[Taxacom] progress on globalnames.org

Peter DeVries pete.devries at gmail.com
Thu May 14 21:54:55 CDT 2009 

Two more points that I forgot to mention:
1) Lets say that everyone who collected information on Ochlerotatus
triseriatus/Aedes triseriatus in North America all
tagged their data with the same species concept identifier.

Now someone could come by later, look at all that information, sequence the
specimens, organize the photographs and observations and then analyze it to
see if those components are or not part of one valid species. If the data
supports a valid species, then that information helps to further define the
attributes and limits of that species. The species concept get better
defined as more information is added.

2) I did not want to give the impression that I am against using UUID's.
They are great, especially when you have to integrate data from
several different sources. I developed the shorter identifier to separate my
ideas from any particular kind of identifier. Some of the comments I have
received made me think that people were throwing out the baby with the bath
water. The bath water being UUID's.

There is no better way that to create unique identifiers than with UUID's.
:-)

Respectfully,

- Pete





On Thu, May 14, 2009 at 9:29 PM, Peter DeVries <pete.devries at gmail.com>wrote:

> Hi Tony,
> The idea of the CAAB type identifiers are not new they exist as foreign
> keys in most of the taxonomic databases.
> However, what I am proposing is different in a number of ways most
> importantly:
>
> 1) LinkedData compliant resolvable identifiers for species concepts for the
> semantic web. If you want to know what it
>     means just use the identifier as a URL to the concept.
>
> 2) The strategy of starting with a resolvable identifier and then point
> various names, and other data at that identifier.
>
> 3) The identifier is not tied to any particular taxonomic hypothesis or
> hierarchy other than that it is about an entity
>     at the species level. Acknowledging that species are fundamentally
> different than higher clades.
>
> This is basically bootstrapping the species concept; which gets better
> defined as more appropriate items are pointed at it.
> This gives those who need to work with species and species concepts an
> identifier to work with quickly that also becomes
> more informative over time.
>
> There are a lot of people who don't really care what genus a particular
> mosquito is in, they just want be able to use
> a stable resolvable identifier with which they can tag their data. They
> also want to find articles about that species
> without having to know each and every name variant.
>
> It is my understanding that the EOL has a more bottom up strategy which
> involves arrays of names and no documented
> plan to expose linked data. I hope to learn more next week; but based on my
> email discussions with them, what I am
> proposing and what they are working on are different.
>
> Also, I applaud their effort to clean up the higher classifications, that
> will be a huge accomplishment. :-)
>
> Respectfully,
>
> - Pete
>
>
> On Thu, May 14, 2009 at 8:09 PM, <Tony.Rees at csiro.au> wrote:
>
>>   Hi Pete,
>>
>>
>>
>> Well, the idea is not new; our group here has being doing this for 20+
>> years for Australian marine species with out “CAAB” identifiers which are
>> intended to be stable although names may change through time (e.g. see
>>
>>
>>
>>
>> http://www.marine.csiro.au/caabsearch/caab_search.caab_report?spcode=28711050
>>
>>
>>
>> )
>>
>>
>>
>> We have achieved a de-facto currency for these identifiers throughout our
>> (geographically and habitat) restricted user community, but obviously have
>> no mandate or desire to do it for the world…
>>
>>
>>
>> Also if you are not careful you end up with needing a synonymy of concept
>> identifiers, plus the ongoing and creeping problems resulting from splitting
>> / merging / redefining concepts as previously alluded to.
>>
>>
>>
>> Anyway I thought uBio / EoL Union were going to do this with their
>> “reconciliation groups” of names, e.g. see Paddy’s post near the bottom of
>> http://forum.eol.org/viewtopic.php?p=2897 – again we don’t want rampant
>> duplication (but I agree, we do need something!!)
>>
>>
>>
>> I am doing something similar with IRMNG too, but only internally at this
>> time and for my own purposes.
>>
>>
>>
>> Just some more food for thought…
>>
>>
>>
>> Cheers - Tony
>>
>>
>>  ------------------------------
>>
>> *From:* Peter DeVries [mailto:pete.devries at gmail.com]
>> *Sent:* Friday, 15 May 2009 10:58 AM
>>
>> *To:* Rees, Tony (CMAR, Hobart)
>> *Cc:* dremsen at gbif.org; taxacom at mailman.nhm.ku.edu; trobertson at gbif.org
>>
>> *Subject:* Re: [Taxacom] progress on globalnames.org
>>
>>
>>
>> Hi Tony,
>>
>>
>>
>> Your concerns are noted and that is one reason that I have set things up
>> on "mobile" domains.
>>
>>
>>
>> I have needed this sort of thing for a while and have periodically posted
>> about it. It did not seem to be happening, so I did it on my GeoSpecies site
>> using UUID's.
>>
>>
>>
>> I have thought that it might be better to separate the species concepts to
>> a lighter framework that did not directly include photos etc.
>>
>>
>>
>> Also my use of UUIDs seemed to put some people off, so I came up with
>> smaller unique identifiers.I can explain those in a later post.
>>
>>
>>
>> I would be happy to work with others on creating this, but I also needed
>> something that can be made workable in a non-TDWG time frame.
>>
>>
>>
>> Think of it this way. The taxonconcept.org site will be for trying this
>> idea, seeing what works and what does not, so that in the end we have
