Quick notes on "taxon concepts". In order to navigate through taxon names I plan to have at least one taxonomic classification in BioNames. GBIF makes the most sense at this stage. The model I'm adopting is that the classification is a graph where nodes have the id used by the external database (in this case GBIF). Each node has one or more names attached, and where possible the names are linked to the original description.
Donald Hobern drew my attention to nice the way iNaturalist displays taxonomic splits: In this example, observations identified as Rhipidura fuliginosa are being split into Rhipidura fuliginosa and Rhipidura albiscapa . This immediately reminds me of the idea which keeps circulating around, namely using version control tools to manage taxonomic classification.
On eof the things BioNames will need to do is match taxon names to classifications. For example, if I want to display a taxonomic hierarchy for the user to browse through the names, then I need a map between the taxon names that I've collected and one or more classifications. The approach I'm taking is to match strings, wherever possible using both the name and taxon authority.
Somehow I get the feeling that botanists haven't got the "open data" religion. Not only is the list of plant names list behind a really bad license, but the Global Plants Initiative (GPI) hides its type images behind a JSTOR Plant Sciences paywall. Why is botany determined to keep its data under wraps?
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.
We all have a "past" that we might not advertise widely, and my past includes flirting with panbiogeography.
If we are ever going to link biodiversity data together we need to have some way of ensuring persistent links between digital records. This isn't going to happen unless people take persistent identifiers seriously. I've been trying to link specimen codes in publications to GBIF, with some success, so imagine my horror when it started to fall apart.
Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories, the recent GBIC2012 meeting (I'm still digesting that meeting), and mulling over the book A Vast Machine I keep thinking about the possible parallels between climate science and biodiversity science.
Next week I'm in Copenhagen for GBIC, the Global Biodiversity Informatics Conference. The goal of the conference is to: The collaboration referred to is the agreement to mobilise data and informatics capability to met the Aichi Biodiversity Targets. I confess I have mixed feelings about the upcoming meeting. There will be something like 100 people attending the conference, with backgrounds ranging from pure science to intergovernmental policy.
