Complete lighting of key knowledge beacons by Oct 2017

NCATS-Tangerine / translator-knowledge-beacon

NCATS Translator Knowledge Beacon Application Programming Interface plus Sample code

MIT License

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Complete lighting of key knowledge beacons by Oct 2017 #22

Open cmungall opened 6 years ago

cmungall commented 6 years ago

See https://github.com/NCATS-Tangerine/translator-knowledge-beacon/blob/develop/api/knowledge-beacon-list.yaml for master list

[x] SemMedDB - @RichardBruskiewich
[x] Wikidata (aka garbanzo) - @stuppie
[x] String-db.org wrapper - @lhannest <-- first add link to github repo in beacon-list.yaml
[ ] Red - @victorganic
[x] Monarch Biolink - @lhannest
[ ] Monarch Ontologies - @kshefchek
[ ] Bio2RDF - @micheldumontier
[ ] Pharos - @amalic
[ ] ISB Translator API - Blue team
[x] nDex Bio - @meera-gd

lhannest commented 6 years ago

@cmungall The string-db API does not support pagination, seemingly by design. They suggest that if you need to use large batches of the data then you should download it yourself:

As mentioned above, if you need to do large-scale analysis, please download full data set. Otherwise you may flood the string server with api requests, in particular if you run scripts in parallel. -https://string-db.org/cgi/help.pl

It's quite a lot to download, though: https://string-db.org/cgi/download.pl

stuppie commented 6 years ago

I'd think restricting the data to human, mouse, rat, yeast, c. elegans, drosphila, zebrafish is probably sufficient, if that is a way to overcome a practicality constraint