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

[John Wieczorek]

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 at 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 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
> _______________________________________________
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> 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
>
>
> .
>
>
>
>
> --
> 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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