Annotation Conf. Call, February 25, 2014: Difference between revisions

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two new molecular functions describing the activities of the E2 and E3
two new molecular functions describing the activities of the E2 and E3
enzymes separately. Please visit the source forge item if you have comments.  
enzymes separately. Please visit the source forge item if you have comments.  
http://sourceforge.net/p/geneontology/ontology-requests/10635/
http://sourceforge.net/p/geneontology/ontology-requests/10635/ <br>
There will be lot of reannotation required when the terms go obsolete.
There will be lot of reannotation required when the terms go obsolete.



Revision as of 17:30, 24 February 2014

Agenda

Symbiotic relationships (David OS)

Formalizing the representation of symbiotic relationships and annotations to describe them in the ontology. GO annotations include many that involve an interaction between two organisms. These include: annotation to a cell component of the host of the organisms expressing the gene being annotated. annotation to a biological process involving a virus and and its host. In these cases we have a mechanism for recording multiple taxon IDs for interacting organisms, but not the relationship between the two organisms , e.g one might be host to the other or vector for the other. We also don't have a way to record which of the two interacting organisms a cell component is located in or a biological process is occurring in. My proposal aims to solve this problem, by allowing annotators to link taxon IDs using a relationship such as host_of or vector_for. Additionally you will be able to use annotation extension to record which of the two organisms an annotated CC is located in or a biological process occurs in. Along with this extension to annotation, I plan to rearrange parts of the CC hierarchy - particularly those relating to host cell. My presentation will include details of these changes.

Requesting new GO Complex terms (Jane) Policy

E2/E3 terms (David Hill)

Ontology group will likely be obsoleting the 'ubiquitin-protein ligase activity' and creating two new molecular functions describing the activities of the E2 and E3 enzymes separately. Please visit the source forge item if you have comments. http://sourceforge.net/p/geneontology/ontology-requests/10635/
There will be lot of reannotation required when the terms go obsolete.

Curation questions

From SGD:

PHO92 has been shown to bind to the 3'-UTR of PHO4 mRNA (PMID: 24206186) and 
can be annotated to GOID: 3730 (mRNA 3'-UTR binding). It would be useful to indicate that it 
is the mRNA of PHO4 using col-16. How can this be annotated?

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.