New Darwin Core terms proposed relating to material samples
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....). 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)
Although it's been more than 30 days since John opened the public comment on this proposal, there hasn't been much discussion and no notification that the comment period has been closed. So I'm going to make a comment requesting some clarification about this proposal, stimulated by a comment about namespaces made by Dag Endresen in a different context.
I re-read the Issue Tracker posting: http://code.google.com/p/darwincore/issues/detail?id=167 and the email below. I think that the proposal was to "import" the ID term mixs:materialSampleID if GSC adopts it (I don't know if they did or not). That is pretty straightforward.
With regards to the type vocabulary term, I'm really confused. My understanding of the current precedent is that for applications which provide a literal value for basisOfRecord, the pattern would call for the string "MaterialSample" to be given (for consistency with "PreservedSpecimen", "MachineObservation", etc.). The URIs for existing DwC-defined DwC type vocabulary terms follow the pattern: http://rs.tdwg.org/dwc/dwctype/%5BLocalName] where [LocalName] is the controlled text value. Following that pattern, the type vocabulary term URI would be http://rs.tdwg.org/dwc/dwctype/MaterialSample or dwctype:MaterialSample where dwctype: is the abbreviation for the namespace "http://rs.tdwg.org/dwc/dwctype/".
However, in the email below, the proposed type vocabulary term is given the URI http://rs.tdwg.org/dwc/terms/MaterialSample which uses the "main" DwC namespace (dwc: = http://rs.tdwg.org/dwc/terms/ ) rather than the dwctype: namespace, while the "namespace" in the proposal is listed as http://purl.obolibrary.org/obo/OBI_0000747 . But that's not a namespace, its a term.
If the intention is to import the OBO term, then the URI for the type vocabulary term would be http://purl.obolibrary.org/obo/OBI_0000747 (namespace: "http://purl.obolibrary.org/obo/"). Under the proposal, I'm not sure if the controlled text value would be "MaterialSample" (following the existing convention using words and capitalization) or "OBI_0000747" (following the existing convention that the local name from the URI is used as the text controlled value.
I have another question, but I think it would be better to have a separate email for it. 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 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.... http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/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)
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 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.... http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/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)
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/MaterialSamplehttp://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http:/rs.tdwg.org/dwctype/ 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.
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/MaterialSampleIDhttp://rs.tdwg.org/dwc/terms/MaterialSamplehttp://gensc.org/ns/mixs/materialSampleID
Namespace: http://rs.tdwg.org/dwc/terms/http://rs.tdwg.org/dwc/terms/MaterialSamplehttp://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: 2013-05-25
Has Domain:
Has Range:
Version: materialSampleID-2013-05-25
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Occurrencehttp://purl.obolibrary.org/obo/OBI_0000747
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....). 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
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John and John,
OK, great! I think this all makes sense to me now. I think that that in the wiki discussion you might eventually make the comment that although materialSampleID is conveniently grouped with other terms under the Occurrence class, a material sample does not have to be a sample from a living organism which is documented in an Occurrence. It could be something that may or may not be known to contain one or more living organisms (e.g. water samples), part of one or more organisms (e.g. tissue samples), or even no known living organisms (e.g. rock samples). Well anyway, you should say that if it is true. I think that was the intention when the term was being discussed. You can confirm whether I have this right or not.
Steve
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 http://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http:/rs.tdwg.org/dwctype/ 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.
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 http://rs.tdwg.org/dwc/terms/MaterialSample http://gensc.org/ns/mixs/materialSampleID
Namespace: http://rs.tdwg.org/dwc/terms/ http://rs.tdwg.org/dwc/terms/MaterialSample 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: 2013-05-25
Has Domain:
Has Range:
Version: materialSampleID-2013-05-25
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Occurrence http://purl.obolibrary.org/obo/OBI_0000747
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 mailto: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 <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.org/obo/OBI_0000747 <http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/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 <tel:%28615%29%20343-4582>, fax: (615) 322-4942 <tel:%28615%29%20322-4942> 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 <mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content-- John Deck (541) 321-0689
Hi All,
I'm on my way home from Berlin, and catching up on this thread.
I wanted to take this opportunity to describe what Rob Whitton and I have been working on over the past year or so, along these lines.
Basically, we've been running with the idea of an "Individual" class - as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW: https://code.google.com/p/darwin-sw/wiki/ClassIndividual
We have (or intend to) drop the "Organism" part, so it's just an "Individual" - because in our data model it doesn't need to be limited to an organism.
Anyway, the reason I mention this here is that we have found it to be a very powerful tool for tracking our data much more closely to "reality" than is achieved when force-fitting everything into the Occurrence class. I also mention it because we are using it for the same function that the proposed MaterialSample/ID seems to be used for.
We define an "Individual" as the physical "something" that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID), and also to the meaning of "CollectionObject" from the old ASC/MVZ data model (see also: https://www.idigbio.org/wiki/images/c/c9/Phase_I_Report.pdf).
So far, it seems to be a very stable and functional unit for tracking myriad kinds of biodiversity information. It is linked from the Occurrence table, and is the thing to which taxon determinations are applied. It's also the thing that represents museum collections objects. The key is that it is hierarchical. For example, there may be one instance of an "Individual" that is a school of fish observed on a reef, representing an occurrence. That Individual instance may have a child "Lot" of, say 5 specimens that were speared and preserved for a Museum. Each of the five specimens might then be assigned its own individual instance, as children of the "Lot". Then, when one or more tissue samples are extracted from one or more of the specimens, those are represented as additional "Individual" instances that are children of the respective specimen individual.
What's nice about the way we manage this is that there is inheritance up and down the hierarchy chain. For example, if the "School" individual is associated with an Occurrence (observation/collection event), then all of its children can inherit this information. Likewise, a taxonomic determination can be applied to any individual in the hierarchy, and that identification can be inherited up or down the hierarchy as appropriate (the meaning of "appropriate" is a bit involved, but I'd be happy to elaborate).
I've been out of this discussion for a while, but I guess my main question/point is to ask whether there has been any progress towards incorporating the concept of the Darwin-SW concept of "Individual" (https://code.google.com/p/darwin-sw/wiki/ClassIndividual) into DWC, and if so, whether this might be a better way of managing materialSample/ID.
Aloha, Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Saturday, May 25, 2013 1:08 AM To: John Deck Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
John and John,
OK, great! I think this all makes sense to me now. I think that that in the wiki discussion you might eventually make the comment that although materialSampleID is conveniently grouped with other terms under the Occurrence class, a material sample does not have to be a sample from a living organism which is documented in an Occurrence. It could be something that may or may not be known to contain one or more living organisms (e.g. water samples), part of one or more organisms (e.g. tissue samples), or even no known living organisms (e.g. rock samples). Well anyway, you should say that if it is true. I think that was the intention when the term was being discussed. You can confirm whether I have this right or not.
Steve
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/MaterialSamplehttp://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http:/http://rs.tdwg.org/dwctype/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.
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/MaterialSampleIDhttp://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http://rs.tdwg.org/dwc/terms/http://rs.tdwg.org/dwc/terms/MaterialSample
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.edumailto: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:/http://rs.tdwg.org/dwc/termshttp://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....). 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) 343-4582tel:%28615%29%20343-4582, fax: (615) 322-4942tel:%28615%29%20322-4942
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.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- John Deck (541) 321-0689
--
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
________________________________ This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
Hi Rich, I'm on my way home from Copenhagen and leaving very soon so will write just a quick response to you. The view of those folks who submitted the MaterialSample ticket ( https://code.google.com/p/darwincore/issues/detail?id=167) is defined well by the following paragraph:
A “material sample” can pertain to general matter in which organisms may exist, in whole, in part, or in conjunction with many other organisms. The “material sample” may exist for a brief period, such as a tissue that is destructively sampled when it is converted to DNA extract. It may also represent a collection of multiple taxa, such as a soil or water sample that is used with the intention of describing the diversity of organisms, whether the actual organisms are later recovered from such a sample, or whether that sample is processed (sometimes destructively, which is when the entire sample is consumed for an analysis process) in order to generate a set of derivatives directly from organisms (e.g.16S sequences from a metagenomics run). A “material sample” may also yield connections to other indicators of biodiversity aside from taxa, such as a transcriptome, indicating which DNA is actively being expressed at a particular point in time.
In reading your idea of what an individual may be, it is not so different than what we're proposing. However, MaterialSample makes no assumptions about what any affiliated names or properties may or may not be, and can be composed of many possible sub-units. Also, the notion of what you're describing is a bit of a stretch when the common dictionary definition of individual is means "single or separate".
