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---------- Forwarded message ----------
From: Parijata Mackey <parijata@gmail.com>
Date: Wed, Mar 17, 2010 at 12:26 PM
Subject: CHDWiki - Or, Someone Finally Built A Collaborative Genetics Portal That May Not Suck.
To: DIYbio <diybio@googlegroups.com>


Morning, guys! :-)

This might be interesting. Some new Wiki portal for "collaborative annotation and analysis of congenital heart defects" is being said to "highlight the potential of this technology for systems biology studies of other complex biological processes" (BioMed Central). It's called CHDWiki, and it's accessible here. [Barriot et al. (2010) Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome Medicine. 2:16 doi:10.1186/gm137]

"This study describes the first specialized portal to collaboratively annotate and analyze gene-phenotype networks. Of broad interest to the biological community, we argue that such portals will play a significant role in systems biology studies of numerous complex biological processes."

The (open access) article, recently published in Genome Medicine, seemed a bit... overenthused -- we've gotten so used to these things failing. But, after a quick tour of the place, I was pleasantly surprised: there are real tools; real data; it's real. They've been around for a little while, and have built up something of a user base. If they can maintain it or grow it, they might actually do something; it's one of the rare DIY/collaborative biology projects I'd bet something on. Check it out. God knows we can learn from it...

"How to efficiently integrate the daily practice of molecular biologists, geneticists, and clinicians with the emerging computational strategies from systems biology is still much of an open question.... This study describes the first specialized portal to collaboratively annotate and analyze gene-phenotype networks. Of broad interest to the biological community, we argue that such portals will play a significant role in systems biology studies of numerous complex biological processes."

To avoid the dreaded "Tower of Babel of internet-enabled tools," these guys manually built a CHD ontology, linking and categorizing 139 phenotypic defects to the relevant genes found on OMIM and Medline (bioinformaticists everywhere just winced). From the article: 

“Relevant genes and mutations were selected and their corresponding cardiac phenotype were manually gathered and described based on the available literature. The level of support for a gene-phenotype link was defined by its incidence and the number of independent publications reporting it. We only considered such links confirmed if at least two reports from independent groups described the incidence of CHD in patients with a mutation to be greater than 1%. Moreover, the support for the link between every single gene mutation and CHD type was further characterized based on the genetic evidence (inheritance and incidence), in silico predictions, and the functional studies (in vitro analysis and animal models) described in the study.”

“Specific components already available include: numerous data retrievers from our local databases; a chromosome map summarizing genes and genomic regions linked to CHDs; pie chart generation; gene network visualization and exploration; and candidate gene prioritization. This variety of components illustrates the versatility of the approach... More generally, the generic extension proved successful in the fast development of new components working as wrappers for databases, web services, command line tools, and DAS (Distributed Annotation System) servers [16].”

“…In addition, CHDWiki interacts with a patient data repository, CHDBench [15] , for managing patient data published in the literature, and a DAS server [17] feeding CHD genes and genomic regions has been set up to allow one to loop from CHDWiki to the Ensembl genome browser and back.” 

“When more Wiki portals such as CHDWiki are available, the problems of interoperability of these systems and integration of stored knowledge can be managed through standard protocols such as DAS for data access, web services for the programmatic use of knowledge, or dedicated application programming interfaces (APIs), which will have to be further specified by the community. The component-oriented architecture of CHDWiki will make such future developments easy to implement.”

And a refreshing sentence:

“The authors had full access to the data and take responsibility for its integrity.”

Check it out, I'd love your thoughts. This might not fail, if they get support. And if you know nothing of heart disease, you'd probably benefit from looking at their infrastructure, see if there are any tools you can use for a different project.  This CHDWiki portal may not be perfect, but they’ve done a lot of good work, in the right directions. Let’s see what we can do about it...

And if nothing else, it can really help us -- just knowing that something out there is working could do wonders for morale. There's a momentum famine in this community, it's painful to watch; we're always hearing that it's just "too soon" for DIYbio.

And so far, that's been true. But... this, unlike many things, could be a real starting point -- something material, something serious, something organized, something easy... Something we can point to; something with real results; if we take that chance. Technological progress yanks us at a breakneck pace towards that critical point in history, when excuses fall away, and it becomes solely our job to convince the world it isn't "too soon" any longer. 

So let us go forth! Fortes fortuna iuvat; varitatio delectat; sciencia est qui vivificat; all those good things... I wonder, will we make anything happen? (If yes, turn to page 42. If no, turn to page 13.)
Cheers for now,
Jata :-)
---
Parijata Mackey
University of Chicago
parijata@uchicago.edu
www.parijata.com]]

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