Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Following all the excellent contributions on this list relating to expressing abundance data in Darwin Core, I think we may have uncovered a way that does not require any changes to the DwC standard. As has been pointed out, modelling sampling and abundance can be quite complex and challenging and is best done as an ontology (as in the work of the BCO).
From the GBIF perspective, our goal is to make it as simple as possible for
data providers to deliver abundance data (in Darwin Core Archive format) that can support the science for processes such as CBD and IPBES. Here, I am using the term abundance (specifically population abundance) in the sense defined by GEO BON: "Quantity of individuals or biomass of a given taxon or functional group at a given location" [1].
The challenge is to come up with a way for Simple Darwin Core to express abundance data. It looks like we can probably work within the restrictions imposed by Simple Darwin Core [2] and use properties from MeasurementOrFact because, for the use case in question here, we only need to share one MeasurementOrFact per record.
The model: A sample, associated with a sampling protocol has one or more taxon occurrence records each of which has an abundance measure which is expressed using MeasurementOrFact.
At a minimum, we would need the following three MeasurementOrFact properties listed below (with definition and examples):
measurementType The nature of the measurement, fact, characteristic, or assertion. Examples: "tail length", "temperature", "trap line length", "survey area", "trap type".
For abundances we would use: count, percentage
measurementValue The value of the measurement, fact, characteristic, or assertion. Examples: "45", "20", "1", "14.5", "UV-light".
For abundances we would use any numeric value.
measurementMethod A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation.
For abundances we would use: Count/sq metre, count/litre, % of biovolume, % of species, ...
To enable automated processing, we would need to develop a controlled list for measurementMethod and, ideally, there would also be a URI for the sampling protocol used which would be recorded in the dwc:samplingProtocol field.
[1] http://www.earthobservations.org/documents/meetings/201202_geobon_ebv/30_ebv _species_table_v2.pdf [2] http://rs.tdwg.org/dwc/terms/simple/index.htm#rules
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of tdwg-content-request@lists.tdwg.org Sent: 26 September 2013 17:23 To: tdwg-content@lists.tdwg.org Subject: tdwg-content Digest, Vol 53, Issue 2
Send tdwg-content mailing list submissions to tdwg-content@lists.tdwg.org
To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-content or, via email, send a message with subject or body 'help' to tdwg-content-request@lists.tdwg.org
You can reach the person managing the list at tdwg-content-owner@lists.tdwg.org
When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-content digest..."
Today's Topics:
1. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 2. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 3. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 4. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 5. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) 6. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Chuck Miller) 7. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 8. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 9. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 10. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick)
----------------------------------------------------------------------
Message: 1 Date: Thu, 26 Sep 2013 14:44:34 +0200 From: John Wieczorek tuco@berkeley.edu Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf steve.baskauf@vanderbilt.edu Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: CAHwKGGdOf7rMwQ3UCGGw1T53c4J7X=amJ_ibSkSX_WSb5EoqcA@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
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 steve.baskauf@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@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@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
------------------------------
Message: 2 Date: Thu, 26 Sep 2013 14:51:13 +0200 From: John Wieczorek tuco@berkeley.edu Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf steve.baskauf@vanderbilt.edu Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: CAHwKGGdARDj32v9EPaofwHrzwonQ3czgwMaiyDmnj3c7L0tMnA@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
I've been in communication with the OBO-ENVO group (obo-envo@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@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@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@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@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@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
------------------------------
Message: 3 Date: Thu, 26 Sep 2013 15:48:16 +0200 From: John Wieczorek tuco@berkeley.edu Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" dhobern@gbif.org Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: CAHwKGGdrmyEAwZ-TcTxUqcdGemwc330_H51XUTo9abb0Mez8-g@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod?
If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex), which have the following properties?
measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks
The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules.
On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] dhobern@gbif.org wrote:
Thanks - I think I too have missed something. If we want to make these terms usable, there needs to be a simple way to get numbers out of records that can be compared with one another where sampling methods allow such comparisons. The suggested plain text examples for Abundance don't make this possible. Forcing normalisation into percentages seems an
unnecessary
hurdle and risks encouraging the impression that number of ducks on a reservoir is somehow comparable with percentage dry mass, proportional expression of CO1 for a particular species in an ecogenomics sample, or whatever.
I would much rather we ensured we had a standard, preferred field which
the
data publisher can populate directly with whatever number is the most appropriate expression of the relative abundance in the sample. That
gives
consumers a clear expectation of how to interpret and handle it.
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever Sent: Thursday, September 26, 2013 8:44 AM To: tuco@berkeley.edu; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Dear all,
As somewhat of an outsider I have another question with regards to the proposed terms abundance and abundanceAsPercent.
