[Taxacom] progress on globalnames.org
Paul Kirk
p.kirk at cabi.org
Mon May 18 02:40:25 CDT 2009
A name by any other name is the original name proposers species concept ... taxonomy (i.e. concepts) precedes nomenclature (i.e. naming). The original species concept of a name is sometimes based on multiple elements (specimens, illustrations, gene sequences).
The Catalogue of Life would be heading for completion right now if the UK Research Council (BBSRC) had funded a proposal to do just this ... for £4M.
In haste,
Paul
-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Tony.Rees at csiro.au
Sent: 18 May 2009 08:31
To: pete.devries at gmail.com; michael.heads at yahoo.com
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] progress on globalnames.org
Dear Pete, all,
I have pointed out some cases where taxon concepts are not easy to model in databases, but in many cases of course this does not apply. So let us say, where the (species level) concepts are relatively stable / non controversial, my original question is still unanswered, i.e. who has the mandate / capacity / time frame / community buy-in to create (e.g.) LSIDs for these (current estimate) 1.8m extant species concepts, plus maybe 0.2m + fossils? At present by default I am using the "current names" for taxa presently treated by Catalogue of Life as de facto "concepts", but who will do the remaining approx. 50% (and by when?)...
Also what mechanisms might be desired for online editing by relevant experts, correction of errors, addition of new synonyms as encountered, etc. etc.?
I am simply pointing out that the efforts of a single individual in this regard are likely to be seriously overloaded...
That is why I pointed to the "community expert editing" software model of WoRMS as a candidate type of operation, although currently they apply identifiers at the name, rather than the taxon concept.
Regards - Tony
-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter DeVries
Sent: Monday, 18 May 2009 5:12 PM
To: Michael Heads
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] progress on globalnames.org
Nico Franz was kind enough to direct me to some papers. In their references listed a paper which is very similarto what was describing, so I thought I should mention it.
*Scientific Names Are Ambiguous as Identifiers for Biological Taxa: Their Context and Definition Are Required for Accurate Data Integration *
*
*
*Jessie B. Kennedy, Robert Kukla,Trevor Paterson* *Lecture Notes in Computer Science*
*10.1007/11530084*
*http://www.springerlink.com/content/7bv5pa3falxwrrvx/*<http://www.springerlink.com/content/7bv5pa3falxwrrvx/>
A number of papers that discuss the issues of taxonomic concepts use genera as examples. As I had mentioned before, concepts above species are going to be difficult. A species concept can be supported with specimens and other real world attributes like gene sequences and images. Once you go above the species level, it is much harder to define a stable foundation.
I can imagine a group authoring and curating a species concept supported by specimens etc. It does not seem clear to me how this could be done with the higher clades. For instance, is there any formal way to determine if a clade should be a subgenus, genus, family or subfamily?
This may be a problem for EOL/GBIF computers to crunch out. :-)
Respectfully,
- Pete
On Sun, May 17, 2009 at 8:24 PM, Michael Heads <michael.heads at yahoo.com>wrote:
> Hi Pete,
>
> It would be great if species were stable and indivisible but molecular
> work is showing that in many groups some species have not been
> delimited well (e.g. in swifts, owl monkeys). But surely if your
> database is specimen-based (not species-based) you can just change the
> species concept as new data comes in?
> Your point about clades is crucial: many very interesting,
> well-supported molecular (and macromorphological) clades at all levels
> have no name and so don't exist for taxonomy, although for general
> biodiversity, ecology, conservation etc. they are just as 'real' as
> named clades. A taxonomy is just a summary or a framework, not the
> complete picture. Still, even if it doesn't incorporate all the new
> molecular clades it's a great advance to have a major collection
> online, arranged under whatever taxonomy it prefers, rather than not available at all.
>
> Michael Heads
>
>
> Wellington, New Zealand.
