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Documentation /Data & sources

Data sources

NosoGraph connects local records with upstream biomedical resources. This page is the authoritative source matrix: it describes each integration's role and current implementation state, not the scientific quality or clinical validity of the upstream resource.

Machine-readable registry: data/sources/registry.yaml, updated 2026-08-20.

Integration matrix

Source Domain Used for Integration state License/terms
MONDO Disease ontology IDs, hierarchy STABLE import CC-BY-4.0
HPO Phenotypes Comparison, annotations STABLE import HPO-custom
HPOA Phenotype associations Symptom harvest STABLE import HPO-custom
GO Function/process Pathways STABLE import CC-BY-4.0
Reactome Pathways Pathways STABLE import CC-BY-4.0
Uberon Anatomy Anatomy STABLE import CC-BY-4.0
Open Targets Target-disease Knowledge-graph scaffold, connector, sync slice BETA / sync EXPERIMENTAL Open Targets data license
PubMed Literature Evidence Workspace STABLE adapter NCBI terms
ClinicalTrials.gov Trials Trials, Evidence Workspace STABLE adapter ClinicalTrials.gov terms
GWAS Catalog Genetics Evidence Workspace BETA EBI terms
openFDA Labels Evidence Workspace BETA US public domain / FDA
ClinVar Variants Biomedical import BETA NCBI ClinVar
ChEMBL Bioactivity Live connector BETA EBI ChEMBL
PubChem Compounds Live connector BETA NCBI PubChem
GTEx Expression Expression / live connector BETA GTEx policy
UniProt Proteins Live connector BETA UniProt terms
bioRxiv/medRxiv Preprints Evidence Workspace EXPERIMENTAL Per-preprint

How to interpret maturity

STABLE, BETA, and EXPERIMENTAL describe NosoGraph's integration maturity. They do not rank upstream scientific quality, source prestige, reproducibility, or clinical validity. Live, fixture-backed, and experimental behavior depends on the code path; CI is often fixture-backed, and connectors are not continuously updated feeds by default.

Open Targets synchronization is an experimental vertical slice with a dry-run path. Source synchronization belongs in advanced workflows; it is not required for the first-time tutorial.

Terms and provenance

Apache-2.0 applies to NosoGraph source code. Each upstream resource retains its own license and terms; read the data licensing guide before redistributing imported data. Provenance may include source identity, snapshot/version, import stages, and fingerprints where the current adapter supports them. See data provenance.

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