Is there a specific reason for not adopting:
- the abundance field as a field to store only the value and
- a field abundanceUnit/abundanceType to specify whether the value is in %
of species, % of biovolume, % of biomass, individuals/l, ind./m^2,
ind/m^3,
ind./sampling effort,...(instead of having a field specific for %)?
Maybe this has been discussed during the hackathon and I missed it in the report?
Thanks for considering this question.
With best regards, Aaike
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 two related new terms proposed during the workshop and defined in the referenced document.
The formal proposal would add the following new terms:
Term Name: abundance Identifier: http://rs.tdwg.org/dwc/terms/abundance Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance Definition: The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume. In the case of vegetation and colonial/encrusting species, percent cover can be used. Comment: Examples: "4 per square meter", "0.32 per cubic meter", "24%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-03-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundance-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
Term Name: abundanceAsPercent Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance as Percent Definition: 100 times the number of individuals of a taxon found in a sample divided by the total number of individuals of all taxa in the sample. Comment: Examples: "2.4%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-08-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundanceAsPercent-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence 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=142 and https://code.google.com/p/darwincore/issues/detail?id=187
If there are any objections to the changes proposed for these new 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
-- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: aaike.dewever@naturalsciences.be skype: aaikew LinkedIn: http://be.linkedin.com/in/aaikedewever BioFresh: http://www.freshwaterbiodiversity.eu/ and http://data.freshwaterbiodiversity.eu/ Belgian Biodiversity Platform: http://www.biodiversity.be _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
------------------------------
Message: 4 Date: Thu, 26 Sep 2013 16:01:10 +0200 From: "Donald Hobern [GBIF]" dhobern@gbif.org Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: tuco@berkeley.edu Cc: 'TDWG Content Mailing List' tdwg-content@lists.tdwg.org Message-ID: 01fd01cebac0$da9a8550$8fcf8ff0$@gbif.org Content-Type: text/plain; charset="iso-8859-1"
Thanks, John.
You are correct. I think though that abundance is such a commonly needed property that it would be a mistake not to make it work easily even in Simple Darwin Core.
Donald
---------------------------------------------------------------------- Donald Hobern - GBIF Director - dhobern@gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ----------------------------------------------------------------------
-----Original Message----- From: gtuco.btuco@gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever@naturalsciences.be; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod?
If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex), which have the following properties?
measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks
The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules.
On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] dhobern@gbif.org wrote:
Thanks - I think I too have missed something. If we want to make these terms usable, there needs to be a simple way to get numbers out of records that can be compared with one another where sampling methods allow such comparisons. The suggested plain text examples for Abundance don't make this possible. Forcing normalisation into percentages seems an unnecessary hurdle and risks encouraging the impression that number of ducks on a reservoir is somehow comparable with percentage dry mass, proportional expression of CO1 for a particular species in an ecogenomics sample, or whatever.
I would much rather we ensured we had a standard, preferred field which the data publisher can populate directly with whatever number is the most appropriate expression of the relative abundance in the sample. That gives consumers a clear expectation of how to interpret and
handle it.
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever Sent: Thursday, September 26, 2013 8:44 AM To: tuco@berkeley.edu; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Dear all,
As somewhat of an outsider I have another question with regards to the proposed terms abundance and abundanceAsPercent.
Is there a specific reason for not adopting:
- the abundance field as a field to store only the value and
- a field abundanceUnit/abundanceType to specify whether the value is
in % of species, % of biovolume, % of biomass, individuals/l, ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field
specific for %)?
Maybe this has been discussed during the hackathon and I missed it in the report?
Thanks for considering this question.
With best regards, Aaike
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 two related new terms proposed during the workshop and defined in the referenced document.
The formal proposal would add the following new terms:
Term Name: abundance Identifier: http://rs.tdwg.org/dwc/terms/abundance Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance Definition: The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume. In the case of vegetation and colonial/encrusting species, percent cover can be used. Comment: Examples: "4 per square meter", "0.32 per cubic meter", "24%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-03-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundance-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
Term Name: abundanceAsPercent Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance as Percent Definition: 100 times the number of individuals of a taxon found in a sample divided by the total number of individuals of all taxa in the sample. Comment: Examples: "2.4%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-08-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundanceAsPercent-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence 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=142 and https://code.google.com/p/darwincore/issues/detail?id=187
If there are any objections to the changes proposed for these new 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
-- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: aaike.dewever@naturalsciences.be skype: aaikew LinkedIn: http://be.linkedin.com/in/aaikedewever BioFresh: http://www.freshwaterbiodiversity.eu/ and http://data.freshwaterbiodiversity.eu/ Belgian Biodiversity Platform: http://www.biodiversity.be _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
------------------------------
Message: 5 Date: Thu, 26 Sep 2013 08:37:15 -0600 From: Robert Guralnick Robert.Guralnick@colorado.edu Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" dhobern@gbif.org Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: CADAgxGX=ZRknz2T-kd0e9wwwP72pSrtoeRVb175fm1EQQ7iovQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
I agree with Donald here regarding the need for Abundance, but am, to be honest, not quite I understand (or agree) with the logic of the proposal. Abundance is listed as a property of an occurrence, and I wonder if that make sense given the class definition "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)" Is abundance "evidence of an occurrence in nature". To me, abundance is a property of a survey and its associated methodology and is based on multiple occurrences that come from a sample and a definition of extent.
