[tdwg-tag] darwin core terms inside tdwg ontology

"Markus Döring (GBIF)" mdoering at gbif.org
Tue Apr 28 07:15:31 CEST 2009

Im trying my best to catch up with all the mails in this thread  
lately, but surely missed something.
Ive ended up with a rather long post, please excuse, but I think the  
new dwc draft needs some explanations...

The idea of darwin core is to provide a simple list of terms which are  
useful in different contexts - just like dublin core does. We have  
been thinking about giving the terms a "domain", the dublin core  
terminology for binding a property to a class. Although we did declare  
a terms domain in the description, we finally decided that this is not  
more than a grouping of terms. Assigning a domain is a rather  
controversary task as properties can belong to several classes and the  
granularity of class definitions is strongly depending on your views.  
This is likely the mayor obstacle in getting an agreed ontology on the  
road too I believe.

But in order to express the context of a collection of darwin core  
terms we also defined class terms representing a taxon/name, an  
occurrence/specimen, a site, a collecting event and more. Actually  
there are 2 ways of expressing the type of a thing in the new terms -  
using a class term (e.g. as the parent xml element instead of just  
record or inside the rowType attribute of the text archive meta file)  
or using the basis of record when using the simple/classic darwin core  
with a meaningfree DarwinRecord parent element.

During last TDWG I got very attracted to the KISS idea that was  
present all over, but especially in Chucks talk. Why has darwin core  
been so much more successful than other tdwg formats? Why can't we use  
the same approach to share taxonomic or nomenclatural data? In the end  
the core properties for a taxon or name are rather limited and if you  
take TCS apart there is not much more you can do with it than what the  
taxonomic dwc terms provide - leaving concept relations aside. We also  
decided not to separate a name from a taxon. That happens in the  
context and due to the present of a taxonomic status or taxonomic  
classification. In order to save you from looking up the latest draft,  
here is the list of the taxonomic terms with a few quick annoations  
from myself:

[ taken from http://darwincore.googlecode.com/svn/trunk/terms/ 
index.htm ]

taxonID  # the taxon/name ID, preferrably a GUID but local ids are  
permitted too. Any ID
scientificName  # the full name incl authorship
higherTaxonID  # ID pointing to the next higher taxon
higherTaxon  #  full scientific name of the next higher taxon. Can be  
used alternatively or in addition to the ID above
kingdom  # the classic dwc higher ranks to simplify transfer in many  
cases and useful to disambiguate homonyms
specificEpithet  # atomised epitheton part as you would guess
taxonRank  # any rank string, preferrably taken from a controlled list  
such as the TCS one
scientificNameAuthorship  # the authorship alone. Similar to the other  
atomised parts this might not be needed as the complete sciname string  
is good enough, but it seemed desired by many
nomenclaturalCode # the code to disambiguate homonyms across the codes
taxonAccordingTo # the taxon concept sec reference
namePublishedIn # the nomenclatural reference, original publication of  
the name
taxonomicStatus  # a status such as accepted, (heterotypic) synonym,  
missapplied name. Ideally also a vocabulary such as the ontology one  
for nomenclatural note types
nomenclaturalStatus  # similar to above, but only nomenclaturaly  
relevant statuses such as nom. illeg.
acceptedTaxonID  # pointer to accepted taxon in case of synonyms or  
misapplied names
acceptedTaxon  # explicit string version of above
basionymID  #  pointer to the basionym
basionym # explicit string version of above

So frankly I think there is a lot you can do with these terms. Every  
synonym will be a name on its own and link to the accepted taxon,  
having its own taxonomic status that can provide you with details  
about the reason for it being a synonym or misapplied name. If  
combined with 1 to many extensions, you could even exchange pretty  
detailed species information in a *very* simple model.
Imagine you have datat based on extensions for species such as  
distribution (multiple distribution status per area per species),  
descriptions (just a simple title, body, and description type ala SPM  
classes would be great), multimedia, alternative links/guids, types  
data. As an exercise I have also translated parts of the GISIN schema  
into extensions based around species described by darwin core terms  
and it works fine.

Surely darwin core terms can leave you in doubt about the exact  
context, just as dublin core does. But it immediately allows you to  
share data in a simple way that people are comfortable with and it is  
not tight to a technology per se. I see this as the biggest advantage  
of all. It plays nice in the world of xml, rdf, plain text, xhtml,  
microformats - just anything as it is based on just a list of terms  
with an associated globally unique URI. And by decoupling the  
recommendations on how to use the dwc terms in the context of  
different technologies, we can keep the term definitions stable no  
matter what comes next.

Also I wanted to avoid confusion about IPT and the dwc text archives.  
The text archive, extensions and vocabularies idea implemented in the  
IPT are not IPT specific. It's just a very simple exchanging format  
based on the dwc recommendations for how to use darwin core in the  
context of text/csv files. For the interested I am writing on client  
code currently, so there will be a java archive reader in a few days  
that allows you to easily iterate over the core dwc records in an  
archive and pulls out the related extension records together with the  
core record.

I am glad to see this list being so alive again!

