Multiomics Clinical Trials Knowledge Provider (CTKP) Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:multiomics-clinicaltrials
Description: The Multiomics Clinical Trials Knowledge Provider (CTKP) is a Translator Knowledge Provider, developed by the Multiomics team, that provides computable knowledge about clinical trials. Its content is derived from researcher submissions to ClinicalTrials.gov, accessed via the Aggregate Analysis of ClinicalTrials.gov (AACT) database maintained by the Clinical Trials Transformation Initiative. CTKP addresses quality and computability issues in the underlying AACT/ClinicalTrials.gov data, and represents each trial's interventions, the diseases/conditions being studied, trial phase, and related metadata (e.g. NCT identifier, overall status, enrollment, primary purpose, age range). From this data CTKP asserts edges linking an intervention to the disease/condition it was tested in ('in clinical trials for'), and treatment assertions ('treats') derived from interventions studied in Phase 4 trials. The resulting knowledge graph is published in KGX format and is useful for Translator treatment and drug-repurposing query types.
Citations: - Generating Biomedical Knowledge Graphs from Knowledge Bases, Registries, and Multiomic Data (preprint): https://pmc.ncbi.nlm.nih.gov/articles/PMC11601480/
Data Access Locations: - Direct download links for the latest version are given in the manifest file: https://github.com/multiomicsKP/clinical_trials_kp/blob/main/manifest.json
Data Provision Mechanisms: file_download
Data Formats: kgx
Data Versioning and Releases: New versions are released weekly.
Ingest Information¶
Ingest Categories: translator_knowledge_creator
Utility: CTKP provides an improved version of clinical trials information that addresses quality and computability issues with sources it uses (AACT, ct.gov), as well as treatment assertions derived from this data. This type of knowledge is critical for many Translator query types.
Scope: Clinical trials information including interventions, diseases/conditions, and treatment assertions derived from clinical trial outcomes.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| clinical_trials_kg_nodes.jsonl.gz | https://db.systemsbiology.net/gestalt/KG/ | KGX node file for the CTKP knowledge graph (interventions, diseases/conditions, and clinical trial nodes). |
| clinical_trials_kg_edges.jsonl.gz | https://db.systemsbiology.net/gestalt/KG/ | KGX edge file for the CTKP knowledge graph (intervention-to-disease edges derived from AACT/ClinicalTrials.gov data). |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| clinical_trials_kg_edges.jsonl.gz | Clinical trial intervention-to-disease/condition edges, plus treatment assertions for interventions studied in Phase 4 trials. | subject, predicate, object, category, publications, qualifiers, max_research_phase, has_supporting_studies, sources |
Target Information¶
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule, biolink:Procedure | biolink:DiseaseOrPhenotypicFeature | knowledge_assertion | manual_agent | The 'in_clinical_trials_for' predicate reports that an intervention was tested in a clinical trial for a particular disease or condition - based on a registered trial in ClinicalTrials.gov, accessed via the AACT database. Each edge aggregates the supporting trials, with the maximum research phase reached across those trials reported as an edge property. | |
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule, biolink:Procedure | biolink:DiseaseOrPhenotypicFeature | knowledge_assertion | manual_agent | The 'treats' predicate is used for interventions studied in Phase 4 trials, which are performed after a treatment has already been approved and its efficacy demonstrated for a particular disease. The presence of a Phase 4 trial is used by CTKP as evidence that the intervention treats the disease/condition. |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:ChemicalEntity | Free text intervention names in AACT - CTKP maps these to identifiers where possible | |
| biolink:MolecularMixture | Free text intervention names in AACT - CTKP maps these to identifiers where possible | |
| biolink:SmallMolecule | Free text intervention names in AACT - CTKP maps these to identifiers where possible | |
| biolink:Procedure | Free text intervention names in AACT - CTKP maps these to identifiers where possible | Procedure nodes represent non-chemical interventions (e.g. surgical or behavioral procedures) studied in clinical trials. |
| biolink:DiseaseOrPhenotypicFeature | Free text condition names in AACT - CTKP maps these to identifiers where possible | |
| biolink:ClinicalTrial | CLINICALTRIALS | Clinical trial nodes (identified by NCT numbers under the CLINICALTRIALS prefix) are attached to edges as supporting studies via the has_supporting_studies edge property, and carry trial metadata such as phase, overall status, enrollment, primary purpose, and age range. |
Provenance Information¶
Contributors: - Gwenlyn Glusman - code author, domain expertise, data modeling - Matthew Brush - data modeling - Sierra Moxon - code, data modeling