Class: GoTerms

Gene Ontology terms with full metadata. GO provides structured vocabulary for gene products across biological process, molecular function, and cellular component namespaces.

TOTAL TERMS: 48,196 (39,354 non-obsolete)

NAMESPACE BREAKDOWN: - biological_process: 30,817 terms (64%) - molecular_function: 12,805 terms (27%) - cellular_component: 4,573 terms (9%)

USAGE: Use for looking up GO term details. For ancestor/descendant queries, use go_hierarchy_flat which has pre-computed transitive closure.

EXAMPLE QUERIES: - Find non-obsolete terms: WHERE is_obsolete = false - Terms by namespace: WHERE namespace = 'biological_process' - Search by name: WHERE name LIKE '%kinase%'

URI: https://w3id.org/kbase/nmdc_core/GoTerms

classDiagram class GoTerms click GoTerms href "../GoTerms/" GoTerms : definition GoTerms : go_id GoTerms : is_obsolete GoTerms : name GoTerms : namespace GoTerms --> "0..1" GoNamespace : namespace click GoNamespace href "../GoNamespace/" GoTerms : synonyms

Slots

Name	Cardinality and Range	Description	Inheritance
go_id	1 String	GO term ID in GO:NNNNNNN format	direct
name	0..1 String	Primary term name (may include "obsolete" prefix for deprecated terms)	direct
namespace	0..1 GoNamespace	GO namespace (aspect)	direct
definition	0..1 String	Full term definition with citations in double quotes	direct
synonyms	0..1 String	Semicolon-separated list of term synonyms	direct
is_obsolete	0..1 Boolean	Whether term is deprecated	direct

Identifier and Mapping Information

Annotations

property	value
source_table	go_terms

Schema Source

from schema: https://w3id.org/kbase/nmdc_core

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/nmdc_core/GoTerms
native	https://w3id.org/kbase/nmdc_core/GoTerms

LinkML Source

Direct

name: GoTerms
annotations:
  source_table:
    tag: source_table
    value: go_terms
description: 'Gene Ontology terms with full metadata. GO provides structured vocabulary
  for gene products across biological process, molecular function, and cellular component
  namespaces.

  TOTAL TERMS: 48,196 (39,354 non-obsolete)

  NAMESPACE BREAKDOWN: - biological_process: 30,817 terms (64%) - molecular_function:
  12,805 terms (27%) - cellular_component: 4,573 terms (9%)

  USAGE: Use for looking up GO term details. For ancestor/descendant queries, use
  go_hierarchy_flat which has pre-computed transitive closure.

  EXAMPLE QUERIES: - Find non-obsolete terms: WHERE is_obsolete = false - Terms by
  namespace: WHERE namespace = ''biological_process'' - Search by name: WHERE name
  LIKE ''%kinase%'''
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  go_id:
    name: go_id
    description: GO term ID in GO:NNNNNNN format. Seven-digit numeric identifier prefixed
      with "GO:".
    examples:
    - value: GO:0000001
      description: mitochondrion inheritance (biological_process)
    - value: GO:0000006
      description: high-affinity zinc transmembrane transporter activity (MF)
    - value: GO:0008150
      description: biological_process - root term
    - value: GO:0003674
      description: molecular_function - root term
    - value: GO:0005575
      description: cellular_component - root term
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    domain_of:
    - GoTerms
    - GoHierarchyFlat
    range: string
    required: true
    pattern: GO:\d{7}
  name:
    name: name
    description: Primary term name (may include "obsolete" prefix for deprecated terms)
    examples:
    - value: mitochondrion inheritance
      description: Active biological process term
    - value: high-affinity zinc transmembrane transporter activity
      description: Molecular function with specific substrate
    - value: obsolete mitochondrial genome maintenance
      description: Obsolete term - check is_obsolete flag
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  namespace:
    name: namespace
    description: GO namespace (aspect). Determines the type of information the term
      represents.
    examples:
    - value: biological_process
      description: 64% of terms - describes biological goals
    - value: molecular_function
      description: 27% of terms - molecular activities
    - value: cellular_component
      description: 9% of terms - cellular locations
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    range: GoNamespace
  definition:
    name: definition
    description: Full term definition with citations in double quotes. Provides precise
      meaning of the term with source references.
    examples:
    - value: '"The distribution of mitochondria, including the mitochondrial genome,
        into daughter cells after mitosis or meiosis, mediated by interactions between
        mitochondria and the cytoskeleton."'
      description: Definition for GO:0000001
    - value: '"OBSOLETE. Assists in the correct assembly of ribosomes..."'
      description: Obsolete terms have OBSOLETE prefix
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - GoTerms
    - KeggKoTerms
    - TraitUnified
    range: string
  synonyms:
    name: synonyms
    description: Semicolon-separated list of term synonyms. Includes exact, related,
      and narrow synonyms.
    examples:
    - value: mitochondrial inheritance
      description: Single synonym
    - value: high affinity zinc uptake transmembrane transporter activity; high-affinity
        zinc uptake transmembrane transporter activity
      description: Multiple synonyms separated by semicolon
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - GoTerms
    - EcTerms
    - TraitUnified
    range: string
  is_obsolete:
    name: is_obsolete
    description: Whether term is deprecated. About 18% of terms are obsolete. Check
      replacement terms in definition before using obsolete terms.
    examples:
    - value: 'False'
      description: Active term (82% of terms)
    - value: 'True'
      description: Obsolete (18%) - find replacement
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    - EcTerms
    range: boolean

