[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
Kevin Richards
RichardsK at landcareresearch.co.nz
Tue Sep 13 22:39:58 CEST 2011
Thanks John, the ResourceRelationship does satisfy my concerns!
1 person satisfied, 10 to go. :-)
Kevin
-----Original Message-----
From: gtuco.btuco at gmail.com [mailto:gtuco.btuco at 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 at 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 at lists.tdwg.org
> [mailto:tdwg-content-bounces at 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
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