Towards a wiki of phylogenies

At the start of this week I took part in a biodiversity informatics workshop at the Naturhistoriska riksmuseets, organised by Kevin Holston. It was a fun experience, and Kevin was a great host, going out of his way to make sure myself and other contributors were looked after. I gave my usual pitch along the lines of "if you're not online you don't exist", and talked about iSpecies, identifiers, and wikis.

I also ran a short, not terribly successful exercise using iTaxon to demo what semantic wikis can do. As is often the case with something that hasn't been polished yet, the students found the mechanics of doing things less than intuitive. I need to do a lot of work making data input easier (to date I've focussed on automated adding of data, and forms to edit existing data). Adding data is easy if you know how, but the user needs to know more than they really should have to.

The exercise was to take some frog taxa from the Frost et al. amphibian tree (doi:10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2) and link them to GenBank sequences and museum specimens. The hope was that by making these links new information would emerge. You could think of it as an editable version of this. With a bit of post-exercise tidying, we got someway there. The wiki page for the Frost et al.
paper now shows a list of sequences from that paper (not all, I hasten to add), and a map for those sequences that the students added to the wiki:

Although much remains to be done, I can't help thinking that this approach would work well for a database like TreeBASE, where one really needs to add a lot of annotation to make it useful (for example, mapping OTUs to taxon names, linking data to sequences and specimens). So, one of the things I'm going to look at is dumping a copy of TreeBASE (complete with trees) into the wiki and seeing what can be done with it. Oh, and I need to make it much, much easier for people to add data.

When taxonomists wage war in Wikipedia

Stumbled across Alex Wild's post Pyramica vs Strumigenys: why does it matter?, which takes as it's starting point a minor edit war on the Wikipedia page for Pyramica .

Alex gives the background to the argument about whether Pyramica is a synonym of Strumigenys, and investigates the issue using the surprisingly small about of data available in GenBank. The tree he found (shown below) suggests this issue will require some work to resolve:

For fun I constructed a history flow diagram for the edits to the Pyramica page in Wikipedia:

The diagram shows the two occasions when the page has been striped of content (and subsequently restored) as contributors dispute whether Pyramica is a synonym of Strumigenys. It would be useful to have one or more metrics of how controversial a page (and/or a contributor) was, to both identify controversial pages, and to see how controversial taxonomic pages were compared to other Wikipedia topics. The paper On Ranking Controversies in Wikipedia: Models and Evaluation by Ba-Quy Vuong et al. (doi:10.1145/1341531.1341556) would be a good place to start (a video of the presentation of this paper is available here).

Gene Wiki and Google

Andrew Su has posted an analysis of Gene Wiki, a project to provide Wikipedia pages on every human gene:

Here's the take home message: in terms of online gene annotation resources, Gene Cards is the most common top-ranked resource, followed closely by the Gene Wiki / Wikipedia, with NCBI in a very distant third (note the log scale).

This result is interesting in that an existing resource (Gene Cards) beats Wikipedia, but only just. There are various ways we could interpret this, but from the point of view of biodiversity resources I suspect it emphasises that if there is a good, existing resource that has a lot of traction (i.e., Gene Cards) it will do well in Google Searches. If there is no single dominant resource (as is the case for biodiversity), then it leaves the field open to be dominated by Wikipedia.