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Extracting annotation information from EntrezID

Now I have several EntrezIDs list (ex. 101171905, 101164258, 101173884, ...). By using this list, I'd like to add several information (gene name, gene symbol and description) to these lists. I know one of the way to extract these information is Biomart, but I would like to use NCBI database because EntrezID is NCBI ID. Can I use reutils or rentrez? I would be grateful if you could help me.

r gene
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updated by BBioinf • BBioinf • written by tomoya • tomoya

what about esummary -db gene -id YOUR_ID ? (The esummary is also commandline tool)

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written by massa.kassa.sc3na massa.kassa.sc3na

There is a typo in this comment. It should be -db gene.

A more complete solution would be something like this using Entrezdirect:

$ efetch -db gene -id "101173884" -format docsum | xtract -pattern DocumentSummary -element Name,Description
LOC101173884    dual specificity protein phosphatase 13
$ efetch -db gene -id "101171905" -format docsum | xtract -pattern DocumentSummary -element Name,Description
slc16a1 solute carrier family 16 member 1
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written by GenoMax GenoMax

Thank you for several suggestions and I successfully earn the annotation information by using this command.

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written by tomoya • tomoya

1 answer

If you can handle large tables, then these information are available on the NCBI ftp site. (Based on your example you are interested in fish genes)
ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Non-mammalian_vertebrates/All_Non-mammalian_vertebrates.gene_info.gz

Also the NCBI information and the ENSEMBL information are the same in most of the cases, so sometimes it is easier to use ENSEMBL due to the simpler tools.

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written by BBioinf • BBioinf

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