University of Glasgow

Roderic Page

![YtNkVT2U](https://lh3.googleusercontent.com/-A99btr6ERMs/Vl1Wvjp2OtI/AAAAAAAAEFI/7bKdRjNG5w0/ytNkVT2U.jpg?imgmax=800 "ytNkVT2U.jpg"){border="0"
width="128" height="128" style="float:right;"}This guest post by [Tony
Rees](https://about.me/TonyRees) explores some of the themes from his
recent talk [10 years of Global Biodiversity Databases: Are We There
Yet?](http://www.slideshare.net/tony1212/10-years-of-global-biodiversity-databases-are-we-there-yet).

::: {style="margin-bottom:5px"}
**[10 years of global biodiversity databases: are we there
yet?](//www.slideshare.net/tony1212/10-years-of-global-biodiversity-databases-are-we-there-yet "10 years of global biodiversity databases: are we there yet?"){target="_blank"}**
from **[Tony Rees](//www.slideshare.net/tony1212){target="_blank"}**
:::

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?\"](http://www.slideshare.net/rdmpage/why-arent-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](www.iobis.org) and [GBIF](www.gbif.org); 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](http://www.slideshare.net/tony1212/10-years-of-global-biodiversity-databases-are-we-there-yet)),
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](http://www.organismnames.com) 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](http://www.catalogueoflife.org) 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](https://paleobiodb.org/%22%3EPaleoBioDB%3C/a%3E%20has%20increased%20from%2060k%20to%20320%20names%20at%20all%20ranks,%20while%20systems%20for%20non-animal%20groups%20(plus%20habitat-specific%20compendia%20such%20as%20%3Ca%20href=%22http://www.marinespecies.org%22%3EWoRMS%3C/a%3E)%20have%20increased%20similarly.%20So,%20coverage%20is%20getting%20a%20lot%20better%20although%20there%20is%20still%20no%20best%20%22one-stop-shop%22%20for%20a%20list%20of%20all%20valid%20taxa,%20for%20which%20I%20estimate%20around%202.2m%20currently%20valid%20taxa%20or%20in%20excess%20of%205m%20published%20names%20including%20synonyms%20(also%20increasing%20at%20around%2020k%20newly%20described%20species/year).%3C/p%3E%0A%0A%3Cp%3ELinks%20to%20the%20literature%20are%20available%20as%20%22microcitations%22%20in%20various%20nomenclator-style%20compilations,%20and%20patchily%20as%20full%20citations%20in%20various%20databases%20including%20a%20format%20shorn%20of%20its%20authors%20in%20ION%20(link%20to%20the%20full%20publication%20information%20via%20Zoological%20Record%20is%20behind%20a%20paywall).%20Rod%20Page){s=""
<a=""} 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\"](http://www.cmar.csiro.au/datacentre/irmng/) genus- and
species- level compendium which was initially tailored to
[OBIS](http://www.iobis.org) needs for simply differentiating organisms
into extant vs. fossil, marine vs. nonmarine. More comprehensive indexes
exist for specific groups and recently, [Encyclopedia of
Life](http://eol.org) 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](https://twitter.com/google/status/662017916255227904) 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](http://www.lifemapper.org) for terrestrial species
and [AquaMaps](http://www.aquamaps.org) 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](http://www.maraujolab.com/conference-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!


This guest post by Tony Rees explores some of the themes from his recent talk 10 years of Global Biodiversity Databases: Are We There Yet?.
<strong>
 10 years of global biodiversity databases: are we there yet?
</strong>
from
<strong>
 Tony Rees
</strong>
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

Messaggi di Rogue Scholar

Guest post: 10 years of global biodiversity databases: are we there yet?