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

[greg whitbread]

+1 for the TDWG ontology.
Not a standard (yet) but one of the most useful and enduring things
that TDWG has produced ( thanks Roger ).
Overlooked perhaps because it is CSV enough for aggregation.  For real
work it's use should be encouraged.

ALA-NSL uses it as the basis for the LSID vocabularies, RDF and JSON
services delivered from http://biodiversity.org.au

  urn:lsid:biodiversity.org.au:apni.name:54321 ,
http://biodiversity.org.au/apni.name/54321.rdf or
http://biodiversity.org.au/apni.name/54321.json

I will leave the XML response to Paul.

greg

On 2 November 2012 10:55, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> 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, more… the
> nearest would perhaps be AFD/APNI (hence copying Paul on this email) however
> their “ibis” 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 definition http://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-homonym
>
>
> 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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-- 
Greg Whitbread
Australian National Botanic Gardens
Australian National Herbarium
+61 2 62509482
ghw at anbg.gov.au