Saturday, December 24, 2005

The Modern Palimpsest

Leigh Dodds included iSpecies in his recent post on the scientific paper as modern palimpest. He writes:

iSpecies is a nice example of a science "mashup" that illustrates an alternative search interface for finding related content. I used the false results that can appear when performing simple keyword searches to reinforce the need for standard identifiers. (The need for a common, scoped identifier for authors, is a particular hobby horse of mine).

Among the false results is the image of oil tanker (among other things) that Yahoo provides when searching for "Apus apus."

Friday, December 23, 2005

Character coding issues with Google Scholar

Tanja points out that results for articles with German titles can look awful (e.g., try searching on Erica inflata). This is a problem with Google Scholar, which corrupts the characters. To verify this, do the search directly in Google Scholar. A workaround, if one had time, would be to screen scrape some of the source sites. For example, Springer's web site could be scraped to get the correct title, and a DOI. One more thing for the to do list...


NatureServe, a "non-profit conservation organization that provides the scientific information and tools needed to help guide effective conservation action" have announced an XML schema for their proposed web service. NatureServe's focus (I think) is on rare and endangered species in North America, but some of their data and/or schema may be useful for iSpecies.

Friday, December 16, 2005

Science NetWatch

Science magazine's NetWatch column for 16 December 2005 mentions iSpecies.

Thursday, December 01, 2005

The Simplicity of the Semantic Web

This is simply to remind me of where iSpecies needs to be heading...

Sunday, November 06, 2005

Nodalpoint notices

iSpecies was blogged by "Greg" at Nodalpoint, which carried some earlier discussion about LSIDs.

Curiously, LSIDs pop up again:

What is also cool is that each species has RDF formated metadata associated with it via an LSID, see here for an example. It would be nice if each species had its own permanent URL, which would be arguably more useful than an LSID, but I won't go there :)

Actually, iSpecies doesn't link to LSIDs for taxon names (that's done through one of my other toys, the Taxonomic Search Engine). Perhaps it's time to link these two toys together?

Saturday, November 05, 2005

Being too careful

Managed to figure out why the Google Scholar results would sometimes appear and sometimes not. The server hosting iSpecies uses PortSentry to detect and block port scans. PortSentry decided that the Glasgow University proxy was evil. Our proxy has three IP addresses, two of which were blocked by PortSentry. If the DNS resolved the proxy address to a blocked IP, the Google Scholar Perl script would fail (as it connects to the outside world via the proxy). If the DNS happened to resolve it to the unblocked IP, it would work. Found this out by changing
use LWP;
use LWP::Debug '+';
and printing out the response status_line.

iSpecies launched

iSpecies is a very simple test of E O Wilson's idea of a web page for each species. The data displayed are generated "on the fly" by querying other data sources, such as NCBI, Yahoo Images, and Google Scholar. The site was announced on TAXACOM and the Taxonomic Databases Working Group - Structure of Descriptive Data lists on 2 November 2005. It was blogged by Leigh Dodds and Danny Ayers.