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Disease Ontology

Access disease terms via the Disease Ontology API.

Overview

The Disease Ontology provides:

  • Disease Terms - Standardized disease vocabulary
  • Cross-References - Links to MeSH, UMLS, ICD
  • Hierarchy - Parent/child relationships

Quick Start

from biodbs.fetch import do_get_term, do_search

# Get term by DOID
term = do_get_term("DOID:162")  # Cancer

Disease Terms

Get Term

from biodbs.fetch import do_get_term, do_get_terms

# Single term
term = do_get_term("DOID:162")

# Multiple terms
terms = do_get_terms(["DOID:162", "DOID:9256"])

from biodbs.fetch import do_search

results = do_search("breast cancer")

Hierarchy

Parents

from biodbs.fetch import do_get_parents

parents = do_get_parents("DOID:1612")  # Breast cancer

Children

from biodbs.fetch import do_get_children

children = do_get_children("DOID:162")  # Cancer

Ancestors

from biodbs.fetch import do_get_ancestors

ancestors = do_get_ancestors("DOID:1612")

Descendants

from biodbs.fetch import do_get_descendants

descendants = do_get_descendants("DOID:162")

Cross-References

To MeSH

from biodbs.fetch import doid_to_mesh

mesh_ids = doid_to_mesh(["DOID:162", "DOID:1612"])

To UMLS

from biodbs.fetch import doid_to_umls

umls_ids = doid_to_umls(["DOID:162"])

To ICD-10

from biodbs.fetch import doid_to_icd10

icd_codes = doid_to_icd10(["DOID:162"])

Generic Mapping

from biodbs.fetch import do_xref_mapping

mapping = do_xref_mapping(
    ["DOID:162"],
    target_db="MESH"
)

Using the Fetcher Class

from biodbs.fetch.DiseaseOntology import DiseaseOntology_Fetcher

fetcher = DiseaseOntology_Fetcher()
term = fetcher.get_term("DOID:162")
  • Reactome - Find disease-related pathways. Reactome provides disease cross-references via reactome_get_diseases_doid().
  • UniProt - Get disease-associated proteins using UniProt disease annotations.
  • Knowledge Graphs - Build knowledge graphs from Disease Ontology data with build_disease_graph().