September 2011 - tdwg-content

An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

3 5

Occurrences, Organisms, and CollectionObjects: a review
by John Wieczorek 19 Sep '11

19 Sep '11

Dear all, Prepare yourself mentally. After more than a year of discussions, prototypes, scholarly papers, bar room brawls, etc., we are very near having a path forward for two new, related classes for Darwin Core that attempt to remove ambiguity inherent in the Occurrence class as it currently stands. Adding classes is quite a bit more complicated than adding properties (as you'll see if you manage to get through this message), and so it is important to be as thorough as possible to make sure we get it right. I'll try here to synthesize the rough consensus and the remaining issues. Basically, the idea is to pull two distinct concepts out of Occurrence and give them their own classes. Maybe not surprisingly, one of the hardest things to agree upon has been the names for these classes. The class that was proposed first as "Individual" has seen no less than 12 alternate names, none of them satisfying to everyone. The closest thing to an acceptable name was "Organism", with caveats that the definition should make it abundantly clear what is to be included in the class and what is not. I'll use "Organism" here to refer to the class in the hopes of offending the fewest people. The rough consensus on "Organism" is that is should include viruses, symbionts, individuals, colonies, groups of individuals, and even populations, but that there should be taxonomic homogeneity to an instance of an "Organism". There has been some concern about how and where to draw the line on homogeneity. No attempt has yet been made to write a definitive description of the class, though many examples of representatives of the class have been given. What we need to move forward on the "Organism" class are an official definition and an official comment, the combination of which should be sufficient for someone previously unfamiliar with the term and the arguments leading to its existence to understand. Some existing terms (individualCount, sex, lifeStage, reproductiveCondition, behavior, previousIdentifications, associatedTaxa) will have to be reorganized to be under this new class. These terms may require updated definitions for consistency. New terms (organismID, associatedOrganisms, organismRemarks) and an Organism Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "Organism" class: Term Name: Organism Identifier: http://rs.tdwg.org/dwc/terms/Organism Namespace: http://rs.tdwg.org/dwc/terms/ Label: Organism Definition: The category of information pertaining to a specific instance of an organism (virus, symbiont, individual, colony, group of individuals, population) reliably be known to taxonomically homogeneous. Comment: For discussion see http://code.google.com/p/darwincore/wiki/Organism Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: Organism-2011-09-09 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: Organism Identifier: http://rs.tdwg.org/dwc/dwctype/Organism Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: Organism Definition: A resource describing an instance of the Organism 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: 2011-09-09 Date Modified: 2011-09-00 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: Organism-2011-09-09 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD Term Name: organismID Identifier: http://rs.tdwg.org/dwc/terms/organismID Namespace: http://rs.tdwg.org/dwc/terms/ Label: organismID Definition: An identifier for the set of information associated with an Organism. 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: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: organismID-2011-09-09 Replaces: individualID-2009-09-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/UnitID Term Name: organismRemarks Identifier: http://rs.tdwg.org/dwc/terms/organismRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: organismRemarks Definition: Comments or notes about the Organism. 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: 2011-09-09 Date Modified: 2009-09-09 Has Domain: Has Range: Version: organismRemarks-2011-09-09 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/Notes Term Name: associatedOrganisms Identifier: http://rs.tdwg.org/dwc/terms/associatedOrganisms Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedOrganisms Definition: A list (concatenated and separated) of identifiers of other Organism records and their associations to this Organism. Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/Organism Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: associatedOrganisms-2011-09-09 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID The class proposed as "CollectionObject" has seen fewer alternate name proposals than "Organism", but the same call for clarity on inclusion and exclusion has been voiced. The basic idea is to use this class to cover information that could be considered "persistent evidence" that an organism occurred, and that the concept is distinct from both "Organism" and Occurrence. Evidence might include collection-based materials, digital media, written materials, and literature. "Evidence" may be a bit vague as a name for the class, providing no real indication that the "Evidence" should apply to an "Organism" rather than to an Occurrence, Taxon, Identification, or any other class. Nor does it convey the idea that the evidence should be persistent. "PersistentEvidenceThatAnOrganismExisted" gets the idea across pretty well, but it is a bit lengthy (and no one actually proposed this name). ABCD isn't shy about vague term names - it uses "Unit" for roughly this concept. The long-standing term "CollectionObject" is less vague than the proposed alternatives, but it might lead people to assume that the object must be physical, and that it must be housed within a collection, neither of which is strictly required. No one objected to this name for the term, however, so I will continue to use it here to illustrate the proposed changes and additions to accommodate this concept. Some existing terms (institutionID, institutionCode, collectionID, collectionCode, ownerInstitutionCode, catalogNumber, preparations, disposition, otherCatalogNumbers, associatedSequences) will have to be organized under this new class. These terms may require updated definitions for consistency. Note that with the addition of the "CollectionObject" class, the institutionCode, collectionCode, catalogNumber triplet would no longer apply to an Occurrence. New terms (collectionObjectID and collectionObjectRemarks) and an CollectionObject Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "CollectionObject" class: Term Name: CollectionObject Identifier: http://rs.tdwg.org/dwc/terms/CollectionObject Namespace: http://rs.tdwg.org/dwc/terms/ Label: CollectionObject Definition: The category of information pertaining to persistent evidence that an organism existed (specimen, sample, image, sound, drawing, field notes, publication), including digital forms. Comment: For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: CollectionObject-2011-09-09 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: CollectionObject Identifier: http://rs.tdwg.org/dwc/dwctype/CollectionObject Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: CollectionObject Definition: A resource describing an instance of the CollectionObject 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: 2011-09-09 Date Modified: 2011-09-09 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: CollectionObject-2011-09-09 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD Term Name: collectionObjectID Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectID Namespace: http://rs.tdwg.org/dwc/terms/ Label: collectionObjectID Definition: An identifier for the CollectionObject. 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 collectionObjectID globally unique. Comment: For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". 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: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: collectionObjectID-2011-09-09 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/CollectionObject ABCD 2.06: DataSets/DataSet/Units/Unit/UnitGUID Term Name: collectionObjectRemarks Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: collectionObjectRemarks Definition: Comments or notes about the CollectionObject. Comment: Example: "custody transferred in 1995 from National Park Service". 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: 2011-09-09 Date Modified: 2009-09-09 Has Domain: Has Range: Version: collectionObjectRemarks-2011-09-09 Replaces: SampleRemarks-2009-01-18 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/CollectionObject ABCD 2.06: DataSets/DataSet/Units/Unit/Notes Because of these changes for "Organism" and "CollectionObject", the definition of the Occurrence class will have to change and quite a different set of terms organized under it, namely: occurrenceID, occurrenceRemarks, recordNumber, recordedBy, establishmentMeans, and occurrenceStatus The Occurrence definition will change from "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)." to something more akin to "The category of information pertaining to evidence of an occurrence of an Organism in nature." The term occurrenceDetails will be deprecated in favor of the Dublin Core term dcterms:references at the record level. Also, associatedMedia, which was organized under Occurrence, would become a record level term, as it could apply as easily to Occurrences, "Organisms", and "CollectionObjects". If you made it this far, I congratulate you on your dedication to the cause. Please let's clear up the remaining issues as a community and put these new terms to good use. Cheers, John

