24 Jun
2013
24 Jun
'13
19:37
Hi John,
My apologies for the long delay - I wanted to finish reading the draft Darwin Core RDF guide, and recent discussion on it, before responding. I agree with the assertion made in the guide (section 2.6.1) that there's no useful way to use use Darwin Core xxxID terms in RDF. But even were this not the case, I struggle to understand the utility of the xxxID terms.
MaterialSampleID, as currently proposed, serves two purposes: it provides an identifier for the thing it gets slapped onto, and it also indicates that that thing is a MaterialSample. But this second purpose - indicating that the thing is a MaterialSample - can be done either by asserting it to be rdf:type dwctype:MaterialSample or by following the convention described in http://rs.tdwg.org/dwc/terms/guides/text/index.htm .
So all we really need is a mechanism for giving an identifier. Is there a reason not to use dc-elements:identifier for this purpose?
Best, Joel.
On Tue, 11 Jun 2013, John Deck wrote:
On Mon, Jun 10, 2013 at 2:43 PM, joel sachs jsachs@csee.umbc.edu wrote: Hi Everyone,
I was scared to read this thread, but it turned out to be fun. Despite the excellent clarification that occurred, I still have some questions. In relation to the proposal below (to introduce the terms MaterialSample, and MaterialSampleID): 1. Given that the decision was made to put MaterialSample in the "dwctype" namespace, why is the definition still "The category of information pertaining to the physical results of a sampling event …"? Shouldn't the definition be "The physical results of a sampling event ..."? (Ramona pointed this out in a message that didn't get posted to the list, but which Rich responded to [1].)yes, I agree with this... 2. I believe Steve asked why there needs to be a MaterialSampleID, when none of the other dwctype terms (preservedSpecimen, etc.) have IDs. JohnD gave a sound defence of MaterialSampleID [2], but his reasoning seems to apply equally to preservedSpecimenID, DigitalStilImageID, etc. Did I miss the explanation of why MaterialSamples are so different from the other dwctype terms? Or is the idea that we will define, e.g.,
dwctype:preservedSpecimen rdfs:subClassOf dwctype:MaterialSample so that preservedSpecimens will inherit MaterialSampleIDs ?MaterialSample doesn't necessarily have to be an occurrence and there could possibly be multiple occurrences in a sample (or vice versa). Thus we need the Identifier to track this (especially in the context of DwC represented as a flat-file) 3. In RDF, all resources are identified by URI, and (should be) referenced by appropriate predicates (hasIndividual, hasOccurrence, etc.) So my understanding is that all the recent discussion about xxxIDs pertains only to non-RDF records. Is that correct?
Not necessarily. Many thanks for the clarification already provided, and for any yet to come - Joel.
1. http://lists.tdwg.org/pipermail/tdwg-content/2013-May/003008.html 2. http://lists.tdwg.org/pipermail/tdwg-content/2013-May/003006.html On Sat, 25 May 2013, John Deck wrote: Steve, Thanks for your comments. Responding to both of your emails here. We’ve removed the class and now have just the MaterialSample dwctype and a materialSampleID property. dwctype:MaterialSample refines http://purl.obolibrary.org/obo/OBI_0000747. Also, we’ve updated materialSampleID to be a new term in the dwc/terms namespace instead of referencing the MiXS namespace. In our original proposal, we suggested using the MIxS RDF namespace for this property, however, the GSC did not make MIxS-as-RDF a standard, as decided recently at GSC15, so we’ve chosen not to use that term (by convention) and instead propose creating our own materialSampleID property in the dwc/terms namespace. (A side note: the GSC is still very much interested in MIxS as RDF and we’ll continue to maintain and implement https://code.google.com/p/mixs-as-rdf/ in conjunction with the MIxS developers). Modification to proposed terms: Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/dwctype/MaterialSample Namespace: http:/rs.tdwg.org/dwctype/ Label: Material Sample Definition: The category of information pertaining to the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: http://purl.obolibrary.org/obo/OBI_0000747 Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-05-25 Has Domain: Has Range: Refines: Version: MaterialSample-2013-05-25 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: materialSampleID Identifier: http://rs.tdwg.org/dwc/terms/MaterialSampleID Namespace: http://rs.tdwg.org/dwc/terms/ Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-05-25 Has Domain: Has Range: Version: materialSampleID-2013-05-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD (someone please confirm or deny this) John D. and John W. On Mon, May 20, 2013 at 7:39 PM, Steve Baskauf <steve.baskauf@vanderbilt.edu> wrote: Here is the second question. The proposal proposes a new MaterialSample class http://rs.tdwg.org/dwc/terms/MaterialSample which is in the "main" (dwc:=http://rs.tdwg.org/dwc/terms/ ) namespace. I guess my question is why we need this class. I can definitely see a rational for a new class defined as part of the