Broken URLs
The old TreeBASE had a URL API, which databases such as NCBI made use of. For example, the NCBI page for Amphibolurus nobbi has a link to this taxon in TreeBASE. The link is http://www.treebase.org/cgi-bin/treebase.pl?TaxonID=T31183&Submit=Taxon+ID. Now, this is a fragile looking link to a Perl CGI script, and sure enough, it's broken. Click on it and you get a 404. In moving to the new TreeBASE II, all these inward links have been severed. At a stroke TreeBASE has cut itself off from an obvious source of traffic from probably the most important database in biology. Please, please, throw in some mod_rewrite and redirect these CGI calls to TreeBASE II.
New identifiers
All the TreeBASE studies and taxa have new identifiers. Why? Imagine if GenBank decided to trash all the accession numbers and start again from scratch. TreeBASE II does support "legacy" StudyIDs, so you can find a study using the old identifier (you know, the one people have cited in their papers). But there's no support for legacy TaxonIDs (such as T31183 for Amphibolurus nobbi). I have to search by taxon name. Why no support for legacy taxon IDs?
Dumb search
Which brings me to search. The search interface for taxa in TreeBASE is gloriously awful:
So, I have to tell the computer what I'm looking for. I have to tell it whether I'm looking for an identifier or doing a text search, then within those categories I need to be more specific: do I want a TreeBASE taxon ID (new ones of course, because the old ones have gone), NCBI id, or uBio? And this is just the "simple" search, because there's an option for "Advanced search" below.
Maybe it's just me, I get really annoyed when I'm asked to do something that a computer can figure out. I shouldn't have to tell a computer that I'm searching for a number or some text, nor should I tell it what that number of text means. Computers are pretty good at figuring that stuff out. I want one search box, into which I can type "Amphibolurus nobbi", or "Tx1294" or "T31183" or "206552" or "6457215" or "urn:lsid:ubio.org:namebank:6457215" (or a DOI, or a text string, or pretty much anything) and the computer does the rest. I don't ever want to see this:
Computers are dumb, but they're not so dumb that they can't figure out if something is a number or not. What I want is something close to this:
Is this really too much to ask? Can we have a search interface that figures out what the user is searching for?
Note to self: Given that TreeBASE has an API, I wonder how hard it would be to knock up a tool that took a search query, ran some regular expressions to figure out what the user might be interested in, then hit the API with that search, and returned the results?
My concern here is that TreeBASE II is important, very important. Which means it's important to make it usable, which means don't break existing URLs, don't make old identifiers disappear, and don't have a search interface that makes me want to pull my hair out.