14 51

Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
by Chuck Miller 18 Sep '11

18 Sep '11

"the [controlled] vocabularies can be quite dynamic, variable, and/or contentious" Indeed they can. But, avoiding them I think is not the solution for the community. Avoiding them proliferates even more dynamics, variability and contention. However, the standardization of controlled vocabularies needs to be a separate activity, one that TDWG has been somewhat absent from of late and one we need to add to the mix of issues for TDWG to address. I suspect there is a lot of programming time being spent on discovering the dynamics and variability of the vocabularies currently in use and remediating them repeatedly in separate and far corners of the world. Even some small effort to consolidate a few variations or at least sort them out once rather than repeatedly by every new programmer that comes into this community would be beneficial to the biodiversity informatics world. Chuck -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Tuesday, September 13, 2011 3:40 PM To: tuco(a)berkeley.edu Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review Thanks John, the ResourceRelationship does satisfy my concerns! 1 person satisfied, 10 to go. :-) Kevin -----Original Message----- From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Wednesday, 14 September 2011 8:22 a.m. To: Kevin Richards Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review Let's see if I can catch up. On Thu, Sep 8, 2011 at 2:20 PM, Kevin Richards <RichardsK(a)landcareresearch.co.nz> wrote: > Great job John. > > 1 comment - I feel a little uncomfortable about the unstructured nature of the associatedOrganisms term. If I was writing some software to read and import some DwC data, I would be interested in capturing the associations that have been defined (in some structured way). I understand your discomfort. That proposed term is to take the place of the corresponding associatedOccurrences. As with the other "associatedX" terms, it is meant to allow useful information to be retained as part of flat records, not necessarily to be rigorously interpretable for the contents of the list, which would require data content standards as well. > There is possibly a few ways to improve this: > - define a structured way of filling this field, eg "[relationship type (from controlled vocabulary), eg host]:[related Organism ID]" > - add another field for just associatedOrganismIDs, that just has the > IDs and not free form text - not sure how this will help though > - add another class for AssociatedOrganism, that has fromOrganismID, > toOrganismID and relationshipType This is really the realm of more relational representations, in which you could use the ResourceRelationship class to good effect. > I also notice with a few of the DwC terms that it is recommended to use a controlled vocabulary for setting the value of the term, but the controlled vocabulary itself is not provided. Is it not the place for the DwC vocabulary to provide these? Or has the work just not been done to define them? No Darwin Core term enforces controlled vocabularies. Only recommendations are made, and that's on purpose. One of the biggest reasons is that the vocabularies can be quite dynamic, variable, and/or contentious, and we did not want that distraction in the management of the Darwin Core terms. > Kevin > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of John > Wieczorek > Sent: Thursday, 8 September 2011 1:05 p.m. > To: TDWG Content Mailing List > Subject: [tdwg-content] Occurrences, Organisms, and CollectionObjects: > a review > > Dear all, > > Prepare yourself mentally. After more than a year of discussions, prototypes, scholarly papers, bar room brawls, etc., we are very near having a path forward for two new, related classes for Darwin Core that attempt to remove ambiguity inherent in the Occurrence class as it currently stands. Adding classes is quite a bit more complicated than adding properties (as you'll see if you manage to get through this message), and so it is important to be as thorough as possible to make sure we get it right. I'll try here to synthesize the rough consensus and the remaining issues. > > Basically, the idea is to pull two distinct concepts out of Occurrence and give them their own classes. > Maybe not surprisingly, one of the hardest things to agree upon has been the names for these classes. The class that was proposed first as "Individual" has seen no less than 12 alternate names, none of them satisfying to everyone. The closest thing to an acceptable name was "Organism", with caveats that the definition should make it abundantly clear what is to be included in the class and what is not. I'll use "Organism" here to refer to the class in the hopes of offending the fewest people. > > The rough consensus on "Organism" is that is should include viruses, symbionts, individuals, colonies, groups