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

Thu Sep 26 04:03:23 CEST 2013

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 at vanderbilt.edu <mailto:steve.baskauf at 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 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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-- 
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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