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Class: DiseaseSubtype

Molecularly-defined disease subtype derived from clustering analysis (transcriptomics, proteomics, multi-omics). Represents cohort stratification. Links to Disease via is_a relationship; carries distinct clinical correlates.

URI: alskb:DiseaseSubtype

 classDiagram
    class DiseaseSubtype
    click DiseaseSubtype href "../DiseaseSubtype/"
      Disease <|-- DiseaseSubtype
        click Disease href "../Disease/"

      DiseaseSubtype : clinical_correlate

      DiseaseSubtype : cluster_id

      DiseaseSubtype : cluster_method

      DiseaseSubtype : cohort

      DiseaseSubtype : comment

      DiseaseSubtype : definition

      DiseaseSubtype : disease_type





        DiseaseSubtype --> "0..1" DiseaseTypeEnum : disease_type
        click DiseaseTypeEnum href "../DiseaseTypeEnum/"



      DiseaseSubtype : hpo_id

      DiseaseSubtype : icd10_code

      DiseaseSubtype : id

      DiseaseSubtype : ingest_date

      DiseaseSubtype : is_obsolete

      DiseaseSubtype : label

      DiseaseSubtype : last_updated

      DiseaseSubtype : median_survival_months

      DiseaseSubtype : mondo_id

      DiseaseSubtype : n_patients

      DiseaseSubtype : name

      DiseaseSubtype : omim_id

      DiseaseSubtype : onset_type





        DiseaseSubtype --> "0..1" OnsetTypeEnum : onset_type
        click OnsetTypeEnum href "../OnsetTypeEnum/"



      DiseaseSubtype : orphanet_id

      DiseaseSubtype : signature_genes

      DiseaseSubtype : source

      DiseaseSubtype : source_publication

      DiseaseSubtype : source_version

      DiseaseSubtype : subtype_id

      DiseaseSubtype : synonym

      DiseaseSubtype : umls_cui

      DiseaseSubtype : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subtype_id 0..1
String		 Custom subtype identifier direct
cluster_method 0..1
String		 Clustering approach (NMF, WGCNA, scRNA-seq, consensus) direct
cluster_id 0..1
Integer		 Cluster number from analysis direct
signature_genes *
String		 Top discriminative genes for subtype direct
n_patients 0..1
Integer		 Number of patients in subtype direct
cohort 0..1
String		 Source patient cohort (AnswerALS, NYGC, PRO-ACT) direct
clinical_correlate 0..1
String		 Associated clinical feature or phenotype direct
median_survival_months 0..1
Float		 Median survival from symptom onset direct
source_publication 0..1
String		 DOI or PMID reference direct
mondo_id 1
MondoIdentifier		 Disease, DiseaseOrPhenotype
name 0..1
String		 Disease name (preferred from MONDO) Disease
disease_type 0..1
DiseaseTypeEnum		 Disease
onset_type 0..1
OnsetTypeEnum		 Disease
umls_cui 0..1
String		 UMLS Concept Unique Identifier Disease
omim_id 0..1
String		 OMIM (Online Mendelian Inheritance in Man) ID Disease
orphanet_id 0..1
String		 Orphanet rare disease identifier Disease
icd10_code 0..1
String		 ICD-10-CM code for billing/clinical use Disease
hpo_id 0..1
HpoIdentifier		 HPO cross-reference DiseaseOrPhenotype
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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: DiseaseSubtype
description: Molecularly-defined disease subtype derived from clustering analysis
  (transcriptomics, proteomics, multi-omics). Represents cohort stratification. Links
  to Disease via is_a relationship; carries distinct clinical correlates.
from_schema: https://cair2015.github.io/als-kg
is_a: Disease
attributes:
  subtype_id:
    name: subtype_id
    description: Custom subtype identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
  cluster_method:
    name: cluster_method
    description: Clustering approach (NMF, WGCNA, scRNA-seq, consensus)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
  cluster_id:
    name: cluster_id
    description: Cluster number from analysis
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
    range: integer
  signature_genes:
    name: signature_genes
    description: Top discriminative genes for subtype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
    multivalued: true
  n_patients:
    name: n_patients
    description: Number of patients in subtype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
    range: integer
  cohort:
    name: cohort
    description: Source patient cohort (AnswerALS, NYGC, PRO-ACT)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
    - DiseasePhenotypeAssociation
  clinical_correlate:
    name: clinical_correlate
    description: Associated clinical feature or phenotype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
  median_survival_months:
    name: median_survival_months
    description: Median survival from symptom onset
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - DiseaseSubtype
    range: float
  source_publication:
    name: source_publication
    description: DOI or PMID reference
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: dcterms:bibliographicCitation
    domain_of:
    - DiseaseSubtype

