INDRA CoGEx (Context Graph Extension) is an automatically assembled biomedical knowledge graph which integrates causal mechanisms from INDRA with non-causal contextual relations including properties, ontology, and data.
| Knowledge source | Relation | Description |
|---|---|---|
| INDRA | indra_rel | The source regulates or interacts with the target according to an INDRA Statement. |
| INDRA Ontology | isa / partof | The source node is a subclass or part of the target node. |
| Gene Ontology | associated_with | The gene represented by the source is associated with the GO term represented by the target. |
| BGee | expressed_in | The gene represented by the source is expressed in the tissue/cell type represented by the target. |
| CCLE | mutated_in / copy_number_altered_in | The gene represented by the source is mutated or its copy number is altered in the cancer cell line represented by the target. |
| CCLE | sensitive_to | The cancer cell line represented by the source is sensitive to the drug represented by the target. |
| ClinicalTrials.gov | tested_in | The drug represented by the source is tested in the clinical trial represented by the target. |
| ClinicalTrials.gov | has_trial | The disease/condition represented by the source has a clinical trial represented by the target. |
| ChEMBL | has_indication | The chemical represented by the source has been studied for use against the indication represented by the target. |
| SIDER | has_side_effect | The chemical represented by the source has a side effect represented by the target. |
| Reactome | haspart | The pathway represented by the source node contains the gene represented by the target node. |
| WikiPathways | haspart | The pathway represented by the source node contains the gene represented by the target node. |
| Enzyme Codes | has_activity | The relation between a gene and its enzyme class(es). |
| Human Phenotype Ontology | has_phenotype | The disease represented by the source has a phenotype represented by the target. |
| Human Phenotype Ontology | phenotype_has_gene | The phenotype represented by the source has an associated gene represented by the target. |
| NIH reporter | has_publication | The NIH Reporter Project represented by the source has an associated publication represented by the target. |
| NIH reporter | has_clinical_trial | The NIH Reporter Project represented by the source has an associated clinical trial represented by the target. |
| NIH reporter | has_patent | The NIH Reporter Project represented by the source has an associated patent represented by the target. |
Install the indra_cogex package with:
$ git clone https://github.com/bgyori/indra_cogex
$ cd indra_cogex
$ pip install -e .Build the graph then bulk import into Neo4j with:
$ python -m indra_cogex.sources
$ sh import.shThe development of this project is funded under the DARPA Young Faculty Award (ARO grant W911NF2010255).