Annotation Conf. Call October 22, 2013

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Agenda

Highlights from the recent GOC BarHarbor meeting

  • Jenkins email alerts. All the groups submitting a GAF should be getting email alerts about their GAF reports. Please go to: http://build.berkeleybop.org to check your report and please fix the errors.
    • We would like groups to look at their Jenkins reports and report at the next Annotation call.
    • Tony and Heiko will work together to make sure protein2GO checks and Jenkins checks are in sync.
  • GOC website is being moved to Drupal content management system. Editing should be easier with this system (unlike editing in html, checking into SVN etc)
  • AmiGO2: beta version has been available since past July. logistics for moving this to be the production is being worked on. Non-MOD IEAs will be available in AmiGO2
  • Integrating protein binding annotations- a working group will be formed to figure out the details
  • Apoptosis reannotation effort is complete. Curation manual is available on the wiki.
  • Cell Cycle overhaul- val and Jane will give an overview at a future annotation when they are done
  • MF alignment with RHEA
  • There are other Ontology projects (Viral terms, Giardia terms, Uberon/CL/GO alignment etc).
  • SGD is very close to completing a roundtrip with protein2GO migration. MGI is next in line. Claire and Alex are going to work with us to get Uniprot IDs for duplicated genes that have the same protein sequence and other ID issues that MGI have.
  • Textmining tool into Protein2GO- Kimberley showed how they are able to use textPresso to curate for GO and have them inserted into protein2GO via web services. MGI is going to work with CalTech to integrate textpresso.
  • Specs for CAT tool will be drawn by the next GOC meeting, which will be at Texas A&M.
  • Col-16 tutorial outcome
    • Good discussion in the pre-meeting;

Requires_regulator; Requires_regulation_by: There are 9 annotations using these that need to be re-examined. When you use these relationships you are actually annotating in 'reverse' direction. From this discussion we identified that we should to aim to annotate gene products in the forward direction only. i.e. to say protein X has protein kinase activity and it's target is protein Y is annotation in the forward direction. To say protein Y is phosphorylated by protein X is annotating in the reverse direction.

From this discussion we identified that we should to aim to annotate gene products in the forward direction only. Aim that only chemicals will be annotated in ‘reverse’ eg ‘x annotation’ is ‘inhibited’ by ChEBI ID, because we can’t annotate forwards the ChEBI ID. The reverse annotations can be implied using LEGO.

One of the action items was to create a LEGO diagram for each of the 69 relationships, so that they are visualized in forward and reverse direction to confirm that we only need to annotate in one direction.

    • Tutorial

part_of and occurs_in are agreed, have good examples for use to put in documentation

Will create documentation pages on new website for AE examples - more guidelines needed for use of relations

Discussion on has_input vs. has_direct_input. Proposal that has_direct_input should only be used for MF. Action was to check the existing annotations to see if any process annotations use ‘has_direct_input’. Consider adding a rule (or a guideline, if we want to be more relaxed) to restrict has_direct_input for MF and NOT BP annotations. Still under discussion