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Having a file of for about 10k mapping identifiers how can I get the annotations of the proteins from Uniprot ? As it is not possible to do It manually

My mappings are contained in a .csv file They are from STRING database Example 9606.ENSP00000387699

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  • $\begingroup$ Can you please expand on this. What format are your ID's in (csv, excel, etc.)? And what is a mapping identifier, a uniprot accession, some other id? Lastly, Uniprot has a batch download system here, which may suit your needs. $\endgroup$ – emilliman5 May 26 '17 at 20:36
  • $\begingroup$ @emilliman5 I edited the question , they are contained in csv file , and they are stringdb external identifier $\endgroup$ – A M May 26 '17 at 21:20
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This problem is discussed here. Apparently STRING IDs are in KEGG format but these can be mapped on to Uniprot IDs using information downloadable from here. I guess that it is either the protein.aliases data or the mapping_files data that you would need. The first link provides a Python script to extract useful info from the downloaded data. These are big downloads so I haven't actually tried this out myself.

Presumably once you have the STRING→Uniprot conversion done you can query Uniprot with the output as a batch request.

Good luck!

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  • $\begingroup$ @AM please comment again when you know if it worked out. Or even write your own answer. $\endgroup$ – Alan Boyd May 27 '17 at 15:44
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UniProt's batch download system, suggested by Alan Boyd above, also allows you to directly map identifiers, e.g. STRING to UniProtKB, or Ensembl to UniProtKB: http://www.uniprot.org/uploadlists

Once you have your UniProtKB results, you can add or remove columns by clicking on "Columns", and once you are happy, you can download the results in tab-separated format (http://www.uniprot.org/help/customize).

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