New terms need resolution: "Individual"
Darwin Core Issues 69 and 80: http://code.google.com/p/darwincore/issues/list
This issue is related to the issue of Evidence (CollectionObject, Representation, Token, Unit) covered in a previous posting. In the Darwin Core there is currently no separate class to explicitly represent the biological entities involved in an Occurrence. This is problematic when trying to be explicit about the attributes of these entities in the semantic world. Various names have been given to this concept, including "Individual", "BiologicalIndividual", "BiologicalEntity", "Organism", and "DataSets/DataSet/Units/Unit" in ABCD.
Open Issues: Determine if there is a general consensus on the need for new class for this concept.
The best name for this class.
Create a new Type Vocabulary term referring to this new class.
Decide which properties currently organized under Occurrence should instead be organized under this new class.
As a seed for further discussion, here is a complete proposal. ============== Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/terms/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/terms/ Label: BiologicalEntity Definition: The category of information pertaining to an individual organism or a group of organisms that can reliably be known to represent a single taxon. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/dwctype/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: BiologicalEntity Definition: A resource describing an instance of the BiologicalEntity class. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD
Term Name: biologicalEntityID Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityID Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityID Definition: An identifier for the set of information associated with an BiologicalEntity. May be a global unique identifier or an identifier specific to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: biologicalEntityID-2011-07-04 Replaces: individualID-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/
Term Name: biologicalEntityRemarks Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityRemarks Definition: Comments or notes about the BiologicalEntity. Comment: Example: "seen several times in Tilden Park before capture". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: biologicalEntityRemarks-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Notes
Term Name: associatedBiologicalEntities Identifier: http://rs.tdwg.org/dwc/terms/associatedBiologicalEntities Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedBiologicalEntities Definition: A list (concatenated and separated) of identifiers of other BiologicalEntity records and their associations to this BiologicalEntity. Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: associatedBiologicalEntities-2011-07-04 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
Terms to be organized under biologicalEntity rather than Occurrence: previousIdentifications associatedMedia associatedReferences
I have a very slow and tenuous email connection here in the field, so as much as I would like to comment in my usual verbose fashion, that will need to wait until my return to Hawaii at the end of July (sighs of relief and sounds of joy can be heard across the internet....)
Very briefly:
1. I favor the creation of an "Individual" class (indeed, I had planned to propose it myself).
2. I believe that the term "BiologicalEntity" is the best term for this class and its ID attribute.
3. I agree in general with the complete proposal as outlined by John in his original email, but I will have more detailed comments about the included attributes when I return.
4. If this proposal is ratified, then the term "IndividualID" in the Occurrence class should be eliminated. (My first thought was to have it changed to "BiologicalEntityID"; but no other class has these "foreign key" equivalents in them, so best to handle it via Resource Relationship; see #6 below).
5. If this proposal is ratified, I do not think there needs to be a separate class for "Evidence", as outlined in John's other email (at least not at this time).
6. We need to have a good discussion about the appropriate use of http://rs.tdwg.org/dwc/terms/index.htm#ResourceRelationship within DwC. It seems to me that this Class is underutilized. Indeed, I think that it should be the most heavily used Class in all of DwC, if indeed its function is to establish relationships between instances of the same or different (i.e., among or within) DwC classes. If we used it more regularly and consistently, we could eliminate all the "associatedXXX" terms (e.g., "associatedBiologicalEntities), and represent these associations via instances of the resourceRelationship class. Indeed, if we qualified the definition of this class, we may also be able to use it to establish relationships with non-DwC Class identifiers as well (e.g., perhaps negating the need for " dcterms:references/dcterms:source/etc. terms currently being discussed on a parallel thread.
OK....by my standards, at least, that was pretty brief.
Aloha, Rich
P.S. To the BiSciCol'ers (SciColists?): I have CC'd our group because this conversation is highly relevant to our project.
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of John Wieczorek Sent: Monday, July 04, 2011 11:49 PM To: TDWG Content Mailing List Subject: [tdwg-content] New terms need resolution: "Individual"
Darwin Core Issues 69 and 80: http://code.google.com/p/darwincore/issues/list
This issue is related to the issue of Evidence (CollectionObject, Representation, Token, Unit) covered in a previous posting. In the Darwin Core there is currently no separate class to explicitly represent the
biological
entities involved in an Occurrence. This is problematic when trying to be explicit about the attributes of these entities in the semantic world.
Various
names have been given to this concept, including "Individual", "BiologicalIndividual", "BiologicalEntity", "Organism", and "DataSets/DataSet/Units/Unit" in ABCD.
Open Issues: Determine if there is a general consensus on the need for new class for
this
concept.
The best name for this class.
Create a new Type Vocabulary term referring to this new class.
Decide which properties currently organized under Occurrence should instead be organized under this new class.
As a seed for further discussion, here is a complete proposal.
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/terms/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/terms/ Label: BiologicalEntity Definition: The category of information pertaining to an individual organism or a group of organisms that can reliably be known to represent a single
taxon.
Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/dwctype/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: BiologicalEntity Definition: A resource describing an instance of the BiologicalEntity
class.
Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD
Term Name: biologicalEntityID Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityID Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityID Definition: An identifier for the set of information associated with an BiologicalEntity. May be a global unique identifier or an identifier
specific
to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: biologicalEntityID-2011-07-04 Replaces: individualID-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/
Term Name: biologicalEntityRemarks Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityRemarks Definition: Comments or notes about the BiologicalEntity. Comment: Example: "seen several times in Tilden Park before capture". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: biologicalEntityRemarks-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Notes
Term Name: associatedBiologicalEntities Identifier: http://rs.tdwg.org/dwc/terms/associatedBiologicalEntities Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedBiologicalEntities Definition: A list (concatenated and separated) of identifiers of other BiologicalEntity records and their associations to this
BiologicalEntity.
Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: associatedBiologicalEntities-2011-07-04 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/Associat edUnitSourceInstitutionCode
- DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni
- tSourceName
- DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni
- tID
Terms to be organized under biologicalEntity rather than Occurrence: previousIdentifications associatedMedia associatedReferences _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
I agree with Gregor
On Sat, Jul 9, 2011 at 11:03 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
- I believe that the term "BiologicalEntity" is the best term for this
class and its ID attribute.
I disagree on this. Biological entities to me seems a clear superterm, encompassing ecosystems, taxa, individuals, enzymes, and probably more.
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
+1 for keeping Individual as for Gregors reasoning.
In also conservative on "normalising" dwc too much and replace all id terms used as foreign keys with the relations class. Of course we can model things that way (though im sure we'll start seeing more qualifiers on that class then), but dwc is largely successful because of its rather flat and simple nature, so we should be careful to preserve at least the important and often used id terms.
Markus
On 09.07.2011, at 17:51, Bob Morris morris.bob@gmail.com wrote:
I agree with Gregor
On Sat, Jul 9, 2011 at 11:03 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
- I believe that the term "BiologicalEntity" is the best term for this
class and its ID attribute.
I disagree on this. Biological entities to me seems a clear superterm, encompassing ecosystems, taxa, individuals, enzymes, and probably more.