On Apr 28, 2009, at 3:22, Blum, Stan wrote:

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> Please note, the most current draft of the DarwinCore is:
>   here http://code.google.com/p/darwincore/ and
>   here http://rs.tdwg.org/dwc/index.htm,
>   not here http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard) 
> ,
> My primary concern with the latest draft is the absence of an  
> explicit class identifier (and an implicit class definition) that  
> indicates what kind of data object the sender is transmitting.  If  
> an indexer/aggregator is indexing multiple kinds of resources, as  
> GBIF is, and a publisher provides a record with these elements  
> [ScientificName, ScientificNameAuthorship, NamePublishedIn, and  
> Country], how should the indexer interepret this record?  Is it an  
> organism occurrence record, an authoritative taxonomic record (the  
> country name indicating the entire known range of the taxon), or  
> part of a taxonomic checklist for that country?  The term/element  
> [BasisOfRecord] is the first step in narrowing the possible  
> meanings, but it's the only step and it appears not to be a required  
> step.  (I interpret the "Status: recommended" to mean that it's  
> optional.)   At a minimum, BasisOfRecord should be required.  It  
> would still be possible to publish garbage (at least hard to  
> interpret records) because our tools don't constrain structure, and  
> there isn't (yet) any guidance controlling the structures for  
> different classes of objects.
> The new GBIF Internet Publishing Toolkit (IPT) supports one-to-many  
> relationships among a series of flat tables and looks like it's  
> going to make it easier to transmit more complicated data than we  
> were doing with DiGIR and TAPIR.  In conjunction with this new  
> expanded bag of elements we could see a lot more complex data get  
> published.  If I may use a skiing metaphor, we've been on the bunny  
> slopes (for beginners) up until now.  The new DarwinCore looks like  
> a nicely groomed black diamond slope, but we haven't had any lessons  
> or even watched anyone else do what we're going to attempt.  I think  
> we're going to end up in a heap at the bottom of the hill, and the  
> aggregators are going to have to sort it out.  ( Woohoo! Extreme  
> biodiversity informatics! )
> Finally, I did not mean to say that the Ontology should not be  
> ratified, as in not supported; what I meant was that it should not  
> be a standard because we will want to change its contents without  
> versioning the ontology as a whole.  (Also, its not an application  
> schema, so it can't be used directly unless we venture into somewhat  
> uncharted territory.)  Its role is to help us keep our application  
> schemas coordinated.
> The earlier versions of the DarwinCore (or our protocols, or the way  
> we used them together) were too limiting (see Greg's comments); this  
> version allows terms to be combined in nonsensical ways.  It could  
> make life very difficult for data integrators.
> I think the bottom line is that we URGENTLY need a similar concerted  
> effort to advance the TDWG (biodiversity informatics) ontology, and  
> a companion set of application schemas coming forward from the  
> collections, marine biology, paleo, observation, taxon-name-concept  
> groups as soon as possible.
> -Stan
> -----Original Message-----
> From: Chuck Miller [mailto:Chuck.Miller at mobot.org]
> Sent: Monday, April 27, 2009 7:22 AM
> To: Kevin Richards; Blum, Stan; Technical Architecture Group  
> mailinglist; exec at tdwg.org
> Subject: RE: [tdwg-tag] darwin core terms inside tdwg ontology
> Kevin,
> I agree with you and Stan that the ontology is useful to all  
> schemas.  It seems to me that a “TDWG Ontology” is a totally new and  
> different kind of thing than all the data exchange standards of the  
> prior 10 years – DwC, SDD, TCS, etc.  But, it is a very useful and  
> important new kind of thing that should be part of the TDWG  
> standards architecture. It challenges prior thinking about the  
> nature of TDWG standards to grasp what standardizing on an ontology  
> means.  But, I think it’s what is needed.
> If TDWG standardized on one Ontology, then the vocabulary of all  
> data exchange could be standardized on it.  Then all TDWG standards  
> could be revised over time to comply to that vocabulary standard,  
> including DwC.
> Stan said: “ I'd like to hear the rationale for combining taxonomic  
> name/concept with organism occurrence.” An occurrence record  
> generally has an organism’s name associated with it in the real  
> world. It is necessary and inevitable that vocabulary about organism  
> names will be used in an occurrence data exchange schema like DwC.  
> We have been stymied with this idea for years. A standard Ontology/ 
> vocabulary for the elements of name information needed to be  
> associated with an occurrence, or a description, or a taxon concept  
> would go a long way toward solving this duality.  The “standard  
> vocabulary” would not be standardized within DwC but it would be  
> used in DwC.
> Of course there is the problem of the hundreds of installations of  
> DiGIR that use DwC “classic” and are no doubt not going to change  
> for a long time.  I think they just have to be accepted and worked  
> around going forward.  It’s impractical to think of anything else.   
> But, the past should not roadblock the future and we need to get  
> moving toward that future.
> Stan thinks that the Ontology is not appropriate for TDWG  
> ratification.  Why not?  Change has to start somewhere. Yes, other  
> standards would probably be in conflict if the Ontology were  
> ratified, but I think we want to ultimately have consistency across  
> all the standards and that means there has to be change going  
> forward.  I think a ratified TDWG Ontology would provide the  
> foundation upon which to start building those changes.
> Chuck
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