db.execute("INSERT INTO ids VALUES (?)", (record["identifier"],))
+ except sqlite3.IntegrityError as exc:
+ raise ContractError(f"duplicate identifier: {record['identifier']}") from exc
+ framed_update(content, record["identifier"], record["text"])
+ framed_update(display, canonical(record).decode())
+ counts[record["category"]] = counts.get(record["category"], 0) + 1
+ versions.add(record["adapter_version"])
+ count += 1
if not count:
raise ContractError("adapter input contains no records")
if len(versions) != 1:
raise ContractError("adapter versions must agree within one input")
if digest_file(path) != raw.hexdigest():
raise ContractError("adapter input changed while inspecting; rerun")
- return {"count": count, "corpus_sha256": content.hexdigest(),
- "records_sha256": display.hexdigest(), "input_sha256": raw.hexdigest(),
- "categories": counts, "adapter_version": versions.pop()}
+ return {
+ "count": count,
+ "corpus_sha256": content.hexdigest(),
+ "records_sha256": display.hexdigest(),
+ "input_sha256": raw.hexdigest(),
+ "categories": counts,
+ "adapter_version": versions.pop(),
+ }
def encoder_profile(*, library_versions: dict | None = None, device: str = "cpu") -> dict:
- return {"format_version": FORMAT_VERSION, "model": MODEL,
- "revision": MODEL_REVISION, "dimension": MODEL_DIMENSION,
- "normalized": True, "dtype": "float32-le", "max_seq_length": MAX_SEQ_LENGTH,
- "pooling": "sentence-transformers-model", "truncation": "tail",
- "inference_device": device, "weight_dtype": "torch.float32",
- "query_instruction": None, "library_versions": library_versions or {}}
+ return {
+ "format_version": FORMAT_VERSION,
+ "model": MODEL,
+ "revision": MODEL_REVISION,
+ "dimension": MODEL_DIMENSION,
+ "normalized": True,
+ "dtype": "float32-le",
+ "max_seq_length": MAX_SEQ_LENGTH,
+ "pooling": "sentence-transformers-model",
+ "truncation": "tail",
+ "inference_device": device,
+ "weight_dtype": "torch.float32",
+ "query_instruction": None,
+ "library_versions": library_versions or {},
+ }
def validate_profile(profile: dict) -> None:
@@ -139,29 +166,43 @@ def validate_profile(profile: dict) -> None:
r"[0-9a-f]{40}", str(profile.get("revision", ""))
):
raise ContractError("encoder profile must identify an immutable model revision")
- if (type(profile.get("format_version")) is not int
- or profile["format_version"] != FORMAT_VERSION
- or not isinstance(profile.get("model"), str) or not profile["model"]
- or type(profile.get("dimension")) is not int or profile["dimension"] < 2
- or profile.get("normalized") is not True or profile.get("dtype") != "float32-le"
- or type(profile.get("max_seq_length")) is not int
- or profile["max_seq_length"] < 1
- or profile.get("pooling") != "sentence-transformers-model"
- or profile.get("truncation") != "tail"
- or not re.fullmatch(r"cpu|mps(?::\d+)?|cuda(?::\d+)?",
- str(profile.get("inference_device", "")))
- or profile.get("weight_dtype") != "torch.float32"
- or "query_instruction" not in profile or profile["query_instruction"] is not None):
+ if (
+ type(profile.get("format_version")) is not int
+ or profile["format_version"] != FORMAT_VERSION
+ or not isinstance(profile.get("model"), str)
+ or not profile["model"]
+ or type(profile.get("dimension")) is not int
+ or profile["dimension"] < 2
+ or profile.get("normalized") is not True
+ or profile.get("dtype") != "float32-le"
+ or type(profile.get("max_seq_length")) is not int
+ or profile["max_seq_length"] < 1
+ or profile.get("pooling") != "sentence-transformers-model"
+ or profile.get("truncation") != "tail"
+ or not re.fullmatch(
+ r"cpu|mps(?::\d+)?|cuda(?::\d+)?", str(profile.get("inference_device", ""))
+ )
+ or profile.get("weight_dtype") != "torch.float32"
+ or "query_instruction" not in profile
+ or profile["query_instruction"] is not None
+ ):
raise ContractError("invalid encoder profile")
validate_versions(profile.get("library_versions"), "encoder")
canonical(profile)
def validate_versions(value, context: str) -> None:
- if (not isinstance(value, dict) or not value
- or any(not isinstance(name, str) or not name.strip()
- or not isinstance(version, str) or not version.strip()
- for name, version in value.items())):
+ if (
+ not isinstance(value, dict)
+ or not value
+ or any(
+ not isinstance(name, str)
+ or not name.strip()
+ or not isinstance(version, str)
+ or not version.strip()
+ for name, version in value.items()
+ )
+ ):
raise ContractError(f"{context} requires recorded software versions")
@@ -221,8 +262,9 @@ def cached_vector(db, key: str, record: dict, dimension: int):
return blob
-def populate_cache(input_path: Path, cache_path: Path, profile: dict, encoder,
- *, batch_size: int = 64) -> dict:
+def populate_cache(
+ input_path: Path, cache_path: Path, profile: dict, encoder, *, batch_size: int = 64
+) -> dict:
"""Reuse exact records and atomically commit each verified encoded batch."""
