[tdwg-tag] Any TCS users with experiences to report?

Fri Nov 2 18:02:40 CET 2012

Hello Folks (Ghost from the pastŠ)

Interesting discussion on who's using TCS - I was wondering the same
myselfŠ
Belo is short history of TCS from my perspective so you can stop now if
it's not of interest..

The important thing to note is that when TCS was developed, the majority
of the work was trying to negotiate with all the stakeholders on how they
saw taxon concepts and to try and capture this in a format that would
allow people to describe Taxon Concepts in as full a way or minimum way as
possible.

Until that point there were a couple of Taxon Concepts schemas - the
Berlin Model (W. Berendsohn et al) and the Prometheus model (Pullan et
al). These had differences and seemed to be too detailed for certain
groups or didn't specify alternative ways of describing taxon concepts
that other groups wanted. When I was asked to lead the initiative for
TDWG, it became apparent that nearly every group wanted something slightly
different and the job was to try and describe something that everyone
could work with.

However we also wanted to work with all the other standard groups ABCD,
Character description (forgot its name sorry) etc but they weren't
complete nor was the idea of guids which we also wanted to incorporate and
felt were central for the approach to work. We went ahead with the belief
that these would get finalised and we would have a way of cross linking
the different schemas. TCS was therefore never fully specified as I had
hoped. This was also in the time when XML was the thing to do, however the
ideas behind TCS were more about the modelling - XML was just someway to
specify it. As RDF was getting popular we started working on the ontology
for TDWG using again the existing groups as the basis - this is where what
is being referred to as Roger's ontology came from and was an RDF
representation of part of TCS required immediately by some folks.

At that point, as I was no longer working on any project in the area, I
gave up the TCS group and handed to RichŠ .

I very occasionally read emails from the group and often think - oh looks
like we're starting the taxon concept debate again ;-) and realise people
still want proper taxon concepts, but then I find we have not pushed TCS
(in some form useful to people) and haven't move don very much.

I have looked at DWCa recently as I have funding to do some more taxonomy
visualisation and see that it makes a very slight nod to concepts but I do
not think would be of any use to do the job properly. I think the problem
is partly because of the focus on legacy data (which of course is
important) but I think something else is required to improve our data for
the future - this was always my hope.

So before all the effort goes only into DWCa I would encourage folks to
think hard about what it is you want. If it is only to be able to exchange
basic information then fine, if it is do do any real analysis and try to
improve the state of biodiversity data and knowledge then DWCa may not be
the answer IMHO.

So someone who really cares please take on the concept challenge and
create proper taxon concept data (be in XML or whatever) - when enough is
available people will make it work as they'll want to use your dataŠ While
the only data we have is basic DWC specimen records no one will botherŠ.

I think it would be great if the major databases that describe taxa (not
just list names) described their data as concepts and allowed people to
link to their databases when identifying specimens and when sequencing
etc, this would be the start of a really useful biodiversity network.

Oh well back to dreaming and occasional lurking on the mailing listŠ

Hope you're all well and I see you again soon,

Jessie

On 02/11/2012 12:08, ""Markus Döring (GBIF)"" <mdoering at gbif.org> wrote:

