Annotation Call July 22 2014

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Agenda

Present: SGD: Rama, Diane, Edith
EBI: Jane, Rachael, Aleks, Prudence
UCL: Becky
IntAct: Birgit
MGI: Judy, Mary, Li
RGD: Stan
WB: Kimberley
Pombe: Midori
Berkeley: Suzi, Chris
dictyBase: Petra, Bob

Col-16 Questions (SGD)

  • PMID: 11486005
    • Snf1 requires Snf4 for full kinase activity - it's unclear how Snf4 contributes to full Snf1 activity. is_regulated_by is not allowed any more. In this case in_presence_of or dependent_on both work. Which one is correct?
    • Snf1 doesn't phosphorylate Mig1 during salt stress. not_happens_during is not an option any more. What is the correct relationship for this? independent_of doesn't seem right. http://www.yeastgenome.org/locus/S000002885/go
  • PMID: 15652479
    • ste20 is localized to the nucleus when cells are treated with H2O2.

This was originally captured as: Ste20 - nucleus - during:GO:0070301 (cellular response to hydrogen peroxide)

"During" is not allowed in this case, the suggested replacement is exists_during, which doesn't sound right. Does localization_dependent_on fit here or should we use exists_during?

Col-16 Questions (UCL)

  • Can we can specify both the direct target and the downstream modified protein for BP terms such as this example from PMID:24899725:
negative regulation of protein ubiquitination ; GO:0031397
has_input: [ID of ubiquitin ligase enzyme]
has_regulation_target: [ID of protein being ubiquitinated]

IPI evidence code for annotating CC complex formation

Are we annotating consistently with the guidelines for IPI? The documentation says:

Examples where the IPI evidence code should not be used:
Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA,
not IPI with the ID corresponding to the tagged subunit in the with/from  column because not all subunits
of the complex interact directly with the tagged subunit. Thus this type of assay can provide IDA for
annotation to a component term for the specific complex because it is a direct assay for a complex, but it
would not necessarily be true to say that all members of the complex interact directly with the tagged 
subunit.

But there are alot of (some recent) annotations to protein complexes using the IPI evidence code.

Annotating to protein complex identifiers

This has come up while bringing the annotations to protein complex identifiers from the IntAct Complex Portal into the GOA database. We want to be able to bring in annotations for complexes IDs to GO:Cellular Component terms using the IPI evidence, however it's not appropriate to have contents in the with field, which is currently required for IPI. IDA is not ideal to use as we want to capture the physical interaction evidence. Possible solutions are; We could either allow IPI evidence with no entry in the with field if the entity being annotated is a complex, or to use IDA and additionally supply the experimental evidence accession used by IntAct.

rehousing annotations to Cell cycle phase term

We are trying a new approach to help groups rehouse annotations. We will deal with one term at a time. Highlight what the issues are etc so the groups can focus and not be overwhelmed. We can also highlight this term on the GOC website (why we can't have direct anotations to this term etc).

Cell cycle phase should not be used any more for manual annotations.

http://amigo.geneontology.org/amigo/term/GO:0022403

Annotation dispute facility in Protein2GO

Procedure for using the annotation dispute facility;

1. Anyone with a Protein2GO account can dispute annotations (not GOC inferred ones) that are displayed in Protein2GO

2. The dispute will be emailed to the curator who made/last updated the annotation or to the group that curator belongs to if they are not Protein2GO users, e.g. Reactome, or the group that provides the predictions in the case of electronic annotations. In the case of annotations made by ex-curators or ex-curation groups, UniProt-GOA is emailed.

3. A reminder email is sent to the disputer after 30 days if the dispute is not resolved. It is the responsibility of the disputer to further chase up the disputee if they do not respond.

4. Once the dispute has been resolved to the satisfaction of the disputer, it is their responsibility to close the dispute.

See screenshot of Protein2GO disputes File:P2GO Disputes.pptx

Discussion

Col-16 Questions

  • PMID: 11486005
    • Snf1 requires Snf4 for full kinase activity - it's unclear how Snf4 contributes to full Snf1 activity. is_regulated_by is not allowed any more. In this case in_presence_of or dependent_on both work. Which one is correct?
    • Dependent_on would be appropriate here. David OS should take a look at this case
    • Snf1 doesn't phosphorylate Mig1 during salt stress. not_happens_during is not an option any more. What is the correct relationship for this? independent_of doesn't seem right. http://www.yeastgenome.org/locus/S000002885/go
    • Don't bother capturing this detail
  • PMID: 15652479
    • ste20 is localized to the nucleus when cells are treated with H2O2. This was originally captured as: Ste20 - nucleus - during:GO:0070301 (cellular response to hydrogen peroxide). "During" is not allowed in this case, the suggested replacement is exists_during, which doesn't sound right. Does localization_dependent_on fit here or should we use exists_during?
    • localization_dependent_on is more definitive, exists_during is appropriate in this case (this protein exists in location X during Y).
  • UCL question about Ubiquitin ligase annotation.
    • Col-16 team will model this situation and come up with a recommendation.

IPI for complexes

We should allow IPI without 'With' column for complexes (and don't use IDA). Change the documentation (and look into QC checks). We should get the IntAct2GO mapping worked out correctly. Have a look up table for experiment type to ev. codes. In some cases they may not map to one of our 3 letter codes in which case we should come up with new 3 letter codes. Rachael will discuss this with Sandra.

cell cycle phase

  • Jane highlighted the fact that there is a now a new term in Biological process called biological phase which is related by 'is_a disjoint'. Ontology developers have moved all the phase terms under this new term. cell cycle phase is a higher level term and shouldn't be used for manual and computational annotations. Please review your anntoations and rehouse them as appropriate.

protein2GO disputing mechanism

We did not have time to discuss this item. Rachael sent an email out to the go-consortium list post meeting. Please check the email.