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- Robert A. Morris
Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University
email: morris.bob@gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile) _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
In also conservative on "normalising" dwc too much and replace all id
terms
used as foreign keys with the relations class. Of course we can model
things
that way (though im sure we'll start seeing more qualifiers on that class then), but dwc is largely successful because of its rather flat and simple nature, so we should be careful to preserve at least the important and
often
used id terms.
But DwC is already normalized this way. There is no LocalityID term in the Event Class. There is no EventID in the Occurrence class. In fact, the only "foreign key" term I know of in DwC (internet too slow here for me to consult it online) is "IndividualID", and this doesn't even serve the function even a "Foreign Key" because there is not yet any "indivudal" class to provide "PK" of the corresponding linked instance.
So...I've been asking various people how one is supposed to represent the fact that "This Event instance took place at this Locality instance", or "This Identification instance refers to this Taxon instance", or "This Occurrence instance involves this Event instance and this Identified Taxon instance". So far, I don't know the answer to this. For the BiSciCol project, these relationships between instances of DwC classes are the core item being indexed, so we are assuming that the purpose of ResourceRelationship is, in fact, to establish these relationships between instances of DwC classes.
I hope someone will correct me if I'm wrong.
Rich
On 10/07/2011, at 1:03 AM, Gregor Hagedorn wrote:
- I believe that the term "BiologicalEntity" is the best term for this
class and its ID attribute.
I disagree on this. Biological entities to me seems a clear superterm, encompassing ecosystems, taxa, individuals, enzymes, and probably more.
What happened to 'Organism'?
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I thought these examples might help people get their head around this idea of "Individual"
For some email systems the long version of these URI's are escaped so have added bit.ly links to should also work.
They are all collected into this bit.ly bundle http://bitly.com/okM8h0
These are from records that can be browsed here http://ocs.taxonconcept.org/ocs/index.html
http://lod.taxonconcept.org/ses/ICmLC.html *owl:Class* *txn:SpeciesConcept* http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%... http://bitly.com/f9MUfe
*http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html * *txn_se:ICmLC#Occurrence* *txn:Occurrence* http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5... http://bitly.com/h00Q9u
*txn_se:ICmLC#Individual* *txn:SpeciesIndividual* http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Focs.taxonconcept.org%... http://bitly.com/hqaOyS
*txn:SpeciesIndividualTag* http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%... http://bitly.com/oM7X6Q
* Note *is type of txn_ocs*:f522444a-2dd9-400e-be59-47213ef38cb9#Individual
- Pete
On Mon, Jul 4, 2011 at 4:48 PM, John Wieczorek tuco@berkeley.edu wrote:
Darwin Core Issues 69 and 80: http://code.google.com/p/darwincore/issues/list
This issue is related to the issue of Evidence (CollectionObject, Representation, Token, Unit) covered in a previous posting. In the Darwin Core there is currently no separate class to explicitly represent the biological entities involved in an Occurrence. This is problematic when trying to be explicit about the attributes of these entities in the semantic world. Various names have been given to this concept, including "Individual", "BiologicalIndividual", "BiologicalEntity", "Organism", and "DataSets/DataSet/Units/Unit" in ABCD.
Open Issues: Determine if there is a general consensus on the need for new class for this concept.
The best name for this class.
Create a new Type Vocabulary term referring to this new class.
Decide which properties currently organized under Occurrence should instead be organized under this new class.
As a seed for further discussion, here is a complete proposal.
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/terms/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/terms/ Label: BiologicalEntity Definition: The category of information pertaining to an individual organism or a group of organisms that can reliably be known to represent a single taxon. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/dwctype/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: BiologicalEntity Definition: A resource describing an instance of the BiologicalEntity class. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD
Term Name: biologicalEntityID Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityID Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityID Definition: An identifier for the set of information associated with an BiologicalEntity. May be a global unique identifier or an identifier specific to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: biologicalEntityID-2011-07-04 Replaces: individualID-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/
Term Name: biologicalEntityRemarks Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityRemarks Definition: Comments or notes about the BiologicalEntity. Comment: Example: "seen several times in Tilden Park before capture". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: biologicalEntityRemarks-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Notes
Term Name: associatedBiologicalEntities Identifier: http://rs.tdwg.org/dwc/terms/associatedBiologicalEntities Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedBiologicalEntities Definition: A list (concatenated and separated) of identifiers of other BiologicalEntity records and their associations to this BiologicalEntity. Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: associatedBiologicalEntities-2011-07-04 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode
DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName
- DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
Terms to be organized under biologicalEntity rather than Occurrence: previousIdentifications associatedMedia associatedReferences _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
For the record, I am in support of this proposal (which may be redundant given my advocacy for it in the past). I do not have a strong opinion about the name of the class because I think that the definition is more important than the name and it looks to me like the definition says what it should (or at least what I think it should). The definition allows for a small group of organisms if they can reliably be known to represent a single taxon. I think that Individual is probably not a good name due to confusion with the technical use of that term elsewhere.
I don't understand why Rich says that the creation of this class eliminates the need for a class for "evidence". Perhaps he will elaborate when he has better email access.
Steve
On 7/4/2011 4:48 PM, John Wieczorek wrote:
Darwin Core Issues 69 and 80: http://code.google.com/p/darwincore/issues/list
This issue is related to the issue of Evidence (CollectionObject, Representation, Token, Unit) covered in a previous posting. In the Darwin Core there is currently no separate class to explicitly represent the biological entities involved in an Occurrence. This is problematic when trying to be explicit about the attributes of these entities in the semantic world. Various names have been given to this concept, including "Individual", "BiologicalIndividual", "BiologicalEntity", "Organism", and "DataSets/DataSet/Units/Unit" in ABCD.
Open Issues: Determine if there is a general consensus on the need for new class for this concept.
The best name for this class.
Create a new Type Vocabulary term referring to this new class.
Decide which properties currently organized under Occurrence should instead be organized under this new class.
As a seed for further discussion, here is a complete proposal.
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/terms/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/terms/ Label: BiologicalEntity Definition: The category of information pertaining to an individual organism or a group of organisms that can reliably be known to represent a single taxon. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}
Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/dwctype/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: BiologicalEntity Definition: A resource describing an instance of the BiologicalEntity class. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD
Term Name: biologicalEntityID Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityID Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityID Definition: An identifier for the set of information associated with an BiologicalEntity. May be a global unique identifier or an identifier specific to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: biologicalEntityID-2011-07-04 Replaces: individualID-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/
Term Name: biologicalEntityRemarks Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityRemarks Definition: Comments or notes about the BiologicalEntity. Comment: Example: "seen several times in Tilden Park before capture". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: biologicalEntityRemarks-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Notes
Term Name: associatedBiologicalEntities Identifier: http://rs.tdwg.org/dwc/terms/associatedBiologicalEntities Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedBiologicalEntities Definition: A list (concatenated and separated) of identifiers of other BiologicalEntity records and their associations to this BiologicalEntity. Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: associatedBiologicalEntities-2011-07-04 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode
- DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName
- DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
Terms to be organized under biologicalEntity rather than Occurrence: previousIdentifications associatedMedia associatedReferences _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
.
represent a single taxon. I think that Individual is probably not a good name due to confusion with the technical use of that term elsewhere.
