diff --git a/CHANGELOG.md b/CHANGELOG.md index 9b910ee9..bad4fa27 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 See https://github.com/kbase/relation_engine_importers/blob/d8f87fb74e984cae1c94985b82349b13bc7f277e/docs/NCBI_taxa_sciname_lookup_issues_22_07.md - taxonomy_search_species_strain - taxonomy_search_species_strain_no_sort +- The NCBI and GTDB taxon collections were updated to include the new flag. ## [0.0.21] 2022-06-13 ### Added diff --git a/spec/collections/gtdb/gtdb_taxon.yaml b/spec/collections/gtdb/gtdb_taxon.yaml index 80d5bec6..bcb9477d 100644 --- a/spec/collections/gtdb/gtdb_taxon.yaml +++ b/spec/collections/gtdb/gtdb_taxon.yaml @@ -31,3 +31,8 @@ schema: type: string title: Taxonomic rank examples: [domain, phylum] + species_or_below: + type: boolean + title: Species or below + description: A flag that denotes the taxon is of rank species or a lower rank, e.g. + strain, forma, genome, subspecies, etc. diff --git a/spec/collections/ncbi/ncbi_taxon.yaml b/spec/collections/ncbi/ncbi_taxon.yaml index 18810eba..9d46d3fc 100644 --- a/spec/collections/ncbi/ncbi_taxon.yaml +++ b/spec/collections/ncbi/ncbi_taxon.yaml @@ -51,12 +51,22 @@ schema: type: string title: Taxonomic rank examples: ["Domain", "Phylum", "no rank"] + species_or_below: + type: boolean + title: Species or below flag + description: A flag that denotes the taxon is of rank species or a lower rank, e.g. + strain, forma, genome, subspecies, etc. strain: type: boolean - title: Strain flag - description: Whether this node corresponds to a strain. Strains are considered to be nodes + title: Strain flag (DEPRECATED) + description: DEPRECATED. See https://github.com/kbase/relation_engine_importers/blob/29cbf68b289335ec5c27201efba0058a501c6b74/docs/NCBI_taxa_sciname_lookup_issues_22_07.md + This field should not be used in any new code, but is left intact as it may be contained in + already loaded data. + Original description was + "Whether this node corresponds to a strain. Strains are considered to be nodes that have a rank of "no rank" and whose parents' rank is either species or subspecies or - where the parent's strain flag is true. + where the parent's strain flag is true." + ncbi_taxon_id: type: integer title: The NCBI taxon ID as a number