John
On Sun, May 26, 2013 at 3:31 AM, Richard Pyle deepreef@bishopmuseum.orgwrote:
Hi All,****
I’m on my way home from Berlin, and catching up on this thread.****
I wanted to take this opportunity to describe what Rob Whitton and I have been working on over the past year or so, along these lines.****
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:****
https://code.google.com/p/darwin-sw/wiki/ClassIndividual****
We have (or intend to) drop the “Organism” part, so it’s just an “Individual” – because in our data model it doesn’t need to be limited to an organism.****
Anyway, the reason I mention this here is that we have found it to be a very powerful tool for tracking our data much more closely to “reality” than is achieved when force-fitting everything into the Occurrence class. I also mention it because we are using it for the same function that the proposed MaterialSample/ID seems to be used for.****
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID), and also to the meaning of “CollectionObject” from the old ASC/MVZ data model (see also: https://www.idigbio.org/wiki/images/c/c9/Phase_I_Report.pdf).****
So far, it seems to be a very stable and functional unit for tracking myriad kinds of biodiversity information. It is linked from the Occurrence table, and is the thing to which taxon determinations are applied. It’s also the thing that represents museum collections objects. The key is that it is hierarchical. For example, there may be one instance of an “Individual” that is a school of fish observed on a reef, representing an occurrence. That Individual instance may have a child “Lot” of, say 5 specimens that were speared and preserved for a Museum. Each of the five specimens might then be assigned its own individual instance, as children of the "Lot“. Then, when one or more tissue samples are extracted from one or more of the specimens, those are represented as additional “Individual” instances that are children of the respective specimen individual.****
What’s nice about the way we manage this is that there is inheritance up and down the hierarchy chain. For example, if the “School” individual is associated with an Occurrence (observation/collection event), then all of its children can inherit this information. Likewise, a taxonomic determination can be applied to any individual in the hierarchy, and that identification can be inherited up or down the hierarchy as appropriate (the meaning of “appropriate” is a bit involved, but I’d be happy to elaborate).****
I’ve been out of this discussion for a while, but I guess my main question/point is to ask whether there has been any progress towards incorporating the concept of the Darwin-SW concept of “Individual” ( https://code.google.com/p/darwin-sw/wiki/ClassIndividual) into DWC, and if so, whether this might be a better way of managing materialSample/ID.** **
Aloha,****
Rich****
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Steve Baskauf *Sent:* Saturday, May 25, 2013 1:08 AM *To:* John Deck *Cc:* TDWG Content Mailing List *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to material samples****
John and John,
OK, great! I think this all makes sense to me now. I think that that in the wiki discussion you might eventually make the comment that although materialSampleID is conveniently grouped with other terms under the Occurrence class, a material sample does not have to be a sample from a living organism which is documented in an Occurrence. It could be something that may or may not be known to contain one or more living organisms (e.g. water samples), part of one or more organisms (e.g. tissue samples), or even no known living organisms (e.g. rock samples). Well anyway, you should say that if it is true. I think that was the intention when the term was being discussed. You can confirm whether I have this right or not.
Steve
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/MaterialSamplehttp://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http:/rs.tdwg.org/dwctype/ 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.****
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/MaterialSampleIDhttp://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http://rs.tdwg.org/dwc/terms/http://rs.tdwg.org/dwc/terms/MaterialSample
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....). 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****
-- ****
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****
This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
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tissue converted to DNA extract is still tissue (the tissue is still "material sample" after "destructive sampling", and still part of the event, just as is a photograph of the beast in the museum.
On May 25, 2013, at 9:55 PM, John Deck jdeck@berkeley.edu wrote:
Hi Rich, I'm on my way home from Copenhagen and leaving very soon so will write just a quick response to you. The view of those folks who submitted the MaterialSample ticket (https://code.google.com/p/darwincore/issues/detail?id=167) is defined well by the following paragraph:
A “material sample” can pertain to general matter in which organisms may exist, in whole, in part, or in conjunction with many other organisms. The “material sample” may exist for a brief period, such as a tissue that is destructively sampled when it is converted to DNA extract. It may also represent a collection of multiple taxa, such as a soil or water sample that is used with the intention of describing the diversity of organisms, whether the actual organisms are later recovered from such a sample, or whether that sample is processed (sometimes destructively, which is when the entire sample is consumed for an analysis process) in order to generate a set of derivatives directly from organisms (e.g.16S sequences from a metagenomics run). A “material sample” may also yield connections to other indicators of biodiversity aside from taxa, such as a transcriptome, indicating which DNA is actively being expressed at a particular point in time. In reading your idea of what an individual may be, it is not so different than what we're proposing. However, MaterialSample makes no assumptions about what any affiliated names or properties may or may not be, and can be composed of many possible sub-units. Also, the notion of what you're describing is a bit of a stretch when the common dictionary definition of individual is means "single or separate".
John
On Sun, May 26, 2013 at 3:31 AM, Richard Pyle deepreef@bishopmuseum.org wrote: Hi All,
I’m on my way home from Berlin, and catching up on this thread.
I wanted to take this opportunity to describe what Rob Whitton and I have been working on over the past year or so, along these lines.
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
https://code.google.com/p/darwin-sw/wiki/ClassIndividual
We have (or intend to) drop the “Organism” part, so it’s just an “Individual” – because in our data model it doesn’t need to be limited to an organism.
Anyway, the reason I mention this here is that we have found it to be a very powerful tool for tracking our data much more closely to “reality” than is achieved when force-fitting everything into the Occurrence class. I also mention it because we are using it for the same function that the proposed MaterialSample/ID seems to be used for.
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID), and also to the meaning of “CollectionObject” from the old ASC/MVZ data model (see also: https://www.idigbio.org/wiki/images/c/c9/Phase_I_Report.pdf).
So far, it seems to be a very stable and functional unit for tracking myriad kinds of biodiversity information. It is linked from the Occurrence table, and is the thing to which taxon determinations are applied. It’s also the thing that represents museum collections objects. The key is that it is hierarchical. For example, there may be one instance of an “Individual” that is a school of fish observed on a reef, representing an occurrence. That Individual instance may have a child “Lot” of, say 5 specimens that were speared and preserved for a Museum. Each of the five specimens might then be assigned its own individual instance, as children of the "Lot“. Then, when one or more tissue samples are extracted from one or more of the specimens, those are represented as additional “Individual” instances that are children of the respective specimen individual.
What’s nice about the way we manage this is that there is inheritance up and down the hierarchy chain. For example, if the “School” individual is associated with an Occurrence (observation/collection event), then all of its children can inherit this information. Likewise, a taxonomic determination can be applied to any individual in the hierarchy, and that identification can be inherited up or down the hierarchy as appropriate (the meaning of “appropriate” is a bit involved, but I’d be happy to elaborate).
I’ve been out of this discussion for a while, but I guess my main question/point is to ask whether there has been any progress towards incorporating the concept of the Darwin-SW concept of “Individual” (https://code.google.com/p/darwin-sw/wiki/ClassIndividual) into DWC, and if so, whether this might be a better way of managing materialSample/ID.
Aloha,
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Saturday, May 25, 2013 1:08 AM To: John Deck Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
John and John,
OK, great! I think this all makes sense to me now. I think that that in the wiki discussion you might eventually make the comment that although materialSampleID is conveniently grouped with other terms under the Occurrence class, a material sample does not have to be a sample from a living organism which is documented in an Occurrence. It could be something that may or may not be known to contain one or more living organisms (e.g. water samples), part of one or more organisms (e.g. tissue samples), or even no known living organisms (e.g. rock samples). Well anyway, you should say that if it is true. I think that was the intention when the term was being discussed. You can confirm whether I have this right or not.
Steve
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....). 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
-- 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
This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
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-- John Deck (541) 321-0689 _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Thanks John -
Yes, I agree - the description you forwarded definitely fits how we have been using "Individual". The main reason we selected that term was to stay in harmony with the existing "individualID" in DWC. Besides, other candidate terms ( "thing", "stuff", "unit", etc.) all seemed a bit vague. The match is not perfect, though, because some of the things we represent as "individuals" (herd, school, etc.) are not "sampled" (unless a visual observation counts as a sample). So, it would seem that "material sample" would be a subset/subclass of what we have been using for "Individual".
My main question, though, was more along the lines of what progress (if any) has been made towards establishing a formal class in DWC for "Individual" (representing the set of terms applied to attributes of what is intended by the existing DWC "individualID") - presumably modeled after the Darwin-SW "IndividualOrganism". And, whether or not there has been any progress, would there be any value in contemplating both that topic (expansion of dwc:individualID into a class), and this topic (proposed new dwc:materialSample) within the same discussion?
Aloha,
Rich
From: jdeck88@gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Saturday, May 25, 2013 5:55 PM To: Richard Pyle Cc: Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
Hi Rich,
I'm on my way home from Copenhagen and leaving very soon so will write just a quick response to you. The view of those folks who submitted the MaterialSample ticket (https://code.google.com/p/darwincore/issues/detail?id=167) is defined well by the following paragraph:
A "material sample" can pertain to general matter in which organisms may exist, in whole, in part, or in conjunction with many other organisms. The "material sample" may exist for a brief period, such as a tissue that is destructively sampled when it is converted to DNA extract. It may also represent a collection of multiple taxa, such as a soil or water sample that is used with the intention of describing the diversity of organisms, whether the actual organisms are later recovered from such a sample, or whether that sample is processed (sometimes destructively, which is when the entire sample is consumed for an analysis process) in order to generate a set of derivatives directly from organisms (e.g.16S sequences from a metagenomics run). A "material sample" may also yield connections to other indicators of biodiversity aside from taxa, such as a transcriptome, indicating which DNA is actively being expressed at a particular point in time.
