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

Thu Sep 8 03:04:38 CEST 2011

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