I really like the synopsis and the clarity of this proposal. However, I'm going to mud things up a bit by sending your message to the Biodiversity Genomics GSC Group list and alert them to this discussion so they can provide input.<br>
<br>There has been an ongoing effort to bridge DwC and GSC standards (for more information on GSC standards see <a href="http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html">http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html</a>). My sense is that CollectionObject is a nice analogue to what MIMARKS refers to as a Sample. Some possibilities for integration here (assuming i'm on target with sample and collectionObject being analogous):<br>
<br>1. Adopt the term "Sample" instead of "CollectionObject"<br>2. Develop a general understanding of how "Sample" and "CollectionObject" are related (or differ) and write up some explanatory text in the reference (with recognition of both terms).<br>
3. Clarify the differences between CollectionObject and Samples and develop a ResourceRelationship between the two.<br><br>John Deck<br><br><div class="gmail_quote">On Wed, Sep 7, 2011 at 6:04 PM, John Wieczorek <span dir="ltr"><<a href="mailto:tuco@berkeley.edu">tuco@berkeley.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear all,<br>
<br>
Prepare yourself mentally. After more than a year of discussions,<br>
prototypes, scholarly papers, bar room brawls, etc., we are very near<br>
having a path forward for two new, related classes for Darwin Core<br>
that attempt to remove ambiguity inherent in the Occurrence class as<br>
it currently stands. Adding classes is quite a bit more complicated<br>
than adding properties (as you'll see if you manage to get through<br>
this message), and so it is important to be as thorough as possible to<br>
make sure we get it right. I'll try here to synthesize the rough<br>
consensus and the remaining issues.<br>
<br>
Basically, the idea is to pull two distinct concepts out of Occurrence<br>
and give them their own classes.<br>
Maybe not surprisingly, one of the hardest things to agree upon has<br>
been the names for these classes. The class that was proposed first as<br>
"Individual" has seen no less than 12 alternate names, none of them<br>
satisfying to everyone. The closest thing to an acceptable name was<br>
"Organism", with caveats that the definition should make it abundantly<br>
clear what is to be included in the class and what is not. I'll use<br>
"Organism" here to refer to the class in the hopes of offending the<br>
fewest people.<br>
<br>
The rough consensus on "Organism" is that is should include viruses,<br>
symbionts, individuals, colonies, groups of individuals, and even<br>
populations, but that there should be taxonomic homogeneity to an<br>
instance of an "Organism". There has been some concern about how and<br>
where to draw the line on homogeneity. No attempt has yet been made to<br>
write a definitive description of the class, though many examples of<br>
representatives of the class have been given.<br>
<br>
What we need to move forward on the "Organism" class are an official<br>
definition and an official comment, the combination of which should be<br>
sufficient for someone previously unfamiliar with the term and the<br>
arguments leading to its existence to understand. Some existing terms<br>
(individualCount, sex, lifeStage, reproductiveCondition, behavior,<br>
previousIdentifications, associatedTaxa) will have to be reorganized<br>
to be under this new class. These terms may require updated<br>
definitions for consistency. New terms (organismID,<br>
associatedOrganisms, organismRemarks) and an Organism Darwin Core Type<br>
vocabulary term will have to be added. Following is an updated<br>
proposal for changes related to the adoption of a new "Organism"<br>
class:<br>
<br>
Term Name: Organism<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/Organism" target="_blank">http://rs.tdwg.org/dwc/terms/Organism</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: Organism<br>
Definition: The category of information pertaining to a specific<br>
instance of an organism (virus, symbiont, individual, colony, group of<br>
individuals, population) reliably be known to taxonomically<br>
homogeneous.<br>