TaxonInstance seems to me to be perhaps most precise. Personally I have a problem merging individual with population, since population -> metapopulation -> subspecies form a continuum in my understanding. But I am quite willing to be pragmatical :-)
Gregor
I also find TaxonInstance a good alternative to Individual and more precise even. Markus
On Jul 12, 2011, at 10:08, Gregor Hagedorn wrote:
represent a single taxon. I think that Individual is probably not a good name due to confusion with the technical use of that term elsewhere.
TaxonInstance seems to me to be perhaps most precise. Personally I have a problem merging individual with population, since population -> metapopulation -> subspecies form a continuum in my understanding. But I am quite willing to be pragmatical :-)
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
My turn to disagree (strongly, in this case). It's not an instance of a taxon, it's an instance of an Organism. A taxon is merely a non-factual (i.e., opinion-based) attribute of an organism, secondarily associated via an Identification instance.
I could probably be comfortable with "OrganismInstance"; but in that case, why not just "Organism" as Paul suggested? Isn't "Instance" sort of implied by all the classes?
I am certainly open to debate about where the "upper boundary" of an instance of this class, and I agree that "population" could be interpreted more as a low level of "taxon", rather than a high level of "organism". But I certainly don't think that instances of this class should be limited to a singular organism. Would a coral head then constitute thousands of instances of this class? Surely such colonies could be collapsed into a single instance of this class. And the same would likely also be useful for colonies of insects (ants, termites, bees, etc.), as well as small groups (pack of wolves, pod of whales, etc.); not to mention a specimen "lot" in a Museum collection.
I agree it should have only *one* taxon, but that there should be no upper limit on the rank of this taxon. If more than one taxon is identified, then there needs to be a separate instance of this class for each identified taxon. But this only applies when multiple taxa are acknowledged -- it does NOT restrict multiple taxa being linked to the same instance via multiple identifications when there is a difference of opinion about what the correct taxon identity should be. In other words, an instance of this class may be identified as "A" *or* "B", but could not legitimately be identified as "A" *and* "B" simultaneously (except, perhaps in the case of hybrids, but that's another situation altogether).
More later.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of Gregor Hagedorn Sent: Tuesday, July 12, 2011 10:09 AM To: Steven J. Baskauf Cc: tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
represent a single taxon. I think that Individual is probably not a good name due to confusion with the technical use of that term
elsewhere.
TaxonInstance seems to me to be perhaps most precise. Personally I have a problem merging individual with population, since population -> metapopulation -> subspecies form a continuum in my understanding. But I am quite willing to be pragmatical :-)
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On 14 July 2011 08:41, Richard Pyle deepreef@bishopmuseum.org wrote:
My turn to disagree (strongly, in this case). It's not an instance of a taxon, it's an instance of an Organism. A taxon is merely a non-factual (i.e., opinion-based) attribute of an organism, secondarily associated via an Identification instance.
WIth respect to organism: strictly, Viruses are not organisms, but I could live with that. But the goal is to find a term including population. Population definitely is not an organism.
I believe the instances of taxon are organisms, populations, individuals.
Gregor
Gregor said: "I believe the instances of taxon are organisms, populations, individuals."
The main commonality between these three is that they are instances of life (or prior life): How about LifeInstance?
Chuck
On Jul 14, 2011, at 4:52 AM, "Gregor Hagedorn" g.m.hagedorn@gmail.com wrote:
I believe the instances of taxon are organisms, populations, individuals.
I think the key point is that “taxa” represent a set of individuals implicitly (i.e., a taxon definition exists without the need to define or enumerate the complete set of individuals contained within it); whereas the class that I think we need to add to DwC is one that deals with *explicitly* defined or enumerated members. These sets of explicitly defined or enumerated members can be assigned as implicit members of a single taxon (via an instance of dwc:identification), but the difference, I think, is in is the explicit inclusion vs. implicit inclusion of members. This may seem trivial, but I believe it to be fundamental.
The problem with “populations” is that they can be defined either way (either implicitly or explicitly). If you think of them from the implicit perspective, they seem more like taxa. If you think of them from the explicit perspective, they seem more like an extension of an “Organism” instance. In a way, populations are the exception that proves the rule. Or….the exemplar that illustrates the distinction.
Aloha, Rich
"explicit inclusion vs. implicit inclusion of members ". I agree it is fundamental. We have here the two classical definitions of a "set" (mathematical) : - extensional definition it means by the explicit list of its elements or instances - intensional definition it means by properties (implicit inclusion of the members having these properties)
"taxa" and "population" are set of living organisms. The two can be defined implicitly or explicitly. The term "class" or "living_set" could be prefered for extensional definition (and "living_unit" or living_instance" for the members). The term "living_concept" for abstract concept with intensional definition.
Régine
Le 15/07/2011 08:52, Richard Pyle a écrit :
I think the key point is that “taxa” represent a set of individuals implicitly (i.e., a taxon definition exists without the need to define or enumerate the complete set of individuals contained within it); whereas the class that I think we need to add to DwC is one that deals with *explicitly* defined or enumerated members. These sets of explicitly defined or enumerated members can be assigned as implicit members of a single taxon (via an instance of dwc:identification), but the difference, I think, is in is the explicit inclusion vs. implicit inclusion of members. This may seem trivial, but I believe it to be fundamental.
The problem with “populations” is that they can be defined either way (either implicitly or explicitly). If you think of them from the implicit perspective, they seem more like taxa. If you think of them from the explicit perspective, they seem more like an extension of an “Organism” instance. In a way, populations are the exception that proves the rule. Or….the exemplar that illustrates the distinction.
Aloha, Rich
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Thanks, Régine. You wrote:
taxa" and "population" are set of living organisms. The two can be defined implicitly or explicitly
I'm not aware of anyone who has attempted to establish an extensional definition a taxon; but I can imagine both extensional and intensional definitions of populations.
Aloha, Rich
-----Original Message----- From: Régine Vignes Lebbe [mailto:regine.vignes_lebbe@upmc.fr] Sent: Friday, July 15, 2011 10:01 AM To: Richard Pyle Cc: 'Chuck Miller'; 'Gregor Hagedorn'; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
"explicit inclusion vs. implicit inclusion of members ". I agree it is fundamental. We have here the two classical definitions of a "set" (mathematical) :
- extensional definition it means by the explicit list of its elements or
instances
- intensional definition it means by properties (implicit inclusion of the
members having these properties)
"taxa" and "population" are set of living organisms. The two can be defined implicitly or explicitly. The term "class" or "living_set" could be prefered for extensional definition (and "living_unit" or living_instance" for the members). The term "living_concept" for abstract concept with intensional definition.
Régine
Le 15/07/2011 08:52, Richard Pyle a écrit :
I think the key point is that “taxa” represent a set of individuals implicitly
(i.e., a taxon definition exists without the need to define or enumerate the complete set of individuals contained within it); whereas the class that I think we need to add to DwC is one that deals with *explicitly* defined or enumerated members. These sets of explicitly defined or enumerated members can be assigned as implicit members of a single taxon (via an instance of dwc:identification), but the difference, I think, is in is the explicit inclusion vs. implicit inclusion of members. This may seem trivial, but I believe it to be fundamental.
