GOA December 2010: Difference between revisions

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Proteins associated with kidney development and disease are the focus of the GOA Renal Annotation Initiative.
Proteins associated with kidney development and disease are the focus of the GOA Renal Annotation Initiative.


Currently the curators from the GOA and BHF-UCL projects have together completely annotated X% (Y/Z) of supplied Reference Genome Targets.
Currently the curators from the GOA and BHF-UCL projects have together completely annotated 65% (719/1111) of supplied Reference Genome Targets.


Between January 2010 and December 2010, the GOA project provided the GO Consortium with ?? annotation file releases, including non-redundant sets of GO annotations to the human, mouse, rat, zebrafish, Arabidopsis, chicken and cow proteomes, as well as data releases for annotations of all proteins in UniProtKB. Since 12th July 2010, GOA has provided an interim release of the human and chicken gene association files to allow the Reference Genomes PAINT project to collect the most up-to-date annotations for use in the tree curation. The human and chicken files are now released every two weeks, that is as part of the main GOA monthly file release and again two weeks later. GOA now provides over ?? million GO annotations for ?? million proteins in over 2??,000 different taxonomic groups. GOA provides ?? annotations for the human proteome (providing ??% of the human proteome with at least one GO annotation). Over the last year the number of manual annotations has increased by ?? % in the UniProtKB file and the number of manual annotations for the human file has increased by ??%. Between January and December 2010, GOA has continued training, checking and supporting 35 curators in the Swiss-Prot team at the Swiss Institute of Bioinformatics, who have since created over 37,500 manual GO annotations for UniProtKB entries from a range of species.
Between January 2010 and December 2010, the GOA project provided the GO Consortium with ?? annotation file releases, including non-redundant sets of GO annotations to the human, mouse, rat, zebrafish, Arabidopsis, chicken and cow proteomes, as well as data releases for annotations of all proteins in UniProtKB. Since 12th July 2010, GOA has provided an interim release of the human and chicken gene association files to allow the Reference Genomes PAINT project to collect the most up-to-date annotations for use in the tree curation. The human and chicken files are now released every two weeks, that is as part of the main GOA monthly file release and again two weeks later. GOA now provides over ?? million GO annotations for ?? million proteins in over 2??,000 different taxonomic groups. GOA provides ?? annotations for the human proteome (providing ??% of the human proteome with at least one GO annotation). Over the last year the number of manual annotations has increased by ?? % in the UniProtKB file and the number of manual annotations for the human file has increased by ??%. Between January and December 2010, GOA has continued training, checking and supporting 35 curators in the Swiss-Prot team at the Swiss Institute of Bioinformatics, who have since created over 37,500 manual GO annotations for UniProtKB entries from a range of species.

Revision as of 11:00, 4 October 2010

!!Report In Progress!!

Gene Ontology Annotation at UniProtKB, 2010

Staff:

Rolf Apweiler

Claire O'Donovan

Emily Dimmer

Rachael Huntley

Yasmin Alam-Faruque

Daniel Barrell

David Binns

Tony Sawford

Swiss-Prot contributors (EBI, Hinxton, UK and SIB, Geneva, Switzerland): Ioannis Xenarios, Amos Bairoch, Lydie Bougueleret, Serenella Ferro-Rojas

Ghislaine Argoud-Puy, Andrea Auchinchloss, Kristian Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi Quintaje, Lionel Breuza, Alan Bridge, Paul Browne, Wei Mun Chan, Elizabeth Coudert, Isabelle Cusin, Louise Daugherty, Paula Duek Roggli, Ruth Eberhardt, Anne Estreicher, Livia Famiglietti, Marc Feuermann, Rebecca Foulger, Michael Gardner, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Kati Laiho, Duncan Legge, Philippe Lemercier, Damien Lieberherr, Michele Magrane, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Klemens Pichler, Diego Poggioli, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Harminder Sehra, Eleanor Stanley, Andre Stutz, Shyamala Sundaram, Michael Tognolli

Annotation Progress

We continue to put emphasis on the annotation of those genes selected for the Reference Genome Project.

Proteins associated with kidney development and disease are the focus of the GOA Renal Annotation Initiative.

Currently the curators from the GOA and BHF-UCL projects have together completely annotated 65% (719/1111) of supplied Reference Genome Targets.

Between January 2010 and December 2010, the GOA project provided the GO Consortium with ?? annotation file releases, including non-redundant sets of GO annotations to the human, mouse, rat, zebrafish, Arabidopsis, chicken and cow proteomes, as well as data releases for annotations of all proteins in UniProtKB. Since 12th July 2010, GOA has provided an interim release of the human and chicken gene association files to allow the Reference Genomes PAINT project to collect the most up-to-date annotations for use in the tree curation. The human and chicken files are now released every two weeks, that is as part of the main GOA monthly file release and again two weeks later. GOA now provides over ?? million GO annotations for ?? million proteins in over 2??,000 different taxonomic groups. GOA provides ?? annotations for the human proteome (providing ??% of the human proteome with at least one GO annotation). Over the last year the number of manual annotations has increased by ?? % in the UniProtKB file and the number of manual annotations for the human file has increased by ??%. Between January and December 2010, GOA has continued training, checking and supporting 35 curators in the Swiss-Prot team at the Swiss Institute of Bioinformatics, who have since created over 37,500 manual GO annotations for UniProtKB entries from a range of species.

Methods and strategies for annotation

1. Literature curation:

Literature curation continues to be the major focus of our annotation efforts, with an emphasis on the use of experimental evidence codes.

2. Computational annotation strategies:

GOA provides IEA annotations from the following methods:

  1. Swiss-Prot Keyword 2GO (SPKW2GO)1,2
  2. Swiss-Prot Subcellular Locations2GO (SPSL2GO) 1,2
  3. HAMAP2GO2
  4. InterPro2GO2
  5. Ensembl Compara


Legend

1: mapping tables created and maintained by the GOA group

2: electronic annotations generated by the GOA group, using UniProtKB.


3. Priorities for annotation

  1. Genes assigned by Reference Genome Project (Rachael, Emily)
  2. Genes associated with renal processes (Yasmin)
  3. Requests from user community (all curators)
  4. Proteins annotated during Swiss-Prot curation duties (all Swiss-Prot/UniProtKB curators at the EBI and SIB)

Presentations and Publications

GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources

Other Highlights

A. Ontology Development Contributions:

B. Annotation Outreach and User Advocacy Efforts:

C. Other

Changes to SPKW2GO and SPSL2GO


Renal GO annotation initiative funded by Kidney Research UK.


Gene Association File changes