of individuals, and even populations, but that there should be taxonomic homogeneity to an instance of an "Organism". There has been some concern about how and where to draw the line on homogeneity. No attempt has yet been made to write a definitive description of the class, though many examples of representatives of the class have been given. > > What we need to move forward on the "Organism" class are an official definition and an official comment, the combination of which should be sufficient for someone previously unfamiliar with the term and the arguments leading to its existence to understand. Some existing terms (individualCount, sex, lifeStage, reproductiveCondition, behavior, previousIdentifications, associatedTaxa) will have to be reorganized to be under this new class. These terms may require updated definitions for consistency. New terms (organismID, associatedOrganisms, organismRemarks) and an Organism Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "Organism" > class: > > Term Name: Organism > Identifier: http://rs.tdwg.org/dwc/terms/Organism > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Organism > Definition: The category of information pertaining to a specific > instance of an organism (virus, symbiont, individual, colony, group of individuals, population) reliably be known to taxonomically homogeneous. > Comment: For discussion see > http://code.google.com/p/darwincore/wiki/Organism > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: Organism-2011-09-09 > 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: Organism > Identifier: http://rs.tdwg.org/dwc/dwctype/Organism > Namespace: http://rs.tdwg.org/dwc/dwctype/ > Label: Organism > Definition: A resource describing an instance of the Organism 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: 2011-09-09 > Date Modified: 2011-09-00 > Member Of: http://rs.tdwg.org/dwc/terms/DwCType > Has Domain: > Has Range: > Version: Organism-2011-09-09 > Replaces: > Is Replaced By: > Class: > ABCD 2.06: not in ABCD > > Term Name: organismID > Identifier: http://rs.tdwg.org/dwc/terms/organismID > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: organismID > Definition: An identifier for the set of information associated > with an Organism. 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: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: organismID-2011-09-09 > Replaces: individualID-2009-09-24 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: DataSets/DataSet/Units/Unit/UnitID > > Term Name: organismRemarks > Identifier: http://rs.tdwg.org/dwc/terms/organismRemarks > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: organismRemarks > Definition: Comments or notes about the Organism. > 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: 2011-09-09 > Date Modified: 2009-09-09 > Has Domain: > Has Range: > Version: organismRemarks-2011-09-09 > Replaces: > Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: DataSets/DataSet/Units/Unit/Notes > > Term Name: associatedOrganisms > Identifier: http://rs.tdwg.org/dwc/terms/associatedOrganisms > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: associatedOrganisms > Definition: A list (concatenated and separated) of identifiers of > other Organism records and their associations to this Organism. > Comment: Example: "sibling of MXA-231; sibling of MXA-232". For > discussion see http://code.google.com/p/darwincore/wiki/Organism > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: associatedOrganisms-2011-09-09 > Replaces: associatedOccurrences-2009-04-24 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: > DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni > tSourceInstitutionCode > + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedU > + ni > + tSourceName > + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedU > + ni > + tID > > > The class proposed as "CollectionObject" has seen fewer alternate name proposals than "Organism", but the same call for clarity on inclusion and exclusion has been voiced. The basic idea is to use this class to cover information that could be considered "persistent evidence" that an organism occurred, and that the concept is distinct from both "Organism" and Occurrence. Evidence might include collection-based materials, digital media, written materials, and literature. > > "Evidence" may be a bit vague as a name for the class, providing no real indication that the "Evidence" should apply to an "Organism" > rather than to an Occurrence, Taxon, Identification, or any other class. Nor does it convey the idea that the evidence should be persistent. "PersistentEvidenceThatAnOrganismExisted" gets the idea across pretty well, but it is a bit lengthy (and no one actually proposed this name). ABCD isn't shy about vague term names - it uses "Unit" for roughly this concept. The long-standing term "CollectionObject" is less vague than the proposed