Issue 14 - July 2011
Editor - Ruth Lovering
During the summer Varsha will be co-ordinating a heart development annotation project. This is a Reference Genome project and will lead to the annotation of 25 subfamilies of genes involved in regulating transcription and heart development, including GATA4, OVOL2, MSX1, SOX17 and MYCD, across 11 different species by the various GO Consortium (GOC) member groups. The regulation of transcription plays an important role in heart development and Varsha provided a key role in choosing the annotations targets for this project. The transcription ontology has recently been revised by the GOC editors, with Karen Christie, at Saccharomyces Genome Database, investing considerable time on these revisions. The heart development Reference Genome project gives all of the GOC curators an opportunity to fully test the new transcription ontology.
Evelyn Camon left us in April, after a very productive time with the BHF-UCL annotation team. Evelyn read 300 papers and created over 1000 experimentally supported GO annotations to 200 proteins. With a recent PhD in immunology she was able to fully curate immunological papers in great detail. This project has now associated 20,000 GO terms to almost 2,800 proteins, 14,500 of which are to around 1,700 human proteins (based on the EBI statistics, 25th June 2011).
Ruth attended an apoptosis ontology development workshop in June, organised by Paola Roncaglia, a GOC editor, in collaboration with the APO-SYS consortium. Discussions to develop this area of the ontology are still ongoing, but good progress is being made. To date over 1000 GO terms have been approved and requested by the Cardiovascular GO annotation Initiative. Using the GOC browser AmiGO, it is now possible to see all of these terms, by searching for GOC:BHF in ‘terms’.
We will be running our third 2-day GO Annotation Workshop, 27-28th September 2011. This workshop aims to provide a quick overview of several bioinformatics resources and their use. In addition, attendees are encouraged to improve the profile of their papers in the world’s leading biological databases, such as EntrezGene, UniProt and GeneCards and analyse some high-throughput datasets. Please contact us or use the Eventbrite registration form, if you are interested in attending this workshop.
This year’s Genetics of Human Disease MSc students submitted 600 correct annotations, which have been included in the GOA dataset, by reading 162 publications. It took us several weeks to check all of the annotations the students had suggested and, based on the papers the students had annotated, we were able to add an additional 1000 annotations to the database.
Ruth and Varsha attended the Conference Enabling Systems Biology at UCL in April, presenting a poster, Bringing Gene Ontology to cardiovascular research. In May, Ruth presented two talks at the GOC meeting at University of Southern Californian, Los Angeles. The first described community annotation at UCL, the other outlined how we prioritise genes for annotation and the impact the Cardiovascular GO Annotation Initiative has had on the interpretation of high-throughput data analysis.
Page last modified on 30 jun 11 09:11
The work of the Cardiovascular Gene Annotation group is supported by British Heart Foundation grant RG/13/5/30112