Proposed new Darwin Core environmental terms from ENVO
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
I attempted to dereference the URIs below as RDF/XML to see how the terms were defined. I kept getting redirected from one URL to another to another (I think about 4 or 5 times). Finally I got to a URI with a response that said "Ontology not specified or not supported". Can somebody post a link to some document somewhere that shows how the ENVO terms are defined in the RDF of the ontology? Plus, somebody should fix the dereferencing so that a client requesting an RDF/XML representation gets a 303 redirect to an RDF file that defines the terms.
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
.
Steve,
I don't know which URLs you're specifically referring to and what you're doing to resolve them, but the ENVO term URIs work perfectly fine for me.
For example, the following curl command returns an OWL document with the term's class definition:
curl -L -H "Accept: application/rdf+xml" http://purl.obolibrary.org/obo/ENVO_00002036
If you paste http://purl.obolibrary.org/obo/ENVO_00002036 into your browser's address bar, it gets resolved to an HTML page showing the class, its properties, and its axioms within the ENVO ontology in a form meant for human consumption.
As per the OBO ID convention [1], the ontology in OWL format is available from the following URL: http://purl.obolibrary.org/obo/envo.owl
-hilmar
[1] http://www.obofoundry.org/id-policy.shtml
On Sep 25, 2013, at 5:04 PM, Steve Baskauf wrote:
I attempted to dereference the URIs below as RDF/XML to see how the terms were defined. I kept getting redirected from one URL to another to another (I think about 4 or 5 times). Finally I got to a URI with a response that said "Ontology not specified or not supported". Can somebody post a link to some document somewhere that shows how the ENVO terms are defined in the RDF of the ontology? Plus, somebody should fix the dereferencing so that a client requesting an RDF/XML representation gets a 303 redirect to an RDF file that defines the terms.
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
.
-- 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
Thanks for the information, Hilmar. I don't have curl installed on my machine at work, so I used http://linkeddata.informatik.hu-berlin.de/uridbg/ which I have previously found to reliably show me what happens when I dereference a URI with Accept-Header application/rdf+xml When I did it for http://purl.obolibrary.org/obo/ENVO_00002036 , I got:
HTTP/1.1 302 Moved Temporarily http://www.berkeleybop.org/ontologies/ENVO_00002036%20
Dereferencing http://www.berkeleybop.org/ontologies/ENVO_00002036%20 produced
HTTP/1.1 303 See Other http://purl.obolibrary.org/obo/ENVO/about/ENVO_00002036
Dereferencing that gave: HTTP/1.1 302 Moved Temporarily http://www.berkeleybop.org/ontologies/ENVO/about/ENVO_00002036
Dereferencing that gave: HTTP/1.1 302 Found http://www.ontobee.org/browser/rdf.php?o=ENVO%26iri=http://purl.obolibrary.o...
Dereferencing that gave: HTTP/1.1 200 OK The RDF file... !
That didn't happen last time I tried it, so I suppose I did something wrong that time. 4 redirects seems odd but I guess in the end it does work. My bad...
Steve
Hilmar Lapp wrote:
Steve,
I don't know which URLs you're specifically referring to and what you're doing to resolve them, but the ENVO term URIs work perfectly fine for me.
For example, the following curl command returns an OWL document with the term's class definition:
curl -L -H "Accept: application/rdf+xml" http://purl.obolibrary.org/obo/ENVO_00002036
If you paste http://purl.obolibrary.org/obo/ENVO_00002036 into your browser's address bar, it gets resolved to an HTML page showing the class, its properties, and its axioms within the ENVO ontology in a form meant for human consumption.
As per the OBO ID convention [1], the ontology in OWL format is available from the following URL: http://purl.obolibrary.org/obo/envo.owl
-hilmar
[1] http://www.obofoundry.org/id-policy.shtml
On Sep 25, 2013, at 5:04 PM, Steve Baskauf wrote:
I attempted to dereference the URIs below as RDF/XML to see how the terms were defined. I kept getting redirected from one URL to another to another (I think about 4 or 5 times). Finally I got to a URI with a response that said "Ontology not specified or not supported". Can somebody post a link to some document somewhere that shows how the ENVO terms are defined in the RDF of the ontology? Plus, somebody should fix the dereferencing so that a client requesting an RDF/XML representation gets a 303 redirect to an RDF file that defines the terms.
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
.
