Annotation Conf. Call, February 25, 2014

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Agenda

Present:
SGD: Rama, Selina, Diane, Stacia
MGI: Judy, David, Karen, Li
Dicty: Pascale
WB: Kimberley
Pombase: Midori
UCL: Ruth, Paul, Anna
EBI: Aleks, Rachael, Jane, Paola
Berkeley: Moni, Chris
Reactome: Peter
TAIR: Tanya (arrived at 8:15)

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. 

Sandra's presentation

Sandra Orchard will present the IntAct Complex Portal on Tuesday 4th March at 8am PT / 10am CT / 11am ET / 4pm BST / 5pm CEST. This is relevant to the current discussions on annotating to identifiers other than gene/protein accessions, but everybody is welcome.

Discussion

Complexes (Jane)

Jane showed a new template in TermGenie to request/define complex terms based an activity/function. If you don't know the function of the complex, go the usual route of requesting via SourceForge.

Symbiotic relationships (David OS)

File:MultiOrgAnn.pdf

  • Pascale asked if we could make another quailifer 'located in host_cell' for these annotations rather than just 'locatedin'. part_of and located_in may not be sufficient for these cases.
  • Will these 'host cell**' terms be obsolteted? No, they will merged with regular terms.
  • How do we handle annotations where we have to say colocalizes_with and located_in in the qualifier column?
  • This new proposal is not sufficient for the end user. David will work on it and present it at the Texas meeting.

E2/E3 terms

  • GO:4842 is going to be obsoleted as it includes ATP hydrolysis in the definition and this is not true. E2 and E3 are synonyms of this term.

Several hundred annotations will have to be rehoused as a consequence. How can we do the rehousing in an efficient way? At MGI if they don't have time to annotate to the granular MF term they annotate to an equivalent BP term and move on. The annotation group should look into solutions for rehousing.

  • Please, please take a look at the SF item and add your comments. DavidH is not an expert in this area and he would love your feedback.
  • it will be another 2 months before these terms go obsolete.

Curation

  • Pho92 annotation: use has_direc_input or has_input (depending on the assay) as the relationship and perhaps transcript ID if available. OTherwise gene ID is fine since the term name includes the mRNA part.
  • We did not get to the second question from Karen. Punted to next call