Wednesday, February 04, 2009

Wiki demo

Reading a recent TAXACOM thread (Species Pages - purpose) my sense is that some people are arguing that "species pages" would be time consuming to create, aren't much good for taxonomists (to quote Mike Dallwitz "In brief, to make simplified and attractive information about taxa easily available to casual users?"), and nobody gets credit for making them. In short, "they're not for me, I don't get credit for making them, so why bother?"

Others (e.g., Doug Yanega) see species pages -- properly constructed -- to be a research tool. If we extend this to its logical conclusion, we could envisage these pages being the primary source of information on taxa. Indeed, new taxa could be described in this way. In short, "this is the future of taxonomic publication".

One obvious way to realise species pages sensu Doug Yanega is using a wiki, but then there are those that horrified by the prospect of just "anyone" being able to edit that content. In short, "wikis are not for serious people, the ignorant might mess up my stuff". Others have had a more positive experience.

I realise this doesn't do justice to these positions, but this make things a little concrete, I've put together a demo based on a wiki I'm constructing. The aim of this wiki is to link together taxonomic names, specimens, images, classifications, publications, phylogeny, people in one place. It's a bit like a wiki version of my Elsevier Challenge entry.

This is some way off being ready for prime time, but I thought it might be useful to show the sort of thing that can be done.

As a starting point, is a page about Chromis circumaurea, one of the fish Rich Pyle et al recently described in Zootaxa. This page contains a map and some specimen images, and an abbreviated description copied from the Zootaxa article. The images and the map are generated automaticaly by the wiki, based on the links it has to the specimens, e.g.:

The USNM specimen is linked to a GenBank sequence . Specimens themselves are linked to Museum collections (using data from Biodiversity Collections Index ).

The name itself is linked to a publication:

which is also linked to the authors. The wiki supports GUIDs, so that you can link to the page about Chromis circumaurea using it's ZooBank LSID, for example:

What I hope this crude example demonstrates is a framework where we can support all the kinds of objects we care about, and easily create links between them that can generate useful information. For example, the page for Chromis circumaurea doesn't explicitly list the images shown, they are there because of the links between Chromis circumaurea, the specimens, and the images of those specimens. The same applies to the map. What this means is that very little information needs be entered, it's mostly a matter of joining the dots.

Note that these wiki pages already have more information than either iSpecies or EOL.

This example has been assembled by hand, but much of the data required can be entered automatically (e.g., for sequences, specimens, publications, etc.), and tools such as text mining or XML markup (e.g., TaxonX) could be easily exploited. I also realise that as it stands the demo has very limited information about the organism itself, but I don't this this as intractable.

If we could build things like this (and I believe we can, with a lot less effort than might be thought), the question becomes this the kind of "species page" that would be useful?


Anonymous said...

Great stuff! You're single-handedly demonstrating the vacuity of the whole EOL farce.

Karen said...

I think this is the direction that we need to go. I do wonder about the balance between information for expert and non-expert users. The former seems more amenable to automated links to external databases / publications. For non-experts, I think the pages need (at minimum) a descriptive paragraph that answers the question "what IS this thing?".

Pete DeVries said...

Very Cool!
I like the idea of using a Wiki model for this. The one issue that I had for our users was if learning WikiMarkup would inhibit them from contributing.
I liked the confluence wiki software because of it's WYSWIG editor but is not free, does not currently have semantic web extensions and runs slower on the same hardware as MediaWiki.

Awesome Demo!

Udi Oron said...

Very nice!

Following all your twitter msgs, I have been wondering when you will give us a sneak preview...
Waiting to see how are you going to import and implement classification(s)...


Anonymous said...

I still think that there is an use for both kinds of "species pages". There has to be an open one, of course, but the necessity and the quality of the information from cured species pages is analogous to the situation the protein databases faced some years ago.
They seem to be living OK with both. So do the astronomers. Why can't we?

Wikis go chaotic pretty quickly. If you want an example, check out the wikipedia in Portuguese.