diff --git a/docs/configuration/table.md b/docs/configuration/table.md index a52b738..4c87f12 100644 --- a/docs/configuration/table.md +++ b/docs/configuration/table.md @@ -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). |