Class: Gene

Human gene entity (Entrez/NCBI model). Separate from protein product to properly distinguish genotype from phenotype. Key ALS genes: C9orf72, SOD1, TARDBP, FUS, TBK1, NEK1, SQSTM1, VCP, OPTN.

URI: biolink:Gene

 classDiagram
    class Gene
    click Gene href "../Gene/"
      MolecularEntity <|-- Gene
        click MolecularEntity href "../MolecularEntity/"


      Gene <|-- TranscriptionFactor
        click TranscriptionFactor href "../TranscriptionFactor/"


      Gene : als_risk_tier

      Gene : chromosome

      Gene : comment

      Gene : definition

      Gene : ensembl_id

      Gene : genomic_pos_end

      Gene : genomic_pos_start

      Gene : hgnc_symbol

      Gene : id

      Gene : ingest_date

      Gene : is_obsolete

      Gene : label

      Gene : last_updated

      Gene : ncbi_gene_id

      Gene : source

      Gene : source_version

      Gene : synonym

      Gene : xref

Inheritance

NamedEntity
- OntologyClass
  - MolecularEntity
    - Gene
      - TranscriptionFactor

Class Properties

Property	Value
Class URI	biolink:Gene

Slots

Name	Cardinality and Range	Description	Inheritance
ncbi_gene_id	1 NcbiGeneIdentifier		direct
hgnc_symbol	0..1 String	Official HGNC gene symbol	direct
ensembl_id	0..1 String	Ensembl gene identifier	direct
chromosome	0..1 String	Cytogenetic location (e	direct
genomic_pos_start	0..1 Integer	GRCh38 start coordinate (1-based)	direct
genomic_pos_end	0..1 Integer	GRCh38 end coordinate	direct
als_risk_tier	0..1 String	Evidence tier for ALS association (ALSoD classification) - definitive, strong...	direct
source_version	0..1 String	Source database/ontology version	OntologyClass
ingest_date	0..1 String	When entity was imported into ALS-KG	OntologyClass
id	1 String	Persistent unique identifier (IRI)	NamedEntity
label	1 String	Preferred human-readable label	NamedEntity
definition	0..1 String	Formal textual definition	NamedEntity
synonym	0..1 String	Alternative names	NamedEntity
xref	0..1 String	Cross-references to external ontologies	NamedEntity
comment	0..1 String	Informal notes or comments	NamedEntity
is_obsolete	0..1 String	Deprecation flag	NamedEntity
source	0..1 String	Original source/database	NamedEntity
last_updated	0..1 String	Last modification timestamp	NamedEntity

Usages

used by	used in	type	used
GeneDiseaseAssociation	has_gene	range	Gene
TranscriptionFactorRegulationAssociation	target_gene	range	Gene
GeneExpressionAssociation	has_gene	range	Gene

Identifier and Mapping Information

Schema Source

from schema: https://cair2015.github.io/als-kg

Mappings

Mapping Type	Mapped Value
self	biolink:Gene
native	alskb:Gene

LinkML Source

Direct

name: Gene
description: 'Human gene entity (Entrez/NCBI model). Separate from protein product
  to properly distinguish genotype from phenotype. Key ALS genes: C9orf72, SOD1, TARDBP,
  FUS, TBK1, NEK1, SQSTM1, VCP, OPTN.'
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  ncbi_gene_id:
    name: ncbi_gene_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    domain_of:
    - Gene
    range: NcbiGeneIdentifier
    required: true
  hgnc_symbol:
    name: hgnc_symbol
    description: Official HGNC gene symbol
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
    - Protein
  ensembl_id:
    name: ensembl_id
    description: Ensembl gene identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
  chromosome:
    name: chromosome
    description: Cytogenetic location (e.g. 21q22.11 for SOD1)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
  genomic_pos_start:
    name: genomic_pos_start
    description: GRCh38 start coordinate (1-based)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
    range: integer
  genomic_pos_end:
    name: genomic_pos_end
    description: GRCh38 end coordinate
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
    range: integer
  als_risk_tier:
    name: als_risk_tier
    description: Evidence tier for ALS association (ALSoD classification) - definitive,
      strong, moderate, or candidate
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Gene
    range: string
class_uri: biolink:Gene

Induced

name: Gene
description: 'Human gene entity (Entrez/NCBI model). Separate from protein product
  to properly distinguish genotype from phenotype. Key ALS genes: C9orf72, SOD1, TARDBP,
  FUS, TBK1, NEK1, SQSTM1, VCP, OPTN.'
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  ncbi_gene_id:
    name: ncbi_gene_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    alias: ncbi_gene_id
    owner: Gene
    domain_of:
    - Gene
    range: NcbiGeneIdentifier
    required: true
  hgnc_symbol:
    name: hgnc_symbol
    description: Official HGNC gene symbol
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: hgnc_symbol
    owner: Gene
    domain_of:
    - Gene
    - Protein
    range: string
  ensembl_id:
    name: ensembl_id
    description: Ensembl gene identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: ensembl_id
    owner: Gene
    domain_of:
    - Gene
    range: string
  chromosome:
    name: chromosome
    description: Cytogenetic location (e.g. 21q22.11 for SOD1)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: chromosome
    owner: Gene
    domain_of:
    - Gene
    range: string
  genomic_pos_start:
    name: genomic_pos_start
    description: GRCh38 start coordinate (1-based)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: genomic_pos_start
    owner: Gene
    domain_of:
    - Gene
    range: integer
  genomic_pos_end:
    name: genomic_pos_end
    description: GRCh38 end coordinate
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: genomic_pos_end
    owner: Gene
    domain_of:
    - Gene
    range: integer
  als_risk_tier:
    name: als_risk_tier
    description: Evidence tier for ALS association (ALSoD classification) - definitive,
      strong, moderate, or candidate
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: als_risk_tier
    owner: Gene
    domain_of:
    - Gene
    range: string
  source_version:
    name: source_version
    description: Source database/ontology version
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:hasVersion
    alias: source_version
    owner: Gene
    domain_of:
    - OntologyClass
    - Association
    range: string
  ingest_date:
    name: ingest_date
    description: When entity was imported into ALS-KG
    from_schema: https://cair2015.github.io/als-kg
    alias: ingest_date
    owner: Gene
    domain_of:
    - OntologyClass
    - Relationship
    - Association
    range: string
  id:
    name: id
    description: Persistent unique identifier (IRI)
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: schema:identifier
    alias: id
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
    required: true
  label:
    name: label
    description: Preferred human-readable label
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:label
    alias: label
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
    required: true
  definition:
    name: definition
    description: Formal textual definition
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: IAO:0000115
    alias: definition
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
  synonym:
    name: synonym
    description: Alternative names
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasRelatedSynonym
    alias: synonym
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
  xref:
    name: xref
    description: Cross-references to external ontologies
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasDbXref
    alias: xref
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
  comment:
    name: comment
    description: Informal notes or comments
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:comment
    alias: comment
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
  is_obsolete:
    name: is_obsolete
    description: Deprecation flag
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: owl:deprecated
    ifabsent: 'false'
    alias: is_obsolete
    owner: Gene
    domain_of:
    - NamedEntity
    range: string
  source:
    name: source
    description: Original source/database
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:source
    alias: source
    owner: Gene
    domain_of:
    - NamedEntity
    - Relationship
    - Association
    range: string
  last_updated:
    name: last_updated
    description: Last modification timestamp
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:modified
    alias: last_updated
    owner: Gene
    domain_of:
    - NamedEntity
    - Association
    range: string
class_uri: biolink:Gene