-- 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
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
.
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
.
-- 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
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 mailto: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
.
-- 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 mailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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
.
-- 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
I've been in communication with the OBO-ENVO group (obo-envo@lists.sourceforge.net) about the proposed re-use of the ENVO terms. The ENVO ontology remains in active development, with a proposed forthcoming guide on how to use ENVO. I have agreed to forward an invitation extended by Pier Buttigieg to the TDWG community to actively contribute.
"To be clear, the habitat class itself isn't queued for obsoletion, but its current subclasses are. Once habitat is better-defined, new subclasses will be created. If anyone in TDWG wishes to help shape the definition of this concept or share any observations to promote its usefulness to the biodiversity community we're certainly open to input."
On Thu, Sep 26, 2013 at 2:44 PM, John Wieczorek tuco@berkeley.edu 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
.
-- 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
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
.
-- 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
.
It is true that the organizedInClass attribute of any given Darwin Core term does nothing more than associate properties with classes as an organizational aid. It says nothing about the class being the domain of the property, and with good reason. Darwin Core in its current manifestation is just not semantically detailed enough to make domain declarations. Most of our classes combine multiple concepts and get used in multiple ways. Occurrence is the best worst example of this.
The environment properties are organized under Event because of their time-dependent nature - habitats and biomes definitely can change over museum time scales. Location alone does not have a time component - the definition of Location is "A spatial region or named place. For Darwin Core, a set of terms describing a place, whether named or not." Darwin Core has no other spatiotemporal concept except the Event, which combines everything in Location with time properties and sampling properties - the definition of an Event is: "The category of information pertaining to an event (an action that occurs at a place and during a period of time)."
If we had a purely spatiotemporal class, then I would organize the environmental properties there. Without one, I would organize the properties in the class that does have time properties, namely Event.
Until your message, no one has discussed the addition of an ecoregion term on tdwg-content.
As to the question of country, I see On Tue, Oct 1, 2013 at 5:24 PM, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
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
.
-- 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
.
-- 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
John,
Thank you for your response. I agree that anything that may change over time should probably be grouped under Event. I guess in the case of biomes I am thinking about this in a practical sense, i.e. realistically how is somebody going to assign a particular event to a biome? A likely scenario would be that they would take the location of an event, use its latitude and longitude to find where it falls on a map such as http://en.wikipedia.org/wiki/Biome#Map_of_biomes and then assign it to whatever biome region it falls within on the map. That is a different approach from assessing the biological and climatological characteristics occurring at an event, comparing it with an ontology that defines biomes, and then making the assignment based on how the event lines up with the ontology. I suppose that in theory people might do that, but realistically, it seems more likely that they would look it up on a map. Under the scenario that they look it up on a map, it is logical to consider biome to be a property of a location. Yes, biomes might change over time, but then so do the names and boundaries of countries, but we don't consider them to be properties of Event, we consider them as properties of Location. We periodically update the maps of countries, just as we might update the maps of biomes once a century or so. But if there is a consensus that dwc:biome belongs under Event, I can live with it.
The other thing I'm wondering about the values of dwc:biome would be how a user would indicate the controlled vocabulary one is using. The ENVO ontology is mentioned. Under the scenario of the draft RDF guide, the term dwcuri:biome would have a URI value of http://purl.obolibrary.org/obo/ENVO_01000195. That would be unambiguous. However, if dwc:biome is reserved for literal values (as the RDF guide suggests it should be) then how does a machine know that "flooded grassland biome" is a label from ENVO and not a literal description of a biome from the Whittaker, Walter, Bailey, etc. systems which are probably currently in much wider use than ENVO and therefore likely controlled vocabularies of choice for many users?
As far as dwc:ecoregion as a term is concerned, I was mostly just testing the waters. I could submit it as a term addition in the DwC issue tracker, but I'm not going to do that if I'm the only person who cares about it. If anybody besides me cares, they can say so on the list.
Thanks for clarifying, Steve
John Wieczorek wrote:
It is true that the organizedInClass attribute of any given Darwin Core term does nothing more than associate properties with classes as an organizational aid. It says nothing about the class being the domain of the property, and with good reason. Darwin Core in its current manifestation is just not semantically detailed enough to make domain declarations. Most of our classes combine multiple concepts and get used in multiple ways. Occurrence is the best worst example of this.
