Add processors for drug indications and side effects #40
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cthoyt
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| print("Mapping out of UMLS") | ||
| print(tabulate(biomappings_from_umls.most_common())) | ||
| print("Mapping into UMLS") | ||
| print(tabulate(biomappings_to_umls.most_common())) |
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An alternative approach here could be to propagate these mappings into INDRA (see https://github.com/sorgerlab/indra/blob/master/indra/resources/biomappings.tsv) and add them to the BioOntology there, then the usual standardization procedure would take care of the necessary mappings. What do you think?
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Yeah I think this was ultimately unnecessary since I rely on the BioOntology standardization after. I guess I wonder if it's handling UMLS xrefs at the moment imported from biomappings. I thought that there were a lot of namespaces that got excluded from the importer, but after rereading https://github.com/sorgerlab/indra/blob/7ecb6be4603d54d55eaf7da8d3687294362907f5/indra/resources/update_resources.py#L699-L780, I think that's not the case.
| chemical.db_id, | ||
| indication.db_ns, | ||
| indication.db_id, | ||
| "causes", |
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Hmm... the fact that these are explicitly causal makes me wonder if this should be implemented as an INDRA source producing e.g., Activation statements. It might require more work but something worth discussing.
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I'm open to either. I thought for the time being, we were trying to keep a more molecular focus in INDRA, but the indirect causal nature of this information could also fit within INDRA statements. One thing I didn't include here is the side effect frequencies, maybe the fact that these exist on a spectrum might also be important to consider
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The test failure says is a new module missing from version control? |
Nice typo catch. I fixed it in 852eb40. |
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This is already covered by the harness
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Closes #39
This PR adds a processor over the ChEMBL database based on SQL queries executed by the
chembl_downloader. It standardizes the ChEMBL identifiers for chemicals and the MeSH identifiers for indications using the INDRA BioOntology. The code that does this is probably generally reusable so I gave it a its own utility function.This PR also adds the processor for SIDER side effects since it shares some of the standardization code from the ChEMBL processor