Annotation Conf. Call, March 11, 2014

Agenda

Present:
SGD:
MGI:
Dicty:
WB:
Pombase:
UCL:
EBI:
Berkeley:
Reactome:
TAIR:
RGD:
Zfin:

Hardware changes (Rama)

We moved many of the GO services (website, SVN, CVS etc) to a new virtual machine (@Stanford).

• GO SVN repository has been moved to this new machine. If you are having trouble checking your GAF or any other file into SVN, please send an email to GO-admin: go-admin@genome.stanford.edu or to go-helpdesk@geneontology.org.
• The GO wiki has also moved to the new machine, and the software has been upgraded. The GO wiki now requires that every page has at least one category. You will not be able to create a new page or successfully edit an existing page if it does not contain a category. Existing GO categories are listed at: http://wiki.geneontology.org/index.php/Special:Categories. More information about categories is available: http://www.mediawiki.org/wiki/Help:Categories.

Curation question

From MGI (Karen):

I am annotating some genes to the component term (colocalizes with)
"nuclear chromatin". I would like to indicate a specific kind of region
within nuclear chromatin, specificlly RNA polymerase III promoters, with a
SO term: "RNApol_III_promoter  ; SO:0000171"


I am already using the colocalizes qualifier since the experiment is a
ChIP, but I don't see what existing relationship I could use in order to
include a SO term to describe the specific types of regions within the
chromatin. 

E2/E3 terms

FYI- http://sourceforge.net/p/geneontology/ontology-requests/10635/

Differential Expression Experiments and IEP Evidence Code

From Kimberly VA (WB)

• Background: We recently had a WB user request that we annotate some genes based on the results of differential expression experiments, specifically microarrays and qRT-PCR.

• In the past, we've been very conservative about annotating to Biological Process terms from differential expression experiments, but this request has raised the issue again and we are re-visiting our annotation practices.

• In this particular case, these are experiments testing the transcriptional response to infection with pathogenic bacteria although we have a number of similar papers and experiments that examine the transcriptional response to various other stressors, such as oxidative stress, thermal stress, etc.

• The authors have asked that we annotate the statistically significantly expressed genes to 'defense response' and 'innate immune response'. Note that we had already annotated genes from this paper for which the authors performed follow-up RNAi experiments to try to assess functional significance.

• Many of these genes do not have other GO annotations and the gene products do not have domains that yield annotations based on sequence aimilarity.

• The paper in question was published in 2006, but using Textpresso to search the literature, we find that a number of these genes are considered biomarkers for infection response, even in the absence of functional data.

• We are considering annotating to a high-level response term, e.g. 'response to bacterium', but not to the more descriptive, and functionally suggestive, terms of 'defense response to bacterium' and 'innate immune response'.

• The issue of annotating based on differential expression experiments has come up before in GO. What are groups currently doing and why, and what, if any, feedback have groups gotten from users wrt these types of annotations? Does GO need to provide more annotation guidelines to curators for this area of annotation?

Previous discussion on this issue (written by Alex Diehl) link