The OpenHelix Blog

In the continuing effort to get scientists and researchers to annotate and curate data and to capture the huge amount of knowledge available, UCSC Genome Browser has added a wiki annotation track to the browser. It’s not the first effort of course, GeneWiki is an effort, with mixed results so far, to annotate gene function information as a community exercise using Wikipedia. Some journals are requiring wiki entries, and several databases have opened wikis for curation. Wikis could be a solution for capturing the exponentially increasing amount of data,

or they could be just another place for adding confusion… or both. I suspect out of the plethora the wikis coming available for annotation and curation of genomic data, something will stick and find that Goldilocks balance of a dedicated community, ease of use, usability, and other aspects that will be needed for this to work.

Perhaps UCSC Genome Browser has that balance. It will remain to be seen, but let’s get started. Today’s tip is introducing the new wiki track in the UCSC Genome Browser.

I wish I had more time to go into this paper in more detail–but I wanted to let you know that the paper is out there now.  It came in my recent Nature Methods in paper version, and if I wasn’t crazy busy on a very cool project that we hope to launch this week I’d go deeper….

The paper is:  Literature-curated protein interaction datasets by Cusick et al. Nature Methods 6, 39 – 46 (2009)  2008 | doi:10.1038/nmeth.1284

I knew from the abstract that it was going to cause some conflama. And I was right.  Soon after an article in Bioinform addressed some of the issues.  Requires a subscription, but here’s the title and the link if you do have one:  Study Finding Erroneous Protein-Protein Interactions in Curated Databases Stirs Debate, by Vivien Marx.

This paper gets at a question that people ask us all the time–how do I know which database to use for X purpose?  So if your question is which database to use for protein interactions, you should read this paper and consider the points they make.   They don’t compare all protein interaction databases, of course–but for those they do examine (IntAct, DIP, MINT) they provide informative comparisons that you should consider for any database.  What does it contain?  What is it missing?  They have some nice Venn diagrams to illustrate the content.  The one I used here is just a representation of that, not attempting to be accurately proportional, go to the paper to see the real ones.

Our position is that you should use all of them, of course    Project goals and funding issues, species specialties, scope…all of this impacts what will be in a database.  (In fact, please go to MINT and support their funding by signing their protest of funding cuts).

One point embedded in the paper caught my attention, though.  One major curation issue was that the species designation of the protein in the interactions was not clear.   I know sometimes this is a problem with the original source paper.  Sometimes it is a curation issue.  But this worries me because of the concern I raised with Wikipedia gene entries.  I made the point that there was no way to distinguish between human genes and mouse genes of the same name (MEF2/Mef2).  This could be true of similar genes in other species too–where the gene might not even be the same gene, just a naming coincidence. I can see it has arisen again.  But if we expect to rely on Wikification projects like Gene Wiki for more and more, I think that would need to be addressed.

PLoS Biology has an article out today entitled “A Gene Wiki for Community Annotation of Gene Function.” The article describes the authors attempts to create a comprehensive gene wiki of gene functions by ’seeding’ Wikipedia with a foundation of ’stub’ articles with information from existing databases (such as Entrez Gene). This foundation would then be built upon in Wikipedia fashion by community editing.

Bioinformatics and Genomics sometimes (always?) brings together two very different groups: biologists and computer scientists. They are often biologists who know something about computers and computer scientists who know something about biology and sometimes they are computational biologists who do both. We (OpenHelix scientists) train biologists who want to use genomics tools that computational biologists (or a team of computer scientists and biologists) have developed. Sometimes those biologists want to do more and sometimes computer scientists need to learn a bit of biology. So, in that vein…

ScienceRoll links to a search engine for Radiology, links to a post about a “Gene Wiki” project, from which I re-find the excellent blog by Deepak Singh. From there I find this interesting resource: FreeBase, which is different that Wikipedia (it doesn’t have ‘articles’, it has stats), which reminds me of that Google project I mentioned earlier and leads me to GoogleBase.

It’s all about finding that info!