The problem with “populations” is that they can be defined either way
(either implicitly or explicitly). If you think of them from the implicit perspective, they seem more like taxa. If you think of them from the explicit perspective, they seem more like an extension of an “Organism” instance. In a way, populations are the exception that proves the rule. Or….the exemplar that illustrates the distinction.
Aloha, Rich
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
--
Régine Vignes Lebbe Laboratoire Informatique et Systématique Université Pierre et Marie Curie- Paris6 CR2P UMR 7207
MNHN Département Histoire de la Terre Bâtiment de Géologie CP48 57 rue Cuvier F-75005 Paris (France)
tél : 01.40.79.80.61
Let's drop taxon! populations are definitively NOT always taxa. They may be in some specific circumstances but dont deserve the general term I support Rich's argument albeit not in full because taxa are actually not opinions based but hypotheses inferred by phylogenies, unless a tested hypothesis qualifies for an opinion. In any case, whatever we may mean with taxa, populations are clearly not covered in most cases.
Nico
Sent from my iPhone
On Jul 14, 2011, at 4:51 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
On 14 July 2011 08:41, Richard Pyle deepreef@bishopmuseum.org wrote:
My turn to disagree (strongly, in this case). It's not an instance of a taxon, it's an instance of an Organism. A taxon is merely a non- factual (i.e., opinion-based) attribute of an organism, secondarily associated via an Identification instance.
WIth respect to organism: strictly, Viruses are not organisms, but I could live with that. But the goal is to find a term including population. Population definitely is not an organism.
I believe the instances of taxon are organisms, populations, individuals.
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hmmm....in the spirit of this statement:
populations are definitively NOT always taxa. They may be in some specific circumstances but dont deserve the general term
....I would respond to the following statement:
taxa are actually not opinions based but hypotheses inferred by phylogenies, unless a tested hypothesis
qualifies
for an opinion.
With this statement:
[taxa] are definitively NOT always [hypotheses]. They may be in some specific circumstances but dont deserve the general term
...but I think we digress.....
:-)
Aloha, Rich
Viruses differ in other ways as well (no Linnean-style names, different fundamental concepts for what a "Taxon" is, many biologists don't even include them within the scope of "life", etc.) I'm not sure "Organism" is any more inconsistent with population than it is with a coral colony or two members of the same species; but I agree more careful though would be useful here.
I'm not married to "organism", but I *really* don't like the word "taxon" embedded in the term. Taxa are abstract notions, invented by humans. What I think we need a term for is an explicit indication of the physical "stuff of life".
I think that DwC is very, very close to having what we need to represent almost all of the information we're interested in. I think one of the main problems with the existing DwC is that "Occurrence" is overloaded -- too many disparate things are being force-fit into instances of that class, and it gets a bit messy. Most of the other DwC classes are pretty consistently understood and utilized by the community. I think this conversation we're having now (the introduction of a new class) should really focus on how best to define that class in such a way that it maximally enhances data sharing. In other words, it should solve a problem, and should enable new features for information exchange that satisfy a need. Also, as we define it, part of the definition is figuring out which existing attributes of "Occurrence" that the new class should inherit.
My own understanding of the core DwC classes (with my own interpretation of "Occurrence" added) are as follows:
Locality: A defined place.
Event: The intersection of a Locality and a specific window of time, with metadata pertaining to some action that happened at that place & time.
Taxon: an *implicit* set of organisms circumscribed by a taxon concept and labeled with a taxon name
Organism: an *explicit*set of one or more instances of organisms (sensu lato, including viruses?).
Occurrence: the intersection of an Event and an Organism.
Identification: the intersection of an Organism and a Taxon.
Steve created some very useful diagrams of this sort of thing the last time we had this conversation (Steve: can you re-post the link to your diagrams?)
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Thursday, July 14, 2011 11:52 AM To: Richard Pyle Cc: Steven J. Baskauf; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
On 14 July 2011 08:41, Richard Pyle deepreef@bishopmuseum.org wrote:
My turn to disagree (strongly, in this case). It's not an instance of a taxon, it's an instance of an Organism. A taxon is merely a non-factual (i.e., opinion-based) attribute of an organism, secondarily associated via an Identification instance.
WIth respect to organism: strictly, Viruses are not organisms, but I could
live
with that. But the goal is to find a term including population. Population definitely
is not
an organism.
I believe the instances of taxon are organisms, populations, individuals.
Gregor
I really don't know why you insist in saying that taxa are abstract concepts. Yes, linnean taxa are but othrwise taxa are very real, so real that they are = to clades. I assume DwC will deal with taxa in general and not just Linnean artifacts.
Nico
Sent from my iPhone
On Jul 14, 2011, at 10:31 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
Viruses differ in other ways as well (no Linnean-style names, different fundamental concepts for what a "Taxon" is, many biologists don't even include them within the scope of "life", etc.) I'm not sure "Organism" is any more inconsistent with population than it is with a coral colony or two members of the same species; but I agree more careful though would be useful here.
I'm not married to "organism", but I *really* don't like the word "taxon" embedded in the term. Taxa are abstract notions, invented by humans. What I think we need a term for is an explicit indication of the physical "stuff of life".
I think that DwC is very, very close to having what we need to represent almost all of the information we're interested in. I think one of the main problems with the existing DwC is that "Occurrence" is overloaded -- too many disparate things are being force-fit into instances of that class, and it gets a bit messy. Most of the other DwC classes are pretty consistently understood and utilized by the community. I think this conversation we're having now (the introduction of a new class) should really focus on how best to define that class in such a way that it maximally enhances data sharing. In other words, it should solve a problem, and should enable new features for information exchange that satisfy a need. Also, as we define it, part of the definition is figuring out which existing attributes of "Occurrence" that the new class should inherit.
My own understanding of the core DwC classes (with my own interpretation of "Occurrence" added) are as follows:
Locality: A defined place.
Event: The intersection of a Locality and a specific window of time, with metadata pertaining to some action that happened at that place & time.
Taxon: an *implicit* set of organisms circumscribed by a taxon concept and labeled with a taxon name
Organism: an *explicit*set of one or more instances of organisms (sensu lato, including viruses?).
Occurrence: the intersection of an Event and an Organism.
Identification: the intersection of an Organism and a Taxon.
Steve created some very useful diagrams of this sort of thing the last time we had this conversation (Steve: can you re-post the link to your diagrams?)
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Thursday, July 14, 2011 11:52 AM To: Richard Pyle Cc: Steven J. Baskauf; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
On 14 July 2011 08:41, Richard Pyle deepreef@bishopmuseum.org wrote:
My turn to disagree (strongly, in this case). It's not an instance of a taxon, it's an instance of an Organism. A taxon is merely a non-factual (i.e., opinion-based) attribute of an organism, secondarily associated via an Identification instance.
WIth respect to organism: strictly, Viruses are not organisms, but I could
live
with that. But the goal is to find a term including population. Population definitely
is not
an organism.
I believe the instances of taxon are organisms, populations, individuals.
Gregor
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hi Rich,
Steve created some very useful diagrams of this sort of thing the last time we had this conversation (Steve: can you re-post the link to your diagrams?)
