Gene Wiki and Wikidata: an overview of 2015

2015 was a busy year for the Gene Wiki/Wikidata team—a naturally collaborative and evolving group of researchers from our lab, UCLA, the University of Maryland, Micelio, and more. The team imported about 132 thousand genes (59,530 human, 73,130 mouse) from NCBI into Wikidata and about 44 thousand proteins (27,662 human, 16,728 mouse) proteins from Swissprot. In addition to importing human and...
read more

Poof it works – using wikidata to build Wikipedia articles about genes

The Gene Wiki team has been hard at work filling wikidata with useful content about genes, diseases, and drugs using the new and improved ProteinBoxBot.  Now, we are starting to see the fruits of this labor in the context of Wikipedia. Infobox for ARF6, rendered entirely from content WikidataThe Gene Wiki project has programmatically created and maintained the infoboxes to the right of all...
read more

1st BD2K/3rd Network of Biothings Hackathon Recap

Let me clarify one thing from the start: My programming skills are extremely limited. That said, I was still very curious as to what a hackathon would be like and concerned about whether or not I’d be able to find a project to which I might make some sort of contribution. 2015.05.07 The first night of the hackathon was the meet, greet, and project pitches. Of the 45 or so people that...
read more

Open source, open science, citizen science – Join us!

If you follow our lab at all you’ve probably noticed some themes emerging in how we approach bioinformatics and biomedical research. To enumerate a few of those themes, we believe in: Open source: We have benefited from the long tradition of open source software in bioinformatics, and we in turn release code through our lab’s open source repositories. We have a particular emphasis on...
read more

BioGPS Featured Article – Study of five novel non-synonymous polymorphisms in human brain-expressed genes in a Colombian sample

BioGPS has become the valuable resource that it is because of the contributions from our wonderful user community. Thank you for contributing plugins, suggestions, and ideas–all of which have improved BioGPS for everyone. In order to celebrate the contributions of BioGPS users to the scientific research community, this series will feature publications and articles generated by BioGPS...
read more

Wikipedia as a basic scientific reference

Wikipedia is probably the most current, extensive, and accessible knowledge base available. Currently, there are over 10,000 Wikipedia entries for human genes of interest thanks to the Gene Wiki project and the contributions of the dedicated and altruistic Wikipedia community. Unfortunately, many of these articles are out-of-date or are just stubs in desperate need of content. If you are in...
read more