[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review

Richard Pyle deepreef at bishopmuseum.org
Fri Sep 9 01:01:50 CEST 2011


This is *exactly* what I'm talking about.  What is dwc:ResourceRelationship
for, if not exactly what Kevin is discussing below?

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: Thursday, September 08, 2011 11:20 AM
> To: tuco at berkeley.edu; TDWG Content Mailing List
> Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects:
> a review
> 
> 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).
> 
> 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
> 
> 
> 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?
> 
> 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/AssociatedUnitS
> ourceInstitutionCode
> + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni
> + tSourceName
> + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni
> + 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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