>> something that works and persists.
>>
>>
>>
>> Also I am not the only one in this space that is setting up taxonomic
>> services without a large infrastructure and guaranteed permanence.
>>
>>
>>
>> I also used to be the network manager for a sizable chunk of the UW
>> campus, so I have infrastructure experience.
>>
>>
>>
>> I will be visiting EOL next week to do a talk, and I plan on discussing
>> this idea with them. There is also another group that I have
>>
>> talked with.
>>
>>
>>
>> You seem supportive of the concept, however, it is not clear at all from
>> messages on this list that something like this is needed or a even a valid
>> idea. There are a number of people for whom the name is the species concept.
>>
>>
>>
>> Respectfully,
>>
>>
>>
>> - Pete
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Thu, May 14, 2009 at 7:01 PM, <Tony.Rees at csiro.au> wrote:
>>
>> Dear Pete, all,
>>
>> What you are proposing is something I have been anticipating to eventuate
>> out of uBio / NameBank / Eol / GBIF / Cat of Life or some combination of the
>> above, so (with respect) I think it is not a decision that can be taken
>> unilaterally by one worker at one agency with unstated permanence /
>> resourcing / long term support / community buy-in etc. etc. My feeling is
>> that such a key central resource needs a rock solid hosting and ongoing
>> governance structure for the future so should probably be a high priority
>> topic for discussion at e-Biosphere. Nobody doubts that taxon concepts are
>> the way to go (hence all the global and regional "species information" sites
>> - you want to attach the species related info to the taxon concept, not
>> every name) - however there are still residual problems of either lumping or
>> splitting through time, regional or other misidentifications, and
>> differences of opinion regarding circumscription (lumpers, splitters, and
>> taxonomic reallocations of subsidiary taxa).
>>
>> I for one look forward to this being a hot topic next month in London...
>>
>> Regards - Tony
>>
>> Tony Rees
>> Manager, Divisional Data Centre,
>> CSIRO Marine and Atmospheric Research,
>> GPO Box 1538,
>> Hobart, Tasmania 7001, Australia
>> Ph: 0362 325318 (Int: +61 362 325318)
>> Fax: 0362 325000 (Int: +61 362 325000)
>> e-mail: Tony.Rees at csiro.au
>> Manager, OBIS Australia regional node, http://www.obis.org.au/
>> Biodiversity informatics research activities:
>> http://www.cmar.csiro.au/datacentre/biodiversity.htm
>> Personal info:
>> http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
>>
>>
>>
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
>> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter DeVries
>> Sent: Friday, 15 May 2009 8:02 AM
>> To: David Remsen (GBIF)
>> Cc: taxacom at mailman.nhm.ku.edu; Tim Robertson
>> Subject: Re: [Taxacom] progress on globalnames.org
>>
>> I think that the effort to organize information about species has been
>> moving so slowly in part because of it's focus on names. Our goal is to
>> organize information about species, names are just the handle that we use
>> to
>> tag a species.
>>
>> The efforts would go much more quickly if we create identifiers for
>> species
>> concepts and then point the various names to that identifier.
>>
>> I did a check via Google Scholar for papers published this year that
>> mention
>> the *Puma concolor*, and *Felis concolor.*
>> *
>> *
>> Both of these names for the same species are still being used.
>>
>> It would make sense to mint global URI for that species concept and then
>> tag
>> all papers, images, observations to that species concept.
>>
>> As these documents are being processed, more and more information will be
>> tied to that identifier.
>>
>> Identifiers for "good" species could be created quickly. New observations
>> could start to be tagged with that identifier along with whatever name the
>> recorder would like to use. e.g. Aedes/Ochlerotatus
>>
>> These concepts could be mapped to the GNI data in the following way
>>
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/3165624
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/505310
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/10330292
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/6689244
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/3169574
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/10568463
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/12104361
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/1758834
>> http://www.taxonconcept.org/spcs/v6n7p  *hasNameID*
>> http://globalnames.org/name_strings/11818218
>>
>> I have not had much success getting this idea accepted in a number of
>> these
>> communities.
>>
>> So I have a proposal. Let my group start making species concept
>> identifiers.
>> If this concept is adopted, I have succeeded in proving my point. If this
>> concept fails, then I am wrong. Either way, we should have an answer by
>> the
>> end of the decade.
>>
>> Respectfully,
>>
>> - Pete
>>
>> P.S. This is not about changing the system of binomial nomenclature, it is
>> about tying data together so we can start to address the world's problems
>> in
>> a efficient manner. Binomial nomenclature stays. ;-)
>>
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>>
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>>
>>
>>
>> --
>> ---------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> ------------------------------------------------------------
>>
>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
>



-- 
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
------------------------------------------------------------

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