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

Steve Baskauf steve.baskauf at vanderbilt.edu
Wed Oct 2 16:12:54 CEST 2013


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 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
> > _______________________________________________
> > 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 <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 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 <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
>

-- 
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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