Matt, all ontology work within TDWG so far should be classified as experimental in my opinion. As you have pointed out, none of this work has gone through a proper standards process (with the exception of NCD maybe), but was driven by immediate needs for LSID resolution.
Also there is a large overlap between the xml schema based TDWG standards such as ABCD, TCS, DWC, NCD and SDD. Plus pretty much all of them use different schema design patterns, so it wouldn't be trivial to integrate them into one. Some standards like TCS actually have placeholders (TCS even has a PlaceholderType complex type) to refer to specimens or publications, as it was not considered the job of TCS to define those. But then again one needed to express the relationship to those objects at a time when the those standards were not yet finalised or used different, incompatible design patterns.
To me the only way out would be to step back and try to reconcile all those standards into a single ontology with an corresponding xml schema. The new DarwinCore terms dont exactly try to do that, but at least they represent a consistent way of representing the basics of our domain, in particular specimen, names & taxonomies. Please keep in mind when looking at the DwC terms that the development had the flexibility and simplicity of Dublin Core in mind rather than a true RDF ontology. It therefore also tries to be technology independent in its core, but provides guidelines for the different implementation/ serialisation technologies like XML, (X)HTML, RDF or tab delimited text files that make use of the same term definitions.
I am really glad that you pointed out all these problems, as I think we still have serious work in front of us.
Markus
On Feb 23, 2009, at 21:51, Matt Jones wrote:
This thread has prompted me to ask some naive questions about the process under which the vocabularies are formed. Maybe I'm the only one who is confused about the vocabularies, their status, and the process of forming new terms, but it seems maybe I'm not alone. And clarification on some of these points will help me with our direction on the development of the Observation Ontology under the OSR group, which I think will fit right in with Stan's point about fitting some of the concepts into a broader Observation framework.
For me there is a lot of confusion over the TDWG vocabularies, partly because they capture concepts that are present in existing TDWG standards, but are generally incomplete. For example, the TCS standard provides the field 'Specimens/Specimen', which I think is relevant to Hilmar's question. However, the listed TDWG vocabulary for TCS is the TaxonConcept vocabulary (http://rs.tdwg.org/ontology/voc/TaxonConcept), which does not provide a class for the TCS 'Specimen' concept. In addition, the ABCD TDWG standard also seem to have a way for specimens to be represented, but they are generalized as 'Unit's with a 'RecordBasis' of 'PreservedSpecimen'. So there are at least two official TDWG 'standards' for representing Specimen information, in addition to whatever DwC does. It seems to me that the best thing to do would be to finish the LSID vocabularies for TCS and ABCD so that they completely represent the concepts in TCS and ABCD, then get that approved as a valid way to represent these TDWG standards. In the process, one could try to resolve the differences in modeling approaches employed by the different standards, such as mapping the Specimen concept in TCS to its corresponding concept in DwC and ABCD. This would help avoid multiple TDWG standards defining overlapping versions of these concepts, and let people use the vocabularies in place of the XML schema versions of these standards.
What is the process for approval of the LSID vocabularies? They seem to be bypassing the normal TDWG standards track. Some of the vocabularies have a status of 'Available' (like TaxonConcept, even though it is incomplete), while others are marked as 'Developmental'.
The page on OntologyGovernance (http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntologyGovernance) states: "Relationship Between TDWG Standards and the Ontology -- Concepts are standardized by being included in TDWG Standards. Once they have been mentioned in a standard the Ontology Manager has the responsibility of maintaining their URIs and descriptions as per the standard. Concepts must be promoted to the live branch before the standard enters the standards process. "
So it seems that the OntologyManager replaces the standards process for the purpose of the vocabularies. Is this correct? And does the OntologyManager make sure that concepts like 'Specimen' that are defined in TCS make it into the corresponding LSID vocabulary before it is classified as 'Available'? And how does the OntologyManager decide which concept and representation for 'Specimen' to use -- the one from TCS or the one from ABCD? Does 'Available' have the same weight as a published TDWG standard, and if so, shouldn't these vocabularies be listed on the Standards page as well? Finally, does the existence of a concept such as 'Specimen' in TCS have any bearing on the development of new standards such as DwC that may want to define the concept differently, or more completely?
Matt
On Mon, Feb 23, 2009 at 11:22 AM, Blum, Stan sblum@calacademy.org wrote:
Given that this ontology work has to be formally correct in a several ways, I'd like to suggest (strongly) that the
name of "TaxonOccurrence" concept
be changed to
"OrganismOccurrence".
One of the properties of OrganismOccurrence would be the TaxonomicIdentification.
If this has a parent "thing", it should be something like the ObservationMeasurement thing that Simon Cox (or other larger ontologies) described at least year's meeting.
-Stan
-----Original Message----- From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Monday, February 23, 2009 11:26 AM To: Hilmar Lapp; Technical Architecture Group mailing list; rogerhyam Hyam Cc: Enrico Pontelli; Rutger A. Vos; Arlin Stoltzfus; Brandon Chisham; nexml-discuss@lists.sourceforge.net Subject: Re: [tdwg-tag] Embedding specimen (and other) annotations in NeXML
Was this particular question answered?
"2) Is there a TDWG vocabulary (in RDF or OWL) that has a relation for referring to a specimen record, or are you aware of another one that has this?"
Is the Occurrence RDF vocab at http://rs.tdwg.org/ontology/voc/TaxonOccurrence what you are looking for? I'm not sure I fully understood what you are after, but have a look and see if it matches your requirements.
Kevin
-----Original Message----- From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Hilmar Lapp Sent: Monday, 23 February 2009 11:04 a.m. To: Technical Architecture Group mailing list; rogerhyam Hyam Cc: Enrico Pontelli; Rutger A. Vos; Arlin Stoltzfus; nexml-discuss@lists.sourceforge.net; Brandon Chisham Subject: [tdwg-tag] Embedding specimen (and other) annotations in NeXML
Hi Roger and everyone else involved in DwC and the core ontology,
in preparation for the upcoming hackathon [1] here we've worked our way through a number of use-cases for attaching metadata to data elements in NeXML [2] in a way that is semantically defined. The results are here:
http://evoinfo.nescent.org/Database_Interop_Hackathon/ Metadata_Support
If you can take a critical look specifically at the section on 'Specimens within collections' (http://tinyurl.com/djdby3) that'd be great.
Specific questions related to that:
Is this using DarwinCore in a correct and/or sanctioned way?
Is there a TDWG vocabulary (in RDF or OWL) that has a relation for
referring to a specimen record, or are you aware of another one that has this?
- I could only find the XML schema for DarwinCore. Are there any
plans for (or did I miss the existence of) a corresponding ontology defined in OWL or RDF, similar Dublin Core (which has a RDF ontology at http://purl.org/dc/elements/1.1 and DCterms ontology at http://purl.org/dc/terms) .
- It wasn't immediately clear how one would use the TDWG core
ontology for doing the same thing in RDF (or OWL) - is this ontology supposed to be used yet, and are there usage examples, or does someone have a recommendation for how one would write the same example using the core ontology?
I know it's a rather tiny subset of DwC that we're using here but that's only a start and one use-case.
Of course, any other feedback to or suggestions for this or any of the other stuff on that page is welcome too!
Cheers,
-hilmar[1] http://evoinfo.nescent.org/Database_Interop_Hackathon [2] http://nexml.org
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Matthew B. Jones Director of Informatics Research and Development National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara jones@nceas.ucsb.edu Ph: 1-907-523-1960 http://www.nceas.ucsb.edu/ecoinfo
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