if batch_size < 1:
raise ContractError("batch size must be positive")
@@ -243,12 +285,21 @@ def save_batch():
# Validate the WHOLE batch before starting its transaction.
blobs = [vector_bytes(vector, profile["dimension"]) for vector in vectors]
with db:
- db.execute("INSERT OR IGNORE INTO profiles VALUES (?, ?)",
- (key, canonical(profile).decode()))
+ db.execute(
+ "INSERT OR IGNORE INTO profiles VALUES (?, ?)",
+ (key, canonical(profile).decode()),
+ )
for record, blob in zip(pending, blobs, strict=True):
- db.execute("INSERT OR REPLACE INTO vectors VALUES (?, ?, ?, ?, ?)",
- (key, record["identifier"], record["text_sha256"], blob,
- hashlib.sha256(blob).hexdigest()))
+ db.execute(
+ "INSERT OR REPLACE INTO vectors VALUES (?, ?, ?, ?, ?)",
+ (
+ key,
+ record["identifier"],
+ record["text_sha256"],
+ blob,
+ hashlib.sha256(blob).hexdigest(),
+ ),
+ )
encoded_count += len(pending)
pending.clear()
@@ -273,21 +324,30 @@ def versions(names: tuple[str, ...]) -> dict[str, str]:
def local_encoder(device: str | None = None):
from sentence_transformers import SentenceTransformer
- model = SentenceTransformer(MODEL, revision=MODEL_REVISION,
- trust_remote_code=False, device=device)
+ model = SentenceTransformer(
+ MODEL, revision=MODEL_REVISION, trust_remote_code=False, device=device
+ )
model.max_seq_length = MAX_SEQ_LENGTH
model.tokenizer.truncation_side = "right"
- profile = encoder_profile(library_versions=versions(
- ("sentence-transformers", "transformers", "tokenizers", "torch", "numpy")
- ), device=str(model.device))
+ profile = encoder_profile(
+ library_versions=versions(
+ ("sentence-transformers", "transformers", "tokenizers", "torch", "numpy")
+ ),
+ device=str(model.device),
+ )
if str(next(model.parameters()).dtype) != profile["weight_dtype"]:
raise ContractError("model weights must use the declared float32 precision")
if model.get_sentence_embedding_dimension() != MODEL_DIMENSION:
raise ContractError("model returned an unexpected embedding dimension")
def encode(texts):
- return model.encode(texts, batch_size=len(texts), normalize_embeddings=True,
- convert_to_numpy=True, show_progress_bar=False)
+ return model.encode(
+ texts,
+ batch_size=len(texts),
+ normalize_embeddings=True,
+ convert_to_numpy=True,
+ show_progress_bar=False,
+ )
return profile, encode
@@ -295,11 +355,13 @@ def encode(texts):
def select_records(input_path: Path, maximum: int, seed: int) -> list[dict]:
if maximum < 3:
raise ContractError("map selection maximum must be at least three")