Steve is traveling in Costa Rica with intermittent internet access. The diagrams he previously posted became integrated into the Darwin-SW model, which is based on DwC Classes. The equivalent diagram is at:
http://code.google.com/p/darwin-sw/
The name IndividualOrganism is used for the proposed DwC Individual class.
Best,
Cam
Populations and metapopulations are real entities but subspecies is definitively an artificial concept. Now that is I deed an opinion! I don't get your flow Greg. But aren't individuals populations taxa etc etc all biologicalEntities?
Nico
Sent from my iPhone
On Jul 12, 2011, at 3:08 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
represent a single taxon. I think that Individual is probably not a good name due to confusion with the technical use of that term elsewhere.
TaxonInstance seems to me to be perhaps most precise. Personally I have a problem merging individual with population, since population -> metapopulation -> subspecies form a continuum in my understanding. But I am quite willing to be pragmatical :-)
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On 14 July 2011 15:18, Nico Cellinese ncellinese@flmnh.ufl.edu wrote:
Populations and metapopulations are real entities but subspecies is definitively an artificial concept. Now that is I deed an opinion!
I don't know the difference between a geographically defined subspecies and a meta-meta population. Do you define them differently? I believe (sic!) you can define either either exact or poorly.
But aren't individuals populations taxa etc etc all biologicalEntities?
Yes, but so, I believe, are ecosystems, organelles, enzymes, and probably much more. Also, crucially, the term and concept sought here seeks to exclude taxa, while you include it into your list.
In my thinking taxa classify individuals or populations. Without objects that they classify, they don't make (biological) sense. That is why I proposed (past tense) this term, but with widespread opposition it is not a good term.
LifeInstances - why not? Or IndividualOrPopulation?
Gregor
I don't know the difference between a geographically defined subspecies and a meta-meta population. Do you define them differently? I believe (sic!) you can define either either exact or poorly.
Meta-population is an entity and subspecies is the rank you may apply to this entity, if that is how you like to label that group.
In my thinking taxa classify individuals or populations.
I guess that is where we disagree.
Well perhaps Organism is a good compromise. I understand viruses are not but I would prefer to live with that than any other term that would imply worse consequences.
I am eager to extend the DwC to also cover concepts that are important to people like me :-) so that when I think about developing phylogenetic databases, holding phylogenetic concepts, I don't feel badly constrained by these terms. I would like the DwC to work across the border. I'm sure I'm not alone in desiring an extensible DwC. So, forgive me.
Nico
Without objects that they classify, they don't make (biological) sense. That is why I proposed (past tense) this term, but with widespread opposition it is not a good term.
LifeInstances - why not? Or IndividualOrPopulation?
Gregor
((who would not forgive you?))
but you think "Organism" includes "population" and metapopulation? We are defining is-a relationships here (subclassing was already discussed), so "a (meta-) population is an organism" should make sense. It does not to me.
Gregor
"a (meta-) population is a LifeInstance" does seem to make sense to me.
"a (meta-) population is a taxon" does not make sense to me. Nor does "a (meta-) population is an Organism"
But "a (meta-) population is a TaxonInstance" sort of makes sense, but Rich dislikes the inherent ambiguity that occurs when using the string "taxon" or "taxa" in a case like this because it opens the can of worms about names and concepts and spins off into endless related, but disassociated, debates. The word "taxon" has several meanings that can only be understood by a clear context within which the word is used or by an accompanying long definition that spells out which meaning is being used. Rich has written on this multiple times.
Chuck
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Gregor Hagedorn Sent: Thursday, July 14, 2011 12:18 PM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
((who would not forgive you?))
but you think "Organism" includes "population" and metapopulation? We are defining is-a relationships here (subclassing was already discussed), so "a (meta-) population is an organism" should make sense. It does not to me.
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Some other suggestions for names of this Class, following my enumeration of examples prompted by Hilmar's post:
BiologicalUnit BiologicalItem BiologicalInstance BiologicalObject BiologicalRepresentative OrganismalUnit OrganismUnit UnitOrganism OrganismInstance OrganismalEntity
I tend not to like "Instance", because (as already stated), all classes have instances so it's redundant, and if meant in a different way, then we have confusion of homonymy. However, if that's what people really like, I won't fight it.
I would prefer "Biological" as a prefix, rather than "Life", because as far as I can tell, they mean essentially the same thing, so in my opinion it's best to go with the more scientific term.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of Chuck Miller Sent: Thursday, July 14, 2011 7:32 PM To: Gregor Hagedorn; Nico Cellinese Cc: tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
"a (meta-) population is a LifeInstance" does seem to make sense to me.
"a (meta-) population is a taxon" does not make sense to me. Nor does "a (meta-) population is an Organism"
But "a (meta-) population is a TaxonInstance" sort of makes sense, but
Rich
dislikes the inherent ambiguity that occurs when using the string "taxon"
or
"taxa" in a case like this because it opens the can of worms about names
and
concepts and spins off into endless related, but disassociated, debates.
The
word "taxon" has several meanings that can only be understood by a clear context within which the word is used or by an accompanying long
definition
that spells out which meaning is being used. Rich has written on this
multiple
times.
Chuck
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Gregor Hagedorn Sent: Thursday, July 14, 2011 12:18 PM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] New terms need resolution: "Individual"
((who would not forgive you?))
but you think "Organism" includes "population" and metapopulation? We are defining is-a relationships here (subclassing was already discussed), so
"a
(meta-) population is an organism" should make sense. It does not to me.
Gregor _______________________________________________ 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 Jul 14, 2011, at 12:13 PM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
But aren't individuals populations taxa etc etc all biologicalEntities?
Yes, but so, I believe, are ecosystems, organelles, enzymes, and probably much more.
Good observation. You could actually use this as a basis for first crafting a definition of the term, and worry about the label you'll assign to it later. For example, using the genus-differentia pattern, you can start with "<X> is a biological entity that <Y>", where <X> is the label, to be deferred to later, and <Y> are the criteria (properties, or to be more precise, property restrictions) that distinguish the class of things we want to define from all other things that are also biological entities. These criteria would need to be chosen such that they apply to *all* members of the class (not only to some), and while a subset of these properties may apply to instances that are not members, there is no instance to which the conjunction of properties applies but that is not a member of the class.
Frankly, I'm not even sure that this is the best place to start for the definition. Perhaps it's better to take one step back further, and enumerate a variety of example instances of biological entities that we all agree should be in the class, and a contrary enumeration of example biological entities that we all agree should not be in the class. If you include less obvious and possibly controversial ones in these lists, it may help to narrow down what the differentiating criteria really are. And while this exercise may sound trivial, it hasn't been done yet as far as I'm aware, and from a number of the posts in this thread I sense that there is actually not consensus on which side of the divider the border-cases go. And you can't hope for consensus on the label (or the definition) if there isn't first consensus on how we want the instances classified.
Just to throw in an example, I might argue that at least some organelles should actually be among the biological entities included in the class. Some organelles have their own genome and evolutionary history, and were once independent organisms. If we accept this, then we might say that biological entities to be included have a genome or a pool of genomes with a (shared in the case of a pool) evolutionary history, and those to be excluded do not. This would exclude vacuoles from the class, but include plastids, viruses, cows, and buffalo herds.
-hilmar
Sent with a tap.