>Hi,
>apart from GBIF the Catalogue of Life is now heavily engaged in using
>DwC-A to exchange taxonomic data between its various components. They
>have established a more rigorous specification being a subset of what dwc
>actually allows. Many other including EOL and EDIT already make use of
>dwc archives, but I dont know about the exact usages.
>
>The only problems I am aware of right now is indeed like Kevin pointed
>out with fully taxon concept oriented systems, having multiple concepts
>for the same name and qualified relations between them. But said that I
>think its mainly a lack of experience and clear guidelines so far that
>leaves us with open questions, not so much the format itself.
>
>I hope we can arrange some workshop in the near year to work out the
>remaining issues that people have with dwc for taxonomic data. So far I
>have Kevin and some people from CoL on my radar, but I would be
>interested to know if more people are interested in such an event.
>
>Markus
>
>
>
>On 02.11.2012, at 02:13, Richard Pyle wrote:
>
>> As the Convenor of the TDWG Taxon Names and Concept group, I have
>>failed in one of my core duties to address this issue.  My inability to
>>attend TDWG this year has only exacerbated this problem.
>>
>> Having said thatŠ.. I have had many discussions with many folks over
>>the past couple of years on this issue, and for various reasons the time
>>is now ripe to re-visit this age-old problem and make some decisions
>>about how to move forward.
>>
>> For the ZooBank LSID resolver, we used Roger¹s vocabularies; and to
>>some extent, the DwC terms harmonize (but not completely).  A few years
>>ago I made a push to either revitalize TCS (e.g., through TCS 2.0), or
>>to allow it to retire (if it hasn¹t already done so de facto).
>>
>> Having just emerged from nearly two very thick years of development on
>>ZooBank, GNA/GNUB, etc., I am now more energized (and liberated, in
>>terms of available time) to re-focus on how to move forward.  My hope is
>>that we can make some core decisions about how to move forward well
>>before next year¹s TDWG meeting.
>>
>> I would very-much welcome feedback from people on:
>>
>> 1)      Who is actively using TCS?  Does it work?  Can it be improved?
>>Should it be retired?
>> 2)      Who is using Roger¹s vocabulary? Does it work?  Can it be
>>improved?
>> 3)      How much of DwC:Taxon is in active use?  Just the ³traditional²
>>terms; or some of the new ones introduced with the ratified DwC? Does it
>>work?  Can it be improved?
>> 4)      What other standards are being used in this space?
>>
>> Now that we have launched the new ZooBank, we will turn our attention
>>to GNUB services that will start to put that content to work.  It is
>>therefore very much in our interest to support the sorts of data
>>exchange mechanisms that people most need and, ideally, collapse the
>>various ³flavors² into something we can all rally around.
>>
>> Aloha,
>> Rich
>>
>>
>> Richard L. Pyle, PhD
>> Database Coordinator for Natural Sciences
>> Associate Zoologist in Ichthyology
>> Dive Safety Officer
>> Department of Natural Sciences, Bishop Museum
>> 1525 Bernice St., Honolulu, HI 96817
>> Ph: (808)848-4115, Fax: (808)847-8252
>> email: deepreef at bishopmuseum.org
>> http://hbs.bishopmuseum.org/staff/pylerichard.html
>>
>> Note: This disclaimer formally apologizes for the disclaimer below,
>>over which I have no control.
>>
>>
>>
>> From: tdwg-tag-bounces at lists.tdwg.org
>>[mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Roderic Page
>> Sent: Thursday, November 01, 2012 1:56 PM
>> To: <Tony.Rees at csiro.au>
>> Cc: pmurray at anbg.gov.au; <tdwg-tag at lists.tdwg.org>; Simon.Pigot at csiro.au
>> Subject: Re: [tdwg-tag] Any TCS users with experiences to report?
>>
>> A TDWG standard not actually being used, surely not ;)
>>
>> Leaving aside the wisdom of XML schema (yuck) and developing standards
>>independently of actual products, it does puzzle me that the work Roger
>>Hyam did on the LSID vocabularies is consistently overlooked. The is a
>>RDF version of TCS
>> http://rs.tdwg.org/ontology/voc/TaxonConcept
>>
>>
>> This was used by CoL in their LSIDs, but because they usually broke I
>>suspect nobody used them.
