November 2007 Monthly Report

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Ruth Lovering


I have met up with Drs Aroon D Hingorani and Tina Shar, Department of Medicine, UCL on Tuesday 27th November. They are working on Pharmacogenetics (see PMID: 16359930). They are currently reviewing the Pharmacogenetic literature associated with approx 1000 genes. I have encouraged them to classify these genes using GO terms (little demonstration of g:profiler). We are looking at whether any of the functional information they accumulate can be incorporated into the GOA database.

Cardiovascular processes

I provided a list of genes associated with Cardiovascular processes to Dr Andrew Smith, Centre for Cardiovascular Genetics, Department of Medicine, UCL, although I didn't really explain much about GO to him. He was already familiar with GO.

I am meeting with Mike Dunn, UCD, on 18th December and hoping this month to meet with Brendan Keating (University of Pennsylvania) who has developed a Cardiovascular specific illumina chip and has supplied us with a list of 2000 CV related genes.


Rachael Huntley and Emily Dimmer gave a talk and tutorial on GOA as part of the Wellcome Trust Advanced Course in 'Proteomics Bioinformatics' which was held on the 19th November 2007

Jennifer Deegan and Emily Dimmer met with Esther Schmidt to discuss the conclusions of the Princeton Consortium meeting on how Reactome can send annotations to GO. Emily explained the conclusions to Esther and Esther is going to write some scripts to produce their annotations in the correct formats.


The Plant Physiology Journal have agreed with TAIR that they will incorporate a submission form into their online submission process that will capture the AGI number of the gene/s the paper talks about and any functional information that the paper asserts. It's an online version of the submission form on the TAIR website. The info requested is of a format that is neither TAIR nor Arabidopsis specific so it could be used for SGD or MGI or any other MOD requesting the same type of information for their organisms' genes. (Just the MOD-specific db identifier would change.) - Contact Tanya Berardini for more details.