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add controlled vocab of missing values for tax_id
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cpauvert committed Jun 27, 2023
1 parent 410aeb2 commit 2d32175
Showing 1 changed file with 29 additions and 2 deletions.
31 changes: 29 additions & 2 deletions src/miiid_schema/schema/miiid_schema.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ prefixes:
EDAM_TOPIC: http://edamontology.org/topic_
NCIT: http://purl.obolibrary.org/obo/NCIT_
OBI: http://purl.obolibrary.org/obo/OBI_
GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_
default_prefix: miiid
default_range: string

Expand Down Expand Up @@ -76,9 +77,12 @@ slots:
description: Names of the microbial entities, with descriptions of any genetic manipulations performed.
tax_id:
required: true
range: NCBITaxId
any_of:
- range: NCBITaxId
- range: MissingValue
multivalued: true
description: NCBI Taxonomy identifiers at the relevant taxonomic level. Novel taxa lacking identifiers are denoted by N/A.
description: NCBI Taxonomy identifiers at the relevant taxonomic level.
comments: For novel taxa lacking identifiers, please use the controlled vocabulary NOT_PROVIDED.
evidence_type:
required: true
range: string
Expand Down Expand Up @@ -135,3 +139,26 @@ enums:
meaning: OBI:0000659
examples:
- value: co-occurrences drawn from analyses of abundances obtained from in situ or in vivo sampling

MissingValue:
description: >-
List of missing values reporting terms according based on the International
Nucleotide Sequence Database Collaboration (INSDC )
permissible_values:
NOT_APPLICABLE:
description: >-
The information is inappropriate to report, this can indicate that the
standard itself fails to model or represent the information appropriately
meaning: GENEPIO:0001619
NOT_COLLECTED:
description: >-
The information of an expected format was not given because it has not been collected
meaning: GENEPIO:0001620
NOT_PROVIDED:
description: >-
The information of an expected format was not given, a value may be given at the later stage
meaning: GENEPIO:0001668
RESTRICTED_ACCESS:
description: >-
The information exists but can not be released openly because of privacy concerns
meaning: GENEPIO:0001810

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