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biothings / mygene.info

MyGene.info: A BioThings API for gene annotations
http://mygene.info
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my gene.info R - homologous genes #86

Open lucolotto opened 4 years ago

lucolotto commented 4 years ago

Hi, I would like to use mygene with R to convert entrezid from one species (a non model species, taxid= 56716) to zebrafish (basically I need the homologous genes), but from the vignette is not clear if (and how) this can be done. Could you help me, please? Thanks

kevinxin90 commented 4 years ago

Hi @lucolotto, we do have homologene data for zebrafish, for example, http://mygene.info/v3/gene/100004372?fields=homologene, though I don't see taxid "56716" as part of the response. We retrieve homologene data from NCBI and PantherDB. If your specific data has to be retrieved from another data source, pls let us know and we can work on how to get that integrated. Thanks!

lucolotto commented 4 years ago

Hi @kevinxin90, thanks for your reply. I see that for zebrafish the homologene is working. The species I am trying to convert the ids is the fish Cottoperca gobio, recently annotated by both NCBI (https://www.ncbi.nlm.nih.gov/genome/?term=cottoperca+gobio) and ENSEMBL (http://www.ensembl.org/Cottoperca_gobio/Info/Index). I would like to find the ortholog genes between C. gobio and zebrafish (in the form of entrezids). On ENSEMBL (via biomaRt), the ortholog genes can be downloaded, but only in the form of ENSEMBL ids of the two species, while my gene ids in C. gobio are in the form of Entrezids. I understood that gene.info was taking information from both databases (i.e. NCBI and ENSEMBL) so I was wondering if it was possible to download the ortholog genes in the form of Entrezids via gene.info? But maybe my task would require another implementation? I don't know if I explained myself, if you have doubts, please let me know.
Thanks