May 2015

Editor - Ruth Lovering

Gene annotation

We are pleased to announce our first release of GO annotations describing the biological roles of microRNAs (miRNAs). Previously, we have concentrated on providing annotations to proteins and, more recently, macromolecular complexes. In November we began a project to curate miRNAs that are involved with cardiovascular development and related processes. In conjunction with this effort we have curated the roles of the key human proteins that are involved in miRNA processing, such as Drosha and Dicer. Inevitably, new GO terms have also been created to enable descriptive annotation of the proteins involved in miRNA processing and the miRNAs themselves, such as "pre-miRNA transporter activity" and "endoribonuclease activity, cleaving miRNA-paired mRNA".

The RNA annotations are available in the regular GOA release files (available from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/) and in AmiGO2 e.g. miR-133a). Furthermore, these annotations will soon be available in the new version of QuickGO. There are currently around 115 annotations provided by the UCL team to RNAcentral identifiers, but this is due to increase substantially as the project progresses.

Based on the EBI statistics, 25th April 2015, this project has associated over 33,000 GO terms to 4,600 gene products, 22,912 of which are to 2,542 human gene products. In addition, we have submitted 1,158 protein-protein interactions (PPIs) to IntAct, from the curation of 131 papers. All of our annotations are exported to public databases.

Community engagement

38 scientists attended our eighth 2-day Bioinformatics and GO Annotation Workshop in April. With such a large group to teach, four of us were involved to ensure someone was available to assist people with the hands-on exercises. The workshop provides an introduction to bioinformatics tools and instruction on how to functionally annotate papers using GO. Many of the attendees brought papers they had authored to annotate and showed great interest in the curation process. We received very positive feedback on the workshop and have plans to increase our repertoire of bioinformatics workshops - watch this space!

We are also pleased to announce that we have been awarded a UCL CALT small grant for educational development of £750, to enable us to improve the teaching materials for our MSc Bioinformatics module.

Meetings attended

In March, Ruth presented a poster, in a poster discussion session, entitled: The Cardiovascular Gene Annotation Initiative: Impact on Data Analysis at the 83rd European Atherosclerosis Society Congress, in Glasgow. There was some discussion afterwards, which led to Ruth highlighting that the functional analysis tool DAVID has not updated the annotation data it uses for over 5 years.

Publications

Upregulation of gingival tissue miR-200b in obese periodontitis subjects. Kalea AZ, Hoteit R, Suvan J, Lovering RC, Palmen J, Cooper JA, Khodiyar VK, Harrington Z, Humphries SE, D'Aiuto F. J Dent Res. 2015 Mar;94(3 Suppl):59S-69S. PMID: 25630869.

Gene Ontology Consortium: going forward. Gene Ontology Consortium. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. PMID: 25428369.

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