+
# Bottom-k hashes are deterministic, bounded and independent of input order.
def ranked():
for record in records(input_path):
key = hashlib.sha256(canonical([seed, record["identifier"]])).digest()
yield key, record["identifier"], record
+
return [record for _, _, record in heapq.nsmallest(maximum, ranked())]
@@ -317,10 +379,19 @@ def atomic_json(path: Path, value: dict) -> None:
temporary.unlink(missing_ok=True)
-def build_map(input_path: Path, cache_path: Path, output: Path, profile: dict,
- *, maximum: int = 50000, seed: int = 42, neighbors: int = 15,
- projector=None, projection_versions: dict | None = None,
- title: str = "Semantic text map") -> dict:
+def build_map(
+ input_path: Path,
+ cache_path: Path,
+ output: Path,
+ profile: dict,
+ *,
+ maximum: int = 50000,
+ seed: int = 42,
+ neighbors: int = 15,
+ projector=None,
+ projection_versions: dict | None = None,
+ title: str = "Semantic text map",
+) -> dict:
import numpy as np
inputs = inspect_inputs(input_path)
@@ -347,17 +418,29 @@ def build_map(input_path: Path, cache_path: Path, output: Path, profile: dict,
projection_details = {"implementation": "injected-projector", "effective_pairs": None}
if projector is None:
import pacmap
+
projection_versions = versions(("pacmap", "numpy", "numba", "scikit-learn", "faiss-cpu"))
- reducer = pacmap.PaCMAP(n_components=2, n_neighbors=neighbor_count,
- MN_ratio=0.5, FP_ratio=2.0, random_state=seed,
- distance="euclidean", lr=1.0, num_iters=(100, 100, 250),
- apply_pca=True, knn_backend="faiss")
+ reducer = pacmap.PaCMAP(
+ n_components=2,
+ n_neighbors=neighbor_count,
+ MN_ratio=0.5,
+ FP_ratio=2.0,
+ random_state=seed,
+ distance="euclidean",
+ lr=1.0,
+ num_iters=(100, 100, 250),
+ apply_pca=True,
+ knn_backend="faiss",
+ )
coordinates = reducer.fit_transform(matrix, init="pca")
neighbor_count = int(reducer.n_neighbors)
projection_details = {
"implementation": "pacmap.PaCMAP",
- "effective_pairs": {"neighbors": neighbor_count,
- "mid_near": int(reducer.n_MN), "further": int(reducer.n_FP)},
+ "effective_pairs": {
+ "neighbors": neighbor_count,
+ "mid_near": int(reducer.n_MN),
+ "further": int(reducer.n_FP),
+ },
}
else:
coordinates = projector(matrix, seed=seed, neighbors=neighbor_count)
@@ -371,54 +454,82 @@ def build_map(input_path: Path, cache_path: Path, output: Path, profile: dict,
try:
map_rows = []
for record, xy in zip(selected, coordinates, strict=True):
- map_rows.append({name: record[name] for name in REQUIRED_FIELDS if name != "text"}
- | {"x": float(xy[0]), "y": float(xy[1])})
+ map_rows.append(
+ {name: record[name] for name in REQUIRED_FIELDS if name != "text"}
+ | {"x": float(xy[0]), "y": float(xy[1])}
+ )
(stage / "points.json").write_bytes(canonical(map_rows) + b"\n")
- (stage / "index.html").write_text(render_html(title, map_rows, inputs["count"]),
- encoding="utf-8")
+ (stage / "index.html").write_text(
+ render_html(title, map_rows, inputs["count"]), encoding="utf-8"
+ )
manifest = {
- "format_version": FORMAT_VERSION, "representation": "semantic-text",
+ "format_version": FORMAT_VERSION,
+ "representation": "semantic-text",
"generated_at_utc": dt.datetime.now(dt.timezone.utc).isoformat(),
- "encoder": profile, "encoder_profile_sha256": key, "inputs": inputs,
- "projection": {"method": "pacmap", "dimensions": 2, "seed": seed,
- "requested_neighbors": neighbors, "neighbors": neighbor_count,
- "MN_ratio": 0.5, "FP_ratio": 2.0, "distance": "euclidean",
- "learning_rate": 1.0, "iterations": [100, 100, 250],
- "apply_pca": True, "knn_backend": "faiss",
- "initialization": "pca", "library_versions": projection_versions or {},
- **projection_details},
- "coverage": {"total": inputs["count"], "eligible": inputs["count"],
- "displayed": len(selected), "omitted": inputs["count"] - len(selected),
- "selection": "bottom-k-sha256(seed,identifier)", "maximum": maximum},
- "source_vectors": {"sha256": vector_checksum,