In reading your idea of what an individual may be, it is not so different than what we're proposing. However, MaterialSample makes no assumptions about what any affiliated names or properties may or may not be, and can be composed of many possible sub-units. Also, the notion of what you're describing is a bit of a stretch when the common dictionary definition of individual is means "single or separate".
John
On Sun, May 26, 2013 at 3:31 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
Hi All,
I'm on my way home from Berlin, and catching up on this thread.
I wanted to take this opportunity to describe what Rob Whitton and I have been working on over the past year or so, along these lines.
Basically, we've been running with the idea of an "Individual" class - as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
https://code.google.com/p/darwin-sw/wiki/ClassIndividual
We have (or intend to) drop the "Organism" part, so it's just an "Individual" - because in our data model it doesn't need to be limited to an organism.
Anyway, the reason I mention this here is that we have found it to be a very powerful tool for tracking our data much more closely to "reality" than is achieved when force-fitting everything into the Occurrence class. I also mention it because we are using it for the same function that the proposed MaterialSample/ID seems to be used for.
We define an "Individual" as the physical "something" that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID), and also to the meaning of "CollectionObject" from the old ASC/MVZ data model (see also: https://www.idigbio.org/wiki/images/c/c9/Phase_I_Report.pdf).
So far, it seems to be a very stable and functional unit for tracking myriad kinds of biodiversity information. It is linked from the Occurrence table, and is the thing to which taxon determinations are applied. It's also the thing that represents museum collections objects. The key is that it is hierarchical. For example, there may be one instance of an "Individual" that is a school of fish observed on a reef, representing an occurrence. That Individual instance may have a child "Lot" of, say 5 specimens that were speared and preserved for a Museum. Each of the five specimens might then be assigned its own individual instance, as children of the "Lot". Then, when one or more tissue samples are extracted from one or more of the specimens, those are represented as additional "Individual" instances that are children of the respective specimen individual.
What's nice about the way we manage this is that there is inheritance up and down the hierarchy chain. For example, if the "School" individual is associated with an Occurrence (observation/collection event), then all of its children can inherit this information. Likewise, a taxonomic determination can be applied to any individual in the hierarchy, and that identification can be inherited up or down the hierarchy as appropriate (the meaning of "appropriate" is a bit involved, but I'd be happy to elaborate).
I've been out of this discussion for a while, but I guess my main question/point is to ask whether there has been any progress towards incorporating the concept of the Darwin-SW concept of "Individual" (https://code.google.com/p/darwin-sw/wiki/ClassIndividual) into DWC, and if so, whether this might be a better way of managing materialSample/ID.
Aloha,
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Saturday, May 25, 2013 1:08 AM To: John Deck Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
John and John,
OK, great! I think this all makes sense to me now. I think that that in the wiki discussion you might eventually make the comment that although materialSampleID is conveniently grouped with other terms under the Occurrence class, a material sample does not have to be a sample from a living organism which is documented in an Occurrence. It could be something that may or may not be known to contain one or more living organisms (e.g. water samples), part of one or more organisms (e.g. tissue samples), or even no known living organisms (e.g. rock samples). Well anyway, you should say that if it is true. I think that was the intention when the term was being discussed. You can confirm whether I have this right or not.
Steve
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 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/ 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/terms/MaterialSample http://rs.tdwg.org/dwc/dwctype/MaterialSample
Namespace: http:/ http://rs.tdwg.org/dwc/terms 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 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 http://www.w3.org/2000/01/rdf-schema#Class
Refines: http://purl.obolibrary.org/obo/OBI_0000747 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/MaterialSample http://rs.tdwg.org/dwc/terms/MaterialSampleID
Namespace: http://rs.tdwg.org/dwc/terms/MaterialSample 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 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 http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines: http://purl.org/dc/terms/identifier 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 http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org /obo/OBI_0000747 &iri=http://purl.obolibrary.org/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)
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc.
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.comwrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
to represent "material sample" and derivaties.
I believe we need "materialSample subclassOf sample" not the other way round (which way is it presently?). A sample can be the recording of temperature, humidity, rainfall etc. at a given location and time, the count of a population, or a media recording (image, sound, video) of an organism.
Gregor
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is: 1. define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions) 2. use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other 3. examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions. 4. use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal: http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questions http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value
- for a term to represent "material sample" and derivaties. It seems
that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn <g.m.hagedorn@gmail.com mailto:g.m.hagedorn@gmail.com> wrote:
> Basically, we’ve been running with the idea of an “Individual” class – as > originally proposed by Steve and discussed at some length on this list a > while ago. This has been documented for DSW: > > https://code.google.com/p/darwin-sw/wiki/ClassIndividual > We define an “Individual” as the physical “something” that underpins an > Occurrence. In the case of organisms, this can be a group (herd, school, > flock, etc.), specimen (either a single specimen, or a lot of multiple > specimens), or any sort of derivative of a specimen (part, tissue sample, > dna extraction, etc.). It corresponds to the intended meaning of I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content
One observation I would like to inject into this thread is the role of English language semantics. In addition to the pursuit of a set of terms and their relationships with each other, I see Gregor and Rob saying things like " "individual" doesn't quite seem to capture the concept or usage" which I read as "the English word "individual" has a dictionary definition that doesn't match this usage and therefore will confuse the usual English speaker.
Perhaps one permutation in solving the puzzle of a complete semantic model is to look for alternate words that convey the semantic concept without causing ambiguity with standard English definitions, like the invention of THeE. Would a Latin term serve for instance?
Just a thought. Overcoming the ME and YOU conflicts, may require a third WE approach.
Chuck
On May 26, 2013, at 8:07 AM, "Steve Baskauf" <steve.baskauf@vanderbilt.edumailto:steve.baskauf@vanderbilt.edu> wrote:
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is: 1. define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions) 2. use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other 3. examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions. 4. use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal: http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questions http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn <g.m.hagedorn@gmail.commailto:g.m.hagedorn@gmail.com> wrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- 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.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Thanks for the *EXCELLENT* post -- this gets to the heart of what I was trying to ask. I don't have time to respond in detail, but will come back to this in a bit.
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, May 26, 2013 3:09 AM To: Robert Guralnick Cc: TDWG Content Mailing List; Robert Whitton; John Deck; rlwalls2008@gmail.com Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is: 1. define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions) 2. use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other 3. examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions. 4. use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal: http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questions http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we've been running with the idea of an "Individual" class - as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an "Individual" as the physical "something" that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hi all, I just returned from a DwC workshop in Copenhagen, but we haven't completed the report yet. Until it is available I wanted to throw into this discussion some main ideas which I think are very relevant:
First of all I see an essential difference in character between the current dwc idea of Individual(ID) and a MaterialSample, Occurrence, Evidence or alike: The Individual has no notion of time and space, whereas the others all have. IndividualID was primarily added to Darwin Core to group occurrence records about the same "Individual", e.g. when dealing with bird ringing, whale tracking or tree tagging. It could also provide useful to track herbarium duplicates. The actual Individual class does not hold any direct dwc term as they are all dependent on time or locality (think about occurrence classics such as life stage, sex, behavior etc). So in this light MaterialSample and Individual are very different concepts which we should keep distinct I believe.
Another surprising outcome of an exercise to actually map a large number of use cases to darwin core records with real values (using the text guidelines) was that we ended up preferring a dynamically typed Occurrence class via the basisOfRecord property and mostly did away with any class terms. This actually draws on Steves proposal to only add a new dwc type term to basisOfRecord instead of creating a new MaterialSample class term. Along with a much richer, hierarchical and probably ontology controlled definition of such basisOfRecord terms we felt we can go a long, long way.
best, Markus
On 26.05.2013, at 23:34, Richard Pyle wrote:
Thanks for the *EXCELLENT* post -- this gets to the heart of what I was trying to ask. I don’t have time to respond in detail, but will come back to this in a bit.
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, May 26, 2013 3:09 AM To: Robert Guralnick Cc: TDWG Content Mailing List; Robert Whitton; John Deck; rlwalls2008@gmail.com Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is:
- define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions)
- use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other
- examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions.
- use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal:http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questionshttp://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- 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
One minor point about what Markus said below: "
instead of creating a new MaterialSample class term
". DwC is defined in its normative form as RDF. If one looks at the defining RDF for the DwC type vocabulary terms (http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwctype.rdf ), one will see that they are defined as rdf:type rdfs:Class, just like the class terms in the "basic" DwC vocabulary (http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf ). So if we create dwctype:MaterialSample, we actually will be creating a MaterialSample class term - it just will be in the dwctype: namespace rather than the dwc: namespace.
