UCL Institute of Cardiovascular Science


January 2015

Editor - Paul Denny

One of the themes of 2014 was how useful it has been for us to participate in conferences and workshops. At the Parkinson's UK Research Conference, Rebecca and Paul were inspired by what they learned about Parkinson's disease biology and also by the people who have to cope with the disease. Rebecca's presentation raised the profile of our project and drew some favourable comments and intriguing questions about capturing the context of experimental data e.g. proteins that interact only under conditions of stress. Rebecca also played a significant role at the 2nd Workshop on Systematic Curation of Molecular Pathways implicated in Parkinson's Disease, participating actively in a discussion group on the topic of the oxidative stress response. Both these meetings prompted us to add new priorities to our lists of proteins, relevant biological processes and papers to annotate and lead to the creation of new PD-relevant GO terms.

Gene Annotation

Our focus on annotating proteins involved in the biological processes of cellular response to oxidative stress, regulation of neuron death and synaptic vesicle transport ended early in October 2014. We have now switched to working on endoplasmic reticulum (ER) stress and the unfolded protein response, as well as mitophagy. Based on the EBI statistics, (January 3rd 2015), Ruth, Rebecca and Paul have associated 2490 GO terms to 534 proteins, including 268 human proteins.

Gene Ontology

Part of our project is aimed at improving the ontology for aspects of biology relevant to PD. With help and advice from the GO Consortium editors, we requested the creation of 153 new GO terms in 2014. Discussions are ongoing about further terms covering aspects of ER stress and mitophagy.

Community engagement

We are now using Twitter to communicate our work to a wider audience - follow us on @UCLgene. Furthermore, as part of a 'Bioinformatics' module within the UCL Genetics of Human Disease MSc program, we have been teaching students about Gene Ontology and other bioinformatics resources.

Call for contributions from the Parkinson's Community

Each time we complete annotations of proteins described in a single publication, we invite feedback from the authors; but we are, of course, pleased to receive feedback from other experts about missing or inaccurate annotations by email.

Meetings Attended

In October Ruth attended the GO Consortium meeting in Barcelona, contributing to many aspects of the wider goals of the consortium e.g. extending the richness of the Gene Ontology to allow curators to capture experimental data better. Rebecca participated in the 2nd Workshop on Systematic Curation of Molecular Pathways implicated in Parkinson's Disease, at the Luxembourg Centre for Systems Biomedicine in October and had discussions with the Parkinson's Disease map to co-ordinate curation efforts. Paul and Rebecca went to the Parkinson's UK Research Conference in York in November, where Rebecca gave a platform presentation. We both also talked about our project using a poster and a live demonstration of Gene Ontology resources, on a laptop.

Upcoming events

We will be hosting a Parkinson's UK project visit on March 31st. In April Paul will also discuss our work with members of the Cheltenham and Gloucestershire local branches of Parkinson's UK.

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