The environment properties are organized under Event because of their time-dependent nature - habitats and biomes definitely can change over museum time scales. Location alone does not have a time component - the definition of Location is "A spatial region or named place. For Darwin Core, a set of terms describing a place, whether named or not." Darwin Core has no other spatiotemporal concept except the Event, which combines everything in Location with time properties and sampling properties - the definition of an Event is: "The category of information pertaining to an event (an action that occurs at a place and during a period of time)."
If we had a purely spatiotemporal class, then I would organize the environmental properties there. Without one, I would organize the properties in the class that does have time properties, namely Event.
Until your message, no one has discussed the addition of an ecoregion term on tdwg-content.
As to the question of country, I see On Tue, Oct 1, 2013 at 5:24 PM, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
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
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
.
-- 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 tel:%28615%29%20343-4582, fax: (615)
322-4942 tel:%28615%29%20322-4942
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 tel:%28615%29%20343-4582, fax: (615)
322-4942 tel:%28615%29%20322-4942
If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu
.
-- 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 tel:%28615%29%20343-4582, fax: (615)
322-4942 tel:%28615%29%20322-4942
If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu
On Wed, Oct 2, 2013 at 4:12 PM, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
The other thing I'm wondering about the values of dwc:biome would be how a user would indicate the controlled vocabulary one is using. The ENVO ontology is mentioned. Under the scenario of the draft RDF guide, the term dwcuri:biome would have a URI value of http://purl.obolibrary.org/obo/ENVO_01000195. That would be unambiguous. However, if dwc:biome is reserved for literal values (as the RDF guide suggests it should be) then how does a machine know that "flooded grassland biome" is a label from ENVO and not a literal description of a biome from the Whittaker, Walter, Bailey, etc. systems which are probably currently in much wider use than ENVO and therefore likely controlled vocabularies of choice for many users?
A machine will have no way to know from which vocabulary a value for a property comes unless the value says so. That is common to all terms that recommend a controlled vocabulary, but do not enforce it. It would be no different for dwc:biome. The only way to be unambiguous is to provide an unambiguous value, which, as you noted, http://purl.obolibrary.org/obo/ENVO_01000195 is.
In Audubon Core [1], there are sometimes other terms that are associated with a string term whose purpose is to indicate the controlled vocabulary being used in the other term (e.g. Iptc4xmpExt:CVterm for a controlled value term and ac:subjectCategoryVocabulary to indicate the vocabulary from which the controlled value term comes). I reviewed the DwC terms and I guess there is no precedent for that kind of thing in DwC. I suppose if people want to be unambiguous, they should just use URIs. Unfortunately, I'm not aware of URIs for the terms from various systems of describing biomes. I suppose someone could mint terms if they cared about this. Or use ENVO uris.
Steve
[1] http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29
John Wieczorek wrote:
On Wed, Oct 2, 2013 at 4:12 PM, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
The other thing I'm wondering about the values of dwc:biome would be how a user would indicate the controlled vocabulary one is using. The ENVO ontology is mentioned. Under the scenario of the draft RDF guide, the term dwcuri:biome would have a URI value of http://purl.obolibrary.org/obo/ENVO_01000195. That would be unambiguous. However, if dwc:biome is reserved for literal values (as the RDF guide suggests it should be) then how does a machine know that "flooded grassland biome" is a label from ENVO and not a literal description of a biome from the Whittaker, Walter, Bailey, etc. systems which are probably currently in much wider use than ENVO and therefore likely controlled vocabularies of choice for many users?
A machine will have no way to know from which vocabulary a value for a property comes unless the value says so. That is common to all terms that recommend a controlled vocabulary, but do not enforce it. It would be no different for dwc:biome. The only way to be unambiguous is to provide an unambiguous value, which, as you noted, http://purl.obolibrary.org/obo/ENVO_01000195 is.
.
On Oct 3, 2013, at 6:42 AM, Steve Baskauf wrote:
I suppose if people want to be unambiguous, they should just use URIs.
Exactly that.
Unfortunately, I'm not aware of URIs for the terms from various systems of describing biomes.
To the extent that unawareness is to be supported, this can be solved through better documentation.
I suppose someone could mint terms if they cared about this.
Certainly not - minting random terms whose semantic content consists solely of a non-resolving URI string or a string in whatever natural language is barely better than providing no value at all.
Or use ENVO uris.
