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August 2017

Editor - Ruth Lovering

New Biocurator to join the team

We are pleased to welcome Vanessa Acquaah to our biocuration team in September. Vanessa has been working on her MSc project with us since January and will join us for an additional three months to continue curation of cardiovascular-related miRNAs.

BHF-funded miRNA Gene Ontology (GO) annotations now available from Ensembl and NCBI

After working with the teams at Ensembl and NCBI, we are pleased to announce that our miRNA GO annotations are now incorporated into these resources. This is a significant achievement, enabling cardiovascular researchers worldwide to access miRNA functional annotations to further their research. For examples, see human miR-21 annotations in Ensembl and human miR-1 annotations in NCBI-Gene.

Gene annotation

Nancy added an impressive 354 molecular interactions to the IntAct database by curating a recent BHF-funded paper entitled: ‘Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signaling and Angiogenesis’ written by our colleague Dr Ian Evans. Whereas Rachael created GO annotations for another BHF paper, ‘Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation’ written by Manuel Mayr’s group. This was the first proteomics study to analyze the human cardiac extracellular matrix and Rachael used GO annotations to describe the location of 95 proteins in the extracellular matrix of the atrial appendages of the myocardium. We would be happy to annotate any suitable papers sent to us directly by email (goannotation@ucl.ac.uk). Annotated papers have an increased exposure, as they are then linked from gene/protein specific web pages at many popular knowledgebases including: NCBI-Gene, UniProt, Ensembl and GeneCards.

A combined effort by the annotation team has led to the comprehensive annotation of lipid metabolism and transport. We have been annotating proteins involved in lipid processes for the past 10 years, however the recent launch of Swiss-Lipids provided a mechanism to check all proteins associated with lipid processes had been annotated. We were pleased to find 90% of the 449 Swiss-Lipids proteins were associated with a lipid relevant GO term, and we completed the annotation of the remaining 10% this month, these new annotations will be available in September via QuickGO.

Based on the EBI statistics, 1st July 2017, the cardiovascular gene annotation team has associated 41,663 GO annotations with 6,032 gene products, 28,764 of which are to 3,432 human gene products.

Introduction to Bioinformatics workshop

Following our successful June workshop, attended by more than 40 staff and students, Nancy has completed checking community annotations contributed by attendees. The annotations were impressive in quality and quantity which shows the relative ease with which bench scientists can learn how to curate their own papers and benefit from the added value that brings to them, as well as the scientific community. For example, a BHF-funded paper was annotated by Laura Denti, a member of the Ruhrberg Lab at UCL Institute of Ophthalmology.

Meetings attended

In June, Rachael attended the Translational Bioinformatics conference at the Wellcome Genome Campus in Hinxton, where she presented a poster entitled ‘Functional Annotation of Cardiovascular microRNAs with GO’. The GO Consortium meeting, in Corvallis, was attended by Ruth, where she presented further modifications to the transcription factor annotation guidelines. One of the key issues discussed at this meeting was the removal of single step processes from the ontology, which duplicate molecular function terms, such as ‘phosphorylation’ and ‘kinase activity’.

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