[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review [SEC=UNCLASSIFIED]
greg whitbread
ghw at anbg.gov.au
Tue Sep 13 16:32:20 CEST 2011
One of the problems with living on the other side of the world is the
difficulty with getting
a word into the appropriate place in a conversation that has been
raging all night. Usually
I tend to sigh and just let it pass - taking note of your various
positions and simply trying
to live with the consequences. But I do need to comment here.
The current debate reminds me a little of one of Bob's favourite
theorems - if we had an organism we could make an occurrence - if we
had a taxon. Darwin Core began its life as an flattened set of
standardized biodiversity data access points employed at the
aggregation and interrogation of content from built for purpose
[collection] metadata systems. The use case here was to provide
standardized content for value added projects with a focus on
occurrence that could benefit from the large datasets that it made
possible. This "Occurrence" was an abstraction derived from point in
time sampling from our collection metadata repositories using
"current" determinations. We do not build occurrence systems.
At the back end, in the real world, our use cases evolve from
requirements that we manage collections of biodiversity content (...,
individuals, parts, impressions, cultures, molecules, observations,
events, images, names, taxa, citations and annotation histories) as a
resource for scientific inquiry and research and for the development
of practical tools for biodiversity management and data interchange.
Without these efforts toward establishment of taxonomic hypotheses the
very concept of "occurrence" is meaningless.
So, to me, it now seems a little absurd that with a bit of tweaking
and classing the TDWG Domain Model might be derivable from this
"occurrence" set. Darwin Core is extremely useful as a vocabulary. It
is beautifully documented and entirely suited to its aggregation use
case. It has been taken up in many quarters. The last thing we should
be thinking about now is how to set about breaking it.
A workable domain model deserves to be a high priority with
Interoperability across our standard offerings a primary goal. Roger's
existing work at rs.tdwg.org may not have that standards ratification
but it has been widely used and tested and forms the basis (along with
TCS) of ongoing semantic systems research and linked data developments
within the biodiversity space. The difficulty in maintaining LSID
traction, the general lack of interest (especially in the vested
interests) in RDF, the pressure of real work and the focus on
application level schema and aggregation have all contributed to the
current state of progress there. Never-the-less it should still be our
point of reference as we try to boot-strap this modelling effort.
There is a proposal to form an DwC RDF task group that comes from the
primary advocates of the Darwin Core changes under discussion here.
It would seem to make sense to leave the Darwin Core alone until this
group reports. There is a parallel movement in the TAG to resurrect
the domain model effort leveraging experiences with the candidate TDWG
ontologies. Hopefully we will have time to air these options during
TDWG 2011.
greg
A few observations:
The real database is in the collection and the labels on the objects
there contained, the real metadata. Our electronic versions are in
effect meta-metadata.
Falsification of an occurrence may very well be the primary function
of a scientific voucher.
There is no avenue of connection from "occurrence" to "taxon" other
than through typification, direct citation of vouchered material or
annotation by the taxon authority. Mostly they simply share taxon
name string
On 8 September 2011 11:04, John Wieczorek <tuco at berkeley.edu> wrote:
> 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
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--
Greg Whitbread
Australian National Botanic Gardens
Australian National Herbarium
+61 2 62509482
ghw at anbg.gov.au
"And therfore, at the kynges court, my brother,
Ech man for hymself, ther is noon oother."
The Knight's Tale, l. 1181-1182
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