UCL Institute of Cardiovascular Science


May 2014


Editor - Ruth Lovering

New Recruits

We are pleased to welcome Dr Rebecca Foulger who joins the Parkinson's UK annotation team this month. Rebecca has extensive experience as both a Gene Ontology (GO) annotator and a GO editor, having worked on the GO project for over twelve years. For more information about the Parkinson's UK project please sign up for their newsletter.

We are also looking to recruit one more biocurator, following the departure of Anna Melidoni, and would be grateful if this newsletter could be circulated to anyone who might be interested in contributing to the cardiovascular annotation project. The post should be advertised early in May, full details via the UCL jobs website (searching with the word 'biocurator') and our website.

Gene annotation

Based on the EBI statistics, 12th April 2014, this project has associated over 30,000 GO terms to 4,100 proteins, 20,853 of which are to 2,358 human proteins. For a short time details of the numbers of annotations created by this project are being displayed in two rows in the current composition table at the EBI: 'Manual GO annotation by BHF-UCL' and 'Manual GO annotation by BHF-UCL for Automated Function Prediction SIG'. This is because we are contributing annotations to support to the second 'Critical Assessment of protein Function Annotation experiment'. The BHF team is supporting this experiment by manually curating proteins included in CAFA2, which are also on our cardiovascular priority gene list. The manual annotations we submit can then be compared to the predicted annotations generated by CAFA2.

In addition, we have submitted 660 protein-protein interactions (PPIs) to IntAct, from the curation of 104 papers, which are now exported to public PPI databases. Since February we have completed the re-annotation of papers describing WNT signalling, thanks to Anna for her hard work here, and have made substantial progress on papers describing lipid metabolism.

We are pleased to announce that the UCL Cardiovascular Gene Annotation Initiative is now listed on the IMEx consortium website as contributing PPIs, and our PPI annotations are available as a unique dataset using the EBI IMEx and EBI PSICQUIC browsers. A table and graph of the BHF-UCL submitted PPIs can be viewed, or downloaded, by clicking on the 'bhf-ucl' and selecting either the table or graph tab.

Community engagement

Over 30 biologists attended for our seventh 2-day Bioinformatics and GO Annotation Workshop, and the attendees submitted annotations for a variety of papers. This 2-day course provides hands-on training in the use of GO, as well as other bioinformatics resources, such as UniProt, Ensembl, IntAct and Cytoscape. If you would be interested in having this course run in your department/group please contact Ruth Lovering.


Meetings attended

Ruth attended the March GO Consortium (GOC) meeting in College Station, Texas. This was a very interesting meeting, some of the highlights included a demonstration of the new Molecular Modeling Environment tool, which will enable GO curators to build complex pathways describing protein function within a process, and the launch of the new GOC website, wiki pages and browser, AmiGO 2. Furthermore, Ruth led a productive workshop session that discussed the establishment of guidelines for the annotation of microRNAs.

Upcoming meetings

In June there are two London computational biology meetings: the 3rd RA Fisher Centre Meeting, and the annual CLMS symposium.

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