Pensoft have recently introduced “nanopubs”, small structured publications that can be thought of as containing the minimum possible statement that could be published. Nanopubs are promoted as FAIR, that is findable, accessible, interoperabile, and reusable. I like the idea of nanopubs, but the examples I have seen so far are problematic.

Note to self. The challenge of finding specimen citations in papers keeps coming around. It seems that this is basically the same problem as finding citations to papers, and can be approached in much the same way. If you want to build a database of reference from scratch, one way is to scrape citations from papers (e.g., from the "literature cited" section), convert those strings into structured data, and add those to your database.

Garnett et al. recently published a paper in PLoS Biology that starts with the sentence "Lists of species matter": This paper (one of a forthcoming series) is pretty much the kind of paper I try and avoid reading.

I'm going to the TDWG Identifier Workshop this weekend, so I thought I'd jot down a few notes. The biodiversity informatics community has been at this for a while, and we still haven't got identifiers sorted out. From my perspective as both a data aggregator (e.g., BioNames) and a data provider (e.g., BioStor) there are four things I think we need to tackle in order to make significant progress.

Given that it's the start of a new year, and I have a short window before teaching kicks off in earnest (and I have to revise my phyloinformatics course) I'm playing with a few GBIF-related ideas. One topic which comes up a lot is annotating and correcting errors. There has been some work in this area [1][2] bit it strikes me as somewhat complicated. I'm wondering whether we couldn't try and keep things simple.

I've been banging on about having citable, persistent identifiers for specimens, so was suitably impressed when Derek Sikes posted a comment on iPhylo that Arctos already does this. For example, here is a DOI for a specimen: http://dx.doi.org/10.7299/X7VQ32SJ. So, we're all done, right? Not quite.

Continuing the theme of trying to map specimens cited in the literature to the equivalent GBIF records, consider the GBIF record http://data.gbif.org/occurrences/685591320, which according to GBIF is specimen "ZFMK 188762" (a [sic] holotype of Praomys hartwigi ). This is odd, because the original publication of this name (Eisentraut, M. 1968 .Beitrag zur Saugetierfauna von Kamerun.

The Integrated Digitized Biocollections (iDigBio) project aims to advance digitising US biodiversity collections. They recently published a GUID Guide for Data Providers. In the PDF document I read this: My heart sank.

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.

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.