>
> My papers on biogeography are at: http://tiny.cc/RiUE0
>
> --- On Mon, 5/18/09, Peter DeVries <pete.devries at gmail.com> wrote:
>
>
> From: Peter DeVries <pete.devries at gmail.com>
> Subject: Re: [Taxacom] progress on globalnames.org
> To: "Michael Heads" <michael.heads at yahoo.com>
> Cc: taxacom at mailman.nhm.ku.edu
> Date: Monday, May 18, 2009, 10:51 AM
>
>
> Hi Michael,
>
>
> Yes, I am not saying that the other levels are not important. I think
> what I am proposing still connect to the higher levels.
>
>
> The particular genus something is put into is a statement about where
> it fits in the tree of life. Workers can differ on the taxonomic
> placement of a particular species concept, but agree that they are
> talking about the same species concept.
>
>
> Something also needs to be done about how we represent clades, any takers?
>
>
> In this example the clades have remained the same, it is just that
> Ochlerotatus was moved from a subgenus to a genus. (some accept this,
> others do not)
>
>
> Yes, there is a difference of opinion on whether species are different
> than the other clades. I think they are.
>
>
> One simple reason is that members of a species are pretty good at
> recognizing each other.
>
>
> The issue of "find ability" would be solved if we had semantic
> identifiers on those pages that would allow you to do a search for
> pages that contain information about the genus "Ochlerotatus".
>
>
> The identifier would make it clear that by the string "Ochlerotatus"
> you mean a genus.
>
>
> That specific genus could also have it's own uri hidden in each page
> that would serve a similar purpose.
>
>
> This problem may go away if more people start marking up their web
> pages with semantic identifiers.
> Google just announced they are going to be supporting this, but they
> do not yet have an identifier for "genus" or "Ochlerotatus"
>
>
> - Pete
>
>
>
>
>
> On Sun, May 17, 2009 at 4:57 PM, Michael Heads
> <michael.heads at yahoo.com>
> wrote:
>
>
>
>
>
>
> Hi Peter, Paul et al.,
>
> In theoretical terms, the species is special in the J.Huxley/Mayr
> 'modern synthesis'. But in other syntheses a species difference is not
> regarded as absolute but only relative (e.g. it's a level of
> differentiation between subspecies and subgenera in that group).
>
> In practical terms, many otherwise excellent websites are completely
> species-centric and so, for example, you can't draw a genus map. This
> means that if you want to get an overview of a genus with, say, 500
> species, you have to look at 500 pages and so the site is pretty well
> useless for this purpose.
> I think the idea should be to look at biodiversity, not just species.
>
> Michael Heads
>
> Wellington, New Zealand.
>
> My papers on biogeography are at: http://tiny.cc/RiUE0
>
> --- On Mon, 5/18/09, Peter DeVries <pete.devries at gmail.com> wrote:
>
>
> From: Peter DeVries <pete.devries at gmail.com>
>
> Subject: Re: [Taxacom] progress on globalnames.org
> To: "Paul van Rijckevorsel" <dipteryx at freeler.nl>
>
> Cc: taxacom at mailman.nhm.ku.edu
> Date: Monday, May 18, 2009, 9:05 AM
>
>
>
>
>
> My main goal in this is to try out ways to tie specimens and data
> related to specimens to species concepts.
> It is not that the higher clades are not important. I think:
>
> 1) Species are fundamentally different than the higher clades (others
> may
> disagree)
> Following the metapopulation idea.
>
> 2) For the kinds of questions I would like to ask species are the priority.
> (many others in the same boat)
>
> 3) From my limited understanding of the EOL approach based on the blog
> post, it seems that what they
> are proposing makes sense for the higher taxa. Also the higher
> clades org will require a lot more buy in
> from all the interested parties. If someone works to define a
> concept for a particular species, others can
> take it or leave it.
>
> I use the *Puma concolor* example because it seemed that scientist
> publishing papers in 2009 about this well known species should be
> using the modern nomenclature. It seems to me that the community
> should not be as split on this particular species as it is.
