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Update collection specs for species_or_below field #165

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Merged
MrCreosote merged 1 commit into from
Aug 5, 2022
Merged

Update collection specs for species_or_below field #165

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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5 changes: 5 additions & 0 deletions spec/collections/gtdb/gtdb_taxon.yaml
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Expand Up @@ -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.
16 changes: 13 additions & 3 deletions spec/collections/ncbi/ncbi_taxon.yaml
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Expand Up @@ -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
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@MrCreosote MrCreosote Aug 5, 2022

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I wanted to use a colon here but that makes Original description was a jsonschema field

"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
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