alternatives, but it might lead people to assume that the object must be physical, and that it must be housed within a collection, neither of which is strictly required. No one objected to this name for the term, however, so I will continue to use it here to illustrate the proposed changes and additions to accommodate this concept. > > Some existing terms (institutionID, institutionCode, collectionID, collectionCode, ownerInstitutionCode, catalogNumber, preparations, disposition, otherCatalogNumbers, associatedSequences) will have to be organized under this new class. These terms may require updated definitions for consistency. Note that with the addition of the "CollectionObject" class, the institutionCode, collectionCode, catalogNumber triplet would no longer apply to an Occurrence. > > New terms (collectionObjectID and collectionObjectRemarks) and an CollectionObject Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "CollectionObject" class: > > Term Name: CollectionObject > Identifier: http://rs.tdwg.org/dwc/terms/CollectionObject > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: CollectionObject > Definition: The category of information pertaining to persistent > evidence that an organism existed (specimen, sample, image, sound, drawing, field notes, publication), including digital forms. > Comment: For discussion see > http://code.google.com/p/darwincore/wiki/CollectionObject > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: CollectionObject-2011-09-09 > 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: CollectionObject > Identifier: http://rs.tdwg.org/dwc/dwctype/CollectionObject > Namespace: http://rs.tdwg.org/dwc/dwctype/ > Label: CollectionObject > Definition: A resource describing an instance of the CollectionObject 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: 2011-09-09 > Date Modified: 2011-09-09 > Member Of: http://rs.tdwg.org/dwc/terms/DwCType > Has Domain: > Has Range: > Version: CollectionObject-2011-09-09 > Replaces: > Is Replaced By: > Class: > ABCD 2.06: not in ABCD > > Term Name: collectionObjectID > Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectID > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: collectionObjectID > Definition: An identifier for the CollectionObject. 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 collectionObjectID globally unique. > Comment: For a specimen in the absence of a bona fide global > unique identifier, for example, use the form: > "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. > Examples: "urn:lsid:nhm.ku.edu:Herps:32", > "urn:catalog:FMNH:Mammal:145732". 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: http://purl.org/dc/terms/identifier > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: collectionObjectID-2011-09-09 > Replaces: > Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/CollectionObject > ABCD 2.06: DataSets/DataSet/Units/Unit/UnitGUID > > Term Name: collectionObjectRemarks > Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectRemarks > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: collectionObjectRemarks > Definition: Comments or notes about the CollectionObject. > Comment: Example: "custody transferred in 1995 from National > Park Service". 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: 2011-09-09 > Date Modified: 2009-09-09 > Has Domain: > Has Range: > Version: collectionObjectRemarks-2011-09-09 > Replaces: SampleRemarks-2009-01-18 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/CollectionObject > ABCD 2.06: DataSets/DataSet/Units/Unit/Notes > > > Because of these changes for "Organism" and "CollectionObject", the definition of the Occurrence class will have to change and quite a different set of terms organized under it, namely: > > occurrenceID, occurrenceRemarks, recordNumber, recordedBy, > establishmentMeans, and occurrenceStatus > > The Occurrence definition will change from "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)." to something more akin to "The category of information pertaining to evidence of an occurrence of an Organism in nature." > > The term occurrenceDetails will be deprecated in favor of the Dublin Core term dcterms:references at the record level. Also, associatedMedia, which was organized under Occurrence, would become a record level term, as it could apply as easily to Occurrences, "Organisms", and "CollectionObjects". > > If you made it this far, I congratulate you on your dedication to the cause. Please let's clear up the remaining issues as a community and put these new terms to good use. > > Cheers, > > John > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > Please consider the environment before printing this email > Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. > The views expressed in this email may not be those of Landcare > Research New Zealand Limited. http://www.landcareresearch.co.nz > Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

