[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
Richard Pyle
deepreef at bishopmuseum.org
Wed Sep 14 20:17:59 CEST 2011
Count me satisfied as well! (Thanks, John , for the answer to my query on
ResourceRelationship, which I both understand, and fully agree with).
2/10
Aloha,
Rich
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-
> bounces at lists.tdwg.org] On Behalf Of Kevin Richards
> Sent: Tuesday, September 13, 2011 10:40 AM
> To: tuco at 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 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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> >
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