GOA, September 2009: Difference between revisions

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a.'' Papers with substantial GO content''
a.'' Papers with substantial GO content''


The GOA database in 2009--an integrated Gene Ontology Annotation resource.(2009) Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. Nucleic Acids Res. 37:D396-403.  
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''
b. ''Presentations including Talks and Tutorials and Teaching''


December 2009 Hands-on training at EBI - Joint EBI-Wellcome Trust Proteomics workshop  'Gene Ontology as a data classification tool' (Rachael; GO/GOA talk and tutorial)
June 2009 - Presentation of GOA and the Renal Annotation Initiative at Edinburgh University (GUDMAP Consortium), Yasmin Alam-Faruque
 
22nd January 2009 Transcriptomics workshop (Rachael GO/GOA talk and tutorial)  


21st March 2009 Perspectives in Stem Cell Proteomics Training Workshop, EBI (Emily GO/GOA talk and tutorial)
7-8th September 2009 - Renal Gene Ontology Annotation Initiative Poster and presentation for the Kidney Research Fellows Day, Yasmin Alam-Faruque


16-19 April 2009 3rd International Biocuration Conference, Berlin (Rachael; GOA Poster)
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


= Other Highlights=
= Other Highlights=

Revision as of 10:50, 4 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.


GOA UniProt gene association file release stats (comparison of March 09 and September 2009 releases)

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.


  1. 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. EC2GO2
  6. Ensembl Compara

Legend

1: mapping tables created and maintained by the GOA group

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


  1. 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 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

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.