Annotate Uniprotac With Taxonomic Lineage
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11.3 years ago

Hello!

I need your advice on how to annotate the protein (uniprotAC) with taxonomy lineage.

http://www.uniprot.org/uniprot/?query=$(QueryProperty)&format=tab&columns=$(columns)

where columns are

id,genes,domains,ec,database(PDB),organism,organism-id

Actually I got lost on the step to provide the correct name for taxonomy lineage column. Any suggestions?

Many thanks!

uniprot • 3.3k views
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Sorry, but I don't understand what you are trying to do. Could you add an example of what your input is, and what you expect as output?

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on the uniprot page there is a info: Taxonomic lineage Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

I want to download that data...

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You have to parse the xml or text file by a python or other program.

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I was looking for other solutions, parsing txt/xml will take a lot of time. I am currently using only mammals list - that can help, but it need an update.

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Sorry to burst your bubble, but parsing txt/xml is incredibly fast. Just use a library such as lxml or w/e. Or get it on json instead, and use a simplejson flavor.

Anyway, the easiest solution would probably be:

Get all IDs for your query using http://www.uniprot.org/uniprot/?query=$(QueryProperty)&format=tab&columns=$(columns)

Then download the respective text file: http://www.uniprot.org/uniprot/$(id).txt and extract the OC lines.

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Yes, I did that way. But I was looking for "online" solution, so I can check on the flight, esp. when the UNIPROT is updated regularly...thus I need update the list, also regularly.

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You might have better luck using the Uniprot API, though I've never used it, so I don't know if more options are available. If you will be doing it very often, I would drop a mail to the Uniprot helpdesk, asking for that piece of information to be added. Seeing as they release every four weeks, you might get lucky.

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9.7 years ago
txino • 0

Instead of suggesting a problem in the question you could answer what the guy is asking:

http://www.uniprot.org/uniprot/?query=accession:Q7DDU3&columns=id,lineage(ALL)&format=tab

I found the answer checking uniprot cookies

OCS

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