>>
>>
>> We seem to be in a muddled state at present where there are competing
>>vocabularies in use for taxonomic names and concepts, and these two
>>notions are often not cleanly separated. Whereas nomenclators such as
>>IPNI and Zoobank use the LSID taxon name vocabulary, other databases use
>>vocabularies such as Darwin Core, which rather conflate  names and
>>concepts. It's not clear to me how this situation arose, but it somewhat
>>defeats the point of having standards.
>>
>>
>> Regards,
>>
>>
>> Rod
>>
>>
>>
>>
>>
>> Sent from my iPhone
>>
>> On 1 Nov 2012, at 22:41, <Tony.Rees at csiro.au> wrote:
>>
>> Hi TDWG persons,
>>
>> I am involved in an activity here to set a local standard for storing
>>taxonomic name, identifier and (probably) hierarchy information in
>>metadata records using our profile of ISO 19115 for the latter, and the
>>question will come up as to whether to use elements from TCS, DwC, EML,
>>NCBII extension to ISO 19115, or other. By default I would expect the
>>front runner to be TCS but it appears few if any major systems have ever
>>gone that route  I have looked at ITIS, COL, TROPICOS, WoRMS, IPNI,
>>GBIF, AFD/APNI, moreŠ the nearest would perhaps be AFD/APNI (hence
>>copying Paul on this email) however their ³ibis² schema, though
>>apparently based originally on TCS,
>>http://biodiversity.org.au/xml/ibis-20120909.xsd , does not make any
>>explicit reference to the TCS schema so far as I can see. (Note also the
>>cited schema definitionhttp://biodiversity.org.au/xml/ibis [or
>>presumably http://biodiversity.org.au/xml/ibis.xsd] does not seem to
>>exist, but maybe I am missing something).
>>
>> I am in the interesting position of also wishing to make apps which
>>both publish and consume taxonomic name information so *could* implement
>>TCS for these, but if no-one else is doing so maybe that is not a path
>>to future data harmonisation, and something like DwC might be better.
>>
>> It does seem odd that we have a standard endorsed in 2005 by TDWG which
>>is apparently unused by any current major players in the real world. Any
>>thoughts?
>>
>> 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
>> LinkedIn profile: http://www.linkedin.com/pub/tony-rees/18/770/36
>>
>> From: tdwg-tag-bounces at lists.tdwg.org
>>[mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Paul Murray
>> Sent: Wednesday, 7 March 2012 12:52 PM
>> To: Steve Baskauf
>> Cc: "Éamonn Ó Tuama (GBIF)"; TDWG TAG
>> Subject: Re: [tdwg-tag] Creating a TDWG standard for documenting Data
>>Standards [SEC=UNCLASSIFIED]
>>
>>
>> On 07/03/2012, at 3:11 AM, Steve Baskauf wrote:
>>
>>
>>
>> Dag and Éamonn,
>>
>> In the context of the discussion which has been going on in the TDWG
>>RDF mailing list, I have been thinking more about the issue of how to
>>deal with DwC terms which state "Recommended best practice is to use a
>>controlled vocabulary...".  That would be dcterms:type, dwc:language,
>>dwc:basisOfRecord, dwc:sex, dwc:lifeStage, dwc:reproductiveCondition,
>>dwc:behavior, dwc:establishmentMeans, dwc:occurrenceStatus,
>>dwc:disposition, dwc:continent, dwc:waterBody, dwc:islandGroup,
>>dwc:island, dwc:country, dwc:verbatimCoordinateSystem,
>>dwc:georeferenceVerificationStatus,
>>dwc:identificationVerificationStatus, dwc:taxonRank;
>>dwc:nomenclaturalCode, dwc:taxonomicStatus, dwc:relationshipOfResource,
>>and dwc:measurementType .
>>
>>
>> We here have had all sorts of problems using other people's
>>vocabularies - they never quite match the data we have. Our solution has
>>been to use the standard terms where possible, but to mint our own where
>>needed. We create RDF objects and to declare them as being the correct
>>type.
>>
>> For instance,
>>           http://biodiversity.org.au/voc/afd/AFD#RelationshipTypeTerm
>>
>> Is declared to be a subclass of
>>
>>http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonRelationshipTerm
>>
>> And we have a few specific items of that type:
>>
>>http://biodiversity.org.au/voc/afd/RelationshipTypeTerm#has-emendation
>>
>>http://biodiversity.org.au/voc/afd/RelationshipTypeTerm#has-invalid-name
>>
>>http://biodiversity.org.au/voc/afd/RelationshipTypeTerm#has-junior-homony
>>m
>>
>>http://biodiversity.org.au/voc/afd/RelationshipTypeTerm#has-miscellaneous
