Open Question: What data sources should be included in MyGeneset? - Githubissues

biothings / mygeneset.info

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Open Question: What data sources should be included in MyGeneset? #9

Open dongbohu opened 3 years ago

dongbohu commented 3 years ago

The public non-user genesets in Tribe come from three data sources:

[x] GO: http://geneontology.org/
- plugin: https://github.com/ravila4/go
[x] KEGG: https://www.genome.jp/kegg/
- plugin: https://github.com/greenelab/kegg_geneset
[x] DO: https://sourceforge.net/projects/diseaseontology/
- plugin: https://github.com/greenelab/disease_ontology_geneset

Other possible data sources include:

[x] wikipathways
- plugin: https://github.com/ravila4/wikipathways
[x] MSigDB: https://www.gsea-msigdb.org/gsea/msigdb
[x] reactome: https://reactome.org/download/current/ReactomePathways.gmt.zip
[x] CTD (Comparative Toxicogenomics Database): https://ctdbase.org/
[x] SMPDB: http://cpdb.molgen.mpg.de/
[ ] CPDB: http://cpdb.molgen.mpg.de/
[ ] Biocarta: https://maayanlab.cloud/Harmonizome/dataset/Biocarta+Pathways
[ ] DSigDB: http://dsigdb.tanlab.org/DSigDBv1.0/collection.html
netpath
pid
Pfam: https://pfam.xfam.org/
InterPro: https://www.ebi.ac.uk/interpro/
whichgenes.org: http://www.whichgenes.org/api/sources
MATADOR: http://matador.embl.de/

Please feel free to add any others.

cgreene commented 3 years ago

I think we should go ahead and include the organisms for each of these that are already supported in mygene.info.

ravila4 commented 3 years ago

Just to add to the list: Pfam and InterPro for domain-related genesets?

dongbohu commented 3 years ago

@ravila4: I am not familiar with neither of the two genesets. Can you add their website URLs? Thanks.

ravila4 commented 3 years ago

Pfam: https://pfam.xfam.org/ InterPro: https://www.ebi.ac.uk/interpro/

dongbohu commented 3 years ago

Thank you @ravila4. I added them in the main thread.

dongbohu commented 3 years ago

Referecence: Data sources of whichgenes.org: http://www.whichgenes.org/api/sources

ravila4 commented 3 years ago

Reactome looks like an easy to parse dataset. The dataset can be found here: https://reactome.org/download/current/ReactomePathways.gmt.zip

ravila4 commented 3 years ago

Another possible data source is CTD (Comparative Toxicogenomics Database): https://ctdbase.org/

ravila4 commented 3 years ago

MATADOR: http://matador.embl.de/

ravila4 commented 3 years ago

Biocarta: https://maayanlab.cloud/Harmonizome/dataset/Biocarta+Pathways

ravila4 commented 3 years ago

DSigDB: http://dsigdb.tanlab.org/DSigDBv1.0/collection.html