Add Amsterdam 10-species gut invasion SynCom

[realmarcin]

Summary

• add CommunityMech:000382 for the Amsterdam ten-strain human gut DSMZ SynCom from PMID:41960919 / DOI:10.1128/msystems.00113-26
• curate taxonomy, conditioned-medium pairwise interactions, GLV co-culture prediction, E. coli and B. ovatus invasion outcomes, anaerobic YCFA growth metadata, and exact full-text snippets
• cache the PubMed/open-access PMC source text
• add append-only curation history and regenerate the committed docs browser/index/detail page

Validation

• PYTHONPATH=src tmp/linkml-env/bin/linkml-validate --schema src/communitymech/schema/communitymech.yaml --target-class MicrobialCommunity kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/evidence_snippet_audit.py kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml --list-mismatch --list-rendering --list-assembled --list-nocontent
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/validate_strict.py kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml --out tmp/strict-41960919.tsv --workers 1
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/validate_gtdb_coherence.py kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/validate_cross_repo_ids.py kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/validate_yaml_scalars.py kb/communities/Amsterdam_10Species_Gut_Invasion_SynCom.yaml references_cache/PMID_41960919.txt
• tmp/linkml-env/bin/linkml-validate --schema src/communitymech/schema/history.yaml --target-class HistoryRecord history/records/Amsterdam_10Species_Gut_Invasion_SynCom/2026-09-15T063606Z-codex-708f6927.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python -m communitymech.render
• PYTHONPATH=src tmp/linkml-env/bin/python src/communitymech/render_community_pages.py --kb /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/kb/communities --out-dir /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/tmp/community-pages-test --index-dir /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/tmp/community-index-test --force
• PYTHONPATH=src tmp/linkml-env/bin/python -m pytest tests/test_no_duplicate_yaml_keys.py tests/test_participating_taxa.py tests/test_snippet_audit_artefact_classes.py tests/test_reference_cache_resolution.py tests/test_published_pages_name_real_records.py -q
• git diff --cached --check

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[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 13 warning across 4 records with findings
Only error-severity findings fail the build.

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.