https://github.com/gyorilab/indra_cogex
INDRA Context Graph Extension
https://github.com/gyorilab/indra_cogex
Last synced: 23 days ago
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INDRA Context Graph Extension
- Host: GitHub
- URL: https://github.com/gyorilab/indra_cogex
- Owner: gyorilab
- License: bsd-2-clause
- Created: 2021-04-06T18:31:47.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-04-24T23:15:06.000Z (29 days ago)
- Last Synced: 2025-04-30T14:27:22.203Z (23 days ago)
- Language: Jupyter Notebook
- Size: 35 MB
- Stars: 10
- Watchers: 2
- Forks: 13
- Open Issues: 28
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
INDRA CoGEx
===========
[](https://github.com/bgyori/indra_cogex/actions/workflows/tests.yml)
[](https://github.com/psf/black)
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.
## Content
| Knowledge source | Relation | Description |
|---------------------------------------------------------------------|-------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|
| [INDRA](https://indra.bio) | indra_rel | The source regulates or interacts with the target according to an INDRA Statement. |
| [INDRA Ontology](https://indra.bio) | isa / partof | The source node is a subclass or part of the target node. |
| [Gene Ontology](http://geneontology.org/) | associated_with | The gene represented by the source is associated with the GO term represented by the target. |
| [BGee](https://bgee.org/) | expressed_in | The gene represented by the source is expressed in the tissue/cell type represented by the target. |
| [CCLE](https://www.cbioportal.org/study/summary?id=ccle_broad_2019) | 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](https://www.cbioportal.org/study/summary?id=ccle_broad_2019) | sensitive_to | The cancer cell line represented by the source is sensitive to the drug represented by the target. |
| [ClinicalTrials.gov](https://clinicaltrials.gov/) | tested_in | The drug represented by the source is tested in the clinical trial represented by the target. |
| [ClinicalTrials.gov](https://clinicaltrials.gov/) | has_trial | The disease/condition represented by the source has a clinical trial represented by the target. |
| [ChEMBL](https://www.ebi.ac.uk/chembl/) | has_indication | The chemical represented by the source has been studied for use against the indication represented by the target. |
| [SIDER](http://sideeffects.embl.de/) | has_side_effect | The chemical represented by the source has a side effect represented by the target. |
| [Reactome](https://reactome.org/) | haspart | The pathway represented by the source node contains the gene represented by the target node. |
| [WikiPathways](https://www.wikipathways.org/) | haspart | The pathway represented by the source node contains the gene represented by the target node. |
| [Enzyme Codes](https://www.ebi.ac.uk/intenz/) | has_activity | The relation between a gene and its enzyme class(es). |
| [Human Phenotype Ontology](https://hpo.jax.org/app/) | has_phenotype | The disease represented by the source has a phenotype represented by the target. |
| [Human Phenotype Ontology](https://hpo.jax.org/app/) | phenotype_has_gene | The phenotype represented by the source has an associated gene represented by the target. |
| [NIH reporter](https://reporter.nih.gov) | has_publication | The NIH Reporter Project represented by the source has an associated publication represented by the target. |
| [NIH reporter](https://reporter.nih.gov) | has_clinical_trial | The NIH Reporter Project represented by the source has an associated clinical trial represented by the target. |
| [NIH reporter](https://reporter.nih.gov) | has_patent | The NIH Reporter Project represented by the source has an associated patent represented by the target. |
| [DisGeNet](https://www.disgenet.org/) | gene_disease_association | Literature curated associations between genes and diseases |
| [DisGeNet](https://www.disgenet.org/) | variant_disease_association | Literature curated associations between variants (e.g., identified by dbSNP) and diseases |
| [DisGeNet](https://www.disgenet.org/) | variant_gene_association | Literature curated associations between genes and variants (e.g., from dbSNP) |
| [GWAS](https://www.ebi.ac.uk/gwas/home) | variant_phenotype_association | Large literature curated collection of human genome-wide association studies. Phenotype and variant associations (e.g., from dbSNP) are extracted. |
| [PubMed](https://ncbi.nlm.nih.gov/) | annotated_with | The publiction represented by the source is annotated with the MeSH entity represented by the target. |
| [PubMed](https://ncbi.nlm.nih.gov/) | has_citation | The Evidence represented by the source is supported by the publication represented by the target. |
| [PubMed](https://ncbi.nlm.nih.gov/) | published_in | The publication represented by the source is published in the journal represented by the target. |
| [CellMarker](http://xteam.xbio.top/) | has_marker | The cell type represented by the source node has the gene marker represented by the target node. |
| [InterPro](https://www.ebi.ac.uk/interpro/) | has_domain | The gene represented by the source node has a protein domain represented by the target node. |
| [DepMap](https://depmap.org/portal/) | codependent_with | The gene represented by the source node is codependent with the gene represented by the target node in cancer cell lines. |
## Installation
Install the `indra_cogex` package with:
```shell
git clone https://github.com/bgyori/indra_cogex
cd indra_cogex
pip install -e .
```
## Build
Build the graph then bulk import into Neo4j with:
```shell
python -m indra_cogex.sources
sh import.sh
```
## Funding
The development of this project is funded under the DARPA Young Faculty Award
(ARO grant W911NF2010255).