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) describes his quest to track all genus
names ever published (plus a subset of the species...).

A "holy grail" for biodiversity informatics is a suitably quality
controlled, human- and machine-queryable list of all the world's
species, preferably arranged in a suitable taxonomic hierarchy such as
kingdom-phylum-class-order-family-genus or other. To make it truly
comprehensive we need fossils as well as extant taxa (dinosaurs as well
as dinoflagellates) and to cover all groups from viruses to vertebrates
(possibly prions as well, which are, well, virus-like). Linnaeus had
some pretty good attempts in his day, and in the internet age the
challenge has been taken up by a succession of projects such as the
"NODC Taxonomic Code" (a precursor to ITIS, the [Integrated Taxonomic
Information System](http://www.itis.gov/) - currently 722,000 scientific
names), the [Species 2000 consortium](http://www.sp2000.org/), and the
combined ITIS+SP2000 product ["Catalogue of
Life"](http://www.catalogueoflife.org/), now in its 16th annual edition,
with current holdings of 1,635,250 living and 5,719 extinct valid
("accepted") species, plus an additional 1,460,644 synonyms (information
from <http://www.catalogueoflife.org/annual-checklist/2016/info/ac>).
This looks pretty good until one realises that as well as the estimated
"target" of 1.9 million valid extant species there are probably a
further 200,000-300,000 described fossils, all with maybe as many
synonyms again, making a grand total of at least 5 million published
species names to acquire into a central "quality assured" system, a task
which will take some time yet.

Ten years ago, in 2006, the author participated in a regular meeting of
the steering committee for OBIS, the [Ocean Biogeographic Information
System](http://www.iobis.org) which, like GBIF, aggregates species
distribution data (for marine species in this context) from multiple
providers into a single central search point. OBIS was using the
Catalogue of Life (CoL) as its "taxonomic backbone" (method for
organising its data holdings) and, again like GBIF, had come up against
the problem of what to do with names not recognised in the then-latest
edition of CoL, which was at the time less than 50% complete
(information on 884,552 species). A solution occurred to me that since
genus names are maybe only 10% as numerous as species names, and every
species name includes its containing genus as the first portion of its
binomial name (thanks, Linnaeus!), an all-genera index might be a
tractable task (within a reasonable time frame) where an all-species
index was not, and still be useful for allocating incoming "not
previously seen" species names to an appropriate position in the
taxonomic hierarchy. OBIS, in particular, also wished to know if species
(or more exactly, their parent genera) were marine (to be displayed) or
nonmarine (hide), similar with extant versus fossil taxa. Sensing a
challenge, I offered to produce such a list, in my mind estimating that
it might require 3 months full-time, or the equivalent 6 months in part
time effort to complete and supply back to OBIS for their use.

To cut a long story short... the project, which I christened the Interim
Register of Marine and Nonmarine Genera or IRMNG (originally at CSIRO in
Australia, now hosted on its own domain
["www.irmng.org"](http://www.irmng.org) and located at VLIZ in Belgium)
has successfully acquired over 480,000 published genus names, including
valid names, synonyms and a subset of published misspellings, all
allocated to families (most) or higher ranks (remainder) in an
internally coherent taxonomic structure, most with marine/nonmarine and
extant/fossil flags, all with the source from which I acquired them,
sources for the flags, and more; also for perhaps 50% of genera, lists
of associated species from wherever it has been convenient to acquire
them (Catalogue of Life 2006 being a major source, but many others also
used). My estimated 6 months has turned into 10 years and counting, but
I do figure that the bulk of the basic "names acquisition" has been done
for all groups (my estimate: over 95% complete) and it is rare (although
not completely unknown) for me to come across genus names not yet held,
at least for the period 1753-2014 which is the present coverage of
IRMNG; present effort is therefore concentrated on correcting internal
errors and inconsistencies, and upgrading the taxonomic placement (to
family) for the around 100,000 names where this is not yet held (also
establishing the valid name/synonym status of a similar number of
presently "unresolved" generic names).

With the move of the system from Australia to VLIZ, completed within the
last couple of months, there is the facility to utilise all of the
software and features presently developed at VLIZ that currently runs
WoRMS, the [World Register of Marine
Species](http://www.marinespecies.org) and its many associated
subsidiary databases, as well as (potentially) look at forming a
distributed editing network for IRMNG in the future, as already is the
case for WoRMS, presuming that others are see a value in maintaining
IRMNG as a useful resource e.g. for taxonomic name resolution, detection
of potential homonyms both within and across kingdoms, and generally
acting as a hierarchical view of "all life" to at least genus level. A
recently implemented addition to IRMNG is to hold
[ION](http://www.organismnames.com) identifiers (also used in
[BioNames](http://bionames.org)), for the subset of names where ION
holds the original publication details, enabling "deep links" to both
ION and BioNames wherein the original publication can often be
displayed, as previously described [elsewhere in this
Blog](http://iphylo.blogspot.com/2016/08/displaying-original-species.html).
Similar identifiers for plants are not yet held in the system but could
be, (for example Index Fungorum identifiers for fungi), for cases where
the potential linked system adds value in giving, for example, original
publication details and onward links to the primary literature.

All in all I feel that the exercise has been of value not only to OBIS
(the original "client") but also to other informatics systems such as
[GBIF](http://www.gbif.org), [Encyclopedia of
Life](http://www.eol.org/), [Atlas of Living
Australia](http://www.ala.org.au/), [Open Tree of
Life](http://www.opentreeoflife.org/) and others who have all taken
advantage of IRMNG data to add to their systems, either for the
marine/nonmarine and extant/fossil flags or as an addition to their
primary taxonomic backbones, or both. In addition it has allowed myself,
the founding IRMNG compiler, to "scratch the taxonomic itch" and finally
flesh out what is meant by statements that a certain group contains *x*
families or *y* genera, and what these actually might be. Finally, many
users of the system via its web interface have commented over time on
how useful it is to be able to input "any" name, known or unknown, with
a good chance that IRMNG can tell them something about the genus (or
genus possible options, in the case of homonyms) as well as the species,
in many cases, as well as discriminate extant from fossil taxon names,
something not yet offered to any significant extent by the current
Catalogue of Life.

Readers of iPhylo are encouraged to try IRMNG as a "taxonomic name
resolution service" by visiting [www.irmng.org](http://www.irmng.org)
and of course, welcome to contact me with suggestions of missed names
(concentrating at genus level at the present time) or any other ideas
for improvement (which I can then submit for consideration to the team
at VLIZ who now provide the technical support for the system).


This guest post by Tony Rees describes his quest to track all genus names ever published (plus a subset of the species…).  A “holy grail” for biodiversity informatics is a suitably quality controlled, human- and machine-queryable list of all the world’s species, preferably arranged in a suitable taxonomic hierarchy such as kingdom-phylum-class-order-family-genus or other.

Messaggi di Rogue Scholar

Guest post: Absorbing task or deranged quest: an attempt to track all genus names ever published