- "shape": list(matrix.shape), "dtype": "float32-le",
- "order": "points.json", "storage": "local-profile-bound-cache"},
- "files": {name: digest_file(stage / name)
- for name in ("points.json", "index.html")},
+ "encoder": profile,
+ "encoder_profile_sha256": key,
+ "inputs": inputs,
+ "projection": {
+ "method": "pacmap",
+ "dimensions": 2,
+ "seed": seed,
+ "requested_neighbors": neighbors,
+ "neighbors": neighbor_count,
+ "MN_ratio": 0.5,
+ "FP_ratio": 2.0,
+ "distance": "euclidean",
+ "learning_rate": 1.0,
+ "iterations": [100, 100, 250],
+ "apply_pca": True,
+ "knn_backend": "faiss",
+ "initialization": "pca",
+ "library_versions": projection_versions or {},
+ **projection_details,
+ },
+ "coverage": {
+ "total": inputs["count"],
+ "eligible": inputs["count"],
+ "displayed": len(selected),
+ "omitted": inputs["count"] - len(selected),
+ "selection": "bottom-k-sha256(seed,identifier)",
+ "maximum": maximum,
+ },
+ "source_vectors": {
+ "sha256": vector_checksum,
+ "shape": list(matrix.shape),
+ "dtype": "float32-le",
+ "order": "points.json",
+ "storage": "local-profile-bound-cache",
+ },
+ "files": {name: digest_file(stage / name) for name in ("points.json", "index.html")},
}
(stage / "manifest.json").write_bytes(canonical(manifest) + b"\n")
validate_bundle(stage, input_path=input_path)
bundle = hashlib.sha256(canonical(manifest)).hexdigest()
destination = output / bundle
os.rename(stage, destination)
- atomic_json(output / "current.json", {"bundle": bundle,
- "manifest_sha256": digest_file(destination / "manifest.json")})
+ atomic_json(
+ output / "current.json",
+ {"bundle": bundle, "manifest_sha256": digest_file(destination / "manifest.json")},
+ )
return {"bundle": str(destination), "coverage": manifest["coverage"]}
finally:
if stage.exists():
shutil.rmtree(stage)
-def validate_bundle(bundle: Path, *, input_path: Path | None = None,
- cache_path: Path | None = None) -> dict:
+def validate_bundle(
+ bundle: Path, *, input_path: Path | None = None, cache_path: Path | None = None
+) -> dict:
if bundle.is_symlink() or (bundle / "manifest.json").is_symlink():
raise ContractError("bundle and manifest must not be symbolic links")
manifest = json.loads((bundle / "manifest.json").read_text())
if not isinstance(manifest, dict) or manifest.get("format_version") != FORMAT_VERSION:
raise ContractError("unsupported map bundle format")
- if (manifest.get("representation") != "semantic-text"
- or any(not isinstance(manifest.get(name), dict) for name in
- ("encoder", "inputs", "files", "coverage", "projection", "source_vectors"))):
+ if manifest.get("representation") != "semantic-text" or any(
+ not isinstance(manifest.get(name), dict)
+ for name in ("encoder", "inputs", "files", "coverage", "projection", "source_vectors")
+ ):
raise ContractError("invalid map bundle metadata")
if manifest.get("encoder_profile_sha256") != profile_id(manifest["encoder"]):
raise ContractError("encoder profile checksum mismatch")
@@ -436,77 +547,103 @@ def validate_bundle(bundle: Path, *, input_path: Path | None = None,
raise ContractError("map points must contain at least three records")
coverage = manifest["coverage"]
projection = manifest["projection"]
- if (projection.get("method") != "pacmap" or projection.get("dimensions") != 2
- or type(projection.get("seed")) is not int
- or type(projection.get("neighbors")) is not int
- or not 1 <= projection["neighbors"] < len(points)
- or type(projection.get("requested_neighbors")) is not int
- or projection["requested_neighbors"] < 1
- or projection.get("initialization") != "pca"
- or projection.get("MN_ratio") != 0.5 or projection.get("FP_ratio") != 2.0
- or projection.get("distance") != "euclidean"
- or projection.get("learning_rate") != 1.0
- or projection.get("iterations") != [100, 100, 250]
- or projection.get("apply_pca") is not True
- or projection.get("knn_backend") != "faiss"):
+ if (
+ projection.get("method") != "pacmap"