Yes, indeed. If they don't exist yet, ask that they do. That's the way to build community ontologies - by a community actively working to make the ontology what it needs it to be.
-hilmar
I suppose if people want to be unambiguous, they should just use URIs.
Exactly that.
I know this discussion is mainly focussing on RDF and such like, but the DwC-A format was designed to make vocabularies a little more accessible for people using spreadsheets / databases etc.
In a data file, you might have a CSV with:
1, Puma concolor, male
And in the meta.xml file, you could have the following, which declares the vocabulary used for the :
<core encoding="utf-8" fieldsTerminatedBy="," linesTerminatedBy="\n" rowType="http://rs.tdwg.org/dwc/terms/Occurrence"> <files> <location>occurrence.txt</location> </files> <id index="0" /> <field index="1" term="http://rs.tdwg.org/dwc/terms/occurrenceID"/><archive xmlns="http://rs.tdwg.org/dwc/text/" metadata="eml.xml"> <field index="2" term="http://rs.tdwg.org/dwc/terms/scientificName"/> <field index="3" term="http://rs.tdwg.org/dwc/terms/sex" vocabulary="http://rs.gbif.org/vocabulary/gbif/sex.xml"/> </core>
This is a primitive example, but keeping content and mapping somewhat separate helps keeps this accessible for wider audiences without having to rewrite content every time standards, namespaces, versions etc all change. The data will simply get outdated quickly as I strongly suspect most content is immutable once written once, most data mappings are immutable once created once and most application developers do not use RDF aware technologies (why I originally went for XML and not RDF in DwC-A meta definition despite DwC itself being in RDF).
I complete agree that we need to provide the means to declare (strongly versioned) vocabularies, but I tend to suspect that they should be separated from the content for the most part for better reusability - that was the rationale when I introduced it to the DwC-A. Perhaps it is time to consider a review of the DwC-A meta format though, to play better with (e.g.) SKOS, but I don't think I understand the versioning aspects there - everything seems in constant flux to me.
Cheers, Tim
On Oct 3, 2013, at 2:25 PM, Hilmar Lapp wrote:
On Oct 3, 2013, at 6:42 AM, Steve Baskauf wrote:
I suppose if people want to be unambiguous, they should just use URIs.
Exactly that.
Unfortunately, I'm not aware of URIs for the terms from various systems of describing biomes.
To the extent that unawareness is to be supported, this can be solved through better documentation.
I suppose someone could mint terms if they cared about this.
Certainly not - minting random terms whose semantic content consists solely of a non-resolving URI string or a string in whatever natural language is barely better than providing no value at all.
Or use ENVO uris.
Yes, indeed. If they don't exist yet, ask that they do. That's the way to build community ontologies - by a community actively working to make the ontology what it needs it to be.
-hilmar
=========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hilmar Lapp wrote:
I suppose someone could mint terms if they cared about this.
Certainly not - minting random terms whose semantic content consists solely of a non-resolving URI string or a string in whatever natural language is barely better than providing no value at all.
Well, I wasn't thinking of just any "somebody" creating random terms with non-dereferencing URIs. I was thinking about using the new GBIF terms management capabilities which I think is probably intended to (among other things) host controlled vocabularies. Also, I was assuming SKOS or some other well-known mechanism for expressing relationships would be used to describe the controlled-value-URI-identified resources.
Or use ENVO uris.
Yes, indeed. If they don't exist yet, ask that they do. That's the way to build community ontologies - by a community actively working to make the ontology what it needs it to be.
Well, the problem here is that there is only one ENVO ontology. There are many systems for defining what a biome is (see wikipedia for examples). Data producers will use the biome system they believe in and are already using, and that won't necessarily be the one system that ENVO comes up with. We can't legislate that everyone use ENVO. So create controlled vocabularies for the various extant systems and use SKOS or something like that to describe how they are related so that a machine can understand the relationships.
Steve
On Oct 3, 2013, at 9:08 AM, Steve Baskauf wrote:
Or use ENVO uris.
Yes, indeed. If they don't exist yet, ask that they do. That's the way to build community ontologies - by a community actively working to make the ontology what it needs it to be.
Well, the problem here is that there is only one ENVO ontology.
I would consider that a fortunate fact, not a problem.
There are many systems for defining what a biome is (see wikipedia for examples).
