GO annotation activities by central GO Consortium members

Additional responsibilities of active GO annotation groups.

• Be responsive to requests from other curators/external users to correct their annotations when necessary, and to integrate accepted corrections from external sources.

• Be responsive to correct annotations in which problems are uncovered using the GOC soft/hard QC checks.

• Each annotation group should be represented on the GO Consortium fortnightly annotation calls and frequently attend GO Consortium meetings, to ensure all groups are kept up-to-date with developments in the GO Consortium.

Additional responsibilities of providers who act as the authoritative source for a species

• Authoritative providers of annotations for a particular species should integrate manual and electronic annotations from external sources (e.g. GOC, RefGenome, UniProt, Reactome) on a monthly basis, providing up-to-date set of merged annotations for their species (as the authoritative source) to the GOC. If an external source includes data in the annotation_extension field or gene_product_form_id (columns 16 and 17 of GAF2.0), then the species owner is required to include this data, even if they themselves are not annotating to this field themselves.

• It is preferable that all annotations are mapped to a common identifier type to enable users to retrieve a standardized annotation format (this could be the group’s MOD identifier type).

* Authotiative species-owning groups should only minimally filter their annotation set to reduce annotation redundancy in their annotation file. The GO Consortium will make available less-redundant annotation sets to users, however it is important that the Consortium receives all annotations supplied by GOC (automatic and manual) annotation efforts.

Document describing the advised mechanism for filtering for annotation redundancy:

http://wiki.geneontology.org/index.php/Mechanisms_for_reducing_annotation_redundancy : Currently under discussion

Activities required of dedicated NIH funded GO curators (optional for others)

Annotation activities

• Supply appropriately formatted GO annotations at a minimum frequency of once/month. Initially these will be supplied in GAF 2.0 (as above) but GO bio-curators will be required to transition to releasing files to the GO Consortium in GPAD/GPI format. GPAD format

• Transition to annotate to identifiers describing specific protein/complex forms as necessary. Possible ids include protein isoforms, post-translationally modified proteins, functional RNAs, protein complexes) e.g. UniProtKB accessions, PRO ids or IntAct complex ids.

• Add information into annotations to describe the biological context of a GO annotation (cell type, anatomical structure, other spatial and temporal attributes), as well as add data to linking functions, processes and components in an annotation. This will require at a minimum annotation extensions (column 16 in GAFs) – i.e. a minimum of GAF2.0 OR GPAD expressivity. It may also involve annotation relations, which requires at a minimum GPAD. This includes enhancements that will become available in the future, such as specifications for more expressive annotations (e.g. LEGO-style annotation, with arbitrary levels of nesting), supported by the appropriate annotation tools becoming available.

• Carry out phylogenetically-based annotations of PANTHER protein families using PAINT, (secondary to curating annotations derived from experimental data.)

• Commit to submit annotations for all species that are described in the papers they are curating, that is annotation data for species not typically captured by the MOD. This would improve efficiency of literature curation when a paper characterizes gene products from >1 species. This will be facilitated through the use of the Community Annotation Tool.

Other activities

• Mentor emerging annotation groups outside of the established functional annotation stream as resources allow; allocation of mentoring responsibilities defined by GOC.

• Participate in the review of annotations contributed by external community experts (as emailed to GO Help or brought in via the CANTO tool)

• Contribute to the development of the expressivity of GO annotations (at least in the format defined by the GO Consortium, if not in the MODs web-display) and determine the priority of these extensions.

• Participate in the testing and development of the Central GO Common Annotation Framework. The Framework comprises both a front-end UI and a back-end system for reasoning, QA and deposition in the GO database, and dedicated curators will participate in the development of either one or both of these elements. The Framework will support multiple UIs as long as they conform to the back-end specifications and respond in a timely manner to updates in these specifications.

• Provide a GPI file (rather than a gp2protein file)

| GPI file format

• • The GPI file must include identifiers and description of macromolecular complexes that have been annotated.