Comment: For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/Organism" target="_blank">http://code.google.com/p/darwincore/wiki/Organism</a><br>
Type of Term: <a href="http://www.w3.org/2000/01/rdf-schema#Class" target="_blank">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: Organism-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class:<br>
ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or<br>
DataSets/DataSet/Units/Unit/MycologicalUnit or<br>
DataSets/DataSet/Units/Unit/HerbariumUnit or<br>
DataSets/DataSet/Units/Unit/BotanicalGardenUnit or<br>
DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or<br>
DataSets/DataSet/Units/Unit/ZoologicalUnit or<br>
DataSets/DataSet/Units/Unit/PalaeontologicalUnit or<br>
DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}<br>
<br>
Term Name: Organism<br>
Identifier: <a href="http://rs.tdwg.org/dwc/dwctype/Organism" target="_blank">http://rs.tdwg.org/dwc/dwctype/Organism</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/dwctype/" target="_blank">http://rs.tdwg.org/dwc/dwctype/</a><br>
Label: Organism<br>
Definition: A resource describing an instance of the Organism class.<br>
Comment: For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary" target="_blank">http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary</a><br>
Type of Term: <a href="http://www.w3.org/2000/01/rdf-schema#Class" target="_blank">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-00<br>
Member Of: <a href="http://rs.tdwg.org/dwc/terms/DwCType" target="_blank">http://rs.tdwg.org/dwc/terms/DwCType</a><br>
Has Domain:<br>
Has Range:<br>
Version: Organism-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class:<br>
ABCD 2.06: not in ABCD<br>
<br>
Term Name: organismID<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/organismID" target="_blank">http://rs.tdwg.org/dwc/terms/organismID</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: organismID<br>
Definition: An identifier for the set of information associated with<br>
an Organism. May be a global unique identifier or an<br>
identifier specific to the data set.<br>
Comment: For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/BiologicalEntity" target="_blank">http://code.google.com/p/darwincore/wiki/BiologicalEntity</a><br>
Type of Term: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines: <a href="http://purl.org/dc/terms/identifier" target="_blank">http://purl.org/dc/terms/identifier</a><br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: organismID-2011-09-09<br>
Replaces: individualID-2009-09-24<br>
Is Replaced By:<br>
Class: <a href="http://rs.tdwg.org/dwc/terms/Organism" target="_blank">http://rs.tdwg.org/dwc/terms/Organism</a><br>
ABCD 2.06: DataSets/DataSet/Units/Unit/UnitID<br>
<br>
Term Name: organismRemarks<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/organismRemarks" target="_blank">http://rs.tdwg.org/dwc/terms/organismRemarks</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: organismRemarks<br>
Definition: Comments or notes about the Organism.<br>
Comment: Example: "seen several times in Tilden Park before capture".<br>
For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/CollectionObject" target="_blank">http://code.google.com/p/darwincore/wiki/CollectionObject</a><br>
Type of Term: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2009-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: organismRemarks-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class: <a href="http://rs.tdwg.org/dwc/terms/Organism" target="_blank">http://rs.tdwg.org/dwc/terms/Organism</a><br>
ABCD 2.06: DataSets/DataSet/Units/Unit/Notes<br>
<br>
Term Name: associatedOrganisms<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/associatedOrganisms" target="_blank">http://rs.tdwg.org/dwc/terms/associatedOrganisms</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: associatedOrganisms<br>
Definition: A list (concatenated and separated) of identifiers of<br>
other Organism records and their associations to this<br>
Organism.<br>
Comment: Example: "sibling of MXA-231; sibling of MXA-232". For<br>
discussion see <a href="http://code.google.com/p/darwincore/wiki/Organism" target="_blank">http://code.google.com/p/darwincore/wiki/Organism</a><br>
Type of Term: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: associatedOrganisms-2011-09-09<br>
Replaces: associatedOccurrences-2009-04-24<br>