Induced

name: GoTerms
annotations:
  source_table:
    tag: source_table
    value: go_terms
description: 'Gene Ontology terms with full metadata. GO provides structured vocabulary
  for gene products across biological process, molecular function, and cellular component
  namespaces.

  TOTAL TERMS: 48,196 (39,354 non-obsolete)

  NAMESPACE BREAKDOWN: - biological_process: 30,817 terms (64%) - molecular_function:
  12,805 terms (27%) - cellular_component: 4,573 terms (9%)

  USAGE: Use for looking up GO term details. For ancestor/descendant queries, use
  go_hierarchy_flat which has pre-computed transitive closure.

  EXAMPLE QUERIES: - Find non-obsolete terms: WHERE is_obsolete = false - Terms by
  namespace: WHERE namespace = ''biological_process'' - Search by name: WHERE name
  LIKE ''%kinase%'''
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  go_id:
    name: go_id
    description: GO term ID in GO:NNNNNNN format. Seven-digit numeric identifier prefixed
      with "GO:".
    examples:
    - value: GO:0000001
      description: mitochondrion inheritance (biological_process)
    - value: GO:0000006
      description: high-affinity zinc transmembrane transporter activity (MF)
    - value: GO:0008150
      description: biological_process - root term
    - value: GO:0003674
      description: molecular_function - root term
    - value: GO:0005575
      description: cellular_component - root term
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    alias: go_id
    owner: GoTerms
    domain_of:
    - GoTerms
    - GoHierarchyFlat
    range: string
    required: true
    pattern: GO:\d{7}
  name:
    name: name
    description: Primary term name (may include "obsolete" prefix for deprecated terms)
    examples:
    - value: mitochondrion inheritance
      description: Active biological process term
    - value: high-affinity zinc transmembrane transporter activity
      description: Molecular function with specific substrate
    - value: obsolete mitochondrial genome maintenance
      description: Obsolete term - check is_obsolete flag
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: name
    owner: GoTerms
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  namespace:
    name: namespace
    description: GO namespace (aspect). Determines the type of information the term
      represents.
    examples:
    - value: biological_process
      description: 64% of terms - describes biological goals
    - value: molecular_function
      description: 27% of terms - molecular activities
    - value: cellular_component
      description: 9% of terms - cellular locations
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: namespace
    owner: GoTerms
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    range: GoNamespace
  definition:
    name: definition
    description: Full term definition with citations in double quotes. Provides precise
      meaning of the term with source references.
    examples:
    - value: '"The distribution of mitochondria, including the mitochondrial genome,
        into daughter cells after mitosis or meiosis, mediated by interactions between
        mitochondria and the cytoskeleton."'
      description: Definition for GO:0000001
    - value: '"OBSOLETE. Assists in the correct assembly of ribosomes..."'
      description: Obsolete terms have OBSOLETE prefix
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: definition
    owner: GoTerms
    domain_of:
    - GoTerms
    - KeggKoTerms
    - TraitUnified
    range: string
  synonyms:
    name: synonyms
    description: Semicolon-separated list of term synonyms. Includes exact, related,
      and narrow synonyms.
    examples:
    - value: mitochondrial inheritance
      description: Single synonym
    - value: high affinity zinc uptake transmembrane transporter activity; high-affinity
        zinc uptake transmembrane transporter activity
      description: Multiple synonyms separated by semicolon
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: synonyms
    owner: GoTerms
    domain_of:
    - GoTerms
    - EcTerms
    - TraitUnified
    range: string
  is_obsolete:
    name: is_obsolete
    description: Whether term is deprecated. About 18% of terms are obsolete. Check
      replacement terms in definition before using obsolete terms.
    examples:
    - value: 'False'
      description: Active term (82% of terms)
    - value: 'True'
      description: Obsolete (18%) - find replacement
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: is_obsolete
    owner: GoTerms
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    - EcTerms
    range: boolean