Skip to content

fix: repair the broken taxon filtering link fragment in the table config reference #231

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
SkyeAv merged 1 commit into from
Oct 21, 2026
Merged

fix: repair the broken taxon filtering link fragment in the table config reference #231

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion docs/configuration/table.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ Defines how to extract and resolve entities.
| `method` | String | No | `"value"` (literal) or `"column"` (source column letters). Defaults to `"value"`. |
| `encoding` | String\|Int\|Float | Yes | Literal value or source column letters, depending on `method` |
| `taxon` | PositiveInt | No | NCBI Taxon ID for filtering (e.g., `9606` for human); defaults to `9606` (Homo sapiens), set null to disable |
| `taxon_from` | String | No | Per-row taxon scoping: name another resolved node column of the same statement (a CURIE-ranged qualifier key, or `subject`/`object`) whose resolved NCBITaxon CURIE scopes this column's entity resolution row by row, instead of the static `taxon`. The named column is resolved first; rows whose taxon cell is blank fall back to the `9606` default, and a non-null cell that does not resolve to an NCBITaxon CURIE fails the build (`taxon-from-not-ncbitaxon`). Mutually exclusive with an explicit `taxon` (`taxon-from-conflict`); an unknown, self-referencing, or cyclic target is rejected at config time (`taxon-from-unknown-column` / `taxon-from-self` / `taxon-from-cycle`). The source column itself usually wants `taxon: null` (see [Taxon Filtering](#taxonomic-filtering)) |
| `taxon_from` | String | No | Per-row taxon scoping: name another resolved node column of the same statement (a CURIE-ranged qualifier key, or `subject`/`object`) whose resolved NCBITaxon CURIE scopes this column's entity resolution row by row, instead of the static `taxon`. The named column is resolved first; rows whose taxon cell is blank fall back to the `9606` default, and a non-null cell that does not resolve to an NCBITaxon CURIE fails the build (`taxon-from-not-ncbitaxon`). Mutually exclusive with an explicit `taxon` (`taxon-from-conflict`); an unknown, self-referencing, or cyclic target is rejected at config time (`taxon-from-unknown-column` / `taxon-from-self` / `taxon-from-cycle`). The source column itself usually wants `taxon: null` (see [Taxonomic Filtering](#taxonomic-filtering)) |
| `prioritize` | List[String] | No | Preferred Biolink categories (must be valid `Categories` enum values such as `Gene`, `Protein`) |
| `avoid` | List[String] | No | Excluded Biolink categories (must be valid `Categories` enum values). Setting `avoid` makes the column an allow-list by complement: categories the `Categories` enum cannot name (fullmap-emitted Biolink mixins; see `biolink.CATEGORY_OVERRIDES`) are dropped as well, so the guard has no silent hole |
| `exclude_prefixes` | List[String] | No | CURIE namespace prefixes excluded during entity resolution: the prefix is the text before the first `:` of a resolved CURIE, and every candidate whose prefix is listed is dropped. Matching is exact and case-sensitive (`OMIM` drops `OMIM:100100` but not `OMIMPS:100` or `omim:100100`). Optional; defaults to null (no prefix filtering). See [Resolution Filters](#resolution-filters). |
Expand Down
Loading