2 1

Inclusion of geo:lat, geo:long, geo:alt in Darwin Core unresolved
by John Wieczorek 15 Sep '11

15 Sep '11

Dear all, I have reviewed both the recent and ancient discussions regarding the proposal to include geo:lat, geo:long, and geo:alt among the recommended terms from Darwin Core. This particular proposal is not being voted on for inclusion by the TAG at this point, because further research has revealed some issues that need to be addressed. I'll include here the issues I raised to the TAG in the hope of stimulating further discussion in pursuit of a public consensus. The proposal is to recommend the inclusion of the terms from the geo: namespace (xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#"). Support in tdwg-content for this request comes from multiple independent sources. There has been a long history of discussion (http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/000050.html), beginning in anticipation of the 2010 TDWG BioBlitz. The proposal has gone through the minimum 30-day public review and discussion on the forum tdwg-content at lists.tdwg.org: http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002581.html There seems to be general support for the additions. However, after reviewing the discussions and the references. I have the following observations/concerns: 1) The discussions presented geo:lat and geo:long as W3C standards. This is not actually the case. These terms were created by the W3C Semantic Web Interest Group in 2003. The documentation for these terms (http://www.w3.org/2003/01/geo/) states: "This document was created as an informal collaboration within W3C's Semantic Web Interest Group. This work is not currently on the W3C recommendation track for standardization, and has not been subject to the associated review process, quality assurance, etc. If there is interest amongst the W3C membership in standards work on a location/mapping RDF vocabulary, this current work may inform any more formal efforts to follow." These terms do seem to have widespread usage in the semantic web. Should we be concerned that they are not part of a standard? 2) geo:lat and geo:long are not semantically equivalent to the existing Darwin Core terms decimalLatitude and decimalLongitude, which have been a part of the Darwin Core since it 2003 (or before, if we ignore the missing Datum term in earlier versions). The addition of the geo: terms as a third set of geolocation terms for Darwin Core raised concerns about confusion, having so many spatially-related terms. I share this concern. An option would be to adopt these terms and deprecate dwc:decimalLatitude, dwc:Longitude, and dwc:geodeticDatum. Data that would have occupied these terms would go instead to dwc:verbatimLatitude dwc:verbatimLongitude, and dwc:verbatimSRS. I see a couple of problems with this. First, most of the time the data in the decimal coordinate fields are not the verbatim originals, so this would be a misuse of the Darwin Core terms. Second, this change would make it more difficult for data consumer’s to use existing georeferences. Here’s how. Right now the verbatim fields are meant to hold the original coordinate information, which means they have a wide variety of content - everything from UTMs to custom-encoded coordinates, in any conceivable format. Meanwhile, the data in the decimal coordinates fields can be much more readily transformed into the desired standardized spatial reference system afforded by the geo: terms, because the values are at least standardized on geographic coordinates in decimal degrees and only a datum transformation has to be done on them to get geo_lat and geo:long. Do we abandon the dwc: terms decimalLatitude, decimalLongitude, and geodeticDatum? Do we abandon them now? Do we build the simplest possible tools necessary for anyone to do the transformations so that these terms are no longer needed? If so, do we wait until those tools exist before we abandon the terms and make millions of georeferenced records less readily usable? 3) A request was expressed by one reviewer that the term geo:alt should be added. No one has made a formal request for this. However, if the other geo: terms were adopted, it might be silly not to adopt this one as well. Doing so would raise a host of issues similar to those raised for lat and lng, but related to the Darwin Core elevation terms. No discussion of these issues has yet taken place. Cheers, John

3 2

Purpose of ResourceRelationship
by Richard Pyle 13 Sep '11

13 Sep '11

On a separate but related issue, I don't think I ever received any feedback on my question some months back regarding the scope of function of the ResourceRelationship class in DwC. I suspect that hardly anyone is using it, and I get the sense that most people assume that it is intended to allow cross-linking instances of DwC classes with objects external to DwC-class items. However, in my mind it serves as the *perfect* mechanism to cross-link instances of DwC classes to each other (e.g., an Occurrence to an Event; an Identification to a Taxon and Organism; a Location to an Event; etc., etc.). It also seems to me to be the perfect mechanism to represent recursive links within a Class. It's this last bit that John's recent email reminded me of. To wit: > Term Name: associatedOrganisms > Identifier: http://rs.tdwg.org/dwc/terms/associatedOrganisms > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: associatedOrganisms > Definition: A list (concatenated and separated) of identifiers of > other Organism records and their associations to this Organism. > Comment: Example: "sibling of MXA-231; sibling of MXA-232". ... as well as associatedOccurrences, associatedTaxa, and possibly other "associated[xxxxx]" terms... Shouldn't these "associations" among instances between and within DwC classes be represented as series of ResourceRelationship instances? Is this not the intended purpose for ResourceRelationship? Or, is it the intended purposes, but the various "associated[xxxx]" terms are there in order to provide a "flattened" or "denormalized" concatenation of identifiers? Aloha, Rich

2 1

dwc: relating dwc:Identification objects to dwc:Taxon objects
by Bob Morris 12 Sep '11

12 Sep '11

As far as I understand for DwC, in order to associate a dwc:Identification with a dwc:Occurrence we need to define a dwc:ResourceRelation analogous to http://rs.tdwg.org/ontology/voc/OccurrenceRecord#identifiedTo (The context is the building of examples of data annotations for the data extensions to the W3 incubation group document Annotation Ontology http://code.google.com/p/annotation-ontology/). The examples will be RDF). a. Am I right? b. Is there one already blessed by TAG? c. If b. is "No", does it make sense to put one on the table? -- 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(a)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)