And so there are for what a gene function is, what a disease phenotype is, what an animal anatomy element is, and so on. Yet, for all of these rather domain cross-cutting subject areas, it has been possible for different communities to converge on advancing together one or a few common ontologies. This can require a lot of work, but the eventual pay-off has been huge and is growing. I really don't see why we can't strive for the same for environmental terms and concepts.
-hilmar
The problem is that in TDWG we have some people writing and using OWL ontologies and we have other people using Excel spreadsheets. I am fully in support of developing community ontologies. The challenge is to find a way to help the Excel spreadsheet people start where they are and move towards something more semantically sophisticated. That's what I'm trying to suggest here.
Hilmar Lapp wrote:
On Oct 3, 2013, at 9:08 AM, Steve Baskauf wrote:
Or use ENVO uris.
Yes, indeed. If they don't exist yet, ask that they do. That's the way to build community ontologies - by a community actively working to make the ontology what it needs it to be.
Well, the problem here is that there is only one ENVO ontology.
I would consider that a fortunate fact, not a problem.
There are many systems for defining what a biome is (see wikipedia for examples).
And so there are for what a gene function is, what a disease phenotype is, what an animal anatomy element is, and so on. Yet, for all of these rather domain cross-cutting subject areas, it has been possible for different communities to converge on advancing together one or a few common ontologies. This can require a lot of work, but the eventual pay-off has been huge and is growing. I really don't see why we can't strive for the same for environmental terms and concepts.
-hilmar
--
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org
http://informatics.nescent.org :
I think we should leave it to the specific technology that implements Darwin Core how to refer to a qualified value. For RDF URIs are ideal, but for Darwin Core Archives and XML they might not necessarily be.
In DwC archives we actually have 2 mechanisms in use already:
1) The DwC text guidelines specify that every mapped term in the meta.xml can have a "vocabulary" attribute which takes a URI defining a vocabulary source. This could be a link to a webpage, SKOS or RDF vocabulary. Right now it is mostly used with IPT vocabularies, e.g. http://rs.gbif.org/vocabulary/gbif/rank.xml
2) For dwc:locationID (and I think a few other terms too) we have the practice to put a prefix in front of the actual value similar to namespace qualified elements in xml. These prefixes are not explicitly defined inside the archive (might be worth doing?), but they are based on conventions in the data sharing community. For example GBIF recommends these prefixes for various area standards: http://rs.gbif.org/areas/
Both solutions work very well in the csv file world. Markus
On 03.10.2013, at 12:42, Steve Baskauf wrote:
In Audubon Core [1], there are sometimes other terms that are associated with a string term whose purpose is to indicate the controlled vocabulary being used in the other term (e.g. Iptc4xmpExt:CVterm for a controlled value term and ac:subjectCategoryVocabulary to indicate the vocabulary from which the controlled value term comes). I reviewed the DwC terms and I guess there is no precedent for that kind of thing in DwC. I suppose if people want to be unambiguous, they should just use URIs. Unfortunately, I'm not aware of URIs for the terms from various systems of describing biomes. I suppose someone could mint terms if they cared about this. Or use ENVO uris.
Steve
[1] http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29
John Wieczorek wrote:
On Wed, Oct 2, 2013 at 4:12 PM, Steve Baskauf
steve.baskauf@vanderbilt.edu wrote:
The other thing I'm wondering about the values of dwc:biome would be how a user would indicate the controlled vocabulary one is using. The ENVO ontology is mentioned. Under the scenario of the draft RDF guide, the term dwcuri:biome would have a URI value of
http://purl.obolibrary.org/obo/ENVO_01000195 . That would be unambiguous. However, if dwc:biome is reserved for literal values (as the RDF guide suggests it should be) then how does a machine know that "flooded grassland biome" is a label from ENVO and not a literal description of a biome from the Whittaker, Walter, Bailey, etc. systems which are probably currently in much wider use than ENVO and therefore likely controlled vocabularies of choice for many users?
A machine will have no way to know from which vocabulary a value for a property comes unless the value says so. That is common to all terms that recommend a controlled vocabulary, but do not enforce it. It would be no different for dwc:biome. The only way to be unambiguous is to provide an unambiguous value, which, as you noted,
http://purl.obolibrary.org/obo/ENVO_01000195 is.
.
-- 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.
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participants (5)
-
Hilmar Lapp -
John Wieczorek -
Markus Döring -
Steve Baskauf -
Tim Robertson [GBIF]