GOA, September 2009
Gene Ontology Annotation at UniProtKB, 2009
Report on the GOA team's activities between March 2009 and September 2009.
Staff:
Rolf Apweiler
Claire O'Donovan
Emily Dimmer
Rachael Huntley
Yasmin Alam-Faruque
Daniel Barrell
David Binns
Tony Sawford
Annotation Progress
We continue to put emphasis on the annotation of those genes selected for the Reference Genome Project.
In addition, with the newly started kidney-centric annotation project, additional emphasis has been placed on certain genes associated with renal development and disease.
Methods and strategies for annotation
- Literature curation:
Literature curation continues to be the major focus of our annotation efforts, with an emphasis on the use of experimental evidence codes.
- Computational annotation strategies:
GOA provides IEA annotations from the following methods:
- Swiss-Prot Keyword 2GO (SPKW2GO)1,2
- Swiss-Prot Subcellular Locations2GO (SPSL2GO) 1,2
- HAMAP2GO2
- InterPro2GO2
- EC2GO2
- Ensembl Compara
Legend
1: mapping tables created and maintained by the GOA group
2: electronic annotations generated by the GOA group, using UniProtKB.
- Priorities for annotation
- Genes assigned by Reference Genome Project (Rachael, Emily)
- Genes associated with renal processes (Yasmin)
- Requests from user community (all curators)
- Proteins annotated during Swiss-Prot curation duties (all Swiss-Prot curators at the EBI and SIB)
Presentations and Publications
a. Papers with substantial GO content
Atherosclerosis. 2009 Jul;205(1):9-14. Improvements to cardiovascular gene ontology. Lovering RC, Dimmer EC, Talmud PJ.
PLoS Comput Biol. 2009 Jul;5(7):e1000431. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. Reference Genome Group of the Gene Ontology Consortium.
b. Presentations including Talks and Tutorials and Teaching
June 2009 - Presentation of GOA and the Renal Annotation Initiative at Edinburgh University (GUDMAP Consortium), Yasmin Alam-Faruque
7-8th September 2009 - Renal Gene Ontology Annotation Initiative Poster and presentation for the Kidney Research Fellows Day, Yasmin Alam-Faruque
23rd April, 1st July, 2nd SeptemberGO annotation training of Swiss-Prot curators at the Swiss Institute of Bioinformatics, Geneva, Switzerland, Emily Dimmer and Rachael Huntley
17-18th September British Atherosclerosis Society Autumn Meeting; 'Genetics of Complex Diseases'. Introduction to GO. Emily Dimmer and Ruth Lovering.
Other Highlights
A. Ontology Development Contributions:
33 GO terms have been created during annotation efforts by the group
B. Annotation Outreach and User Advocacy Efforts:
GOA is currently training curators at the Swiss Institute of Bioinformatics. Rachael and Emily from GOA and Michele Magrane from the Swiss-Prot group at the EBI travelled to Geneva on the 28th-29th January to train 8 curators. Rachael and Emily then checked all annotations generated by this group over the following 2 months before making the annotations public. The Swiss-Prot team in Geneva have so far generated approximately 4,000 manual GO annotations. Annotations are created in GOA's protein2go tool, and released in the groups gene association files. Such annotations use the existing source 'UniProtKB' (for column 15 of the gene association file).
Emily will visit SIB in April to train another 5 curators.
GOA will continue to train and mentor SIB curators over 2009.
C. Other
Renal GO annotation initiative funded by Kidney Research UK.
This grant will start on the 1st April, and will be run by Yasmin Alam-Faruque, who will join GOA from the Swiss-Prot team at the EBI.
This initiative will generate high-quality manual annotation for those genes/processes found to be implicated in kidney development and disease.
Human Gene Association File changes.. In February 2009, the production of the gene_association.goa_human file changed from using the International Protein Index (IPI) to using the complete human proteome set available from UniProtKB/Swiss-Prot (http://www.uniprot.org/news/2008/09/02/release).
The name and format of this human file has remained the same, however annotations are now assigned to proteins from just the 'UniProtKB' (column 1) database source. Human IPI identifiers continue to be included in column 11 of annotations.
In addition, new releases of the cross-references file for human IPI set (human.xrefs.gz), will no longer be provided. Instead, identifier mapping is possible using the UniProt ID mapping file, available from: ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz
idmapping.dat.gz is a tab-delimited table, which includes mappings for 20 different sequence identifier types, including IPI identifiers.