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Class: TranscriptionFactor

Gene encoding a transcription factor (TF). Subclass of Gene, carries both :Gene and :TranscriptionFactor labels. Source: DoRothEA + ENCODE TF annotations.

URI: alskb:TranscriptionFactor

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

      TranscriptionFactor : als_risk_tier

      TranscriptionFactor : chromosome

      TranscriptionFactor : comment

      TranscriptionFactor : definition

      TranscriptionFactor : dorothea_confidence

      TranscriptionFactor : ensembl_id

      TranscriptionFactor : genomic_pos_end

      TranscriptionFactor : genomic_pos_start

      TranscriptionFactor : hgnc_symbol

      TranscriptionFactor : id

      TranscriptionFactor : ingest_date

      TranscriptionFactor : is_obsolete

      TranscriptionFactor : label

      TranscriptionFactor : last_updated

      TranscriptionFactor : ncbi_gene_id

      TranscriptionFactor : source

      TranscriptionFactor : source_version

      TranscriptionFactor : synonym

      TranscriptionFactor : tf_family

      TranscriptionFactor : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
tf_family 0..1
String		 Structural family (C2H2-ZF, bHLH, Homeodomain, etc direct
dorothea_confidence 0..1
String		 DoRothEA confidence level (A=high, D=low) direct
ncbi_gene_id 1
NcbiGeneIdentifier		 Gene
hgnc_symbol 0..1
String		 Official HGNC gene symbol Gene
ensembl_id 0..1
String		 Ensembl gene identifier Gene
chromosome 0..1
String		 Cytogenetic location (e Gene
genomic_pos_start 0..1
Integer		 GRCh38 start coordinate (1-based) Gene
genomic_pos_end 0..1
Integer		 GRCh38 end coordinate Gene
als_risk_tier 0..1
String		 Evidence tier for ALS association (ALSoD classification) - definitive, strong... Gene
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
TranscriptionFactorRegulationAssociation transcription_factor range TranscriptionFactor

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self alskb:TranscriptionFactor
native alskb:TranscriptionFactor

LinkML Source

Direct

name: TranscriptionFactor
description: 'Gene encoding a transcription factor (TF). Subclass of Gene, carries
  both :Gene and :TranscriptionFactor labels. Source: DoRothEA + ENCODE TF annotations.'
from_schema: https://cair2015.github.io/als-kg
is_a: Gene
attributes:
  tf_family:
    name: tf_family
    description: Structural family (C2H2-ZF, bHLH, Homeodomain, etc.)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - TranscriptionFactor
  dorothea_confidence:
    name: dorothea_confidence
    description: DoRothEA confidence level (A=high, D=low)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - TranscriptionFactor

Induced

name: TranscriptionFactor
description: 'Gene encoding a transcription factor (TF). Subclass of Gene, carries
  both :Gene and :TranscriptionFactor labels. Source: DoRothEA + ENCODE TF annotations.'
from_schema: https://cair2015.github.io/als-kg
is_a: Gene
attributes:
  tf_family:
    name: tf_family
    description: Structural family (C2H2-ZF, bHLH, Homeodomain, etc.)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: tf_family
    owner: TranscriptionFactor
    domain_of:
    - TranscriptionFactor
    range: string
  dorothea_confidence:
    name: dorothea_confidence
    description: DoRothEA confidence level (A=high, D=low)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: dorothea_confidence
    owner: TranscriptionFactor
    domain_of:
    - TranscriptionFactor
    range: string
  ncbi_gene_id:
    name: ncbi_gene_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    alias: ncbi_gene_id
    owner: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    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: TranscriptionFactor
    domain_of:
    - NamedEntity
    - Association
    range: string