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NCATS-Tangerine / ncats-ingest

Management of ingestion of sources for NCATS-translator
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Pull genes annotated to FA related GO terms #24

Open mellybelly opened 7 years ago

mellybelly commented 7 years ago

We need to pull a series of data to inform which genes to look for variants in.

There is a google doc here for reference, https://docs.google.com/spreadsheets/d/1yX-5sfrC3vrahf4_k7-5rl4Oqzm853ollIMmUo1PTc0/edit#gid=1185309083

This relates to Set-8.

but essentially we need a gene set based upon GO associations with our primary genes (some may have alternate primary symbols): FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCD2, FANCI, UBE2T FANCD1 (BRCA2), FANCJ, FANCN, FANCO, FANCP, FANCQ, FANCR, FANCS, FANCV, FANCU FAAP100, FAAP24, FAAP20, FAAP16 (MHF1), FAAP10 (MHF2)

This is an overlapping set with what Mike Yu presented on our call from the data-driven ontology. Essentially, take all GO terms associated with our 21 genes above and their orthologs, and identify any other genes also enriched for these GO terms, and return their human orthologs.

@dnahotline will advise as needed

newgene commented 7 years ago

@mellybelly @cmungall You guys probably have the required gene annotations in your Dipper/Bridge system already, but in case needed (or partially needed), MyGene.info API should have included the latest gene-to-GO mappings and gene orthologs which can be queried for listed FA genes. The current data were updated on 03/12, and we do weekly update.

kshefchek commented 7 years ago

This notebook seems related: https://github.com/NCATS-Tangerine/cq-notebooks/tree/master/OrangeQ1.2_GO_Functional_Similarity

@cmungall do you have an opinion on a service that provides GO semantic similarity? I recall you mentioned we could add this to our owlsim3 instance or a test instance on the monarch VMs.

cmungall commented 7 years ago

It would probably be fastest to just do this via biolink/ontobio. I know it seems duplicative but it took a few minutes to implement jaccard. And it already has full access to GO.

kshefchek commented 7 years ago

@cmungall that works for me, I'll go that route.