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

Thu Sep 26 14:51:13 CEST 2013

I've been in communication with the OBO-ENVO group
(obo-envo at 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 at 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 at 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 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
>>
>>
>> _______________________________________________
>> 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