I've had some time to read through the proposed changes more closely and had a question.
I realize that when a property is listed under a class in the /dwc:/ namespace, that is kind of a suggestion about the type of resource for which that term would be an appropriate property (vs. a formal domain declaration which would force the subject resource to BE an instance of that class). So one doesn't really "break the rules" if one uses a DwC term as a property of a resource that isn't a member of the class that the term is listed under. Nevertheless, for the sake of consistency and to make it possible for consuming applications to know what to "expect" as properties for particular types of things, it would be good to place DwC properties under the "right" class headings.
So my question is, why are the terms/ dwc:habitat/ and /dwc:biome/// being placed under the /dwc:Event/ class? I'll start with /dwc:biome/ because that's the most straightforward one. It seems to me that /dwc:biome/ should be organized under the class /dcterms:Location/ rather than /dwc:Event/. For example, I would say
http://bioimages.vanderbilt.edu/baskauf/d0127#loc /dwc:biome/ "temperate broadleaf forest"
(where http://bioimages.vanderbilt.edu/baskauf/d0127#loc is a /dcterms:Location/) or something like that. Although I suppose over time climate change could cause that location to be part of a different biome, that probably wouldn't happen on a timescale the would be relevant. One could probably also make the case that /dwc:habitat/ is a property of a location, although I suppose that the habitat type of a location could change, for example if it were a forest, but then somebody chopped down all of the trees and converted it to agricultural use. In that case, it might be desirable to record what the state of that location was at a particular time (which is the way I think about /dwc:Event/ - something that happens at a particular place and time). Then it would make sense to group it under /dwc:Event/. But we have other properties of location that could change over time, such as /dwc:country/ for which we have several examples in Europe within the past few decades.
I suppose the thinking is that the proposed terms (habitat, biome, environmentalFeature, environmentalMaterial) would comprise a set of properties that would be associated with a collecting or sampling event. But it doesn't really make sense to me to call /dwc:biome/ a property of an event.
I'm also wondering if there was any consideration about creating a /dwc:ecoregion/ property, which I would consider to be something intermediate in scale between a biome and a habitat. I would actually use that term a lot, but I may be the only one (and I would use it as a property of a location). If one were to create such a term, it would probably be good to have some other term that specified the system used to define the controlled vocabulary (e.g. Bailey vs. WWF ecoregions). Or use URIs but that's a different issue and the DwC RDF guide would have a solution for that (dwcuri:biome, dwcuri:ecoregion, etc.).
Steve
John Wieczorek wrote:
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 _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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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
.