From the standpoint of RDF, either the class terms from the basic vocabulary or the type vocabulary terms could be used to type resources. However, since the whole point of having a type vocabulary is to describe what type of thing a resource is, it makes sense that we recommend that the DwC type vocabulary be used to declare the type of a resource in RDF (rather than the dwc: classes). That is what we will probably recommend in the RDF guide and is consistent with the use of the string versions of the type vocabulary terms as controlled values for dwc:basisOfRecord in text-based systems.
Steve
Markus Döring (GBIF) wrote:
Another surprising outcome of an exercise to actually map a large number of use cases to darwin core records with real values (using the text guidelines) was that we ended up preferring a dynamically typed Occurrence class via the basisOfRecord property and mostly did away with any class terms. This actually draws on Steves proposal to only add a new dwc type term to basisOfRecord instead of creating a new MaterialSample class term. Along with a much richer, hierarchical and probably ontology controlled definition of such basisOfRecord terms we felt we can go a long, long way.
best, Markus
On 26.05.2013, at 23:34, Richard Pyle wrote:
Thanks for the *EXCELLENT* post -- this gets to the heart of what I was trying to ask. I don’t have time to respond in detail, but will come back to this in a bit.
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, May 26, 2013 3:09 AM To: Robert Guralnick Cc: TDWG Content Mailing List; Robert Whitton; John Deck; rlwalls2008@gmail.com Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is:
- define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions)
- use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other
- examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions.
- use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal:http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questionshttp://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
https://code.google.com/p/darwin-sw/wiki/ClassIndividual
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- 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
.
Hi Markus,
Very briefly:
First of all I see an essential difference in character between the
current dwc
idea of Individual(ID) and a MaterialSample, Occurrence, Evidence or
alike:
Yes -- everyone seems to agree that Occurrence, Evidence, and Individual are fundamentally different things (as are Event, Location, Taxon, etc.).
The part that is not so clear to me is where the difference is between what was intended to be represented by dwc:individualID, and what is proposed for materialSample(ID). There seems to be some broad overlap in these two things, with no clear distinction of where one ends and the other begins.
The Individual has no notion of time and space, whereas the others all
have.
I don't think it is true that MaterialSample has a notion of space and time -- any more so than individualID does (or should).
The proposed definition of materialSample is:
"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."
There is no class "individual" in DWC; but if there were one, it should have a definition something like this:
"The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the individual is typically a named group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)."
At least, that's how we have interpreted the generalized intended meaning of what an "individualID" should refer to (i.e., identify). Unfortunately, as has already been pointed out repeatedly in this thread, the term "individual" comes with a lot of baggage, and is not the best term to use (for several reasons). Also, the current definition of dwc:individualID is very thin and too narrowly focused on "resampling" -- which is certainly one of the reasons for having such a class, but also certainly not the only reason.
IndividualID was primarily added to Darwin Core to group occurrence
records
about the same "Individual", e.g. when dealing with bird ringing, whale tracking or tree tagging. It could also provide useful to track herbarium duplicates. The actual Individual class does not hold any direct dwc term
as
they are all dependent on time or locality (think about occurrence
classics
such as life stage, sex, behavior etc). So in this light MaterialSample
and
Individual are very different concepts which we should keep distinct I believe.
I don't agree. Our own interpretation of what an individual class would look like was very-much shaped by the earlier (2010) discussions on this list for what was actually needed by more than a few data providers and consumers. While the addition of "dwc:individualID" may have been done hastily and with a narrow purpose in mind, the broader problem is that the "Occurrence" class is overloaded. I agree with you that the properties that you mention (life stage, sex, behavior, etc.) are properly a function of time and space, and therefore are legitimately associated with a specific Occurrence instance; however, certain other terms associated with dwc:Occurrence (such as catalogNumber, preparations, disposition, otherCatalogNumbers, previousIdentifications, associatedSequences, and taxonomic determinations) are independent of time and space, and are inherently properties of the "individual"/"materialSample" instance.
Put another way, the reasons why an instance of "materialSample" is not equivalent to an instance of "Occurrence", are the same reasons why the notion of "Individual" (sensu me) and "IndivisualOrganism" (sensu DSW) are not equivalent to an instance of "Occurrence".
The motivation for my initial posting to this thread was the recognition that many of the reasons for establishing "materialSample" are the same as the reasons why Steve Baskauf, and I, and a number of others saw a need for "IndividualOrganism" (or whatever it should be called). This is not to say that they necessarily *are* the same thing (materialSample and IndividualOrganism) -- but the overlap is broad enough that it bears some deserves some discussion -- if for no other reason than to inform the discussion on "materialSample" by what has already been discussed for "IndividualOrganism"'; and to clarify the definitions of each to make sure the community (both providers and consumers) understand the differences between them.
Another surprising outcome of an exercise to actually map a large number
of
use cases to darwin core records with real values (using the text
guidelines)
was that we ended up preferring a dynamically typed Occurrence class via the basisOfRecord property and mostly did away with any class terms. This actually draws on Steves proposal to only add a new dwc type term to basisOfRecord instead of creating a new MaterialSample class term. Along with a much richer, hierarchical and probably ontology controlled
definition
of such basisOfRecord terms we felt we can go a long, long way.
This is very similar to our thinking on this as well; except we have found reasonably good congruence between many key properties with the specific basisOfRecord, such that some of them (particularly Evidence and IndividualOrganism) emerge in a way that seem to justify recognition at the Class level. In any case, we need to be careful not to overload "Occurrence" even further. I think that, whatever we do, we should focus on reducing confusion, rather than increasing it.
Aloha, Rich
Hi Markus,
You mention below "an exercise to actually map a large number of use cases to darwin core records with real values", which sounds like a potentially illuminating activity. Can you share the results of the exercise?
Best, Joel.
On Mon, 27 May 2013, "Markus Döring (GBIF)" wrote:
Hi all, I just returned from a DwC workshop in Copenhagen, but we haven't completed the report yet. Until it is available I wanted to throw into this discussion some main ideas which I think are very relevant:
First of all I see an essential difference in character between the current dwc idea of Individual(ID) and a MaterialSample, Occurrence, Evidence or alike: The Individual has no notion of time and space, whereas the others all have. IndividualID was primarily added to Darwin Core to group occurrence records about the same "Individual", e.g. when dealing with bird ringing, whale tracking or tree tagging. It could also provide useful to track herbarium duplicates. The actual Individual class does not hold any direct dwc term as they are all dependent on time or locality (think about occurrence classics such as life stage, sex, behavior etc). So in this light MaterialSample and Individual are very different concepts which we should keep distinct I believe.
Another surprising outcome of an exercise to actually map a large number of use cases to darwin core records with real values (using the text guidelines) was that we ended up preferring a dynamically typed Occurrence class via the basisOfRecord property and mostly did away with any class terms. This actually draws on Steves proposal to only add a new dwc type term to basisOfRecord instead of creating a new MaterialSample class term. Along with a much richer, hierarchical and probably ontology controlled definition of such basisOfRecord terms we felt we can go a long, long way.
best, Markus
On 26.05.2013, at 23:34, Richard Pyle wrote:
Thanks for the *EXCELLENT* post -- this gets to the heart of what I was trying to ask. I don’t have time to respond in detail, but will come back to this in a bit.
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, May 26, 2013 3:09 AM To: Robert Guralnick Cc: TDWG Content Mailing List; Robert Whitton; John Deck; rlwalls2008@gmail.com Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity . I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical enti!
ties whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it!
's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots. It is my believe that what needs to happen is:
- define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions)
- use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other
- examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions.
- use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal:http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html . This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questionshttp://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to tak!
e up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an “Individual” as the physical “something” that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- 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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On Mon, Jun 10, 2013 at 2:51 PM, joel sachs jsachs@csee.umbc.edu wrote:
Hi Markus,
You mention below "an exercise to actually map a large number of use cases to darwin core records with real values", which sounds like a potentially illuminating activity. Can you share the results of the exercise?
That will be shared soon --- the group is writing up a report...
John
Best, Joel.
On Mon, 27 May 2013, "Markus Döring (GBIF)" wrote:
Hi all,
I just returned from a DwC workshop in Copenhagen, but we haven't completed the report yet. Until it is available I wanted to throw into this discussion some main ideas which I think are very relevant:
First of all I see an essential difference in character between the current dwc idea of Individual(ID) and a MaterialSample, Occurrence, Evidence or alike: The Individual has no notion of time and space, whereas the others all have. IndividualID was primarily added to Darwin Core to group occurrence records about the same "Individual", e.g. when dealing with bird ringing, whale tracking or tree tagging. It could also provide useful to track herbarium duplicates. The actual Individual class does not hold any direct dwc term as they are all dependent on time or locality (think about occurrence classics such as life stage, sex, behavior etc). So in this light MaterialSample and Individual are very different concepts which we should keep distinct I believe.
