Issue 15 - October 2011

Editor - Ruth Lovering

Gene annotation

Since May Varsha has been co-ordinating a Reference Genome heart development annotation project. This project has taken advantage of the new heart development terms created following a workshop funded by the British Heart Foundation as well as recent revisions to the transcription ontology. This focused annotation project has lead to the creation of over 1000 annotations to nearly 300 different proteins. For example the biological process GO terms 'embryonic heart tube anterior/posterior pattern specification', 'heart trabecula formation', 'embryonic heart tube morphogenesis' and 'cardiac neural crest cell development involved in outflow tract morphogenesis' are now associated with the transcriptions factors GATA4, OVOL2, SOX17 and HAND2, respectively.

We would like to thank Sejal Patel, who completed her MSc project in our group and achieved a distinction. Sejal annotated over 30 papers and creating several hundred annotations describing genes involved in synaptogenesis, as well as requesting specific GO terms to improve the description of this process. The Cardiovascular GO Annotation Initiative has now associated 22,000 GO terms to 3,000 proteins, 15,600 of which are to over 1,800 human proteins (based on the EBI statistics, 17th September 2011).

Gene Ontology

To date 1100 GO terms have been approved following specific requests by the Cardiovascular GO annotation Initiative.

Community annotation

The BHF-UCL team has encouraged 4 of last years Genetics of Human Disease MSc students to take part in the annotation competition, CACAO, being run by Brenley McIntosh at Texas A&M University. The competition runs for ten weeks and encourages the students to submit annotations and challenge the accuracy of annotations made by other competitors. We wish all the competitors luck (and accuracy) in this competition!

Our September 2-day GO annotation workshop was attended by 20 UCL scientists who contributed around 60 GO annotations directly to the GOA database. Andrea Townsend-Nicholson, who attended this workshop last year, incorporated GO annotation in her BSc signalling module. Consequently, her students annotated papers describing signalling processes, and these annotations should be appearing in the GOA database soon.

Meetings attended

In September, Henning Hermjakob, EBI, kindly presented the Cardiovascular Gene Ontology Initiative under the imaginative title 'Human Protein Knowledgebase for the Heart and Soul' at the Cardiovascular Initiative workshop of the HUPO 2011 World Congress in Geneva, Switzerland.

Also in September, Varsha was invited to participate in the UniProt usability workshop. Through a series of games and activities, the participants were asked about their experiences with the UniProt website and came up with potential ways in which the UniProt website and tools could be improved.

Upcoming meetings

UCL will be hosting the GO Consortium meeting in November this year, which both Ruth and Varsha will attend. This meeting will be followed by a cardiac conduction ontology workshop to improve the GO description of these neurological and muscular processes.

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