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Editor - Ruth Lovering
Gene annotation
Dr Evelyn Camon has been very productive during her time with the BHF-UCL annotation team, creating almost 1000 experimentally supported GO annotations to 200 proteins. She has been focusing on the annotation of genes involved in immunity, with priority gene lists provided by Professor Steve Humphries and Professor Derek Gilroy. This project has now associated over 17,000 GO terms to almost 2,500 proteins, 13,000 of which are to 1,500 human proteins (based on the EBI statistics, 5th March 2011).
Gene Ontology
Rebecca Foulger, from the EBI GO Editorial Office, organized a 2-day signalling ontology workshop in February, jointly funded by the GO Consortium and the Cardiovascular GO Annotation Initiative. The meeting was attended by signaling experts, GO curators (including Ruth and Varsha) and GO editors, with Rebecca and Ruth ensuring that specific topics were discussed and, for the most part, resolved. One of the key decisions was agreeing a general rule for the descriptive limits of a signaling pathway: in the majority of cases a signaling pathway begins with receptor-ligand binding and ends with regulation of a downstream process, such as regulation of transcription. This decision means that annotators will now be associating the GO term 'insulin receptor signaling pathway' with insulin, FOXO1, and GSK3, rather than annotating these gene products as regulating this pathway or as targets of this pathway. Strategies to deal with non 1:1 ligand-receptor binding signaling pathways and connecting intracellular signaling cascades with upstream events were also discussed and now need to be developed.
Working with the APO-SYS consortium, the GO Consortium will be running an apoptosis ontology development workshop in June. Ruth has been invited to participate in the workshop and in the coming months will be annotating genes involved in this process, to help identify areas of the apoptosis ontology that need developing or improving.
Community annotation
There are still 3 places available on our second 2-day GO Annotation Workshop, 6-7th April 2011. This workshop is open to all biological or biomedical PhD and Post-Doc research scientists and aims to boost your understanding of bioinformatics resources and their use. In addition you will have the opportunity to improve the profile of your papers in the world's leading biological databases, such as EntrezGene, UniProt and GeneCards and analyse some high throughput datasets. Please contact us if you are interested in attending this workshop, or the next one, which will be run later this year.
Meetings attended
Ruth and Varsha attended the Computational Biology Symposium at UCL in February, presenting a poster entitled 'Bringing Gene Ontology to Cardiovascular Research'.
Upcoming meetings
Ruth and Varsha will be attending the Conference Enabling Systems Biology at UCL in April, and Ruth will be attending the Los Angeles GO Consortium meeting in May.
Publications
The Representation of Heart Development in the Gene Ontology. Varsha K Khodiyar, David P Hill, Doug Howe, Tanya Z Berardini, Susan Tweedie, Philippa J Talmud, Ross Breckenridge, Shoumo Bhattarcharya, Paul Riley, Peter Scambler, Ruth C Lovering. Dev Biol. 2011 Mar 16. [Epub ahead of print] PMID:21419760.
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