Another surprising outcome of an exercise to actually map a large number of use cases to darwin core records with real values (using the text guidelines) was that we ended up preferring a dynamically typed Occurrence class via the basisOfRecord property and mostly did away with any class terms. This actually draws on Steves proposal to only add a new dwc type term to basisOfRecord instead of creating a new MaterialSample class term. Along with a much richer, hierarchical and probably ontology controlled definition of such basisOfRecord terms we felt we can go a long, long way.
best, Markus
On 26.05.2013, at 23:34, Richard Pyle wrote:
Thanks for the *EXCELLENT* post -- this gets to the heart of what I was
trying to ask. I don’t have time to respond in detail, but will come back to this in a bit.
Rich
From: tdwg-content-bounces@lists.**tdwg.orgtdwg-content-bounces@lists.tdwg.org[mailto: tdwg-content-bounces@**lists.tdwg.orgtdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, May 26, 2013 3:09 AM To: Robert Guralnick Cc: TDWG Content Mailing List; Robert Whitton; John Deck; rlwalls2008@gmail.com Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I suppose that Rich and Rob W. have already looked at http://code.google.com/p/**darwin-sw/wiki/**TaxonomicHeterogeneityhttp://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity. I think it pretty much encapsulates what they are talking about. I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism. It can be a collection of organisms (herd, colony, school) or part of an organism (tissue). The basic requirement is that it is a "taxonomically homogeneous entity". In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level). It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it. In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance. What this diagram includes that Rich did not mention are "tokens" (evidence). We defined a class for evidence, but we also considered not having evidence being an explicit class. Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine. However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc. MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G. IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich. If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/**lots. It is my believe that what needs to happen is:
- define clearly what the various stakeholders want to accomplish by
their version of individuals/organisms/samples/**lots (i.e. use cases/competency questions) 2. use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/**lots are related to each other 3. examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/**lots terms and determine how each approach can or cannot satisfy the use cases/competency questions. 4. use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.
In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal: http://lists.tdwg.**org/pipermail/tdwg-content/** 2011-September/002727.htmlhttp://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html. This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/**darwincore/issues/detail?id=**117http://code.google.com/p/darwincore/issues/detail?id=117) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group." So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questionshttp:// code.google.**com/p/tdwg-rdf/wiki/**CompetencyQuestionshttp://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestionsand use cases http://code.google.com/p/tdwg-**rdf/wiki/UseCaseshttp://code.google.com/p/tdwg-rdf/wiki/UseCasesbut has not moved beyond that. So that's a start on Item #1 in the list above. However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will champion this?
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all. So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Steve
Robert Guralnick wrote:
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we’ve been running with the idea of an “Individual” class – as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
https://code.google.com/p/**darwin-sw/wiki/ClassIndividualhttps://code.google.com/p/darwin-sw/wiki/ClassIndividual
We define an “Individual” as the physical “something” that underpins an
Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc. ______________________________**_________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/**listinfo/tdwg-contenthttp://lists.tdwg.org/mailman/listinfo/tdwg-content
-- 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 http://bioimages.vanderbilt.edu ______________________________**_________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/**listinfo/tdwg-contenthttp://lists.tdwg.org/mailman/listinfo/tdwg-content
______________________________**_________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/**listinfo/tdwg-contenthttp://lists.tdwg.org/mailman/listinfo/tdwg-content
Hi Steve,
Again, great post. Some more detailed comments:
I suppose that Rich and Rob W. have already looked at
http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity .
I think it pretty much encapsulates what they are talking about.
Yes (see the P.S. of my reply to Gregor) -- and it's this reasoning that eventually convinced me that you were right about this.
I should note that the way DSW defines dsw:IndividualOrganism does not
require it to be a single organism.
It can be a collection of organisms (herd, colony, school) or part of an
organism (tissue).
Yes -- which is exactly why we defined it this way. The only reason we stripped the "organism" part (or, more precisely, why we think of "individualOrganism" as a subclass of "individual" -- though we haven't formally established it that way yet), is because in our application, we want to track individuals that are not organisms (I'd be happy to provide examples -- but that falls outside the scope of this conversation....and this email list). The point is, our concept of "Individual" is the superclass (perhaps we should all it "Object"?), which includes a subclass of things that would be properly labeled as "IndividualOrganism" (or maybe "BiologicalObject").
The basic requirement is that it is a "taxonomically homogeneous entity".
In a variant form of DSW (dsw_alt.owl) we included "taxonomically
heterogeneous entity" (THeE)
which would basically include what Rich and Rob W. are talking about (lots
of organisms which are seperatable
and aren't necessarily from the same lowest taxonomic level).
No, that's not quite right. We've been defining "Individual" (in the context of organisms) as what you refer to as "taxonomically homogeneous entity". In other words, if more than one taxon is involved, we split them into appropriate subset individual instances (so that each individual is taxonomically homogeneous). Like I said, your arguments won me over. But that doesn't mean that the concept of THeE isn't a necessary one for our community. Examples are things like rocks containing multiple fossil organisms from multiple taxa, a collected rock on the seafloor containing multiple organisms, a soil sample, or a seafloor core (etc.). These are units of information that fall within the realm of "CollectionObject", but not within the concept of a "taxonomically homogeneous entity" (i.e., individualOrganism).
Somehow these things need to be defined well enough that we can develop practical vocabularies and ontologies that are both practical to implement, and meet our data management needs.
It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it.
Again, while I agree there is a need for a THeE "thing", this is not what I'm talking about in this thread. I see that as a separate discussion -- which we need to have, but will probably only confuse this discussion. I think we should focus on the relationship between a "taxonomically homogeneous entity", which is what Rob W. and I -- and also, I believe, what dwc:individualID is intended to represent -- are including within our notion of "individual" as discussed in my earlier posts on this thread, and "materialSample" -- which I generally see as a subclass of "individual" (=dwc:individualID = Pyle/Whitton "Individual" = Baskauf "taxonomically homogeneous entity").
In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by
inheritance.
What this diagram includes that Rich did not mention are "tokens"
(evidence).
Same here. We use the term "Evidence", but I think we define it slightly differently from your "token". Again, this is an important topic -- but one I deliberately left out of my earlier posts, because my real question pertains to the proposal of "materialSample" as a new dwc term (along with materialSampleID). I want to make sure I understand what the relationship is between this concept, and the concept represented by dwc:individualID (e.g., would "dwc:materialSample" constitute a subclass of dwc:individual, if the latter also existed?) I'm not at all opposed to the introduction of "materialSample/ID" in DWC -- but I am not sure there has been enough clarification on the relationship/distinction between what these new terms represent, and what is already represented via dwc:individualID (and, of course, the relevant terms in Darwin-SW and its kin).
We defined a class for evidence, but we also considered not having
evidence
being an explicit class. Not defining an explicit Token class would have
simplified
the diagram at the bottom of the page - one could just say that there
should be
evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical
entity
can be the evidence if somebody "owns" it and makes it available for
people to examine.
However, in DSW, Token and THeE are not synonymous because we allow
evidence
to include things that are not physically derived from the entity (e.g.
images, sounds,
string data records) in addition to physical specimens.
I have much to comment on concerning the above text, but I'll save it for a different thread with a different subject line.
I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc.
Agreed! I hope nobody thinks I was suggesting any of these things about materialSample. If so, I was misunderstood. What I want to discuss is how these things conceptually relate to each other. One of the biggest problems with DWC in actual use is not so much whether we have the right terms, or have too many, or whatever; rather, it's that the terms we have leave enough room for interpretation that people use them in subtly (or not-so-subtly) different ways. This is one of the things I heard repeatedly in Berlin last week -- that different providers use the same terms to represent different information.
I think it's incumbent on us to minimize further generation of this sort of ambiguity, so I want to make sure we are clear in what the terms are, how they are meant to be used, and how they relate to other terms in DWC.
MaterialSample does exactly what the metagenomics people need because they
invented it to serve the purposes they want it to serve (handle material
samples
in which one may or may not ever know what all organisms are included or
even
if there are organisms in it). Individual (sensu Pyle/Whitton)/THeH is
just vague
enough to do what Rich and Rob W. want it to do with their lots and
specimens,
but is too vague for Rob G.
Again, just to be absolutely clear: "Individual (sensu Pyle/Whitton)" <> "THeH (sensu Baskauf)"
IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I
want it to do
with our images, specimens, DNA samples, and data records, and the
requirement that
IndividualOrganism be taxonomically homogeneous allows us to infer that a
determination
applied to one resource also applies to other resources which are derived
from the same
IndividualOrganism (a requirement not stated by the others) but it's too
restrictive for both
Rob G and Rich.
What you describe above is *EXACTLY* what "Individual (sensu Pyle/Whitton)" is intended to be, for *exactly* the same reasons. So I hope we can now dispense completely with the incorrect equivalence of "Individual (sensu Pyle/Whitton)" with "THeH (sensu Baskauf)".
I think "materalSample" is very-much more analogous to (but not identical to) "collectionObject". The similarities include:
- Something extracted from nature that may or may not involve a biological organism (the concept of "collectionObject" could be used for a mineralogy collection, or a soil sample with no organisms in it). - Something that is often taxonomically homogeneous, but not necessarily so - Something that is studied or examined outside of its occurrence in nature
The main difference I see is that, traditionally at least, "collectionObject" refers to something typically intended to be maintained for a long time (like a voucher specimen), whereas "materialSample" explicitly includes things that only exist as such for a temporary period (e.g., are lost or destroyed upon analysis). But I don't think that "collectionObject" necessary excludes things that are temporary, which is why really "materialSample" is either equivalent to an instance of "collectionObject", or is a subclass of "collectionObject".
