[tdwg-tag] Any TCS users with experiences to report?
Kevin Richards
RichardsK at landcareresearch.co.nz
Fri Nov 2 03:01:20 CET 2012
We have used TCS for several projects, TDWG LSID vocabs (ontology) for some and Darwin Core taxon terms for another.
Eg.
Global Compositae Checklist uses a variation on TCS (as we need to provide “provider data” with the generated consensus checklist data).
The web service return this TCS variant, eg
http://dixon.iplantcollaborative.org/CompositaeWebService/TICAChecklistService.asmx/GetTICANameRecordTCS?ticaLSID=urn:lsid:compositae.org:names:0002DB31-87CD-4FC0-8852-7A16080F00BA
TCS works very well for handling taxon names and concepts in their fuller form. Our biggest issue using TCS was data providers not being able to actually give this structured data – it was often just NameId, FullName, ParentNameId, AcceptedNameId data.
I also agree with Rod that RDF is probably a better way to go, so the TDWG LSID vocabs (ontology), http://wiki.tdwg.org/twiki/bin/view/TAG/LsidVocs, are good for – ie the equivalent of the fuller TCS XML but in RDF from.
We have used these vocabs for most LSID resolver that resolve names:
our names at Landcare, eg http://lsid.landcareresearch.co.nz/authority/metadata/?lsid=urn:lsid:landcareresearch.co.nz:names:3BF47627-12C1-4091-A55D-5D004D97ABF6
Index Fungorum names, eg urn:lsid:indexfungorum.org:names:213645 (currently broken, but on the move to a new server)
Recently, with the NZOR project (www.nzor.org)<http://www.nzor.org)> we have delivered our names dataset to GBIF using the Taxon terms of Darwin Core, in the Darwin Core Archive format.
This brought up several issues. Firstly, we still don’t seem to have sorted out what actually constitutes a taxon concept, and what to apply the ID for the concept to. This is evident from the conflation of the name and concept terms in DwC. I think the Darwin-SW stuff Steve mention is a good step towards sorting this out, but it really needs some clarification, especially when applying it in a practical sense, eg as a DwC-A. Other issues where around the flattened nature of DwC and the struggle to get concept data into it.
I agree with Rich that all this stuff needs sorting out and we need to define a way forward – which standards should be recommended for use, etc.
This also overlaps with the TAG work and there has been some talk of a TAG workshop that may be a good place to look at these issues. Eg, if we had a core, technology independent model that all standards could map to, then the standards would be more like applicability statements, best practices etc for particular use cases. There shouldn’t really be any issue with have multiple taxon oriented standards (as there are many use cases that vary slightly), but at least they should all map together and be consistent in some way.
Kevin
From: tdwg-tag-bounces at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
Sent: Friday, 2 November 2012 2:13 p.m.
To: 'Roderic Page'; 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?
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 that….. 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 Roger’s 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 hasn’t 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 year’s 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 Roger’s vocabulary? Does it work? Can it be improved?
3) How much of DwC:Taxon is in active use? Just the “traditional” 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 “flavors” 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<mailto: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<mailto: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<mailto: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> [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#<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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