[tdwg-content] Proposed new Darwin Core environmental terms from ENVO

Thu Sep 26 01:52:21 CEST 2013

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.org/obo/ENVO_00002036

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 at 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 at 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

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