So, we have this cloud of overlapping terms: 'individual" (as implied by dwc:individualID), "individualOrganism" (as defined in DSW), "collectionObject" (as used historically in the ASC and MVZ models, and more recently in the iDigBio document thatI sent the link for), and "materialSample" (as currently proposed).
The overlap of these things vastly exceeds the non-overlap, so I think it's important that we refine the definitions to more precisely articulate how they are the same, and how they are different. Once we get the concepts sorted out, *then* we should figure out the best terms to use.
If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.
ABSOLUTELY! Let's assume that any need expressed by anyone is, by definition, important.
I think that it is clear from this and preceding discussions that there is
a need for some system of tracking things that are like
individuals/organisms/samples/lots.
It is my believe that what needs to happen is:
- define clearly what the various stakeholders want to accomplish by
their
version of individuals/organisms/samples/lots (i.e. use cases/competency
questions)
- use set theory or some other kind of logical system to describe clearly
how the
various versions of individuals/organisms/samples/lots are related to each
other
- examine alternative mechanisms for defining the relationships among the
variously
defined individuals/organisms/samples/lots terms and determine how each
approach
can or cannot satisfy the use cases/competency questions. 4. use one or more mechanisms which pass test #3 to define the terms that
are deemed
necessary and include them in some TDWG standard which may or may not be
Darwin Core.
YES!!! This is *exactly* what I was heading towards, but you captured it much more clearly than I did. But I think it is a bit of a multi-dimensional issue. On one axis is, as you outline above, the hierarchy from "group" things down to "part" things (school, flock, lot, specimen, specimen part, tissue sample, DNA extraction, etc.). Another axis is the "taxonomically homogeneous" vs. "taxonomically heterogeneous" distinction (the latter of which is mostly needed for curated objects, rather than objects as they occur in nature -- although one could conceive of an "ecosystem" as a top-level THeE that our community may want to track). And yet another axis is the whole issue of "what is a 'thing'", contrasted with "what is evidence of a 'thing'" (e.g., a specimen in a jar is a "thing", whereas an image of that specimen is evidence of that "thing").
In September 2011, John Wieczorek had packaged several of the proposed
class additions
to Darwin Core into a concrete proposal:
http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html .
This proposal was deferred by the Executive Committee (see the last
comment at
http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we
can further
examine broader changes including the new classes and any insights that
might come
out of the RDF Interest Group."
Ah! OK, this specifically answers my question concerning "where do we stand on discussions of an "individual" class within DWC? The last thing I want to do is slow down progress, so if a quick addition of materialSample/ID will help solve some problem, then I'm all for it. But to save long/complex conversations later on (which will inevitably happen when we try to reconcile dwc:individualID and the proposed dwc:materialSampleID), it's probably worth at least a bit of discussion now. If that discussion shows no signs of resolution anytime, soon, then by all means, let's not bog the process down unnecessarily. But one of the reasons I spoke up on this thread is that, what is different now from last September, is that we (Rob W. and I) now have about a year's worth of experience dealing with the ontological relationships between "Location", "Event", "Occurrence", "Evidence", "Individual", "Determination" and "Taxon" (among other classes of things, like "Agent" and Reference") -- both in terms of harvesting legacy data, and in building workflows to capture new data in real time. (Indeed, as I write this, Rob W. is currently aboard a NOAA ship somewhere between the Northwestern Hawaiian Islands and Johnston Atoll, on a 1-month cruise gathering in-situ observations, imagery, voucher specimens, and tissue samples, and is using the workflow that he and I developed to integrate these new data with pre-existing images/specimens/observations/literature reports/tissue samples/etc., to build an evidence-based checklist for the Northwestern Hawaiian Islands. In other words, what we have now that we didn't have a year or two ago, is real-world experience organizing this kind of information.
So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications. The RDF TG has assembled competency questions http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that. So that's a start on Item #1 in the list
above.
However, the process has not moved beyond that. I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses. I cannot be the person to move this forward for two reasons. One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4. Who will
champion this?
As soon as Rob W. returns from his cruise, he and I will discuss this in much more detail, and perhaps we can help make progress in this area. In the meantime, I'll review the content at the links you provided.
At the risk of making this email too long, I will add one more comment. There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above. However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases. We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved). I presume that Rich and Rob W. have
in
hand a technical solution to their use cases that doesn't involve RDF at
all.
Indeed, you are correct! Most of our implementation is at the database model and UI workflow level. We have not made an attempt to translate this into RDF/OWL/OBO sorts of documentation -- in part because this is not our area of expertise. We can provide ER-diagrams, a plethora of various use-case examples (from collected specimens with and without tissue samples and their DNA-ish derivatives, to tissue samples without vouchers, to in-situ imagery, to post-collection imagery, to observation-only occurrence, to literature-based occurrence, to telemetry-based occurrence data, to managing misidentifications, to determination and collecting-event inheritance via a hierarchy of individuals, etc.) We are by no means at the end-game of all of this. Rob and I still argue about a number of things (including how to precisely draw the lines between "Location", "Event", and "Occurrence", and which properties should be associated with instances in each class; as well as the question of whether a specimen in a Museum is really an "Occurrence" or an "Individual"); and we have not yet taken a stab at dealing with THeH use-cases. But we do have a lot of real-world experience now dealing with what is probably 90-95% of the data in our community.
So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation. We've been down that road before with the TDWG Ontology and look how that turned out.
Agreed! Again, I'll discuss with Rob after he gets home (mid-June), and we'll try to put together some ER diagrams and a bunch of detailed use-cases. Perhaps others can provide use-cases that they have encountered (the more complex, the better), to challenge our approach to these sorts of things.
Aloha, Rich
Everyone seems to be focused on the "word", but I'm much more interested in the concept. As I said in my reply to John, I use the word "individual" only because DWC has already defined it via dwc:individualID. I honestly don't care what the actual term is - as long as we understand the scope of its conceptual meaning. I have found strong experiential support for collapsing "small group", "single individual", and "part" or "subsample" of a single individual into the same conceptual entity. If we are going to continue to use dwc:individualID, and dwc:materialSample as separate entities in DWC, then we really need robust definitions to distinguish these two things, so we don't end up with massive overlap. Are they different classes of things? Are they both subclasses of something else (e.g., "biologicalObject")?
Aloha,
Rich
From: robgur@gmail.com [mailto:robgur@gmail.com] On Behalf Of Robert Guralnick Sent: Saturday, May 25, 2013 10:05 PM To: Gregor Hagedorn Cc: Richard Pyle; TDWG Content Mailing List; Robert Whitton; John Deck Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
I agree with John and Gregor. The term "individual" doesn't quite seem to capture the concept or usage. However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties. It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.
Best, Rob
On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Basically, we've been running with the idea of an "Individual" class - as originally proposed by Steve and discussed at some length on this list a while ago. This has been documented for DSW:
We define an "Individual" as the physical "something" that underpins an Occurrence. In the case of organisms, this can be a group (herd, school, flock, etc.), specimen (either a single specimen, or a lot of multiple specimens), or any sort of derivative of a specimen (part, tissue sample, dna extraction, etc.). It corresponds to the intended meaning of
I disagree with using "Individual" for sets of objects. It is surprising, and lacking any clear definition when to stop, that means a taxon is an individual, a collection is an individual, etc.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hi Gregor,
I disagree with using "Individual" for sets of objects. It is surprising,
and
lacking any clear definition when to stop, that means a taxon is an
individual,
a collection is an individual, etc.
I refer you to the lengthy discussions on this list a while back, which covered all of this in great detail. Going "up" the hierarchy chain (e.g., beyond "School" or "Herd" or "Colony", etc.) -- to units such as "population" or "taxon" -- things get very messy. During the previous discussion, it seemed that everyone agreed that "taxon" was too broad and not useful for our purposes; whereas "colony", "school", "herd", etc. were absolutely necessary (lest we need to treat every polyp on a coral head as a separate database entry, and many use cases involve treating herd/pod/flock as an important unit to be able to track in exactly the same way that "individuals" are tracked -- which is why the definition of dwc:individualID is as it is). The border-line term is "population" -- which is cleary below the realm of taxon, but perhaps a bit too vauge and poorly defined to be regarded as the same class as an individual.
But the "upper" limit of what the class "individual" would encompass is not relevant to this discussion -- that's a separate issue. The topic here is in the "downward" direction (whole individuals, parts of individuals, parts of parts, etc.), and in that context, our experience has increasingly convinced me that treating such objects as a subclass of what is intended by "dwc:individualID" is a very flexible, useful, and powerful approach to modeling our data -- and also, in my mind at least, the most logically/conceptually defensible approach as well.
