Standard name to exact source

[Maria Alieva Krasheninnikova]

Hello,

I was wondering where can I find a database with the correspondance of the standard name of the pathways (for example for reactome) and the actual exact source name (so the number that reactome uses). See here.   GSEA gmt files provide: REACTOME_INTERLEUKIN_6_SIGNALING while I need R-HSA-1059683. Is there a database with all the names?

The reason is that I use GSEA for my analysis and now I want to make a network using the reactome database, but I can not link both with a correspondance between the names.

Cheers,

Maria

[Anthony Castanza]

Hi Maria,

If you go to the MSigDB Collections page, you can download the "json bundle" for each gene set collection. In that json file, each set has a "exactSource" key that has the Reactome pathway ID that you're looking for. Here's an example of an entry from that file:

  "REACTOME_2_LTR_CIRCLE_FORMATION" : {"systematicName":"M26996","pmid":"","exactSource":"R-HSA-164843","geneSymbols":["BANF1","HMGA1","LIG4","PSIP1","XRCC4","XRCC5","XRCC6"],"msigdbURL":"https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/REACTOME_2_LTR_CIRCLE_FORMATION","externalDetailsURL":["https://reactome.org/PathwayBrowser/#/R-HSA-164843","https://www.reactome.org/content/detail/R-HSA-164843"],"filteredBySimilarity":[],"externalNamesForSimilarTerms":[],"collection":"C2:CP:REACTOME"},

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[David Eby]

Hi Maria,

If you want to do this in bulk, the Collections page has a JSON bundle for the full Reactome collection (similarly for the Mouse collection).  Likewise for such collections as Gene Ontology, Human Phenotype Ontology, etc.

There is also a JSON bundle for the full MSigDB (one each for Human and Mouse), and even more extensive metadata in XML formatted files.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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[Maria Alieva Krasheninnikova]

Thanks! That's exactly what I was looking for.