Induced

name: DiseaseSubtype
description: Molecularly-defined disease subtype derived from clustering analysis
  (transcriptomics, proteomics, multi-omics). Represents cohort stratification. Links
  to Disease via is_a relationship; carries distinct clinical correlates.
from_schema: https://cair2015.github.io/als-kg
is_a: Disease
attributes:
  subtype_id:
    name: subtype_id
    description: Custom subtype identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: subtype_id
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: string
  cluster_method:
    name: cluster_method
    description: Clustering approach (NMF, WGCNA, scRNA-seq, consensus)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: cluster_method
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: string
  cluster_id:
    name: cluster_id
    description: Cluster number from analysis
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: cluster_id
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: integer
  signature_genes:
    name: signature_genes
    description: Top discriminative genes for subtype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: signature_genes
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: string
    multivalued: true
  n_patients:
    name: n_patients
    description: Number of patients in subtype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: n_patients
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: integer
  cohort:
    name: cohort
    description: Source patient cohort (AnswerALS, NYGC, PRO-ACT)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: cohort
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    - DiseasePhenotypeAssociation
    range: string
  clinical_correlate:
    name: clinical_correlate
    description: Associated clinical feature or phenotype
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: clinical_correlate
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: string
  median_survival_months:
    name: median_survival_months
    description: Median survival from symptom onset
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: median_survival_months
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: float
  source_publication:
    name: source_publication
    description: DOI or PMID reference
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: dcterms:bibliographicCitation
    alias: source_publication
    owner: DiseaseSubtype
    domain_of:
    - DiseaseSubtype
    range: string
  mondo_id:
    name: mondo_id
    from_schema: https://cair2015.github.io/als-kg
    identifier: true
    alias: mondo_id
    owner: DiseaseSubtype
    domain_of:
    - DiseaseOrPhenotype
    - Disease
    range: MondoIdentifier
    required: true
  name:
    name: name
    description: Disease name (preferred from MONDO)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: string
  disease_type:
    name: disease_type
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: disease_type
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: DiseaseTypeEnum
  onset_type:
    name: onset_type
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: onset_type
    owner: DiseaseSubtype
    domain_of:
    - Disease
    - DiseasePhenotypeAssociation
    range: OnsetTypeEnum
  umls_cui:
    name: umls_cui
    description: UMLS Concept Unique Identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: umls_cui
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: string
  omim_id:
    name: omim_id
    description: OMIM (Online Mendelian Inheritance in Man) ID
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: omim_id
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: string
  orphanet_id:
    name: orphanet_id
    description: Orphanet rare disease identifier
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: orphanet_id
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: string
  icd10_code:
    name: icd10_code
    description: ICD-10-CM code for billing/clinical use
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: icd10_code
    owner: DiseaseSubtype
    domain_of:
    - Disease
    range: string
  hpo_id:
    name: hpo_id
    description: HPO cross-reference
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: hpo_id
    owner: DiseaseSubtype
    domain_of:
    - DiseaseOrPhenotype
    - Phenotype
    range: HpoIdentifier
  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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    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: DiseaseSubtype
    domain_of:
    - NamedEntity
    - Association
    range: string