Perhaps it's better to take one step back further, and enumerate a variety
of
example instances of biological entities that we all agree should be in
the
class, and a contrary enumeration of example biological entities that we
all
agree should not be in the class. If you include less obvious and possibly controversial ones in these lists, it may help to narrow down what the differentiating criteria really are. And while this exercise may sound
trivial, it
hasn't been done yet as far as I'm aware, and from a number of the posts
in
this thread I sense that there is actually not consensus on which side of
the
divider the border-cases go. And you can't hope for consensus on the label (or the definition) if there isn't first consensus on how we want the
instances
classified.
I agree with Hilmar on this approach.
Just to throw in an example, I might argue that at least some organelles should actually be among the biological entities included in the class.
Some
organelles have their own genome and evolutionary history, and were once independent organisms. If we accept this, then we might say that
biological
entities to be included have a genome or a pool of genomes with a (shared
in
the case of a pool) evolutionary history, and those to be excluded do not. This would exclude vacuoles from the class, but include plastids, viruses, cows, and buffalo herds.
This *might* be close to what my own vision of how to establish the criteria for things to include within this class. But following Himar's suggestion, I will try to list some things that I think may be useful to represent as instances of this class.
I'll start with the entities that most of us probably agree with:
- A single whole-organism specimen curated and preserved at a Museum - A single whole organism (whale, wolf, buffalo, tree, insect, etc.) documented in nature - A single, cohesive colonial organism (e.g., coral head), either preserved in a Museum, or documented in nature
Now some well-enumerated aggregates:
- A single "lot" of multiple whole-organism specimens of the same taxon curated and preserved at a Museum - A well-defined and enumerated set of whole organisms (pod of whales, pack of wolves, etc.) documented in nature
Now some non-enumerated, but still reasonably definable aggregates:
- A colony of ants (or termites, or bees, etc.) in nature - A living culture of bacteria - A flock of birds in nature
Now some parts of a single whole organism:
- A preserved herbarium specimen - A preserved skeleton of a mammal - A preserved skin of a mammal - A preserved head of a fish - A tissue sample extracted from a whale in nature
The preceding set requires some elaboration. For example, a herbarium specimen is usually a clipping or other small part of a larger whole plant. Often multiple clippings from the same individual plant are taken and preserved as separate herbarium specimens. Should there only be one instance of this class representing the whole plant? Or should there be multiple distinct instances of this class, one for each herbarium specimen? If the former, would the herbarium specimens represent instances of the "Evidence" class, linked to the one instance of this class (whole plant)? If the latter, should there be a separate instance of this class to represent the whole plant, and then each of the instances of herbarium specimens be linked via a "derivedFrom" relationship to the whole-plant instance?
Similarly, suppose the mammal skeleton and skin in the above list are from the same individual mammal. Would there be one instance of this class (for the whole organism), and the Skeleton and Skin be treated as instances of the Evidence class? Or, should there be two instances (one for the skin, one for the skeleton)? Or should there be three instances (one for the whole mammal organism, one for the preserved skin derived from it, and one for the preserved skeleton derived from it)?
Take the example of the whale. Suppose there is a pod of 7 whales that is well-defined, cohesive, tagged, and studied in nature. Would there be one instance of this class for the pod, and then 7 additional instances (one for each individual whale) that are linked as "memberOf" the pod instance? What to do with the tissue sample? Is it an instance of the Evidence Class? Is it another instance of this class, "derivedFrom" the instance of this class representing the specific whale from which the sample was taken?
Now some border-line and controversial cases:
- A non-enumerated but otherwise well-defined population of a single species in nature. [How do we distinguish this from a well-defined taxonomic unit?] - A single rock in a Museum collection that has multiple fossils (representing multiple phyla of animals) embedded in it - A single rock preserved in alcohol containing multiple invertebrate specimens from different phyla
I'm sure we can come up with other examples. I do not have web access (only email), so I was unable to look at Peter DeVries' links to examples of what he felt belonged in this class. Pete -- maybe you can summarize them in text form?
I would like to believe that all instances of Occurrence can be rooted into one instance of this proposed new class. So, maybe it would be useful to think about all the different ways that an Occurrence is currently represented in actual instances, and see if we can scope this new class to be the generalized "basis of record" for all Occurrences.
Aloha, Rich
P.S. I have BCC'd the BiSciCol list on this email, because of it's strong relevance to that project.
But Hilmar recommended a companion list of things not in the class. What are some of those?
Chuck
On Jul 17, 2011, at 1:46 AM, "Richard Pyle" deepreef@bishopmuseum.org wrote:
Perhaps it's better to take one step back further, and enumerate a variety
of
example instances of biological entities that we all agree should be in
the
class, and a contrary enumeration of example biological entities that we
all
agree should not be in the class. If you include less obvious and possibly controversial ones in these lists, it may help to narrow down what the differentiating criteria really are. And while this exercise may sound
trivial, it
hasn't been done yet as far as I'm aware, and from a number of the posts
in
this thread I sense that there is actually not consensus on which side of
the
divider the border-cases go. And you can't hope for consensus on the label (or the definition) if there isn't first consensus on how we want the
instances
classified.
I agree with Hilmar on this approach.
Just to throw in an example, I might argue that at least some organelles should actually be among the biological entities included in the class.
Some
organelles have their own genome and evolutionary history, and were once independent organisms. If we accept this, then we might say that
biological
entities to be included have a genome or a pool of genomes with a (shared
in
the case of a pool) evolutionary history, and those to be excluded do not. This would exclude vacuoles from the class, but include plastids, viruses, cows, and buffalo herds.
This *might* be close to what my own vision of how to establish the criteria for things to include within this class. But following Himar's suggestion, I will try to list some things that I think may be useful to represent as instances of this class.
I'll start with the entities that most of us probably agree with:
- A single whole-organism specimen curated and preserved at a Museum
- A single whole organism (whale, wolf, buffalo, tree, insect, etc.)
documented in nature
- A single, cohesive colonial organism (e.g., coral head), either preserved
in a Museum, or documented in nature
Now some well-enumerated aggregates:
- A single "lot" of multiple whole-organism specimens of the same taxon
curated and preserved at a Museum
- A well-defined and enumerated set of whole organisms (pod of whales, pack
of wolves, etc.) documented in nature
Now some non-enumerated, but still reasonably definable aggregates:
- A colony of ants (or termites, or bees, etc.) in nature
- A living culture of bacteria
- A flock of birds in nature
Now some parts of a single whole organism:
- A preserved herbarium specimen
- A preserved skeleton of a mammal
- A preserved skin of a mammal
- A preserved head of a fish
- A tissue sample extracted from a whale in nature
The preceding set requires some elaboration. For example, a herbarium specimen is usually a clipping or other small part of a larger whole plant. Often multiple clippings from the same individual plant are taken and preserved as separate herbarium specimens. Should there only be one instance of this class representing the whole plant? Or should there be multiple distinct instances of this class, one for each herbarium specimen? If the former, would the herbarium specimens represent instances of the "Evidence" class, linked to the one instance of this class (whole plant)? If the latter, should there be a separate instance of this class to represent the whole plant, and then each of the instances of herbarium specimens be linked via a "derivedFrom" relationship to the whole-plant instance?
