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AgBase and TIGR

Fiona McCarthy fmccarthy at
Tue Mar 28 08:37:09 PST 2006

Hi David,

My understanding is that TIGR primarily assigns GO Annotations based on
"inferred from electronic annotation" (IEA). This data is very useful for
getting a broad coverage of gene products but it is assigned
computationally and is not reviewed by curators. I believe that they have
several microbial genomes where they are assigning GO using literature
curation of experimental evidence. However TIGR have a lot of genomes and
they do not try to do manual curation of all genomes.

At AgBase we have been annotating proteins. We do not currently do IEA
annotations; the IEA annotations you see at AgBase are downloaded from
GOA. Instead we work first to get GO annotations inferred from structural
or sequence homology (ISS) , then if there is no sequence homology we will
manually curate the experimental data from published literature. Using ISS
allows us to get a 'breadth' of coverage and then by curating literature
we can get a much finer level of detail and find functions for proteins
that may not have homology to other annotated proteins.

AgBase understands the critical need for better microarray and EST
annotations. We have very recently been working with a researcher at the
University of Delaware to add GO annotations to ESTs and microarray data. 

We are certainly happy to take advice and suggestions from researchers
about how best to direct our annotations so that you can get the GO
annotations you require. All of what we do at AgBase is driven by our own
experimental needs and we certainly understand the frustrations involved
with trying to get a well annotated dataset.

Please don't hesitate to contact us if you have any further questions or
if we can be of assistance.
Fiona McCarthy

AgBase Biocurator
Department of Basic Sciences
Box 6100
MS 39762-6100 
Mississippi State University
Tel:   (+ 1) 662 325 5859
Fax:  (+ 1) 662 325 1031

----- Original Message -----

		Monday, March 27, 2006 1:24:22 PM
From:		Shane Burgess
Subject:	Re: Agbase vs. TIGR
To:		david clayton <dclayton at>
Fiona McCarthy

Thank you so much for your email. I could reply personally but I would
rather refer you to our resident expert Dr Fiona McCarthy. By doing so I
will ensure that you get the best possible information. I know that Fi is
out for the next couple of hours but she should reply to you and the group
very soon.


>Shane - I received your email request for endorsements of your NIH  
>chicken GO proposal, and I am happy to respond formally (will do so  
>shortly). Meantime, however, I wonder if you could clarify for me the  
>relationships between the annotations at AgBase and the ones on TIGR,  
>for example?  We've been using TIGR ( 
>tgi/T_index.cgi?species=g_gallus) as our primary reference for  
>annotating zebra finch ESTs. Is your resource equivalent,  
>complementary, different somehow?
>David F. Clayton, Ph.D.
>University of Illinois
>Professor of Cell & Developmental Biology, Neuroscience, and  
>Member, Beckman Institute and Institute for Genomic Biology
>Associate Director, School of Molecular & Cellular Biology
>phone:  217-244-3668
>fax: 503-213-6611
>mail: 601 S. Goodwin, B107 CLSL, Urbana IL 61801
>email: dclayton at
>Co-founder, Songbird Genome Organization:
>Director, Songbird Neurogenomics Initiative:  http:// 

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