I was assuming that the proposal was that subclasses of envo:habitat would take the place of values for the dwc:habitat property. But perhaps I was naive or misunderstanding?

-hilmar

Sent from away

On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf@vanderbilt.edu> wrote:

OK, now that I've had a chance to look at the RDF, it is as I suspected.  If I am understanding the proposal correctly, the proposal is to replace the term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call envo:00002036 for brevity)  However, the definition of dwc:habitat which you can view at http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf says

 dwc:habitat rdf:type rdfs:Property

whereas the document I received at the end of those four redirects tells me that

envo:00002036 rdf:type owl:Class

Since

owl:Class rdfs:subclassOf rdfs:Class

then we are effectively changing the current DwC "habitat" term from a property into a class similar to dwc:Occurrence, dwc:Identification, dwc:Taxon, etc. which are all of type rdfs:Class

So I'm left wondering what I can do with the new term.  With the old term I could make a statement like

<http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous forest"

or something like that if I take the hint from the DwC class groupings that dwc:habitat might be a property of dwc:Event instances.  But I can't meaningfully say

<http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036  "deciduous forest"

That doesn't make any sense because the way I understand RDF, predicates should be properties, not classes.  Even if we weren't talking about RDF, I'd still have the same problem (we are changing a property into a class) - it's just easier for me to make plain what the issue is by giving RDF examples.  So just exactly what can I "do" with envo:00002036 ?????

I haven't looked up the RDF for the other proposed terms (too much work with the four redirects), but I suspect if I did, I'd find that they are also classes and not properties.  This particular issue is a case of a broader issue that I have about OBO-style ontologies.  They are great for defining how many, many kinds of classes are related to each other.  But they provide very few properties that could be used as predicates to serve as properties of instance data.

Steve

John Wieczorek wrote:
Dear all,

GBIF has just published "Meeting Report: GBIF hackathon-workshop on
Darwin Core and sample data (22-24 May 2013)" at
http://www.gbif.org/orc/?doc_id=5424. Now that this document is
available for public reference, I would like to formally open the
minimum 30-day comment period on the new environmental terms proposed
during the workshop and defined in the referenced document.

The formal proposal would change the term habitat to align it with the
ENVO habitat term. The related issues in the Darwin Core issue tracker
is https://code.google.com/p/darwincore/issues/detail?id=178. The
Darwin Core term habitat would be redefined as follows:

Term Name: habitat
Identifier: http://purl.obolibrary.org/obo/ENVO_00002036
Namespace: http://purl.obolibrary.org/obo/
Label: Habitat
Definition: A spatial region having environmental qualities which may
sustain an organism or a community of organisms.
Comment: Examples: "freshwater habitat",
"http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see
http://code.google.com/p/darwincore/wiki/Event (there will be no
further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2008-11-19
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00002036
Replaces: habitat-2009-04-24
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

The formal proposal would add the following new terms for biome,
environmental feature, and environmental material:

Term Name: biome
Identifier: http://purl.obolibrary.org/obo/ENVO_00000428
Namespace: http://purl.obolibrary.org/obo/
Label: Biome
Definition: A major class of ecologically similar communities of
plants, animals, and other organisms. Biomes are defined based on
factors such as plant structures (such as trees, shrubs, and grasses),
leaf types (such as broadleaf and needleleaf), plant spacing (forest,
woodland, savanna), and other factors like climate. Unlike ecozones,
biomes are not defined by genetic, taxonomic, or historical
similarities. Biomes are often identified with particular patterns of
ecological succession and climax vegetation.
Comment: Examples: "flooded grassland biome",
"http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see
http://code.google.com/p/darwincore/wiki/Event (there will be no
further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00000428
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Term Name: environmental feature
Identifier: http://purl.obolibrary.org/obo/ENVO_00002297
Namespace: http://purl.obolibrary.org/obo/
Label: Environmental Feature
Definition: A prominent or distinctive aspect, quality, or
characteristic of a biome.
Comment: Examples: "meadow",
"http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see
http://code.google.com/p/darwincore/wiki/Event (there will be no
further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00002297
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Term Name: environmental material
Identifier: http://purl.obolibrary.org/obo/ENVO_00010483
Namespace: http://purl.obolibrary.org/obo/
Label: Environmental Material
Definition: Material in or on which organisms may live.
Comment: Examples: "scum",
"http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see
http://code.google.com/p/darwincore/wiki/Event (there will be no
further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00010483
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

The related issues in the Darwin Core issue tracker are
https://code.google.com/p/darwincore/issues/detail?id=189
https://code.google.com/p/darwincore/issues/detail?id=190
and
https://code.google.com/p/darwincore/issues/detail?id=191

If there are any objections to the changes proposed for these terms,
or comments about their definitions, please respond to this message.
If there are no objections or if consensus can be reached on any
amendments put forward, the proposal will go before the Executive
Committee for authorization to put these additions into effect after
the public commentary period.

Cheers,

John
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.

  

-- 
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

postal mail address:
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