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griffithlab / civic-meeting

Repo for advertising and organizing CIViC unconference/meeting activities
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Improve CIViC WikiData integration #35

Closed malachig closed 2 years ago

malachig commented 5 years ago

Elevator pitch to be lead by Greg Stupp (Su lab) @stuppie

stuppie commented 5 years ago

I was thinking this could be a task to incorporate structured information about drugs into civic. Right now, we've mapped all of the drug names returned by the civic API to wikidata QIDs. It would be better if civic returned pubchem IDs which we could retrieve QIDs for.

https://github.com/SuLab/scheduled-bots/blob/master/scheduled_bots/civic/drugs.tsv

stuppie commented 5 years ago

Another idea is to take advantage of the sitelinks and label translations in Wikidata to "internationalize" civic. i.e. make available translations of diseases, drugs, or gene names.

stuppie commented 5 years ago

Pitch deck: https://docs.google.com/presentation/d/1NCmLT7unu6vdhPEBrdYyo30qy10l9EB6gurL8LgiUug/edit?usp=sharing

acoffman commented 5 years ago

wikidata_mapping.tsv.zip

@stuppie, here's the list that @kkrysiak assembled

NuriaQueralt commented 5 years ago

NCIT - therapies: http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C20401

stuppie commented 5 years ago

New updated list current as of oct 15 2018, with pmids https://github.com/SuLab/scheduled-bots/blob/master/scheduled_bots/civic/drugname_pmid_oct_2018.csv

mmayers12 commented 5 years ago

I've combined the two spreadsheets here: https://docs.google.com/spreadsheets/d/1FL_Mim29q5Osloazj7rbNFoD4sdga247GE__qN1b4yc/edit?usp=sharing

stuppie commented 5 years ago

Some interesting drug issues: https://docs.google.com/presentation/d/1C483_2h2cz6A2O4LFvlgGjVXXf1elpNnGW8KQCXuUXM/edit?usp=sharing