Revision as of 10:37, 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

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
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/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

@@ Line 26: / Line 26: @@
 = Annotation Progress =
+= 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)<sup>1,2</sup>
+# Swiss-Prot Subcellular Locations2GO (SPSL2GO) <sup>1,2</sup>
+# HAMAP2GO<sup>2</sup>
+# InterPro2GO<sup>2</sup>
+# Ensembl Compara
+<b>Legend</b>
+<b><sup>1</sup></b>: mapping tables created and maintained by the GOA group
+<b><sup>2</sup></b>: 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/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'''

GOA December 2010: Difference between revisions