3 4

multiplicity whine about DwC
by Bob Morris 10 Sep '11

10 Sep '11

Warning: technical DwC whine I am attempting to use DwC in RDF to model something that is functionally like the predicate lsidvoc:identifiesTo in the LSID vocabularies. If I understand correctly, in DwC I must start with an \instance/ of dwc:ResourceRelationship, lets call it x:identifiesTo and use its dwc:resourceID to provide the source Identification and its dwc:relatedResourceID to provide the instance's object Taxon. The problem is, you can't use the same instance x:identifiesTo for two different (Identification, Taxon) pairs because you won't be able to tell which Identification goes with which Taxon. A little more precisely, if you don't have another instance of dwc:Resource Relationship, you will have: x:identifiesTo rdf:type dwc:ResourceRelationship x:identifiesTo dwc:resourceID Identification1 x:identifiesTo dwc:relatedResoruce Taxon1 x:identifiesTo dwc:resourceID identification2 x:identifiesTo dwc:relatedResourceID Taxon2 (This is a generic multiplicity problem about RDF vocabularies that mean to support flat implementation. In some context recently I made that observation on this list. If I were as careful as Steve B I'd go back to the record, find out where and cite it :-) . But I have to rush off and go collect a few weeds from my lawn and get off to a weekend course on botanical printing on fabric sponsored in part by the Arnold Arboretum !) Probably the only solution is to introduce a real predicate outside of DwC that actually looks like lsidvoc:identifiesTo so the graph looks like x:identifiesTo rdf:type rdfs:Property Identification1 x:identifiesTo Taxon1 Identification2 x:identifiesTo Taxon2 This is essentially the approach of http://code.google.com/p/darwin-sw/. Even this has some implementation issues in an environment where you are facing some RDF that has vocabulary from an ontology named by a URI that you can't resolve, which is what we are exploring in the FilteredPush project about the management of annotations of data. I'd love to be shown why I am wrong about the non-reusability of a dwc:ResourceRelation, or whether there is a different way to solve problems like this in DwC Bob Morris -- 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(a)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)

1 0

Re: [tdwg-content] [tdwg-tag] DwC change review: geo terms
by Hilmar Lapp 09 Sep '11

