[Taxacom] global species lists and taxonomy ( was Re: Draft Checklist ...)

Dave Roberts workpackage6 at gmail.com
Thu Aug 29 08:21:19 CDT 2013

Dear all,

I fear that the comparatively greater complexity of the animals will make such an approach a considerable amount of work, or more bluntly, will be significantly hard.

With the list of names, on which so many people are labouring without, as Rich says, sufficient coordination, we also need a classification bank, a simple way to find in how many arrangements a given taxon has been placed.  That was one of the priorities identified in the Biodiversity Informatics Decadal Vision [1].

The EU's funding programme H2020 is an opportunity to create a large consortium to do exactly that level of coordination.  The problem, though, is to link it in some way to either job creation or policy making at an EU scale.  The advantage is that international collaboration (i.e. outside Europe) is likely to be more tractable in H2020.

Next week's meeting in Rome [2] is a starting point for that kind of discussion.

Cheers, Dave

[1] Hardisty, Alex, Dave Roberts, and The Biodiversity Informatics Community. “A Decadal View of Biodiversity Informatics: Challenges and Priorities.” BMC Ecology 13 (2013): 16. doi:10.1186/1472-6785-13-16.
[2] http://conference.lifewatch.unisalento.it/index.php/EBIC/BIH2013/

On 29 Aug 2013, at 13:08, nicky nicolson <nicky.nicolson at gmail.com> wrote:

> Thanks Karen, yes this is what we are working on in botany and mycology -
> we are using the nomenclators (IPNI and IF) to provide the fundamental
> units (names and the objective relationships between them) and then
> supporting multiple overlapping - even contradictory - classifications to
> be built using these same fundamental units. We are storing enough data on
> the relationships which form the taxonomic classifications to do the kind
> of assessments that Fred suggests - e.g. to take into account how recently
> the hypothesis was published, who published it and where (e.g. was it a
> regional treatment or a globally-scoped monograph).
> I did quite a general talk about this at the Natural History Museum in
> London recently, video here: http://www.youtube.com/watch?v=ynFB6DWCBjc and
> slides here: http://www.slideshare.net/nickyn/nicolson-namesbackbonenhm
> We've a funded project to rebuild Kew's taxonomic systems in this
> environment, and we are working on incorporating the World Checklist system
> at the moment, although our communications standard is TCS so we should be
> able to import / export data from many different sources.
> cheers,
> Nicky
> PS: I'll be at TDWG along with a few people from the Kew team if anybody is
> interested in having a closer look.
> On 29 August 2013 12:18, Karen Cranston <karen.cranston at gmail.com> wrote:
>> It is not too hard to implement this type of system. Both IPNI and Open
>> Tree of Life are currently implementing a relatively new graph database
>> model (database called neo4j) to load and store multiple hierarchies in the
>> same data structure. Then, you can traverse the graph (which contains all
>> of the nodes and edges, and therefore all of the conflict) in various ways
>> in order to summarize / resolve conflicts / find interesting patterns. You
>> could use algorithmic and / or human-curated approaches to annotate or
>> resolve parts of the hierarchy, while still keeping all of the information
>> from the sources. Visualization libraries like d3 make it easy to create
>> images or interactive tools to explore the data in the graph.
>> On Thu, Aug 29, 2013 at 7:03 AM, Erik Rijkers <er at xs4all.nl> wrote:
>>> On Thu, August 29, 2013 12:31, Fred Schueler wrote:
>>>> Maybe we want to take a lesson from the physicists' ideas of infinite
>>>> parallel universes, and program systems where all published
>>>> classifications are represented, but with some sort of combined voting
>>>> or weighting by the recency of publication, and wiki-style comments and
>>>> discussion, to show users which classifications are more currently
>>>> approved and used.
>>> hear, hear!
>>> IMHO, this is the only possible way to get usefully stable global lists.
>>> It amounts to the realisation that the classification business is
>>> producing opinions (however obnoxious this may sound to
>>> the taxonomist).
>>> So databases should amass these opinions with plenty factual detail but
>>> without implicitly endowing any
>>> classification-opinion with the distinction of being "fact".
>>> It would seem this obvious way of doing taxonomical databases is not too
>>> hard to implement but I have never seen it done ,
>>> or even acknowledged as necessary.
>>> Erikjan Rijkers

Dr D.McL. Roberts,        Tel: +44 (0)20 7942 5086
ViBRANT Project Manager,
Dept. Life Sciences,
The Natural History Museum,
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London        SW7 5BD
Great Britain             Email: dmr at nomencurator dot org
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