DwC type vocabulary (i.e. dwctype:MaterialSample). It would be used to type resources that are material samples. But the class terms in the main (dwc:) namespace are used as a convenient way to group DwC property terms that might reasonably be used with instances of that class. However, there really aren't any such terms. We already have a convention in which not every type vocabulary class term has a corresponding class term in the main (dwc:) namespace. There are dwctype:PreservedSpecimen, dwctype:LivingSpecimen, dwctype:FossilSpecimen, dwctype:HumanObservation, dwctype:MachineObservation, and dwctype:NomenclaturalChecklist, none of which have dwc: namespace analogues. So why does MaterialSample need a dwc: namespace analog? Steve John Wieczorek wrote: Dear all, TDWG could see a lot of activity in 2013 in anticipation of the meeting in Florence in October. Much of the activity is related to enabling integration across multiple parts of our domain. We have the Audubon Core under review for biodiversity-related media and an impending RDF Guide to supplement the already extant Text and XML Guides for Darwin Core. This message is to bring your attention to another integrative initiative, to introduce terms into Darwin Core that will form a nexus between Occurrences and the interesting things that happen with physical materials that result from them, such as, but not limited to, genetic sequencing. A series of meetings for a little over the past year have inspired our colleagues in the Genomics Standards Consortium (GSC) to propose to their constituency to align their terms with Darwin Core, including adopting some of the Darwin Core terms in place of their own that have the same meaning. Out of these discussions has come the realization that neither community has terms to accommodate the concept of an identifiable (objectively, not taxonomically), trackable material sample. This message constitutes such a proposal. This proposal would have no impact on those publishing purely taxonomic data. It would also have no impact on those publishing occurrence data unless they want to increase their capacity to distinguish material samples from organisms more rigorously than is now possible using only the dwc:preparations term. The initial request for new terms can be found in the Darwin Core Issue tracker as http://code.google.com/p/darwincore/issues/detail?id=167. Below I have elaborated nad formalized the request into the three distinct terms under consideration, initiating the 30 day minimum public review process to seek consensus on their inclusion in the Darwin Core standard. Your job, should you choose to accept it, is to discuss the merits or any perceived problems in the inclusion of these three terms in Darwin Core. Below I will give the proposed properties of three terms as they would appear in the Darwin Core Quick Reference Guide, though these properties would be included in the RDF of the normative form of the documentation. A new MaterialSample class: This is for the purpose of organizing properties, just as the existing classes (Occurrence, Event, Location, GeologicalContext, Identification, Taxon, etc.) do, without having any terms declare this class as their domain. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http:/rs.tdwg.org/dwc/terms Label: Material Sample Definition: The category of information pertaining to the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed, with the intention of being representative of a greater whole. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) A Darwin Core Type Vocabulary value for basisOfRecord is needed to represent this new class of information. Luckily, a term already exists in the Ontology for Biomedical Investigations (http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.o rg/obo/OBI_0000747). We and the GSC both propose to reuse this class within Darwin Core as below, making it the cross-ver point between the two domains. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http://purl.obolibrary.org/obo/OBI_0000747 Label: material sample Definition: A material entity that has the material sample role Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines:http://purl.obolibrary.org/obo/OBI_0100051 Status: recommended Date Issued: 2013-03-28 Date Modified: 2013-03-28 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD In keeping with all other classes in Darwin Core, the Material Sample class would have a corresponding identifier property. The Genomics Standards Consortium (GSC) is in the process of proposing this term. If it is accepted, we propose to use it, and its properties would be as below, otherwise, the properties would be the same, but have the Darwin Core namespace and identifier URI. Term Name: materialSampleID Identifier: http://gensc.org/ns/mixs/materialSampleID Namespace: http://gensc.org/ns/mixs Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: materialSampleID-2013-03-28 Replaces: IsReplaceBy: Class: http://purl.obolibrary.org/obo/OBI_0000747 ABCD 2.0.6: not in ABCD (someone please confirm or deny this) -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- John Deck (541) 321-0689-- John Deck (541) 321-0689