09 Sep '11

(Sorry if you receive this twice - John asked to repost here.) Where is adopting these terms now going to put us with respect to OGC standards, which, I think, will ultimately be more authoritative than an informal W3C vocabulary. I don't have enough insight into OGC standards for vocabularies for describing geolocations, but I have also learned earlier this year from Flip Dibner (copied here) that there are efforts underway within OGC to create RDF vocabularies (presumably corresponding to OGC's XML standards?). -hilmar On Sep 6, 2011, at 6:33 PM, Javier de la Torre wrote: > Hi John, > > As you mention from previous discussion I would still adopt option > number 1 as I believe there is enough tools out there to handle > transformations. The current situation I think is much worst on the > consumer part and I think is time to think more on data use than on > data mobilization. > > Best, > > Javier. > > On 07/09/2011, at 00:00, John Wieczorek <tuco(a)berkeley.edu> wrote: > >> Perhaps my message was too long for easy digestion and action, as >> I've >> received no responses. I will take the initiative to initiate option >> 3. No further action from the TAG on this at this point. Be prepared >> though, VOTES by the TAG on publicly resolved issues are forthcoming >> very soon. >> >> On Sat, Sep 3, 2011 at 9:34 AM, John Wieczorek <tuco(a)berkeley.edu> >> wrote: >>> Hi TAGers, >>> >>> I am deep in the review process for the proposed changes to Darwin >>> Core, trying to do due diligence. Some of the change requests are >>> challenging to summarize to determine if there is consensus, in >>> spite >>> of, or because of the discussions. One of the requests on which I’d >>> like some TAG help before proposing a solution is the request for >>> the >>> inclusion of the terms from the geo: namespace >>> (xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#"). >>> >>> Support in tdwg-content for this request comes from multiple >>> independent sources. There has been a long history of discussion >>> (http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/000050.html), >>> beginning in anticipation of the 2010 TDWG BioBlitz. The proposal >>> has >>> gone through the minimum 30-day public review and discussion on the >>> forum tdwg-content(a)lists.tdwg.org: >>> >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002581.html >>> >>> There seems to be general support for the additions, however, after >>> reviewing the discussions and the references. I have the following >>> observations/concerns: >>> >>> 1) The discussions presented geo:lat and geo:lng as W3C standards. >>> This is not actually the case. These terms were created by the W3C >>> Semantic Web Interest Group in 2003. The documentation for these >>> terms >>> (http://www.w3.org/2003/01/geo/) states: >>> >>> "This document was created as an informal collaboration within W3C's >>> Semantic Web Interest Group. This work is not currently on the W3C >>> recommendation track for standardization, and has not been subject >>> to >>> the associated review process, quality assurance, etc. If there is >>> interest amongst the W3C membership in standards work on a >>> location/mapping RDF vocabulary, this current work may inform any >>> more >>> formal efforts to follow." >>> >>> These terms do seem to have widespread usage in the semantic web. >>> Should we be concerned that they are not part of a standard? >>> >>> 2) geo:lat and geo:lng are not semantically equivalent to the >>> existing >>> Darwin Core terms decimalLatitude and decimalLongitude, which have >>> been a part of the Darwin Core since it 2003 (or before, if we >>> ignore >>> the missing Datum term in earlier versions). The addition of the >>> geo: >>> terms as a third set of geolocation terms for Darwin Core raised >>> concerns about confusion. I share this concern. An option would be >>> to >>> adopt these terms and deprecate dwc:decimalLatitude, dwc:Longitude, >>> and dwc:geodeticDatum. Data that would have occupied these terms >>> would >>> go instead to dwc:verbatimLatitude dwc:verbatimLongitude, and >>> dwc:verbatimSRS. I see a couple of problems with this. First, most >>> of >>> the time the data in the decimal coordinate fields are not the >>> verbatim originals, so this would be a misuse of the Darwin Core >>> terms. Second, this change would make it more difficult for data >>> consumer’s to use existing georeferences. Here’s how. Right now the >>> verbatim fields are meant to hold the original coordinate >>> information, >>> which means they have a wide variety of content - everything from >>> UTMs >>> to custom-encoded coordinates, in any conceivable format. Meanwhile, >>> the data in the decimal coordinates fields can be much more readily >>> transformed into the desired standardized spatial reference system >>> afforded by the geo: terms, because the values are at least >>> standardized on decimal degrees and only a datum transformation >>> has to >>> be done on them. >>> >>> Do we abandon the dwc: terms decimalLatitude, decimalLongitude, and >>> geodeticDatum? Do we abandon them now? Do we build the simplest >>> possible tools necessary for anyone to do the transformations so >>> that >>> these terms are no longer needed? If so, do we wait until those >>> tools >>> exist? >>> >>> 3) Additional concern was expressed that the term geo:alt should >>> also >>> be added. No one has made a formal request for this. However, if the >>> other geo: terms were adopted, it might be silly not to adopt this >>> one >>> as well. Doing so would raise a host of issues similar to those >>> raised >>> for lat and lng. >>> >>> I don’t have a good solution. The best short-term one, in my >>> opinion, >>> is to leave Darwin Core as it is, and to recommend that if >>> applications (or aggregators) want to share “cleansed” point-based >>> georeferences, that they do so with the geo: tags, the values for >>> which they derive through transformations to WGS84 of the DwC >>> decimal >>> coordinates and geodeticDatum. >>> >>> Options: >>> >>> 1) Accept the proposal, adding geo:lat, geo:lng, and geo:alt to the >>> list of recommended terms for DwC. >>> >>> 2) Reject the proposal pending further directed research into a >>> comprehensive solution that considers all geospatial terms in Darwin >>> Core (including footprintWKT, for example). >>> >>> 3) Reject the proposal for now, reopening the public discussion with >>> these concerns. >>> >>> Others? >>> >> _______________________________________________ >> tdwg-tag mailing list >> tdwg-tag(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-tag > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

3 5