>>-literature-name
>>
>> These individuals are therefore correctly typed to be legitimately be
>>used as a TDWG  relationshipCategory.
>>
>> Your lists of dwc:disposition values does not need to be exhaustive.
>>It's legitimate (from a machine point of view) for a site to create
>>their own terms. However, this does mean that the world becomes
>>fragmented into a number of site-specific vocabularies that cannot be
>>machine-reasoned over. The underlying reason for this is that that is in
>>fact the way the world actually is at the moment, and there's not a lot
>>of help for it.
>>
>> -------------------------------------------------------------
>>
>> There are two or three approaches to using a standard vocabulary when
>>your own data does not quite match it.
>>
>> You can use the standard term that is *closest in meaning* to your own
>>term. The difficulty here is that if the meaning of the standard term
>>implies things that are not true of your data, using it  means that you
>>are asserting things that are in fact not true, and for that reason I
>>suggest that it's not the way to go.
>>
>> You can use the standard term whose definition encompasses your term.
>>The difficulty here is that some vocabularies (notably Taxon Concept
>>Schema) don't have "other" or "unspecified" values for their
>>enumerations - they are not exhaustive.
>>
>> In either of these cases, you will want to supplement the standard term
>>with another value specific to your own data set, whose definition you
>>make available. There are a few ways to do that.
>>
>> You can use the "define your own term" mechanism and assert both
>>   _:_ tdwg:has_relationship_type tdwg:is-subtaxon-of  .
>>   _:_ tdwg:has_relationship_type
>>my-voc:is-recently-declared-subtaxon-of  .
>>
>> You can have a completely separate predicate:
>>   _:_ tdwg:has_relationship_type tdwg:is-subtaxon-of  .
>>   _:_ myvoc:has_relationship_type
>>my-voc:is-recently-declared-subtaxon-of  .
>>
>> You can also be terribly clever and declare your own predicate to be a
>>super-property of the TDWG predicate, one whose range is a union. This
>>isn't terribly useful to people using your data unless the tdwg triple
>>is also asserted.
>>
>> Another alternative is to create an OWL rule that says
>> "if a thing has relationship-type
>>my-voc:is-recently-declared-subtaxon-of, then it also has
>>relationship-type tdwg:is-subtaxon-of"
>>
>> But this creates a performance hit.
>>
>> -------------------------------------------------------------
>>
>> That little discussion aside, my main concern is that you don't get
>>mired in attempting to exhaustively list all the different island types
>>(etc) as part of the vocabulary that you are creating. It's a
>>never-ending job. It might be an idea to have the design guideline that
>>no enumeration class defined by the vocabulary shall have more than 10
>>values. It's arbitrary, but it will keep people from being carried away
>>subdividing types into a hierarchy that they think is a good idea, but
>>which doesn't match the data people already have.
>>
>> I'd also suggest that that every enumeration (ie, ist of individuals)
>>include two special values:
>>
>> NOT_SPECIFIED. This value is not present in the source, underlying
>>data. It isn't in the database, the respondent didn't fill out the form
>>fully. Perhaps "NULL" might be a better name - assuming people at this
>>level know what it means.
>> OTHER. This means the value is some specific value, but it's not
>>covered in the TDWG list. I am not sure if this value should be
>>explicitly used if you are publishing your own vocabulary and using
>>terms from that. I'm inclined to say it should not be, because doing
>>that would result in two values for predicates that naturally should be
>>functional.
>>
>> These special values *can* be done as a single instance, which means
>>you could easily pull all "not specifieds" out of a dataset, but that
>>means that either the ranges would have to be declared as a union, which
>>is messy, or the individuals would have to be declared as having all
>>possible types, which would break disjoint class declarations.
>>
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