Is Replaced By:<br>
Class: <a href="http://rs.tdwg.org/dwc/terms/Organism" target="_blank">http://rs.tdwg.org/dwc/terms/Organism</a><br>
ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode<br>
+ DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName<br>
+ DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID<br>
<br>
<br>
The class proposed as "CollectionObject" has seen fewer alternate name<br>
proposals than "Organism", but the same call for clarity on inclusion<br>
and exclusion has been voiced. The basic idea is to use this class to<br>
cover information that could be considered "persistent evidence" that<br>
an organism occurred, and that the concept is distinct from both<br>
"Organism" and Occurrence. Evidence might include collection-based<br>
materials, digital media, written materials, and literature.<br>
<br>
"Evidence" may be a bit vague as a name for the class, providing no<br>
real indication that the "Evidence" should apply to an "Organism"<br>
rather than to an Occurrence, Taxon, Identification, or any other<br>
class. Nor does it convey the idea that the evidence should be<br>
persistent. "PersistentEvidenceThatAnOrganismExisted" gets the idea<br>
across pretty well, but it is a bit lengthy (and no one actually<br>
proposed this name). ABCD isn't shy about vague term names - it uses<br>
"Unit" for roughly this concept. The long-standing term<br>
"CollectionObject" is less vague than the proposed alternatives, but<br>
it might lead people to assume that the object must be physical, and<br>
that it must be housed within a collection, neither of which is<br>
strictly required. No one objected to this name for the term, however,<br>
so I will continue to use it here to illustrate the proposed changes<br>
and additions to accommodate this concept.<br>
<br>
Some existing terms (institutionID, institutionCode, collectionID,<br>
collectionCode, ownerInstitutionCode, catalogNumber, preparations,<br>
disposition, otherCatalogNumbers, associatedSequences) will have to be<br>
organized under this new class. These terms may require updated<br>
definitions for consistency. Note that with the addition of the<br>
"CollectionObject" class, the institutionCode, collectionCode,<br>
catalogNumber triplet would no longer apply to an Occurrence.<br>
<br>
New terms (collectionObjectID and collectionObjectRemarks) and an<br>
CollectionObject Darwin Core Type vocabulary term will have to be<br>
added. Following is an updated proposal for changes related to the<br>
adoption of a new "CollectionObject" class:<br>
<br>
Term Name: CollectionObject<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/CollectionObject" target="_blank">http://rs.tdwg.org/dwc/terms/CollectionObject</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: CollectionObject<br>
Definition: The category of information pertaining to persistent<br>
evidence that an organism existed (specimen, sample, image, sound,<br>
drawing, field notes, publication), including digital forms.<br>
Comment: For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/CollectionObject" target="_blank">http://code.google.com/p/darwincore/wiki/CollectionObject</a><br>
Type of Term: <a href="http://www.w3.org/2000/01/rdf-schema#Class" target="_blank">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: CollectionObject-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class:<br>
ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or<br>
DataSets/DataSet/Units/Unit/MycologicalUnit or<br>
DataSets/DataSet/Units/Unit/HerbariumUnit or<br>
DataSets/DataSet/Units/Unit/BotanicalGardenUnit or<br>
DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or<br>
DataSets/DataSet/Units/Unit/ZoologicalUnit or<br>
DataSets/DataSet/Units/Unit/PalaeontologicalUnit or<br>
DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject}<br>
<br>
Term Name: CollectionObject<br>
Identifier: <a href="http://rs.tdwg.org/dwc/dwctype/CollectionObject" target="_blank">http://rs.tdwg.org/dwc/dwctype/CollectionObject</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/dwctype/" target="_blank">http://rs.tdwg.org/dwc/dwctype/</a><br>
Label: CollectionObject<br>
Definition: A resource describing an instance of the CollectionObject class.<br>
Comment: For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary" target="_blank">http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary</a><br>
