Tuesday, February 07, 2006

TreeBASE talk at CIPRES

On Saturday I gave a short invited talk at the CIPRES all hands meeting in Austin. Not sure if I'll be invited back after this, but I think it was worth saying a few things that somebody, somewhere should be saying. You can grab the PowerPoint slides here. To give you a sense of the talk (and the style in which it was intended), here's the abstract:

The current TreeBASE is a black hole -- data disappears in and is difficult to extract again. Furthermore, no use is made of the wealth of information that could be linked to data in TreeBASE. The only external links TreeBASE contains are author email addresses. Yet, given a GenBank sequence or a paper title one can go to the Internet and readily extract information on genes, specimen localities, PubMed records, citation links, images, taxonomic authorities, etc. The search interface is limited, and locks users into primitive and often fruitless searches. TreeBASE is a walled garden in a time when the world is discovering data integration, federated searches, and "mashups." Designing new, improved (read bigger) relational database schema does nothing to address these issues. If the community wants a useful tool that tells us what we know (and what we don't know) about the tree of life, and enables the kind of integrated research that we systematists so often say is only possible with a phylogenetic underpinning, then I suggest we need something rather different. This talk will sketch some problems with TreeBASE, discuss some ideas relating to globally unique identifers, metadata, inference, and the Semantic web, and will end with the author running from the room hotly pursued by Bill Piel.

Apart from biological gripes, I was also a little surprised that some of the stuff from the early days of "phyloinformatics" wasn't being picked up on, especially the idea of a phylogenetic query language (e.g., Jamil et al., BIBE 2001 doi:10.1109/BIBE.2001.974405) (and, no, I don't think a CORBA wrapper constitutes a phylogenetic query language).


Vince Smith said...

Rod, I think this ppt file is corrupt. PowerPoint whinges about it on both my mac and pc.

Rod Page said...

I've uploaded it again, this time as a ZIP file. You can get it here. Thanks for pointing this out.