TreeBASE II makes me pull my hair out

I've been playing a little with TreeBASE II, and the more I do the more I want to pull my hair out.

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.

Linked data part 2

Continuing the Friday folly theme, below is a screencast of a linked data browser that uses the same ideas as last week's screencast, but uses a custom browser I've written to display the results in a more user-friendly way.

Linking the data together from Roderic Page on Vimeo.

The demo is live, you can view it at http://iphylo.org/~rpage/browser/www/uri/http://bioguid.info/doi:10.1371/journal.pone.0001787. Under the hood the browser uses bioGUID as the primary linked data provider (although it should consume any valid linked data source, for example Dbpedia). The data is stored in a local triple store (ARC), and the web interface is created by transforming SPARQL queries into HTML using XSLT. You can add data to it by editing the URL in the browser location bar and reloading the page, or entering a URL on the page. Linked data URLs be entered next to the Browse button as is, e.g. http://dbpedia.org/resource/Euphausia, or appended to http://iphylo.org/~rpage/browser/www, e.g. http://http://iphylo.org/~rpage/browser/www/http://dbpedia.org/resource/Euphausi. Other identifiers, such as DOIs, PubMed ids, and specimens need to be resolved via bioGUID, e.g. http://iphylo.org/~rpage/browser/www/uri/http://bioguid.info/gi:86161637.

All still very crude, but I hope you get the idea.

NCBI Taxonomy IDs and Wikipedia

I've written a note on the Wikipedia Taxobox page making the case for adding NCBI taxonomy IDs to the standard Taxobox used to summarise information about a taxon. Here is what I wrote:

Wikipedia's taxon pages have a huge web presence (see my blog post Google and Wikipedia revisited and Page, R. D. M. (2010). "Wikipedia as an encyclopaedia of life". Nature Precedings hdl:10101/npre.2010.4242.1). If a taxon is in Wikipedia it is almost always the first search result in Google. Researchers in other areas of biology are making use of a Wikipedia as a tool to annotate genes Gene Wiki and RNA families Wikipedia:WikiProject_RNA, respectively. Pages for genes, such as Cytochrome_b, have numerous external identifiers in their equivalent of the Taxobox (the Pfam_box). I think we are missing a huge opportunity by not including NCBI taxonomy ids. The advantages would be:

• It would provide a valuable service to Wikipedia readers by enabling them to go to NCBI to discover more about a taxon


• It would help Wikipedia contributors by providing a standardised way to refer to NCBI (and enable bots to add missing NCBI taxonomy ids). Putting them in an External links section makes it harder to be consistent (there are various ways to write a URL linking to the NCBI taxonomy)


• It would facilitate linking from NCBI to Wikipedia. A mapping of Wikipedia pages to NCBI taxonomy ids could be added to NCBI Linkout, generating more traffic to the Wikipedia pages


• Projects that are trying to integrate information from different sources would be able to combine information of genomics from NCBI with other information much more readily

Note that I am not arguing that Wikipedia should "follow" NCBI taxonomy, merely that where the potential to link exists, the links would create value, both within and outside the Wikipedia community.

Some discussion has ensued on the Taxobox page, all positive. I'm blogging this here to encourage anyone who as any more thoughts on the matter to contribute to the discussion.