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.

The first examples of this program in action are already online. The journal is hosting an open access paper that describes a family of RNA molecules found in nematode worms; a corresponding Wikipedia page is already in place. In good Wikipedia form, the phylogenetic analysis of these RNAs is dinged for not providing citations, while the article as a whole is flagged as having excess jargon. (The talk page hosts an interesting discussion of how much jargon can possibly be eliminated from a highly technical description like this.)

So far, everyone is happy with the results. A few scientists have started updating the scientific content of the RNA entries, while the usual Wikipedia denizens have helped out in terms of catching typos and improving the formatting. The people backing the project expect that it will be immune to some of the issues that plague other Wikipedia entries; Nature quotes one of the biologists as saying, “”We don’t think vandalism will ever be as much of a problem for a Wikipedia page on transfer RNAs as it is for a page on George Bush.”

And looking at that one entry, it does seem to. But I have a question, if researchers are soon required not only to submit and/or annotate in a database and to wikis and curate and annotate if they wish to publish, doesn’t this start to place an undue burden on researchers who already have grant writing, teaching, and more in addition to actual research? There does need to be a solution to the growing need for curation and annotation of data, it will be interesting to see if this is one solution that will hold.

The Gene Wiki, like the proposal for the ‘wikification of GenBank‘ and the now online Encyclopedia of Life, is an attempt to harness the power of the community to provide the community with a wealth of annotated information

But, even as the authors admit, the Gene Wiki’s success so far has been muted. Part of the solution to make this a more useful tool is reported in this paper. The authors seeded the gene wiki with entry data from Entrez Gene. This is based on the observation that editors are more likely to add or correct information on a pre-existing article than they are to create a new one. So far the success of this effort of seeding hasn’t been shown (but as the authors suggest, this is recent and as of this paper wasn’t announced).

The authors reference the  Nature article comparing Wikipedia vs. Encyclopedia Britannica showing that Wikipedia stacked up well. I’d caveat that, these were for the most ‘basic’ science comparison, comparisons of scientific concepts that would be expected a college student might get correct. But the authors are suggesting a wiki for something much more complex and deep, the annotation of a gene. Even with the basic comparison, Wikipedia only compared favorably in the sense that it didn’t do nearly as badly as many would expect and only almost as good as Encyclopedia Britannica. Research needs something more than this.

And this would bring me to what I consider the biggest hurdle. The Gene Wiki project is deep and complex science. Wikipedia is doing reasonably well in ‘general science’, but I’m not so sure the model will work for this kind of science. I’m not sure Wikipedia is the venue for this (a similar concern voiced by BBGM) or will be able to bring the level of completeness and accuracy required by scientific research. Wikis have found uses and success, but for every successful wiki, there are a few hundred (thousand) failures littering the internet landscape. For success, a wiki needs a readership knowledgable enough and large enough not only to contribute but to keep data accurate. Too small or too many unknowledgable people adding to an article allows too many errors to creep into and, more importantly in a wiki’s success, to remain in the wiki. I’m not convinced the knowlegable readership of a gene wiki will be large enough.

Perhaps I’d use it like I use Wikipedia now for general use, a starting off point for information and research, but one I never use as a definitive source or reference.

And that is what the authors state in the end:

Importantly, this gene wiki effort  is not meant to be a substitute for existing resources. Gene portals and model organism databases will continue to serve as authoritative references with a specific role for data curation and enforcement of data standards. Moreover, the structured and typed data in gene portals is amenable to incorporation into pipelines and systematic analyses in  a way the information in a gene wiki cannot [22]. Most importantly, because articles are dynamic and not subject to rigorous peer review, the gene wiki is not intended to be a reference that is cited in a traditional peer-reviewed article or used exclusively as a source of gene annotation. Nevertheless, we believe that this gene wiki will be a valuable launch pad for collaboratively summarizing knowledge, and we expect that scientists will synergistically use the gene wiki with traditional gene portals.

Huss, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., Su, A.I. (2008). A Gene Wiki for Community Annotation of Gene Function. PLoS Biology, 6(7), e175. DOI: 10.1371/journal.pbio.0060175

a scheme like those used in herbaria and museums, where specimens often have multiple annotations: listing original and new entries side by side. It would be a community operation, like Wikipedia, in which the users themselves update and add information, but not anonymously.

But the idea is meeting resistance from Genbank’s Managers:

GenBank’s managers are dead set against letting users into GenBank’s files, however. They say there already are procedures to deal with errors in the database, and researchers themselves have created secondary databases that improve on what GenBank has to offer.

But would this work? In Francis Collins’ talk at the GenBank anniversary he mentions the proposal though isn’t sold (video, at 2hr 22min). But Steven Salzberg suggests in an opinion piece in Genome Biology last year that the current solution isn’t working and one possible solution is to add a layer of ‘wiki’ to the database.

“Wikifying” a genome database or Genbank would be one more step beyond even what TAIR is doing. TAIR hopes that authors will curate the database and save on time and money spent on curators. But there is some concern that this might not work as planned.

Though wikis have been quite successful in some instances (of course wikipedia being an example), the internet is littered with dead wikis that never got the community support to keep them going successfully. It is also littered with wikis filled with inaccuracies, spam links, bad information and turf battles. If a wikified GenBank went the way of a lot of other wikis, the solution to fix inaccuracies might be worse than the original problem.

The wikification of GenBank would be allowing only credentialed editors make changes I suppose, but in reaction to a suggestion for academics with research credentials to enroll as identifiable editors of Wikipedia (in order to increase the accuracy of those articles), one blogger writes:

There’s nothing nastier or more tenacious than credentialed scholars squabbling about their area of research.

He might have a point, though this is GenBank and sequences, not the minutiae of population genetics (I’ve seen some quite acrimonious discussions there!) . Perhaps a way could be made for a ‘wikified’ layer of genbank and I can definitely see the usefulness. Wikis can be a great tool for the right community and subject.

It’s all about finding that info!