how to convert SwissProt or UniProt gene names to standard ID
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6.8 years ago
Learner ▴ 260

I know that based on web like david or others you can convert a list of gene with different symbols to IDs. for example DAVID https://david.ncifcrf.gov/content.jsp?file=conversion.html I am looking to find a way which I can do this in R or python

Lets say I have the following symbols, how can I convert them to standard IDs .

CONT_PPIA_HUMAN
DECOY1_53727
CONT_PRDX1_HUMAN
P09041
Q3TV35
CONT_CAS2_BOVIN
Q8BG13
Q3UI43
Q64475
CONT_ANXA5_HUMAN
P38060
R python • 3.3k views
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What do you mean by "standard ID"? There is not really any such thing. Can you give an example of an output ID?

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@Neilfws for example when I use DAVID, It does not recognise all but gives me an conversion like this from the list above. so, I don't know if I can search for different organisms

P38060  443585  
Q64475  427395  
Q3UI43  458616  
Q8BG13  464628  
P09041  481479  
Q3TV35  463168
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A search on Google seems to give no results for a few of your IDs in your original list e.g. CONT_PPIA_HUMAN, DECOY1_53727 and CONT_PRDX1_HUMAN. It's safe bet to think that the first and third IDs correspond to the genes PPIA and PRDX1 in human. You can use the Ensembl REST APIs (which is language agnostic and works with Python) to convert e.g. Q8BG13 into many standard xrefs or the BiomaRt to convert one standard ID (e.g. TrEMBL Q8BG13) to another standard ID (MGI symbol). Perhaps even better, you can use the EBI search through the EB-eye (REST) as in this case you don't need to know Q8BG13 is a TrEMBL in mouse, info you need to know beforehand for BiomaRt and the Ensembl REST APIs.

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There is a legitimate question as to whether DAVID is actually being actively looked after or the site is running in some sort of autopilot mode. Efforts to get a response from emails associated with DAVID have failed. Last update to DAVID was possibly done back in 2010.

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Possibly HGNC ID's.

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@genomax2 stay away from DAVID, means for all functions ? like pathway analysis etc ? do you have any idea on how to use the HGNC based on python ? however, it is not funny website because you must submit the list and wait for their email to be sent

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Possibly, long as you keep the possibility in mind that the data may not be recently updated. There have been past discussions about DAVID DAVID pathway analysis and Is the DAVID knowledgebase not updated any more? You can search biostars via google to get python based solutions for ID conversions.

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You can use HGNC's REST access for programmatic queries: http://www.genenames.org/help/rest-web-service-help

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6.8 years ago
Girolamo ▴ 140

DAVID is outdated i suggest to not use it. what about using http://www.uniprot.org/uploadlists/ to convert the gene id to the desired format

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