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biothings / mygene.info

MyGene.info: A BioThings API for gene annotations
http://mygene.info
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Pathway data updates #104

Closed colleenXu closed 2 years ago

colleenXu commented 3 years ago

According to @kevinxin90, the gene-pathway information is from http://consensuspathdb.org/ . However, this hasn't updated in ~2 years.

Maybe we can get the pathway data from somewhere else. For example, we can get reactome data fairly easily from https://reactome.org/download-data (including gene-pathway data).

newgene commented 3 years ago

@colleenXu Reactome data from mygene.info is up to date from Reactome directly. See "reactome" entry from:

http://mygene.info/v3/metadata

Other pathway data are indeed coming from CPDB

colleenXu commented 3 years ago

Good to know. The other resources have perhaps also updated within the past 2 years?

Edit: For Translator/other open-source projects, we may have to use resources with open licenses. I'm not sure what that means for the Metacyc/Humancyc/etc. pathways.

newgene commented 2 years ago

CPDB Pathway data in MyGene.info is already the latest version Release 35 (05.06.2021) (see "src.cpdb" from http://mygene.info/v3/metadata).

colleenXu commented 2 years ago

Great! I can see on the website that this was the first release in a while.

http://cpdb.molgen.mpg.de/CPDB

19.06.2021 ConsensusPathDB version 35 has been released. In addition to an updated content, this release features new functionality: enrichment and over-representation analysis of functional gene sets defined by transcription factor and miRNA regulatory interactions. 15.01.2019 ConsensusPathDB version 34 has been released.