Steve and others:
The better solution (from an informatics point of view) would be to use the ENVO URI in the field, even if that means changing the DwC guidelines. If it is left as a string, then there would have to be another field that specifies where the term came from, then there would have to be some mechanism to convert the string to a URI. I realize that entering URIs requires some effort, but if someone is looking up the exact label for a term, it is not much harder to find the URI.
Re. adding a term to DwC for ecoregion, I suggest you take that up on the ENVO list first. I don't know if they have considered adding a class for ecoregion. To me it makes sense to first work out the utility,definition, and classes in ENVO before adoption in DwC.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Thu, Oct 3, 2013 at 3:00 AM, tdwg-content-request@lists.tdwg.org wrote:
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Today's Topics:
- Re: Proposed new Darwin Core environmental terms from ENVO (Steve Baskauf)
Message: 1 Date: Wed, 2 Oct 2013 09:12:54 -0500 From: Steve Baskauf steve.baskauf@vanderbilt.edu Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: tuco@berkeley.edu Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: 524C29E6.8030908@vanderbilt.edu Content-Type: text/plain; charset="iso-8859-1"
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@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
"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@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
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@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@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