But again, I am not advocating that DWC be modeled after our approach. I'm just asking to what extent a conversation about the class "individual" (if, indeed, there is or needs to be such a conversation) should be overlapped with the conversation about "materlaiSample".
Aloha, Rich
P.S. Another very messy question -- if a dwc:individual class is established -- is how it relates to the concept of a "CollectionObject". In most cases, it's very straightforward -- individuals are either extracted from nature and placed in a collection (at the colony, lot, singleIndividual, or any sort of "part" level), or they are left in nature. Where it gets tricky is when you have CollectionObjects that are clearly multi-taxon in nature (e.g., a soil sample as per the proposed materialSample, or a single rock containing multiple fossil taxa on the same physical object). This is where Steve Baskauf and I focused much of our debate -- with me eventually coming around to his perspective that an "Individual" should represent what is believed to be a single taxon, and when it is discovered to include more than one taxon, it should be split to multiple individuals such that the 1:1 relationship of individual:purportedTaxon is maintained (see http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity for a more extensive discussion). Perhaps this is where the notion of a "material sample" can help.
"population" or "taxon" -- things get very messy. During the previous discussion, it seemed that everyone agreed that "taxon" was too broad and not useful for our purposes; whereas "colony", "school", "herd", etc. were absolutely necessary (lest we need to treat every polyp on a coral head as a separate database entry, and many use cases involve treating herd/pod/flock as an important unit to be able to track in exactly the same way that "individuals" are tracked -- which is why the definition of dwc:individualID is as it is). The border-line term is "population" -- which is cleary below the realm of taxon, but perhaps a bit too vauge and poorly defined to be regarded as the same class as an individual.
Yes, and I am also thinking of metapopulations, just for fun...
I understand that we need an operationally defined term with a particular use case. Primarily I agree with Chucks observation that an important point is that we believe to understand what an individual is, both in biology and in informatics and philosophy, so I just want to warn about the use of this. Secondarily I do believe we need to define it in a way that the upper limit of the set we want to refer to becomes clear, at least operationally. I was missing that.
WIth respect to the operational usefullness of a term that does not distinguish between part, individual, set of taxonomical homogeneous OR heterogeneous samples (you excluded tax. heterogeneous, which would exclude lichens, most plants (mycorrhiza!) or any other symbiosis like us humans with our skin and intestine microbes) I have two proposals:
Broadly the term "sample" implies not necessarily physical sampling, you can sample observations or data. A sample is a subset of a (statistical) population, selected under operational rules and encompasses the individual and part. Think of sampling music.
The other term is unit. What you describe has been discussed extensively in the CDEFG and later ABCD papers and standard and the term "Unit" was chosen for as far as I understand exactly the concept you are looking for. Perhaps that can be followed, if we accept that these are not "natural" units, but operationally defined units (think of OTU, oper. tax. units). Unit was chosen in ABCD because it applies both in a sampling context, in an analysis context, and in a collection curation context.
Apologies should I repeat something already discussed previously.
Gregor
Hi Gregor,
Again, I think we need to pin down the concepts before we spend too much time thinking about what the terms should be. I understand that it's difficult to discuss the concepts without the terms, but focusing on the terms first is like putting the cart before the horse. Perhaps we should follow Chuck's advice and use latin terms or some other kinds of labels that do not come with so much baggage -- so we don't attach too many pre-conceived notions. The only terms in this space that have "standard" definitions are "Individual" (as inferred from dwc:individualID) and "CollectionObject" (from historical definitions in the MVZ/ASC models). The DSW terms are also useful and well-defined, but are not as well established as standards.
All of the terms you propose ("Sample", "Unit", etc., as well as a number of others such as "item" and "object") were very-much in consideration when we were thinking about these things, but all of them have similar levels of weaknesses to other term options (most people think of a "unit" as a term applied to units of measure, and "Sample" implies the collection or removal of something from nature). We eventually went with "Individual" because it is already defined in DWC (though not well defined).
But let's see if we can have a discussion first about the different concepts we are talking about. Can we nest all of these ideas under a single superclass? Or do we need different top-level classes to define/distinguish:
- Biological things from non-biological things; - Collected/extracted things from things that are observed/documented in-situ; - Things that are taxonomically homogeneous from things that include taxonomic heterogeneity?
Also, to what extent are the things we want to discuss best represented as a nested hierarchy? For example, if an aggregate (school, colony, herd, etc.), has multiple specimens collected at the same time, and then some of those specimens have parts/tissues removed from them, and then some of those tissues have subsamples taken or destroyed for analysis..... are those all instances of the same class of thing related via parent/child hierarchy? Or is each step a separate class of thing? If the latter, how many classes of such things do we need?
I used the word "thing" as much as I could to avoid the term-baggage issue; but another term that I have found useful in these conversation is "Object". As I wrote to Chuck off-list, the top-level superclass might be thought of as "physicalObject"; under-which some of these other concepts (e.g., "biologicalObject" and others) can be represented either as subclasses, or as key properties of instances within the superclass.
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Sunday, May 26, 2013 7:37 PM To: Richard Pyle Cc: Steve Baskauf; John Deck; TDWG Content Mailing List; Robert Whitton; Walter G. Berendsohn; Anton Güntsch Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
"population" or "taxon" -- things get very messy. During the previous discussion, it seemed that everyone agreed that "taxon" was too broad and not useful for our purposes; whereas "colony", "school", "herd", etc. were absolutely necessary (lest we need to treat every polyp on a coral head as a separate database entry, and many use cases involve treating herd/pod/flock as an important unit to be able to track in exactly the same way that "individuals" are tracked -- which is why the definition of dwc:individualID is as it is). The border-line term is "population" -- which is cleary below the realm of taxon, but perhaps a bit too vauge and poorly defined to be regarded as the same
class as an individual.
Yes, and I am also thinking of metapopulations, just for fun...
I understand that we need an operationally defined term with a particular use case. Primarily I agree with Chucks observation that an important
point is
that we believe to understand what an individual is, both in biology and
in
informatics and philosophy, so I just want to warn about the use of this. Secondarily I do believe we need to define it in a way that the upper
limit of
the set we want to refer to becomes clear, at least operationally. I was missing that.
WIth respect to the operational usefullness of a term that does not distinguish between part, individual, set of taxonomical homogeneous OR heterogeneous samples (you excluded tax. heterogeneous, which would exclude lichens, most plants (mycorrhiza!) or any other symbiosis like us humans with our skin and intestine microbes) I have two proposals:
Broadly the term "sample" implies not necessarily physical sampling, you
can
sample observations or data. A sample is a subset of a (statistical) population, selected under operational rules and encompasses the individual and part. Think of sampling music.
The other term is unit. What you describe has been discussed extensively
in
the CDEFG and later ABCD papers and standard and the term "Unit" was chosen for as far as I understand exactly the concept you are looking
for.
Perhaps that can be followed, if we accept that these are not "natural"
units,
but operationally defined units (think of OTU, oper. tax. units). Unit was chosen in ABCD because it applies both in a sampling context, in an
analysis
context, and in a collection curation context.
Apologies should I repeat something already discussed previously.
Gregor
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].)
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 ?
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?
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.org/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
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-- John Deck (541) 321-0689
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):
- 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...
- 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)
- 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.
- http://lists.tdwg.org/**pipermail/tdwg-content/2013-**May/003008.htmlhttp://lists.tdwg.org/pipermail/tdwg-content/2013-May/003008.html
- http://lists.tdwg.org/**pipermail/tdwg-content/2013-**May/003006.htmlhttp://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 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/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/MaterialSamplehttp://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/** DwCTypeVocabularyhttp://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#Classhttp://www.w3.org/2000/01/rdf-schema#Class
Refines: http://purl.obolibrary.org/**obo/OBI_0000747http://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/**MaterialSampleIDhttp://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/MaterialSamplehttp://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#Propertyhttp://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines: http://purl.org/dc/terms/**identifierhttp://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/**Occurrencehttp://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/**MaterialSamplehttp://rs.tdwg.org/dwc/terms/MaterialSample which is in the "main" (dwc:=http://rs.tdwg.org/dwc/**terms/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 vocabularyclass 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 ofthe 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 anotherintegrative 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 purelytaxonomic 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 DarwinCore Issue tracker as http://code.google.com/p/**darwincore/issues/detail?id=**167http://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 asthey 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 oforganizing 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<http://rs.tdwg.org/dwc/terms/MaterialSample> Namespace: http:/rs.tdwg.org/dwc/terms Label: Material Sample Definition: The category of information pertaining to thephysical 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/MaterialSamplehttp://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#Classhttp://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 isneeded 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.org/**obo/OBI_0000747http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/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<http://rs.tdwg.org/dwc/terms/MaterialSample> Namespace: http://purl.obolibrary.org/**obo/OBI_0000747<http://purl.obolibrary.org/obo/OBI_0000747> Label: material sample Definition: A material entity that has the material samplerole Comment: For discussion see http://code.google.com/p/**darwincore/wiki/** DwCTypeVocabularyhttp://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#Classhttp://www.w3.org/2000/01/rdf-schema#Class Refines:http://purl.**obolibrary.org/obo/OBI_0100051http://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, theMaterial 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<http://gensc.org/ns/mixs/materialSampleID> Namespace: http://gensc.org/ns/mixs Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposedto 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/MaterialSamplehttp://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#Propertyhttp://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/**identifierhttp://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_0000747http://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 http://bioimages.vanderbilt.edu
______________________________**_________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/**listinfo/tdwg-contenthttp://lists.tdwg.org/mailman/listinfo/tdwg-content
-- John Deck (541) 321-0689
Hmmmm.....