>
> There seems to be a bit of a disconnect between how specimens are
> determined and labeled and how that label is being perceived.
>
> Most mosquitoes workers use a key. I use Darsie. Most have never seen
> the type specimen. They use the key of their choice and assign a name
> to that specimen. There is little or no real "mapping" from that keyed
> specimen to the typed specimen. Also, not everyone is using the same key.
>
> Assuming that the species concept for each of the specimens in a
> collection are defined directly by the type specimen is a little tenuous.
>
> Assuming that every published use of a name can be directly tied to
> the type specimen is also a little tenuous.
>
> When someone labels a mosquito specimen, "*Aedes triseriatus*", do
> they mean "I believe that this specimen belongs in the genus *Aedes*?"
>
> Or, do most workers really mean "I believe that this specimen maps to
> the species concept currently known as "*Aedes triseriatus*"
>
> I think that some of these issues need be be cleared up. If we do not,
> then researchers will not be able to get what they want once all this
> data has been digitized.
>
> Put another way, people will realize that what they thought they were
> putting into databases is not what they actually did put into the
> databases.
>
> At a minimum, adding a species concept identifier to a named specimen
> helps clarify the intent of the person identifying the specimen.
>
> - Pete
>
>
> On Sun, May 17, 2009 at 1:21 AM, Paul van Rijckevorsel
> <dipteryx at freeler.nl>wrote:
>
> > From: "Geoff Read" <gread at actrix.gen.nz>
> > Sent: Saturday, May 16, 2009 10:01 AM
> > > My point was that both these differences are trivial, they are not
> > > real "different scientific names", and thus poor examples for your
> > > plan. The link is the epithet in both, derived from the basionym,
> > > and I betcha
> the
> > > biologists that work on them happily talk about their 'triseriatus'
> > > experiments and 'concolor' distribution data. Shades of the LITU.
> Search
> > > software should be able to pull together the data on them easily.
> >
> > ***
> > Yes, that is not the issue. On the one hand there are scientific
> > names,
> and
> > on the other hand there are taxon concepts. Any database worth
> > anything will have a 'page' per scientific name, detailing at least
> > the nomenclatural data (publication, typification, etc). However, as
> > such, these data will of
> very
> > limited use to an end-user.
> >
> > The end-user expects 'taxon pages', and here the trouble starts. It
> > is simple where there are 'good' taxa, with one or more "homotypic"
> > or "objective" synonyms. It is not too bad if there are also "heterotypic"
> or
> > "subjective" synonyms, when there is consensus about their status.
> >
> > However, in many cases there is less than universal agreement about
> > the taxon. Even if there is consensus at any one time, this may not
> > be the
> case
> > from a wider historical perspective, and many older taxon concepts
> > will resurface after a few decades. This means that a database will
> > have to
> deal
> > with family Khgtyryuuaceae sensu author A, Khgtyryuuaceae sensu
> > author B, Khgtyryuuaceae sensu author C, etc. Likely these need separate 'pages'.
> > This
> > is even more confusing when it comes to species: a collection from a
> > tree today may be made under a different name (different basionym,
> > different
> > type) than a collection from that same tree twenty years ago, and in
> > another twenty years it may have reverted. When a taxonomist lumps
> > taxa this may lose information: the literature on taxa G, H, I, K
> > and L can be found by anybody who subscribes to a joint taxon K
> > (comprising G, H, I, K and L), but the reverse is not true. The
> > literature on the joint taxon K may resist being broken down by
> > those who subscribe to separate taxa G, H, I, K and
> L
> > (even if the end-user is aware of the situation). And yet, this may
> > be of great practical importance to the end-user.
> >
> > And indeed, common names may be of invaluable use in finding information.
> > And, yes, using common names can lead to huge mistakes.
> >
> > Just stating the obvious (yet again) Paul
> >
> >
> > _______________________________________________
> >
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> >
>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
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>
>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
>
>
>
>
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--
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
------------------------------------------------------------
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