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Class: Protein

Protein product (UniProt model). Distinct from Gene entity to capture protein-specific properties: aggregation propensity, prion-like domains, subcellular localization.

URI: biolink:Protein

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

      Protein : aggregation_prone

      Protein : comment

      Protein : definition

      Protein : has_prion_like_domain

      Protein : hgnc_symbol

      Protein : id

      Protein : ingest_date

      Protein : is_obsolete

      Protein : label

      Protein : last_updated

      Protein : molecular_weight_kda

      Protein : protein_family

      Protein : protein_name

      Protein : source

      Protein : source_version

      Protein : subcellular_location

      Protein : synonym

      Protein : uniprot_id

      Protein : xref

Inheritance

Class Properties

Property Value
Class URI biolink:Protein

Slots

Name Cardinality and Range Description Inheritance
uniprot_id 1
UniprotIdentifier		 direct
protein_name 0..1
String		 Protein name (UniProt recommended name) direct
hgnc_symbol 0..1
String		 Gene name (cross-reference to Gene entity) direct
molecular_weight_kda 0..1
Float		 Molecular weight in kDa direct
protein_family 0..1
String		 Protein family classification (Pfam) direct
subcellular_location *
String		 Cellular compartment(s) where protein is localized (e direct
aggregation_prone 0..1
Boolean		 Known to form aggregates (TDP-43, SOD1, FUS) direct
has_prion_like_domain 0..1
Boolean		 Contains intrinsically disordered prion-like region 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
VariantProteinEffectAssociation has_protein range Protein
ProteinProteinInteractionAssociation protein_1 range Protein
ProteinProteinInteractionAssociation protein_2 range Protein
ProteinPathwayAssociation has_protein range Protein

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Protein
description: 'Protein product (UniProt model). Distinct from Gene entity to capture
  protein-specific properties: aggregation propensity, prion-like domains, subcellular
  localization.'
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  uniprot_id:
    name: uniprot_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: 'UniProtKB:'
    identifier: true
    domain_of:
    - Protein
    range: UniprotIdentifier
    required: true
  protein_name:
    name: protein_name
    description: Protein name (UniProt recommended name)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:name
    domain_of:
    - Protein
  hgnc_symbol:
    name: hgnc_symbol
    description: Gene name (cross-reference to Gene entity)
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Gene
    - Protein
  molecular_weight_kda:
    name: molecular_weight_kda
    description: Molecular weight in kDa
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Protein
    range: float
  protein_family:
    name: protein_family
    description: Protein family classification (Pfam)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Protein
  subcellular_location:
    name: subcellular_location
    description: Cellular compartment(s) where protein is localized (e.g. mitochondrion,
      nucleus, axon)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Protein
    multivalued: true
  aggregation_prone:
    name: aggregation_prone
    description: Known to form aggregates (TDP-43, SOD1, FUS)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Protein
    range: boolean
  has_prion_like_domain:
    name: has_prion_like_domain
    description: Contains intrinsically disordered prion-like region
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Protein
    range: boolean
class_uri: biolink:Protein

Induced

name: Protein
description: 'Protein product (UniProt model). Distinct from Gene entity to capture
  protein-specific properties: aggregation propensity, prion-like domains, subcellular
  localization.'
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  uniprot_id:
    name: uniprot_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: 'UniProtKB:'
    identifier: true
    alias: uniprot_id
    owner: Protein
    domain_of:
    - Protein
    range: UniprotIdentifier
    required: true
  protein_name:
    name: protein_name
    description: Protein name (UniProt recommended name)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:name
    alias: protein_name
    owner: Protein
    domain_of:
    - Protein
    range: string
  hgnc_symbol:
    name: hgnc_symbol
    description: Gene name (cross-reference to Gene entity)
    from_schema: https://cair2015.github.io/als-kg
    alias: hgnc_symbol
    owner: Protein
    domain_of:
    - Gene
    - Protein
    range: string
  molecular_weight_kda:
    name: molecular_weight_kda
    description: Molecular weight in kDa
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: molecular_weight_kda
    owner: Protein
    domain_of:
    - Protein
    range: float
  protein_family:
    name: protein_family
    description: Protein family classification (Pfam)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: protein_family
    owner: Protein
    domain_of:
    - Protein
    range: string
  subcellular_location:
    name: subcellular_location
    description: Cellular compartment(s) where protein is localized (e.g. mitochondrion,
      nucleus, axon)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: subcellular_location
    owner: Protein
    domain_of:
    - Protein
    range: string
    multivalued: true
  aggregation_prone:
    name: aggregation_prone
    description: Known to form aggregates (TDP-43, SOD1, FUS)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: aggregation_prone
    owner: Protein
    domain_of:
    - Protein
    range: boolean
  has_prion_like_domain:
    name: has_prion_like_domain
    description: Contains intrinsically disordered prion-like region
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: has_prion_like_domain
    owner: Protein
    domain_of:
    - Protein
    range: boolean
  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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    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: Protein
    domain_of:
    - NamedEntity
    - Association
    range: string
class_uri: biolink:Protein