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)
This is (again) 100% consistent with our interpretation of our "Individual", as I discussed previously. I don't care what the term is (I agree that "Individual is potentially vague and misleading). But whatever this "thing" is, it always includes "material", but depending on how one defines "sample", our "thing" may or may not always be sampled.
Again, I don't want to re-define MaterialSample, and I don't want to obstruct it from being added to DwC. But I *do* want to make sure I understand its full meaning and scope, so I can conceptually "Venn-diagram" it against the object that we call "Individual" in our model.
Let me ask a few questions (through declarative statements):
1) An instance of MaterialSample may include zero, one, or many taxa represented among its material contents (zero taxa = no organisms). Correct?
2) An instance of MaterialSample may represent a portion or subsample of a whole organism, may be a whole organism, or may be a set of multiple whole organisms. Correct?
3) An instance of MaterialSample always represents material that is extracted from nature. (e.g., a visual observation with no material extracted from nature is not an instance of Material Sample.) Correct?
4) An instance of MaterialSample may represent a subsample of (i.e., be derived from) another, more inclusive instance of a MaterialSample. Correct?
5) If an instance of MaterialSample is associated with an Occurrence, it would be an Occurrence that explicitly involved that instance of MaterialSample (e.g., an Occurrence at which the MaterialSample was extracted from nature). Correct?
The last one probably needs a bit more elaboration. Suppose a whole organism was observed 20 times over 10 years, representing 20 different Occurrences. On the 5th (chronologically) Occurrence, a sample was extracted from the whole organism, and we represent it as an instance of MaterialSample. I would assume that we would also establish some sort of relationship between the MaterialSample instance, and the 5th Occurrence. But would we also directly associate the MaterialSample instance with the first four Occurrences (the implication being that this sample had been part of that whole organism during those first four Occurrences)? What about directly associating the MaterialSample instance with the other Occurrences of the same whole organism that happened chronologically after the MaterialSample was extracted from nature?
By "directly" associate, I mean "represent as a property of", rather than some sort of inherited property through some sort of intermediate object (e.g., the whole organism as a separate object).
Don't get bogged down on this being an Edge Case, because I can come up with hundreds of other such examples, which, while perhaps being Edge Cases individually, collectively add up to non-Edge Cases in aggregate.
Aloha, Rich
I agree with statements #1-#4... As for #5, i believe this was answered with: http://lists.tdwg.org/pipermail/tdwg-content/2013-May/003006.html
John
On Tue, Jun 11, 2013 at 8:04 PM, Richard Pyle deepreef@bishopmuseum.orgwrote:
Hmmmm.....
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)
This is (again) 100% consistent with our interpretation of our "Individual", as I discussed previously. I don't care what the term is (I agree that "Individual is potentially vague and misleading). But whatever this "thing" is, it always includes "material", but depending on how one defines "sample", our "thing" may or may not always be sampled.
Again, I don't want to re-define MaterialSample, and I don't want to obstruct it from being added to DwC. But I *do* want to make sure I understand its full meaning and scope, so I can conceptually "Venn-diagram" it against the object that we call "Individual" in our model.
Let me ask a few questions (through declarative statements):
- An instance of MaterialSample may include zero, one, or many taxa
represented among its material contents (zero taxa = no organisms). Correct?
- An instance of MaterialSample may represent a portion or subsample of a
whole organism, may be a whole organism, or may be a set of multiple whole organisms. Correct?
- An instance of MaterialSample always represents material that is
extracted from nature. (e.g., a visual observation with no material extracted from nature is not an instance of Material Sample.) Correct?
- An instance of MaterialSample may represent a subsample of (i.e., be
derived from) another, more inclusive instance of a MaterialSample. Correct?
- If an instance of MaterialSample is associated with an Occurrence, it
would be an Occurrence that explicitly involved that instance of MaterialSample (e.g., an Occurrence at which the MaterialSample was extracted from nature). Correct?
The last one probably needs a bit more elaboration. Suppose a whole organism was observed 20 times over 10 years, representing 20 different Occurrences. On the 5th (chronologically) Occurrence, a sample was extracted from the whole organism, and we represent it as an instance of MaterialSample. I would assume that we would also establish some sort of relationship between the MaterialSample instance, and the 5th Occurrence. But would we also directly associate the MaterialSample instance with the first four Occurrences (the implication being that this sample had been part of that whole organism during those first four Occurrences)? What about directly associating the MaterialSample instance with the other Occurrences of the same whole organism that happened chronologically after the MaterialSample was extracted from nature?
By "directly" associate, I mean "represent as a property of", rather than some sort of inherited property through some sort of intermediate object (e.g., the whole organism as a separate object).
Don't get bogged down on this being an Edge Case, because I can come up with hundreds of other such examples, which, while perhaps being Edge Cases individually, collectively add up to non-Edge Cases in aggregate.
Aloha, Rich
For reasons elaborated in the DwC RDF guide and probably several places in the RDF Task Group wiki, none of the ID terms as they are presently defined can be used effectively in RDF. I'm not going to elaborate here because anybody who cares can read the details in the draft of the guide. But the crux of the issue is that all of the ID terms are currently defined as subClassOf dcterms:identifier. That means that a client can infer that the identifier given as the value of the term is the identifier of the subject of the triple, not the object of the triple as would be assumed for a predicate like hasIndividual, hasOccurrence, etc.
If we want to use the ID terms in RDF, the subClassOf declarations would have to be removed from their definitions.
Even if the definitions were changed, there is still an ambiguity issue which can be seen in the example in the XML guide. Again, I'm going to refer interested parties to the draft RDF guide. Steve
John Deck wrote:
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.
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
Joel,
John may have an additional response, but I think that one rationale for the ID terms can be seen in the XML guide, notably in http://rs.tdwg.org/dwc/terms/guides/xml/index.htm#classes where ID terms are used not only in the role you suggest for dc-elements:identifier (to show the identifier of the subject resource) but also as a sort of pseudo-object property that provides an IDref to another resource in a different container element. One could also use them as the names of record elements in a flat database table that contains information about several kinds of resources in the same record. So although ID terms don't make much sense from the RDF perspective, they probably are necessary for compatibility with the DwC text and XML guidelines.
Steve
joel sachs wrote:
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....
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
From the clarification email that was sent out in response to the arguments
re: using Individual instead of Material Sample, we indicated the utility of having distinct ID fields:
"...As was already pointed out, there is no restriction on specifying that an occurence is associated with more than one type, so any occurrence can have both an individualID and a materialSampleID."
This allows us to track distinct individuals, occurrences, and material samples in the same archive. Yes, there are other ways this could be modelled but this proposal was constructed to be in line with the current standard.
John
On Mon, Jun 24, 2013 at 3:37 PM, joel sachs jsachs@csee.umbc.edu wrote:
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.htmhttp://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.htmlhttp://lists.tdwg.org/pipermail/tdwg-content/2013-May/003008.html 2. http://lists.tdwg.org/**pipermail/tdwg-content/2013-** May/003006.htmlhttp://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<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/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<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/**DwCTypeVocabularyhttp://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<http://www.w3.org/2000/01/rdf-schema#Class> Refines: http://purl.obolibrary.org/**obo/OBI_0000747<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<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<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<http://www.w3.org/1999/02/22-rdf-syntax-ns#Property> Refines: http://purl.org/dc/terms/**identifier<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<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<http://rs.tdwg.org/dwc/terms/MaterialSample> which is in the "main" (dwc:=http://rs.tdwg.org/dwc/**terms/<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<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<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<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<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.ohttp://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<http://rs.tdwg.org/dwc/terms/MaterialSample> Namespace: http://purl.obolibrary.org/**obo/OBI_0000747<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/**DwCTypeVocabularyhttp://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#Classhttp://www.w3.org/2000/01/rdf-schema#Class
Refines:http://purl.**obolibrary.org/obo/OBI_0100051<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<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<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<http://www.w3.org/1999/02/22-rdf-syntax-ns#Property> Refines: http://purl.org/dc/terms/**identifier<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<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<http://bioimages.vanderbilt.edu> ______________________________**_________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/**listinfo/tdwg-content<http://lists.tdwg.org/mailman/listinfo/tdwg-content> -- John Deck (541) 321-0689-- John Deck (541) 321-0689
participants (10)
-
"Markus Döring (GBIF)" -
Chuck Miller -
Daniel Janzen -
Gregor Hagedorn -
joel sachs -
John Deck -
John Wieczorek -
Richard Pyle -
Robert Guralnick -
Steve Baskauf