Dear all,
The spirit of the proposal is to satisfy use cases defined in the
document "Meeting Report: GBIF hackathon-workshop on
Darwin Core and sample data (22-24 May 2013)" found at
http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO
ontology. Steve is correct. All of the ENVO terms are classes in
keeping with the OBO Foundry way of doing things. As such, they don't
work in the intended Darwin Core context as they currently stand,
where what we want are properties whose values can come from ENVO as a
controlled vocabulary in the way Hilmar described.
To satisfy the spirit of the proposal, I suggest that instead of
replacing the dwc:habitat property with the envo:habitat class and
adding the other three ENVO classes, we modify the existing
dwc:habitat property and introduce new properties whose ranges are
recommended to be the appropriate ENVO classes, as follows:
Retain the property term dwc:habitat, but amend the definition to be:
Term Name: habitat
Identifier: http://rs.tdwg.org/dwc/terms/habitat
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Habitat
Definition: A spatial region having environmental qualities which may
sustain an organism or a community of organisms. Recommended best
practice is to use a controlled vocabulary such as defined by the
habitat class of the Environment Ontology (ENVO).
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/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2008-11-19
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: habitat-2013-09-26
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)
Add the following new property terms for biome,
environmental feature, and environmental material:
Term Name: biome
Identifier: http://rs.tdwg.org/dwc/terms/biome
Namespace: http://rs.tdwg.org/dwc/terms/
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. Recommended best practice
is to use a controlled vocabulary such as defined by the biome class
of the Environment Ontology (ENVO).
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/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: biome-2013-09-26
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: environmentalFeature
Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Environmental Feature
Definition: A prominent or distinctive aspect, quality, or
characteristic of a biome. Recommended best practice is to use a
controlled vocabulary such as defined by the environmental feature
class of the Environment Ontology (ENVO).
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/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: environmentalFeature-2013-09-26
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: environmentalMaterial
Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Environmental Material
Definition: Material in or on which organisms may live. Recommended
best practice is to use a controlled vocabulary such as defined by the
environmental feature class of the Environment Ontology (ENVO).
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/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: environmentalMaterial-2013-09-26
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
I hope this makes better sense.
Cheers,
John
On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf
<steve.baskauf@vanderbilt.edu> wrote:
Well, the proposal says "The Darwin Core term habitat would be redefined..."
. I take that to mean that the term dwc:habitat is being replaced with
envo:00002036 . If that's not what it means, then it would be good to
clarify. If the intention is to provide values for other terms, that should
be stated.
Steve
Hilmar Lapp wrote:
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:
PMB 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
_______________________________________________
tdwg-content mailing list
tdwg-content@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
.