Class: GoHierarchyFlat

Flattened GO hierarchy for efficient ancestor/descendant queries. Pre-computed transitive closure of is_a and part_of relationships.

USAGE: Essential for GO enrichment analysis and hierarchical queries. Use all_ancestors for finding parent terms, all_parents for direct parents. Depth indicates distance from root (root terms have depth 1).

EXAMPLE QUERIES: - Find all ancestors of a term: SELECT all_ancestors WHERE go_id = 'GO:0000001' - Find terms at specific depth: WHERE depth = 5 - Non-obsolete with ancestors: WHERE is_obsolete = false AND all_ancestors IS NOT NULL

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

classDiagram class GoHierarchyFlat click GoHierarchyFlat href "../GoHierarchyFlat/" GoHierarchyFlat : all_ancestors GoHierarchyFlat : all_parents GoHierarchyFlat : depth GoHierarchyFlat : go_id GoHierarchyFlat : is_obsolete GoHierarchyFlat : namespace GoHierarchyFlat --> "0..1" GoNamespace : namespace click GoNamespace href "../GoNamespace/"

Slots

Name	Cardinality and Range	Description	Inheritance
go_id	0..1 String	GO term this row describes	direct
namespace	0..1 GoNamespace	GO namespace of this term	direct
all_parents	0..1 String	Semicolon-separated direct parent GO IDs (immediate is_a/part_of parents)	direct
all_ancestors	0..1 String	Semicolon-separated all ancestor GO IDs (transitive closure)	direct
depth	0..1 Integer	Maximum depth from root (root terms have depth 1)	direct
is_obsolete	0..1 Boolean	Whether term is deprecated	direct

Identifier and Mapping Information

Annotations

property	value
source_table	go_hierarchy_flat

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GoHierarchyFlat
annotations:
  source_table:
    tag: source_table
    value: go_hierarchy_flat
description: 'Flattened GO hierarchy for efficient ancestor/descendant queries. Pre-computed
  transitive closure of is_a and part_of relationships.

  USAGE: Essential for GO enrichment analysis and hierarchical queries. Use all_ancestors
  for finding parent terms, all_parents for direct parents. Depth indicates distance
  from root (root terms have depth 1).

  EXAMPLE QUERIES: - Find all ancestors of a term: SELECT all_ancestors WHERE go_id
  = ''GO:0000001'' - Find terms at specific depth: WHERE depth = 5 - Non-obsolete
  with ancestors: WHERE is_obsolete = false AND all_ancestors IS NOT NULL'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  go_id:
    name: go_id
    description: GO term this row describes
    comments:
    - Foreign key to GoTerms.go_id
    examples:
    - value: GO:0000001
      description: mitochondrion inheritance
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - GoTerms
    - GoHierarchyFlat
    range: string
    pattern: GO:\d{7}
  namespace:
    name: namespace
    description: GO namespace of this term
    examples:
    - value: biological_process
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    range: GoNamespace
  all_parents:
    name: all_parents
    description: Semicolon-separated direct parent GO IDs (immediate is_a/part_of
      parents). Empty for root terms.
    examples:
    - value: GO:0048308;GO:0048311
      description: Two direct parents
    - value: GO:0008150
      description: Single parent (biological_process root)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - GoHierarchyFlat
    range: string
  all_ancestors:
    name: all_ancestors
    description: Semicolon-separated all ancestor GO IDs (transitive closure). Includes
      all terms reachable through is_a and part_of relations.
    examples:
    - value: GO:0006996;GO:0008150;GO:0009987;GO:0016043;GO:0048308
      description: Multiple ancestors from root to direct parents
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - GoHierarchyFlat
    range: string
  depth:
    name: depth
    description: Maximum depth from root (root terms have depth 1). Useful for filtering
      by specificity - higher depth = more specific term.
    examples:
    - value: '1'
      description: Root terms (biological_process, molecular_function)
    - value: '5'
      description: Mid-level terms
    - value: '10'
      description: Highly specific terms
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - GoHierarchyFlat
    range: integer
    minimum_value: 1
  is_obsolete:
    name: is_obsolete
    description: Whether term is deprecated
    examples:
    - value: 'False'
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    - EcTerms
    range: boolean

Induced

name: GoHierarchyFlat
annotations:
  source_table:
    tag: source_table
    value: go_hierarchy_flat
description: 'Flattened GO hierarchy for efficient ancestor/descendant queries. Pre-computed
  transitive closure of is_a and part_of relationships.

  USAGE: Essential for GO enrichment analysis and hierarchical queries. Use all_ancestors
  for finding parent terms, all_parents for direct parents. Depth indicates distance
  from root (root terms have depth 1).

  EXAMPLE QUERIES: - Find all ancestors of a term: SELECT all_ancestors WHERE go_id
  = ''GO:0000001'' - Find terms at specific depth: WHERE depth = 5 - Non-obsolete
  with ancestors: WHERE is_obsolete = false AND all_ancestors IS NOT NULL'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  go_id:
    name: go_id
    description: GO term this row describes
    comments:
    - Foreign key to GoTerms.go_id
    examples:
    - value: GO:0000001
      description: mitochondrion inheritance
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: go_id
    owner: GoHierarchyFlat
    domain_of:
    - GoTerms
    - GoHierarchyFlat
    range: string
    pattern: GO:\d{7}
  namespace:
    name: namespace
    description: GO namespace of this term
    examples:
    - value: biological_process
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: namespace
    owner: GoHierarchyFlat
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    range: GoNamespace
  all_parents:
    name: all_parents
    description: Semicolon-separated direct parent GO IDs (immediate is_a/part_of
      parents). Empty for root terms.
    examples:
    - value: GO:0048308;GO:0048311
      description: Two direct parents
    - value: GO:0008150
      description: Single parent (biological_process root)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: all_parents
    owner: GoHierarchyFlat
    domain_of:
    - GoHierarchyFlat
    range: string
  all_ancestors:
    name: all_ancestors
    description: Semicolon-separated all ancestor GO IDs (transitive closure). Includes
      all terms reachable through is_a and part_of relations.
    examples:
    - value: GO:0006996;GO:0008150;GO:0009987;GO:0016043;GO:0048308
      description: Multiple ancestors from root to direct parents
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: all_ancestors
    owner: GoHierarchyFlat
    domain_of:
    - GoHierarchyFlat
    range: string
  depth:
    name: depth
    description: Maximum depth from root (root terms have depth 1). Useful for filtering
      by specificity - higher depth = more specific term.
    examples:
    - value: '1'
      description: Root terms (biological_process, molecular_function)
    - value: '5'
      description: Mid-level terms
    - value: '10'
      description: Highly specific terms
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: depth
    owner: GoHierarchyFlat
    domain_of:
    - GoHierarchyFlat
    range: integer
    minimum_value: 1
  is_obsolete:
    name: is_obsolete
    description: Whether term is deprecated
    examples:
    - value: 'False'
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: is_obsolete
    owner: GoHierarchyFlat
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - GoHierarchyFlat
    - EcTerms
    range: boolean