UCL Institute of Cardiovascular Science


Issue 16 - January 2012


Editor - Ruth Lovering

Gene annotation

Based on the EBI statistics, 10th December 2011, this project has associated 23,000 GO terms to over 3,000 proteins, 16,350 of which are to 1,900 human proteins.

Gene Ontology

The BHF-UCL team are now focusing on extending the cardiac conduction ontology. In November, Ruth organised an ontology workshop, which was attended by several experts from UCL and UCLH, as well as GO editors and annotators. So far around 100 new cardiac conduction terms have been defined.


Community annotation

Two UCL teams (comprised of 4 Genetics of Human Disease 2010 MSc students) took part in an annotation competition, CACAO, being run by Brenley McIntosh at Texas A&M University. The competition ran for ten weeks and students had to submit annotations and challenge the accuracy of annotations made by other competitors. We are pleased to announce that the UCL teams were awarded first and fourth place (out of 24 teams). The winning team, UCL-Maple Leaf, submitted over 200 annotations. The other teams involved in this challenge were undergraduate students representing six US Universities. The BHF-UCL team would like to congratulate all teams that took part in this very challenging and competitive venture. Thanks also go to Brenley for setting up and organising this interesting competition.  More information about community annotation is available here

Thanks go to Johnathan Watkins, Dept of Biological Sciences, Birkbeck College, who has volunteered to annotate several of our high priority genes including IGF1, KL, GPX1, ELN and NOG. Johnathan learnt about GO annotation by using our MSc student workbooks and lectures and has successfully annotated 2 papers describing Dec2 (BHLHE41).

Our fourth 2-day GO annotation workshop will take place Tuesday 24th to Wednesday 25th April 2012, please book online if you are interested in attending.

Meetings attended

UCL hosted a successful GO Consortium meeting in November, which Ruth and Varsha organised and attended. Among the many GO issues discussed were the management of the GOC, improvements to term genie (a GO term generating tool), the annotation extension field, the apoptosis project, the development of a community annotation tool, and ontology development.

Upcoming meetings

Ruth and Varsha will be attending the GO Consortium meeting in February at Stanford, where the focus of the meeting will be annotation practice; improving consistency and the use of the annotation extension field.


Transcriptomic analyses of murine resolution-phase macrophages. Melanie J. Stables, Sonia Shah, Evelyn B. Camon, Ruth C. Lovering, Justine Newson, Jonas Bystrom, Stuart Farrow, and Derek W. Gilroy. Blood. 2011 Oct 19. PMID: 22012065

The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems. Yasmin Alam-Faruque, Rachael P. Huntley, Varsha K. Khodiyar, Evelyn B. Camon, Emily C. Dimmer, Tony Sawford, Maria J. Martin, Claire O'Donovan, Philippa J. Talmud, Peter Scambler, Rolf Apweiler, Ruth C. Lovering. 2011 PLoS ONE 6(12): e27541. doi:10.1371/journal.pone.0027541




Please register to receive this quarterly Newsletter by email