Multiomics Clinical Trials Knowledge Provider (CTKP) Reference Ingest Guide
Source Information
InfoRes ID: infores:multiomics-clinicaltrials
Description: The Clinical Trials KP provides information on Clinical Trials, ultimately derived from researcher submissions to clinicaltrials.gov, via the Aggregate Analysis of Clinical Trials (AACT) database. Information on select trials includes the NCT Identifier of the trial, interventions used, diseases/conditions relevant to the trial, adverse events, etc.
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 |
|---|---|---|
| CTKP processed data | https://ctkp.ncats.io/ | Clinical trials data processed from AACT/clinicaltrials.gov |
Included Content
| File Name | Included Records | Fields Used |
|---|---|---|
| CTKP processed data | Clinical trial interventions and their associated diseases/conditions, plus treatment assertions for successful trials | NCT Identifier, interventions, diseases/conditions, adverse events, trial phases |
Target Information
Target InfoRes ID: infores:translator-ctkp-kgx
Edge Types
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:ChemicalEntity, biolink:MolecularMixture | 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 - based on a registered trial in ct.gov. | |
| biolink:ChemicalEntity, biolink:MolecularMixture | biolink:DiseaseOrPhenotypicFeature | knowledge_assertion | manual_agent | The treats predicate is used for interventions in Phase 4 trials that are performed for after successful demonstration of efficacy in treating a particular disease. |
Node Types
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:ChemicalEntity | Free text in AACT - no identifiers | |
| biolink:MolecularMixture | Free text in AACT - no identifiers | |
| biolink:SmallMolecule | Free text in AACT - no identifiers | |
| biolink:DiseaseOrPhenotypicFeature | Free text in AACT - no identifiers |
Provenance Information
Contributors: - Gwenlyn Glusman - code author, domain expertise - Matthew Brush - data modeling - Sierra Moxon - data modeling