UCL Institute of Cardiovascular Science


Issue 17 - April 2012


Editor - Varsha Khodiyar

Gene annotation

Based on the EBI statistics, 28th March 2012, this project has associated almost 24,000 GO terms to 3,300 proteins, 16,800 of which are to over 1,960 human proteins. Included in these figures are the annotations of proteomic paper creating 53 annotations describing the extracellular location of 53 pig proteins, and, based on orthology, the annotation, of 64 human proteins. In addition, Varsha has been working on annotating genes involved in the determination of heart left/right asymmetry. So far she has associated this term (or it's child terms) with 20 human proteins. The majority of these annotations were actually based on experimental evidence describing a variety of mammalian orthologs. Varsha would be grateful for any papers to annotate which describe the experimental association of this process with specific genes. Ruth intends to annotate cardiac conduction processes in the coming months, and experimental papers describing genes involved in either of these processes would be appreciated. Papers can be sent to the CV GO annotation team either via our feedback form or by email.

Gene Ontology

83 new GO terms describing cardiac conduction were released last month, with many more expected, which will describe the regulation of cardiac conduction by hormones and neurotransmitters. This brings the total number of GO terms created through the focused annotation of cardiovascular-relevant genes to 1500.

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The QuickGO browser has recently been updated so that all of these terms display a statement confirming that funding from the BHF supported the creation of the term. Thanks to the GOA team (particularly Tony) for organising this!


Community annotation

Later this month, we will be running our fourth GO Annotation Workshop (24-25th April). This workshop is open to all biological or biomedical PhD and Post-Doc research scientists and aims to boost attendees understanding of bioinformatics resources and their use. In addition attendees will have the opportunity to improve the profile of their papers in the world's leading biological databases, such as NCBI Gene, UniProt and GeneCards and analyse some high throughput datasets. Please register for the April workshop, or contact us if you are interested in attending a future workshop.

Meetings attended

In February, Ruth and Varsha attended the GO Consortium meeting at Stanford University. The focus was GO annotation, and thus several model organism database curators new to GO also attended. Amongst the issues discussed, was the question of how the central GOC can help curators, how to increase consistency in GO term annotation between different curation groups, and how specific ontology development projects (such as the apoptosis and transcription overhauls) have impacted on GO curation efforts.

In March, Varsha attended the 34th London Vascular Biology Forum at St Thomas' hospital, where the focus of the meeting was imaging endothelial dysfunction.

Upcoming meetings

In June, Ruth will be attending the Human Variome Project Biennial Meeting, taking place in Paris. Ruth and Varsha will be attending the UCL Computational Life and Medical Sciences Symposium, also taking place in June.





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