meaning of evidence in PDB/UniProt Info
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? Thanks for a great program and best regards -- Luis M. Sánchez
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?
Thanks for a great program and best regards Luis M. Sánchez
On Mon, 18 Feb 2013 19:12:42 +0100, Elaine Meng <meng@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:
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
participants (2)
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Elaine Meng -
Luis M. Sánchez