Similarly, suppose the mammal skeleton and skin in the above list are from the same individual mammal. Would there be one instance of this class (for the whole organism), and the Skeleton and Skin be treated as instances of the Evidence class? Or, should there be two instances (one for the skin, one for the skeleton)? Or should there be three instances (one for the whole mammal organism, one for the preserved skin derived from it, and one for the preserved skeleton derived from it)?
Take the example of the whale. Suppose there is a pod of 7 whales that is well-defined, cohesive, tagged, and studied in nature. Would there be one instance of this class for the pod, and then 7 additional instances (one for each individual whale) that are linked as "memberOf" the pod instance? What to do with the tissue sample? Is it an instance of the Evidence Class? Is it another instance of this class, "derivedFrom" the instance of this class representing the specific whale from which the sample was taken?
Now some border-line and controversial cases:
- A non-enumerated but otherwise well-defined population of a single species
in nature. [How do we distinguish this from a well-defined taxonomic unit?]
- A single rock in a Museum collection that has multiple fossils
(representing multiple phyla of animals) embedded in it
- A single rock preserved in alcohol containing multiple invertebrate
specimens from different phyla
I'm sure we can come up with other examples. I do not have web access (only email), so I was unable to look at Peter DeVries' links to examples of what he felt belonged in this class. Pete -- maybe you can summarize them in text form?
I would like to believe that all instances of Occurrence can be rooted into one instance of this proposed new class. So, maybe it would be useful to think about all the different ways that an Occurrence is currently represented in actual instances, and see if we can scope this new class to be the generalized "basis of record" for all Occurrences.
Aloha, Rich
P.S. I have BCC'd the BiSciCol list on this email, because of it's strong relevance to that project.
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
But Hilmar recommended a companion list of things not in the class. What
are
some of those?
Right -- sorry!
Well, plenty of things are not in the class (Localities, dates, etc., etc.). But more specifically, I would say that any circumscription of organisms that is based on an intensional definition (sensu Régine) would be excluded (and would instead be covered by the "Taxon" class). That is, if a set of organisms is defined by properties, rather than by specific members, it would be excluded from this class. Also excluded from this class would be an organism or set of organisms bounded by time or space. What I mean by this is that the temporal scope of an organism instance begins when the organism(s) is/are born, and ends when the organism(s) disintegrates (I didn't want to say "die", because a dead specimen is still an organism, in my option -- but a disintegrated specimen is not). Also, one cannot define an instance of organism dynamically via space and time, such as "all whales off Maui during the winter months", as the members would change year after year.
This reasoning would tend to exclude "population" from this class; but if population also is excluded from Taxon, then I don't know how one would represent an instance of a population via DwC. Surely there is an informatics need to track/monitor/analyze sets of organisms defined by "population". But how would one represent such a unit in DwC? If not as a Taxon, and not as an Organism, then how would one instantiate a "population" and assign properties to it? Another new class, perhaps? That would make me squeamish.
Incidentally, I have been using the term "Organism" consistently to refer to this class; but as I said previously, I am reasonably open-minded to what the term should be (as long as it doesn't include the word "taxon", and only if there is broad community consensus if it includes the words "Instance" or "Individual").
Aloha, Rich
What is your position about:
- "All the whales that were within 10 km of Maui between 2010-06-01 and 2010-08-31." - "All the whales that will have been within 10 km of Maui between 2012-06-01 and 2012-08-30." - "All the whales that that will have been within 10 km of Maui in the next 91 days"
Also for each of the above, what about - "A whale that..." and
Also per Hillmar, for each of the 6 cases, consider the 6 cases that negate the verbs, e.g. "All the whales that were not within..."
When you are done with that exercise, what about the difference between "A whale" and "The whale"?
{FWIW, for finite sets, the difference between intensional and extensional definition is largely one of practicality based on the set size. That's not the case for infinite sets, for which extensional definitions are impossible. This is one reason I wouldn't be enamored of your criterion. I don't think it in fact includes some actual whales but excludes others.}
Bob
On Tue, Jul 19, 2011 at 2:26 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
But Hilmar recommended a companion list of things not in the class. What
are
some of those?
Right -- sorry!
Well, plenty of things are not in the class (Localities, dates, etc., etc.). But more specifically, I would say that any circumscription of organisms that is based on an intensional definition (sensu Régine) would be excluded (and would instead be covered by the "Taxon" class). That is, if a set of organisms is defined by properties, rather than by specific members, it would be excluded from this class. Also excluded from this class would be an organism or set of organisms bounded by time or space. What I mean by this is that the temporal scope of an organism instance begins when the organism(s) is/are born, and ends when the organism(s) disintegrates (I didn't want to say "die", because a dead specimen is still an organism, in my option -- but a disintegrated specimen is not). Also, one cannot define an instance of organism dynamically via space and time, such as "all whales off Maui during the winter months", as the members would change year after year.
This reasoning would tend to exclude "population" from this class; but if population also is excluded from Taxon, then I don't know how one would represent an instance of a population via DwC. Surely there is an informatics need to track/monitor/analyze sets of organisms defined by "population". But how would one represent such a unit in DwC? If not as a Taxon, and not as an Organism, then how would one instantiate a "population" and assign properties to it? Another new class, perhaps? That would make me squeamish.
Incidentally, I have been using the term "Organism" consistently to refer to this class; but as I said previously, I am reasonably open-minded to what the term should be (as long as it doesn't include the word "taxon", and only if there is broad community consensus if it includes the words "Instance" or "Individual").
Aloha, Rich
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On Jul 19, 2011, at 8:26 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
Well, plenty of things are not in the class (Localities, dates, etc., etc.).
If we agree (do we?) that the class we seek to define is a subclass of biological entity, then I would assume that localities, dates, etc are already excluded. Hence, we only need to look at things that are biological entities, but that are to be excluded from the class (presumably because they are members of other disjoint sibling subclasses of biological entity).
But more specifically, I would say that any circumscription of organisms that is based on an intensional definition (sensu Régine) would be excluded (and would instead be covered by the "Taxon" class). That is, if a set of organisms is defined by properties, rather than by specific members, it would be excluded from this class.
A set defined by shared properties of its members is a class, not an instance.
Also excluded from this class would be an organism or set of organisms bounded by time or space. What I mean by this is that the temporal scope of an organism instance begins when the organism(s) is/are born, and ends when the organism(s) disintegrates
I'm confused by what exactly you mean by intensional definition. Above you say it is a circumscription of organisms, which isn't a biological entity (a circumscription of an organism is not an organism), and thus already excluded. But an organism bounded by space and time is an organism, and thus would be included if we include all organisms (but perhaps we don't?).
Maybe it's just me though - Bob seems to understand what you mean.
Also, one cannot define an instance of organism dynamically via space and time, such as "all whales off Maui during the winter months", as the members would change year after year.
This is a definition for a class (a set of instances) rather than giving examples of instances. We need the latter.
-hilmar
Sent with a tap.
Hi Rich - some comments inline below.