+ or projection.get("dimensions") != 2
+ or type(projection.get("seed")) is not int
+ or type(projection.get("neighbors")) is not int
+ or not 1 <= projection["neighbors"] < len(points)
+ or type(projection.get("requested_neighbors")) is not int
+ or projection["requested_neighbors"] < 1
+ or projection.get("initialization") != "pca"
+ or projection.get("MN_ratio") != 0.5
+ or projection.get("FP_ratio") != 2.0
+ or projection.get("distance") != "euclidean"
+ or projection.get("learning_rate") != 1.0
+ or projection.get("iterations") != [100, 100, 250]
+ or projection.get("apply_pca") is not True
+ or projection.get("knn_backend") != "faiss"
+ ):
raise ContractError("invalid PaCMAP projection metadata")
validate_versions(projection.get("library_versions"), "projection")
if projection.get("implementation") == "pacmap.PaCMAP":
pairs = projection.get("effective_pairs")
- if (not isinstance(pairs, dict)
- or any(type(pairs.get(name)) is not int or not 0 <= pairs[name] < len(points)
- for name in ("neighbors", "mid_near", "further"))
- or pairs["neighbors"] != projection["neighbors"] or pairs["further"] < 1):
+ if (
+ not isinstance(pairs, dict)
+ or any(
+ type(pairs.get(name)) is not int or not 0 <= pairs[name] < len(points)
+ for name in ("neighbors", "mid_near", "further")
+ )
+ or pairs["neighbors"] != projection["neighbors"]
+ or pairs["further"] < 1
+ ):
raise ContractError("invalid effective PaCMAP pair counts")
elif projection.get("implementation") != "injected-projector":
raise ContractError("unidentified projection implementation")
- if (not isinstance(points, list) or len(points) < 3
- or any(type(coverage.get(name)) is not int for name in
- ("displayed", "eligible", "total", "omitted", "maximum"))
- or not 3 <= len(points) <= coverage["maximum"]
- or coverage["omitted"] < 0
- or coverage.get("selection") != "bottom-k-sha256(seed,identifier)"):
+ if (
+ not isinstance(points, list)
+ or len(points) < 3
+ or any(
+ type(coverage.get(name)) is not int
+ for name in ("displayed", "eligible", "total", "omitted", "maximum")
+ )
+ or not 3 <= len(points) <= coverage["maximum"]
+ or coverage["omitted"] < 0
+ or coverage.get("selection") != "bottom-k-sha256(seed,identifier)"
+ ):
raise ContractError("invalid map selection coverage")
source_vectors = manifest["source_vectors"]
- if (source_vectors.get("shape") != [len(points), manifest["encoder"]["dimension"]]
- or source_vectors.get("dtype") != "float32-le"
- or source_vectors.get("order") != "points.json"
- or source_vectors.get("storage") != "local-profile-bound-cache"
- or not re.fullmatch(r"[0-9a-f]{64}", str(source_vectors.get("sha256", "")))):
+ if (
+ source_vectors.get("shape") != [len(points), manifest["encoder"]["dimension"]]
+ or source_vectors.get("dtype") != "float32-le"
+ or source_vectors.get("order") != "points.json"
+ or source_vectors.get("storage") != "local-profile-bound-cache"
+ or not re.fullmatch(r"[0-9a-f]{64}", str(source_vectors.get("sha256", "")))
+ ):
raise ContractError("invalid source vector receipt")
for row in points:
- if (not isinstance(row, dict)
- or any(not isinstance(row.get(name), str) or not row[name].strip()
- for name in REQUIRED_FIELDS if name != "text")
- or not local_link(row["page"]) or not local_link(row["source_path"])
- or not re.fullmatch(r"[0-9a-f]{64}", row["text_sha256"])
- or not all(type(row.get(name)) in (int, float) and math.isfinite(row[name])
- for name in ("x", "y"))):
+ if (
+ not isinstance(row, dict)
+ or any(
+ not isinstance(row.get(name), str) or not row[name].strip()
+ for name in REQUIRED_FIELDS
+ if name != "text"
+ )
+ or not local_link(row["page"])
+ or not local_link(row["source_path"])
+ or not re.fullmatch(r"[0-9a-f]{64}", row["text_sha256"])
+ or not all(
+ type(row.get(name)) in (int, float) and math.isfinite(row[name])
+ for name in ("x", "y")
+ )
+ ):
raise ContractError("invalid map coordinate or record metadata")
- if (coverage["displayed"] != len(points)