Type of Term: <a href="http://www.w3.org/2000/01/rdf-schema#Class" target="_blank">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Member Of: <a href="http://rs.tdwg.org/dwc/terms/DwCType" target="_blank">http://rs.tdwg.org/dwc/terms/DwCType</a><br>
Has Domain:<br>
Has Range:<br>
Version: CollectionObject-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class:<br>
ABCD 2.06: not in ABCD<br>
<br>
Term Name: collectionObjectID<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/collectionObjectID" target="_blank">http://rs.tdwg.org/dwc/terms/collectionObjectID</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: collectionObjectID<br>
Definition: An identifier for the CollectionObject. In the absence of<br>
a persistent global unique identifier, construct one from a<br>
combination of identifiers in the record that will most closely make<br>
the collectionObjectID globally unique.<br>
Comment: For a specimen in the absence of a bona fide global unique<br>
identifier, for example, use the form:<br>
"urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber].<br>
Examples: "urn:lsid:nhm.ku.edu:Herps:32",<br>
"urn:catalog:FMNH:Mammal:145732". For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/CollectionObject" target="_blank">http://code.google.com/p/darwincore/wiki/CollectionObject</a><br>
Type of Term: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines: <a href="http://purl.org/dc/terms/identifier" target="_blank">http://purl.org/dc/terms/identifier</a><br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2011-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: collectionObjectID-2011-09-09<br>
Replaces:<br>
Is Replaced By:<br>
Class: <a href="http://rs.tdwg.org/dwc/terms/CollectionObject" target="_blank">http://rs.tdwg.org/dwc/terms/CollectionObject</a><br>
ABCD 2.06: DataSets/DataSet/Units/Unit/UnitGUID<br>
<br>
Term Name: collectionObjectRemarks<br>
Identifier: <a href="http://rs.tdwg.org/dwc/terms/collectionObjectRemarks" target="_blank">http://rs.tdwg.org/dwc/terms/collectionObjectRemarks</a><br>
Namespace: <a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
Label: collectionObjectRemarks<br>
Definition: Comments or notes about the CollectionObject.<br>
Comment: Example: "custody transferred in 1995 from National Park<br>
Service". For discussion see<br>
<a href="http://code.google.com/p/darwincore/wiki/CollectionObject" target="_blank">http://code.google.com/p/darwincore/wiki/CollectionObject</a><br>
Type of Term: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines:<br>
Status: recommended<br>
Date Issued: 2011-09-09<br>
Date Modified: 2009-09-09<br>
Has Domain:<br>
Has Range:<br>
Version: collectionObjectRemarks-2011-09-09<br>
Replaces: SampleRemarks-2009-01-18<br>
Is Replaced By:<br>
Class: <a href="http://rs.tdwg.org/dwc/terms/CollectionObject" target="_blank">http://rs.tdwg.org/dwc/terms/CollectionObject</a><br>
ABCD 2.06: DataSets/DataSet/Units/Unit/Notes<br>
<br>
<br>
Because of these changes for "Organism" and "CollectionObject", the<br>
definition of the Occurrence class will have to change and quite a<br>
different set of terms organized under it, namely:<br>
<br>
occurrenceID, occurrenceRemarks, recordNumber, recordedBy,<br>
establishmentMeans, and occurrenceStatus<br>
<br>
The Occurrence definition will change from "The category of<br>
information pertaining to evidence of an occurrence in nature, in a<br>
collection, or in a dataset (specimen, observation, etc.)." to<br>
something more akin to "The category of information pertaining to<br>
evidence of an occurrence of an Organism in nature."<br>
<br>
The term occurrenceDetails will be deprecated in favor of the Dublin<br>
Core term dcterms:references at the record level. Also,<br>
associatedMedia, which was organized under Occurrence, would become a<br>
record level term, as it could apply as easily to Occurrences,<br>
"Organisms", and "CollectionObjects".<br>
<br>
If you made it this far, I congratulate you on your dedication to the<br>
cause. Please let's clear up the remaining issues as a community and<br>
put these new terms to good use.<br>
<br>
Cheers,<br>
<br>
John<br>
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</blockquote></div><br><br clear="all"><br>-- <br>John Deck<br>(541) 321-0689<br><br>