Rachael Huntley (UniProt-GOA)
Rama Balakrishnan (SGD)
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 year include;
Jenkins reports: Jenkins validates GAF files for both hard and soft QC checks and generates reports. Groups are reminded via email to check the reports for their GAF files and to correct any errors.
Annotation extension: a) specific examples have been provided on several calls where we aim to reach a consensus on how to annotate the example.
Enzyme regulator activity: There was discussion about how to use this term, should it only be used for gene products that directly regulate, i.e. bind to an enzyme. The consensus was that the curator should use their judgement when interpreting the data. An improved definition for the term was proposed: "Modulates the activity of an enzyme by allostery, direct modification, blocking the catalytic site or any mechanism which involves a direct interaction with the enzyme. An enzyme regulator activity changes the intrinsic catalytic activity of the enzyme toward its substrate, independently of substrate availability."
Apoptosis: The PAINT curators came across several annotation errors involving the apoptosis terms. Annotations had been made incorrectly using assay read-outs rather than an actual involvement of the gene product in the process. Comments have been added to some terms to clarify when they should be used, the apoptosis curation manual has also been updated.
We also had the following talks:
David Osumi-Sutherland "Formalizing the representation of symbiotic relationships and annotations to describe them in the ontology." The focus here is to potentially remove the "host" component and "host" process terms by introducing relationships between taxon IDs.
Sandra Orchard "The IntAct Complex Portal." Sandra described what IntAct defines as a complex, the sources used to populate the complex portal, how they annotate complexes and how to request/create new complexes. The IntAct complex identifiers will be used as a new entity type in the upgraded version of Protein2GO.
New Annotation Datasets
We have been providing annotation guidance to the following groups:
PseudoCAP, who annotate Pseudomonas genes,
Syscilia who are annotating proteins involved with cilium development and disease,
GeneDB, who annotate pathogen gene products.
We have additionally assisted GeneDB and PseudoCAP with providing updated annotation files.
We continue to work with Astrid Lægreid's group (NTNU, Norway) on annotating mammalian transcription factors (PMID:23981286)
We are working with MoonProt Database to help them annotate the moon lighting functions of the proteins in their database using GO. Connie Jefferson came to Stanford for annotation training.
We are working with Giardia researchers to develop the cellular component ontology to describe the structures in Giardia and other flagellates. Scott Dawson (UC Davis) who requested the terms, came over to Stanford for annotation training.
We are currently in the process of porting, and updating, annotation guidance webpages from the current GO Consortium website to the Drupal site. The initial porting of pages has largely been completed and the software group are now testing the new website. Updating of a number of pages still remains to be done.
Annotation Quality Control
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.
Plans for 2014
In the upcoming year we will;
- 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
- Complete the re-organization of the annotation documentation provided by the GO Consortium through its website
- 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
- Ensure use of the new Evidence Code Ontology is adopted by all annotating groups within the GO Consortium by promoting its use and providing up-to-date documentation
- Continue to keep curators informed of updates to the ontology by providing documentation and holding conference calls
- Discuss incorporating Biological Process annotations from IntAct interaction curation
- Discuss "deepening" protein binding (GO:0005515) annotations using rules created by UniProt-GOA