Class: GeneProductProperties

The closed set of properties associated with an entity in a GPI row.

URI: go_standard_annotation_schema:GeneProductProperties

 classDiagram
    class GeneProductProperties
    click GeneProductProperties href "../GeneProductProperties/"
      GeneProductProperties : db_subset

      GeneProductProperties : go_annotation_complete

      GeneProductProperties : go_annotation_summary

      GeneProductProperties : uniprot_proteome

Slots

Name	Cardinality and Range	Description	Inheritance
db_subset	0..1 String	The status of a UniProtKB accession with respect to curator review	direct
uniprot_proteome	0..1 String	The UniProt proteome accession for the set of proteins that constitute an org...	direct
go_annotation_complete	0..1 Date	The date on which a curator determined that the set of GO annotations for an ...	direct
go_annotation_summary	0..1 String	A textual gene or gene-product description	direct

Usages

used by	used in	type	used
Entity	gene_product_properties	range	GeneProductProperties

Notes

Attributes are used instead of slots here because the names of the attributes are somewhat tightly coupled to the GPI file format. They should not be reused or modified in other contexts, as top-level slots might be.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/geneontology/go-standard-annotation-schema

Mappings

Mapping Type	Mapped Value
self	go_standard_annotation_schema:GeneProductProperties
native	go_standard_annotation_schema:GeneProductProperties

LinkML Source

Direct

name: GeneProductProperties
description: The closed set of properties associated with an entity in a GPI row.
notes:
- Attributes are used instead of slots here because the names of the attributes are
  somewhat tightly coupled to the GPI file format. They should not be reused or modified
  in other contexts, as top-level slots might be.
from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
attributes:
  db_subset:
    name: db_subset
    description: The status of a UniProtKB accession with respect to curator review.
    notes:
    - Using equals_string_in instead of an enum here to avoid issues with the specific
      capitalization and punctuation of the values.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    domain_of:
    - GeneProductProperties
    range: string
    required: false
    equals_string_in:
    - TrEMBL
    - Swiss-Prot
  uniprot_proteome:
    name: uniprot_proteome
    description: The UniProt proteome accession for the set of proteins that constitute
      an organism's proteome.
    notes:
    - The GPI grammar says this should be a prefixed identifier, but the example shows
      an unprefixed identifier. It is unclear what is actually used in practice. This
      is being modeled as an unprefixed identifier for now.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    domain_of:
    - GeneProductProperties
    range: string
    required: false
    pattern: ^UP[0-9]+$
  go_annotation_complete:
    name: go_annotation_complete
    description: The date on which a curator determined that the set of GO annotations
      for an entity was complete.
    notes:
    - The GPI grammar and spec say this can be a date or datetime. It is unclear what
      is actually used in practice. This is being modeled as a date to keep it in
      alignment with other date fields for now.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    domain_of:
    - GeneProductProperties
    range: date
    required: false
  go_annotation_summary:
    name: go_annotation_summary
    description: A textual gene or gene-product description.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    domain_of:
    - GeneProductProperties
    range: string
    required: false

Induced

name: GeneProductProperties
description: The closed set of properties associated with an entity in a GPI row.
notes:
- Attributes are used instead of slots here because the names of the attributes are
  somewhat tightly coupled to the GPI file format. They should not be reused or modified
  in other contexts, as top-level slots might be.
from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
attributes:
  db_subset:
    name: db_subset
    description: The status of a UniProtKB accession with respect to curator review.
    notes:
    - Using equals_string_in instead of an enum here to avoid issues with the specific
      capitalization and punctuation of the values.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: GeneProductProperties
    domain_of:
    - GeneProductProperties
    range: string
    required: false
    equals_string_in:
    - TrEMBL
    - Swiss-Prot
  uniprot_proteome:
    name: uniprot_proteome
    description: The UniProt proteome accession for the set of proteins that constitute
      an organism's proteome.
    notes:
    - The GPI grammar says this should be a prefixed identifier, but the example shows
      an unprefixed identifier. It is unclear what is actually used in practice. This
      is being modeled as an unprefixed identifier for now.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: GeneProductProperties
    domain_of:
    - GeneProductProperties
    range: string
    required: false
    pattern: ^UP[0-9]+$
  go_annotation_complete:
    name: go_annotation_complete
    description: The date on which a curator determined that the set of GO annotations
      for an entity was complete.
    notes:
    - The GPI grammar and spec say this can be a date or datetime. It is unclear what
      is actually used in practice. This is being modeled as a date to keep it in
      alignment with other date fields for now.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: GeneProductProperties
    domain_of:
    - GeneProductProperties
    range: date
    required: false
  go_annotation_summary:
    name: go_annotation_summary
    description: A textual gene or gene-product description.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: GeneProductProperties
    domain_of:
    - GeneProductProperties
    range: string
    required: false