On Jul 17, 2011, at 8:43 AM, Richard Pyle deepreef@bishopmuseum.org wrote:
- A well-defined and enumerated set of whole organisms (pod of whales, pack
of wolves, etc.) documented in nature
What distinguishes well-defined from not well-defined? It sounds like this is relatively clear to you. It's not to me, and to see whether there is broad agreement, these things need to be spelled out. (One benefit from thinking about vocabularies in terms of ontologies is that this forces one to be specific and precise, which can help a lot in surfacing and pinpointing disagreements that need to be resolved.)
The preceding set requires some elaboration. For example, a herbarium specimen is usually a clipping or other small part of a larger whole plant. Often multiple clippings from the same individual plant are taken and preserved as separate herbarium specimens. Should there only be one instance of this class representing the whole plant? Or should there be multiple distinct instances of this class, one for each herbarium specimen?
Yes, depending on what roles they play. As you say, a tissue sample can serve as an evidence (as can presumably non-biological entities, too), or may be the specimen being observed.
Similarly, suppose the mammal skeleton and skin in the above list are from the same individual mammal. Would there be one instance of this class (for the whole organism), and the Skeleton and Skin be treated as instances of the Evidence class? Or, should there be two instances (one for the skin, one for the skeleton)? Or should there be three instances (one for the whole mammal organism, one for the preserved skin derived from it, and one for the preserved skeleton derived from it)?
My take is it would depend on what observation you are trying to represent, and hence which instance is the one being observed.
I would like to believe that all instances of Occurrence can be rooted into one instance of this proposed new class.
You may have meant something different, but just in case, instances aren't rooted, in the subsumption sense, in other instances. Only classes are.
-hilmar
Sent with a tap.
I realize that I had missed this email from Steve previously.
I don't understand why Rich says that the creation of this class
eliminates the
need for a class for "evidence". Perhaps he will elaborate when he has better email access.
I guess I'm confused about what the difference between "Evidence" and "Individual" is.
Ultimately, we want an Occurrence to represent the existence of a particular organism at a particular place and time (at least I *think* that's what we want???)
So, if an Event represents a Locality+Time, then an Occurrence serves to represent an Event+Organism.
An Organism is asserted to be a member of a Taxon, as established via an Identification instance. Thus, from Event+Organism, we can derive Event+Taxon (the Taxon inherited via an Organism linked to an Identification linked to a Taxon). Thus, people can get "Taxon at locality & time" through linking a set of instances of these classes (Locality, Event, Occurrence, Organism, Identification, Taxon).
The part I'm a little bit fuzzy on is were "Evidence" fits in to this model. If the function of "Evidence" is to represent proof of the Occurrence (i.e., that the indicated Organism actually was associated with the indicated Event), then I guess I can see the rationale and need for it. I'll need to keep thinking on this one a bit more, but as I write this email, and re-read Steve's earlier post, I'm beginning to get my head around it. But I'd still like to see exactly where it fits in the diagram. Also, does a literature citation of a particular organism at a particular place/time constitute a form of Evidence? Or is that simply captured as an Occurrence, without any tangible evidence (as, I imagine, an Observation would be captured)?
Aloha, Rich
In my haste to write my last post, I garbled up some of my wording.
I said:
An Organism is asserted to be a member of a Taxon, as established via an Identification instance. Thus, from Event+Organism, we can derive Event+Taxon (the Taxon inherited via an Organism linked to an Event+Identification linked to a Taxon).
That last parenthetical should have said:
"(the Taxon inherited via an Organism linked to an Identification)"
Rich
Hi Rich,
I guess I'm confused about what the difference between "Evidence" and "Individual" is. ... The part I'm a little bit fuzzy on is were "Evidence" fits in to this model. If the function of "Evidence" is to represent proof of the Occurrence (i.e., that the indicated Organism actually was associated with the indicated Event), then I guess I can see the rationale and need for it. I'll need to keep thinking on this one a bit more, but as I write this email, and re-read Steve's earlier post, I'm beginning to get my head around it. But I'd still like to see exactly where it fits in the diagram.
Again, for a diagram, please refer to the image on:
http://code.google.com/p/darwin-sw/
Steve and I used `Token' as the class name for anything that provides evidence of a dwc:Occurrence. The Token could be an image, a dried specimen, or...
Also, does a literature citation of a particular organism at a particular place/time constitute a form of Evidence? Or is that simply captured as an Occurrence, without any tangible evidence (as, I imagine, an Observation would be captured)?
... an Observation. I see a literature citation as documentation of an Observation, which provides evidence for an occurrence. If we wanted to integrate Darwin-SW, or even DwC with existing observational ontologies (e.g. OBOE, https://semtools.ecoinformatics.org/oboe), we could allow an oboe:Observation to also be a Token, providing evidence for a dwc:Occurrence.
Please see the discussion of Token at:
http://code.google.com/p/darwin-sw/wiki/ClassToken
Best,
Cam
Thanks, Cam -- this is helpful.
Again, for a diagram, please refer to the image on:
http://code.google.com/p/darwin-sw/
Steve and I used `Token' as the class name for anything that provides evidence of a dwc:Occurrence. The Token could be an image, a dried specimen, or...
OK, I think that answers my question, then. It's intended as evidence of the Occurrence of an Organism at a Place & time (=Event), not simply evidence that the organism exists/existed. In that case, yes: Evidence is quite distinct from Organism. I guess I was thinking too much in terms of specimen, where the evidence *is* the organism. I guess there may be other forms of Evidence as well, such as an electronic tracking tag attached to an organism. This sort of evidence would not help identify the taxon of the organism (as an image and specimen would), but it would certainly represent evidence of an Organism at a place & time. But I see in your diagram (took me ten minutes to open that page from here), that you have a relationship between Token and Identification. I'm assuming that's not a mandatory relationship -- i.e., it would only apply to the subset of Tokens (Evidence instances) that provide taxonomically useful information (which an electronic tracking tag would not).
Also, does a literature citation of a particular organism at a particular place/time constitute a form of Evidence? Or is that simply captured as an Occurrence, without any tangible evidence (as, I imagine, an Observation would be captured)?
... an Observation. I see a literature citation as documentation of an Observation, which provides evidence for an occurrence. If we wanted to integrate Darwin-SW, or even DwC with existing observational ontologies (e.g. OBOE, https://semtools.ecoinformatics.org/oboe), we could allow an oboe:Observation to also be a Token, providing evidence for a dwc:Occurrence.
OK, I can see that. A literature citation could include an image, and could include reference to a specimen, but I suppose in that case the image and the specimen would then each stand alone as their own instance of Evidence (independent of the literature citation), in which case the literature citation becomes effectively the same as a specimen label or a slip of paper documenting an observation record (i.e., Documentation of Evidence, rather than Evidence per se).
Please see the discussion of Token at:
Alas, my internet connection is too slow, so I'll look at it when I get home. You've certainly cleared up my confusion with respect to the respective roles of Evidence and Organism [=Individual], and I fully agree they are fundamentally different.
Aloha, Rich
participants (13)
-
Bob Morris -
Cam Webb -
Chuck Miller -
Gregor Hagedorn -
Hilmar Lapp -
John Wieczorek -
Markus Döring -
Nico Cellinese -
Paul Murray -
Peter DeVries -
Richard Pyle -
Régine Vignes Lebbe -
Steven J. Baskauf