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GO evidence code usage questions

Evelyn Camon camon at ebi.ac.uk
Thu May 19 03:10:47 PDT 2005


Hi

Most of the entrez gene go annotations I believe come from GOA at EBI
so I will attempt to answer your questions.

 >How can it be that 22 "traceable author statements" are not
 >associated with a PMID?
I don't see this in the GOA file but I will check it our further and get 
back to you.
Not sure if Entrez Gene are adding these? I will enquire.

 >2. Why are so many "nontraceable author statements" (nearly 75%)
  > associated with a PMID?  What is the association? 
 >Might I expect to find a statement justifying the annotation in the 
article?
Yes you should find a statement from the author in the papers listed
 inferring these NAS GO annotations.

 >Why are so many (nearly 1000) "inferred by electronic annotation"
 >annotations associated with a pubmed id?  What in an article would
 > trigger an IEA code rather than some other evidence code?

Ok I am looking at BRCA1 in Entrez gene and they show Nucleus GO annotation
with pubmed ID. In GOA no IEA GO annotations have a pubmed ID
See the same annotation in our QuickGO browser:
http://www.ebi.ac.uk/ego/GSearch?query=P38398+&mode=name_syno&ontology=all_ont
So I suspect that NCBI are adding pubmed IDS to IEA GO annotations created
from GOA-Human association file but we need to ask them directly.
 I will send them an e-mail and ask if this is the case.

Thankyou for alerting us.
I suggest you download GOA annotations for Human directly from
the GO Consortium or GOA home pages.
http://www.ebi.ac.uk/GOA

kind regards
Evelyn Camon
GOA Coordinator

Zhiyong Lu wrote:

> Dear GO friends,
>
> I'd like to share some data we collected about GO annotations with
> you, and ask a few related questions of the annotators. 
> The lab where I work is looking at the relationships between pubmed
> entries (mostly abstracts) and various kinds of annotations.  I looked
> at the human gene records in Entrez Gene (as of Jan 19, 2005) to see
> which had GO annotations that were associated with a specific PubMed
> ID.   Looking at that data by evidence code turned up some interesting
> phenomena, and I was wondering of any of the annotators (or anybody
> else) had any comments about them.
> Here's the data:
>
> code   w/PMID        %w      w/o      %w/o   total    IMP       
> 228      98.3%       4      1.7%     232      ND         68       
> 5.9%    1080     94.1%    1148     ISS       572      31.1%    
> 1269     68.9%    1841     TAS     17180      99.9%      22      
> 0.1%   17202    IC        104      96.3%       4      3.7%     
> 108      IGI        14     100.0%       0      0.0%      14       
> NR          8       0.4%    1858     99.6%    1866     IEP       
> 175     100.0%       0      0.0%     175      IEA       872       
> 2.2%   38373     97.8%   39245    NAS      4660      74.8%    1572     
> 25.2%    6232     IPI       402      99.3%       3      0.7%     
> 405      IDA      1959      99.8%       3      0.2%    1962     
> total   26242      37.3%   44188     62.7%   70430  
> w/PMID means the number (or %) of annotations with that evidence code
> which are associated with a specific pubmed id. "w/o" means not
> associated with a specific pubmed id.
>
> My questions are:
>
> 1. How can it be that 22 "traceable author statements" are not
>    associated with a PMID?
> 2. Why are so many "nontraceable author statements" (nearly 75%)
>    associated with a PMID?  What is the association?  Might I expect
>    to find a statement justifying the annotation in the article?
> 3. Why are so many (nearly 1000) "inferred by electronic annotation"
>    annotations associated with a pubmed id?  What in an article would
>    trigger an IEA code rather than some other evidence code?
> Thanks very much!
>
> Zhiyong Lu
> Center for Computational Pharmacology
> University of Colorado
>
>
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