[Chimera-users] meaning of evidence in PDB/UniProt Info

Luis M. Sánchez lmsp at uniovi.es
Tue Feb 19 10:01:52 PST 2013


On Mon, 18 Feb 2013 19:12:42 +0100, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Luis,
> The short answer is that I don't know -- that information is taken  
> directly from UniProt, so I would recommend trying to find out at their  
> website:
>
> <http://www.uniprot.org>
>
> You didn't say which UniProt entry, so I can't look at the same thing,  
> but if you search UniProt for that entry and display it, the "Sequence  
> annotation (features)" part is what Chimera gets.  Chimera gets it in  
> XML format.  You can see if the HTML (user-readable web page) format  
> gives something more informative.
>
> My guess is that the numbers might point to literature references or  
> refer to types of experiments.
>
> Sorry I don't know the answer,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Feb 18, 2013, at 6:59 AM, Luis M. Sánchez wrote:
>
>> In PDB/UniProt Info some features have a line with a numeric value for  
>> evidence. For example:
>> 	N-linked (GlcNAc...) (complex)
>> 	evidence=1 2 3 7 8 9 10 12
>> What do those numbers means?

I am not sure, but it seems that those evidence-associated numbers are  
evidence codes from the Open Biological and Biomedical Ontologies. There  
is a list in http://evidenceontology.googlecode.com/svn/trunk/eco.obo .  
There is also a lookup service in http://www.ebi.ac.uk/ontology-lookup/

-- 
Luis M. Sánchez


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