Annotation Advocacy Q2 2014

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Management

Rachael Huntley (UniProt-GOA)

Rama Balakrishnan (SGD)

Annotation Consistency

Annotation calls

We continue to discuss annotation issues on our biweekly annotation calls. Subjects can be anything from new annotation guidelines, quality control checks, ontology or evidence code-related discussions, tool development or updates from annotating groups.

Some of the discussion we have had this quarter include;

  • Improvements to the E1, E2 and E3 ubiquitin Molecular Function terms
  • Cardinality of the with/from field

We also had the following talks:

David Osumi-Sutherland: "Plans for the extracellular branch of the Cellular Component ontology"

David Osumi-Sutherland: "Introduction to OWL"

Valerie Wood: "PomBase GO Matrix Tool"

Training New Annotation groups

We have been providing annotation guidance to the following groups:

GeneDB, who annotate pathogen gene products.

MoonProtDB (UI Chicago) who annotate a second moonlighting function for proteins

Giardia Lamblia group (UC Davis) to annotate cellular component og G. lamblia

Help the Pseudocap group resubmit their GAF

We continue to work with Astrid Lægreid's group (NTNU, Norway) on annotating mammalian transcription factors (PMID:23981286)

Annotation Guidelines

Annotation Extensions

The Annotation Extension paper was published in BMC Bioinformatics (http://www.biomedcentral.com/1471-2105/15/155/abstract).

The annotation extension working group (core members are Rachael, Val, David H., Chris and Ruth, but others are welcome to join) have been discussing the usage of various annotation extension relations. This has led to assigning to a subset each relation that is valid for use in annotation extensions, which ensures these are the only relations visible in Protein2GO and the QuickGO visualization of relations (http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html). We also agreed to stop use of has_indirect_input and all of the not_* relations, e.g. not_occurs_in. The relation not_dependent_on was agreed to be useful and so it's primary name has changed to independent_of and annotations have been updated.

Ruth is improving the documentation on the GO wiki for individual relations by adding examples of folded and unfolded annotations.


Documentation

Annotation Quality Control

Usage of with/from field

The outcome of discussions in 2013 regarding identifiers in the with/from field was a list of identifier types that are valid for use with each evidence code. These identifier types are being added to the relevant ECO terms as subsets, e.g. valid_with_protein and to GO.xrf_abbs. When complete this will assist with quality control checks on the contents of the with/from field.

We continue to discuss standardization of the with/from field cardinality for each evidence code.

Jenkins reports

Help groups deal with Jenkins reports

GO Helpdesk

GO helpdesk staff

Rama Balakrishnan, Rachael Huntley, Harold Drabkin, Jane Lomax, Kimberly Van Auken, Tanya Berardini, Rebecca Foulger, Poala Roncaglia, David Osumi-Sutherland.

We continue to use a gohelp rota where each person is 'on duty' for 1 week at a time. It is the responsibility of the person on duty to make sure that all queries are answered, either by answering it themselves, or by assigning the issue to someone else to answer. The on duty person is now encouraged to 'tweet' interesting GO-related stories to keep up the public profile of GO.

Other

Plans for Q3

In the upcoming quarter we will;

  • Discuss "deepening" protein binding (GO:0005515) annotations
  • Come up with an annotation manual for mapping E2/E3 terms
  • Work on documentation of annotation extension relations
  • Finalize with/from cardinality issues
  • Create a new subset of do_not_automatically_annotate GO terms

Ongoing tasks;

  • Continue to promote annotation consistency through regular annotation calls and jamborees and through up-to-date guideline documentation
  • Enforce annotation guidelines by implementing further quality control checks as needed
  • Continue to assist external annotating groups who wish to provide annotation sets to the GO Consortium by providing them with the GO Consortium's annotation policies and guidelines and reviewing their annotations as necessary
  • Continue to keep curators informed of updates to the ontology by providing documentation and holding conference calls