In the spirit of the Would you give me a grant experiment? [1] here's the draft of a proposal I'm working on for the Computable Data Challenge. It's an attempt to merge taxonomic names, the primary literature, and phylogenetics into one all-singing, all-dancing website that makes it easy to browse names, see the publications relevant to those names, and see what, if anything, we know about the phylogeny of those taxa.

Dark taxa have become even darker. NCBI has pulled the plug on large numbers of DNA barcode sequences that lack scientific names. For example, taxon Cyclopoida sp. BOLD:AAG9771 (tax_id 818059) now has a sparse page that has no associated sequences. From an earlier download of EMBL I know that this taxon is associated with at least 5 sequences, such as GU679674. But if you go to that sequence you get this:So the the sequence is hidden.

Based on recent discussions my sense is that our community will continue to thrash the issue of identifiers to death, repeating many of the debates that have gone on (and will go on) in other areas. To be trite, it seems to me we have three criteria: cheap , resolvable , and persistent . We get to pick two. Cheap and resolvable means URLs, which everybody is nervous about because they break.

Now we are awash in challenges! EOL has announced its Computable Data Challenge:Some $US 50,000 is on offer. "Challenge" is perhaps a misnomer, as EOL is offering this money not as a prize at the end, but rather to fund one or more proposals (submitted by 22 May) that are accepted.

When I think of the Biodiversity Heritage Library (BHL) or GBIF I tend to think of taxonomy and biodiversity. Folk wisdom has it that BHL is full of old books, mostly pre-1923. Great for finding old taxonomic names, or nice artwork, but not exactly "modern" biology. GBIF is mainly about displaying organism distributions based on museum specimens, the primary data of taxonomic research.

The iEvoBio 2012 Challenge has been announced, and the topic is synthesizing phylogenies. The task:The rules of this challenge are:The set of trees you use must have at least 10,000 leaves in total.

One reason I'm pursuing the theme of specimen identifiers (and identifiers in general) is the central role they play in annotating databases. To give a concrete example, I (among others) have argued for a wiki-style annotation layer on top of GenBank to capture things such as sequencing errors, updated species names, etc. Annotation is a lot easier if we have consistent identifiers for the things being annotated.

Sometimes I need to remind myself just why I'm spending so much time trying to make sense of other people's data, and why I go on (and on) about identifiers. One reason for my obsession is I want data to be "sticky", like the burrs shown in the photo above (Who invented velcro? by A-dep). Shared identifiers are like the hooks on the burrs, if two pieces of data have the same identifier they will stick together.

Brief update on yesterday's post about finding specimens in BioStor. BioStor has some 66,000 articles from BHL, from which I've extracted 143,000 cases of a specimen code being cited in the text.

Following on from exploring links between GBIF and GenBank here I'm going to look at links between GBIF and the primary literature, in this case articles scanned by the Biodiversity Heritage Library (BHL). The OCR text in BHL can be mined for a variety of entities. BHL itself has used uBio's tools to identity taxonomic names in the OCR text, and in my BioStor project I've extracted article-level metadata and geographic co-ordinates.