A couple of months ago I received an invitation to address the upcoming 2015 meeting of the Malacological Society of Australasia (Australian and New Zealand mollusc persons for the uninitiated) on some topic associated with biodiversity databases, and I decided that a decadal review might be an interesting exercise, both for my potential audience (perhaps) and for my own interest (definitely). Well, the talk is delivered and the slides are available on the web for viewing if interested, and Rod has kindly invited me to present some of its findings here, and possibly stimulate some ongoing discussion since a lot of my interests overlap his own quite closely. I was also somewhat influenced in my choice of title by a previous presentation of Rod's from some 5 years back, "Why aren't we there yet?" which provides a slightly pessimistic counterpoint to my own perhaps more optimistic summary.
I decided to construct the talk around 5 areas: compilations of taxonomic names and associated valid/accepted taxa; links to the literature (original citations, descriptions, more); machine-addressable lists of taxon traits; compilations of georeferenced species data points such as OBIS and GBIF; and synoptic efforts in the environmental niche modelling area (all or many species so as to be able to produce global biodiversity as well as single-species maps). Without recapping the entire content of my talk (which you can find on SlideShare), I thought I would share with readers of this blog some of the more interesting conclusions, many of which are not readily available elsewhere, at least not with effort to chase down and/or make educated guesses.
In the area of taxonomic names, for animals (sensu lato) ION has gone up from 1.8m to 5.2m names (2.8m to 3.5m indexed documents) from all ranks (synonyms not distinguished) over the cited period 2005-2015, while Catalogue of Life has gone up from 0.5m species names + ?? synonyms to 1.6m species names + 1.3m synonyms over the same period; for fossils, BioNames database is making some progress in linking ION names to external resources on the web but, at less than 100k such links, is still relatively small scale and without more than a single-operator level of resourcing. A couple of other "open access" biological literature indexing activities are still at a modest level (e.g. 250k-350k citations, as against an estimated biological literature of perhaps 20m items) at present, and showing few signs of current active development (unless I have missed them of course).
Comprehensive databases of taxon traits (in machine addressable form) appear to have started with the author’s own "IRMNG" genus- and species- level compendium which was initially tailored to OBIS needs for simply differentiating organisms into extant vs. fossil, marine vs. nonmarine. More comprehensive indexes exist for specific groups and recently, Encyclopedia of Life has established "TraitBank" which is making some headway although some of the "traits" such as geographic distribution (a bounding box from either GBIF or OBIS) and "number of GenBank sequences" stretch the concept of trait a little (just my two cents' worth, of course), and the newly created linkage to Google searches is to be applauded.
With regard to aggregating georeferenced species data (specimens and observations), both OBIS (marine taxa only) and GBIF (all taxa) have made quite a lot of progress over the past ten years, OBIS increasing its data holdings ninefold from 5.6m to 44.9m (from 38 to 1,900+ data providers) and GBIF more than tenfold from 45m to 577m records over the same period, from 300+ to over 15k providers. While these figures look healthy there are still many data gaps in holdings e.g. by location sampled, year/season, ocean depth, distance to land etc. and it is probably a fair question to ask what is the real "end point" for such projects, i.e. somewhere between "a record for every species" and "a record for every individual of every species", perhaps...
Global / synoptic niche modelling projects known to the author basically comprise Lifemapper for terrestrial species and AquaMaps for marine taxa (plus some freshwater). Lifemapper claims "data for over 100,000 species" but it is unclear whether this corresponds to the number of completed range maps available at this time, while AquaMaps has maps for over 22,000 species (fishes, marine mammals and invertebrates, with an emphasis on fishes) each of which has a point data map, a native range map clipped to where the species is believed to occur, an "all suitable habitat map" (the same unclipped) and a "year 2100 map" showing projected range changes under one global warming scenario. Mapping parameters can also be adjusted by the user using an interactive "create your own map" function, and stacking all completed maps together produces plots of computed ocean biodiversity plus the ability to undertake web-based "what [probably] lives here" queries for either all species or for particular groups. Between these two projects (which admittedly use different modelling methodologies but both should produce useful results as a first pass) the state of synoptic taxon modelling actually appears quite good, especially since there are ongoing workshops e.g. the recent AMNH/GBIF workshop Biodiversity Informatics and Modelling Species Distributions at which further progress and stumbling blocks can be discussed.
So, some questions arising:
- Who might produce the best "single source" compendium of expert-reviewed species lists, for all taxa, extant and fossil, and how might this happen (my guess: a consortium of Catalogue of Life + PaleoBioDB at some future point)
- Will this contain links to the literature, at least citations but preferably as online digital documents where available? (CoL presently no, PaleoBioDB has human-readable citations only at present)
- Will EOL increasingly claim the "TraitBank" space, and do a good enough job of it? (also bearing in mind that EOL is still an aggregator, not an original content creator, i.e. somebody still has to create it elsewhere)
- Will OBIS and/or GBIF ever be "complete", and how will we know when we’ve got there (or, how complete is enough for what users might require)?
- Same for niche modelling/predicted species maps: will all taxa eventually be covered, and will the results be (generally) reliable and useable (and at what scale); or, what more needs to be done to increase map quality and reliability.
Opinions, other insights welcome!