- or coverage["total"] != manifest["inputs"]["count"]
- or coverage["eligible"] != coverage["total"]
- or coverage["omitted"] != coverage["total"] - len(points)
- or len({row["identifier"] for row in points}) != len(points)):
+ if (
+ coverage["displayed"] != len(points)
+ or coverage["total"] != manifest["inputs"]["count"]
+ or coverage["eligible"] != coverage["total"]
+ or coverage["omitted"] != coverage["total"] - len(points)
+ or len({row["identifier"] for row in points}) != len(points)
+ ):
raise ContractError("map coverage or identifiers are inconsistent")
if input_path is not None:
selected = select_records(input_path, coverage["maximum"], projection["seed"])
- expected = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"}
- for row in selected]
- observed = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"}
- for row in points]
+ expected = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"} for row in selected]
+ observed = [{key: row[key] for key in REQUIRED_FIELDS if key != "text"} for row in points]
if observed != expected:
raise ContractError("map records differ from the declared input selection")
if cache_path is not None:
digest = hashlib.sha256()
with cache_connection(cache_path) as db:
- profile_row = db.execute("SELECT json FROM profiles WHERE id=?",
- (manifest["encoder_profile_sha256"],)).fetchone()
+ profile_row = db.execute(
+ "SELECT json FROM profiles WHERE id=?", (manifest["encoder_profile_sha256"],)
+ ).fetchone()
if profile_row is None or profile_row[0] != canonical(manifest["encoder"]).decode():
raise ContractError("cache does not contain the exact encoder profile")
for row in points:
- blob = cached_vector(db, manifest["encoder_profile_sha256"], row,
- manifest["encoder"]["dimension"])
+ blob = cached_vector(
+ db, manifest["encoder_profile_sha256"], row, manifest["encoder"]["dimension"]
+ )
if blob is None:
raise ContractError("source vector is missing from the verified cache")
digest.update(blob)
@@ -525,8 +662,9 @@ def current_bundle(output: Path) -> Path:
return bundle
-def stage_map(output: Path, published_dir: Path, *, input_path: Path,
- expected_bundle: str | None = None) -> dict:
+def stage_map(
+ output: Path, published_dir: Path, *, input_path: Path, expected_bundle: str | None = None
+) -> dict:
"""Stage a verified map into a site build, restoring old files on exceptions.
The caller owns the repository/build lock. The site's later deployment is
@@ -543,11 +681,13 @@ def stage_map(output: Path, published_dir: Path, *, input_path: Path,
raise ContractError("map manifest differs from its immutable generation identity")
if manifest["projection"]["implementation"] != "pacmap.PaCMAP":
raise ContractError("site publication requires the actual PaCMAP implementation")
- if (published_dir.is_symlink()
- or (published_dir.exists() and not published_dir.is_dir())
- or source.resolve().is_relative_to(published_dir.resolve())
- or published_dir.resolve().is_relative_to(output.resolve())
- or input_path.resolve().is_relative_to(published_dir.resolve())):
+ if (
+ published_dir.is_symlink()
+ or (published_dir.exists() and not published_dir.is_dir())
+ or source.resolve().is_relative_to(published_dir.resolve())
+ or published_dir.resolve().is_relative_to(output.resolve())
+ or input_path.resolve().is_relative_to(published_dir.resolve())
+ ):
raise ContractError("unsafe map staging destination")
published_dir.parent.mkdir(parents=True, exist_ok=True)
temporary = Path(tempfile.mkdtemp(prefix=".text-map-stage-", dir=published_dir.parent))
@@ -582,7 +722,7 @@ def render_html(title: str, points: list[dict], total: int) -> str:
payload = canonical(points).decode().replace("<", "\\u003c").replace("&", "\\u0026")
# The site adapter publishes this directory at text-map/. Record pages are
# relative to the site root, one level above this self-contained page.
- return f'''
+ return f"""
{html.escape(title)}