It seems to me to be a bad fit to scrunch abundance into the occurrence class. I recognize that it might not quite fit anywhere in DwC yet. Wouldn't it be better to wait to see if materialSample is ratified as a class within the Darwin Core?
Best, Rob
On Thu, Sep 26, 2013 at 8:01 AM, Donald Hobern [GBIF] dhobern@gbif.orgwrote:
Thanks, John.
You are correct. I think though that abundance is such a commonly needed property that it would be a mistake not to make it work easily even in Simple Darwin Core.
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
-----Original Message----- From: gtuco.btuco@gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever@naturalsciences.be; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Could every concept of abundance be captured in a combination of
abundance,
abundanceUnit, abundanceMethod?
If so, is there justification for creating new terms at all if the
concepts
can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex), which have the following properties?
measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks
The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules.
On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] dhobern@gbif.org wrote:
Thanks - I think I too have missed something. If we want to make these terms usable, there needs to be a simple way to get numbers out of records that can be compared with one another where sampling methods allow such comparisons. The suggested plain text examples for Abundance don't make this possible. Forcing normalisation into percentages seems an unnecessary hurdle and risks encouraging the impression that number of ducks on a reservoir is somehow comparable with percentage dry mass, proportional expression of CO1 for a particular species in an ecogenomics sample, or whatever.
I would much rather we ensured we had a standard, preferred field which the data publisher can populate directly with whatever number is the most appropriate expression of the relative abundance in the sample. That gives consumers a clear expectation of how to interpret
and
handle it.
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever Sent: Thursday, September 26, 2013 8:44 AM To: tuco@berkeley.edu; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Dear all,
As somewhat of an outsider I have another question with regards to the proposed terms abundance and abundanceAsPercent.
Is there a specific reason for not adopting:
- the abundance field as a field to store only the value and
- a field abundanceUnit/abundanceType to specify whether the value is
in % of species, % of biovolume, % of biomass, individuals/l, ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field
specific for %)?
Maybe this has been discussed during the hackathon and I missed it in the report?
Thanks for considering this question.
With best regards, Aaike
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 two related new terms proposed during the workshop and defined in the referenced document.
The formal proposal would add the following new terms:
Term Name: abundance Identifier: http://rs.tdwg.org/dwc/terms/abundance Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance Definition: The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume. In the case of vegetation and colonial/encrusting species, percent cover can be used. Comment: Examples: "4 per square meter", "0.32 per cubic meter", "24%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-03-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundance-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
Term Name: abundanceAsPercent Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent Namespace: http:/rs.tdwg.org/dwc/terms/ Label: Abundance as Percent Definition: 100 times the number of individuals of a taxon found in a sample divided by the total number of individuals of all taxa in the sample. Comment: Examples: "2.4%". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence (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: 2012-08-01 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: abundanceAsPercent-2013-09-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence 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=142 and https://code.google.com/p/darwincore/issues/detail?id=187
If there are any objections to the changes proposed for these new 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
-- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: aaike.dewever@naturalsciences.be skype: aaikew LinkedIn: http://be.linkedin.com/in/aaikedewever BioFresh: http://www.freshwaterbiodiversity.eu/ and http://data.freshwaterbiodiversity.eu/ Belgian Biodiversity Platform: http://www.biodiversity.be _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
I see several problems with using MeasurementOrFact in this way.
What happens when someone wants to add the next MeasurementOrFact to "Simple" Darwin Core? They won't be able to. "Every field in the Simple Darwin Core may appear either once or not at all in a single record - otherwise how could you distinguish one scientificName field from another one? Think of a database table. It will not allow you to have the same name for two different fields. Because of this design restriction (lack of flexibility for the sake of simplicity), the auxiliary fields from the ResourceRelationship and MeasurementOrFact classes are of somewhat limited utility here - you could only share one MeasurementOrFact and one ResourceRelationship per record." [2].
Why should abundance take precedence over any other potential MeasurementOrFact?
Unlike all other terms in Simple Darwin Core, the labels for the MeasurementOrFact terms will not explicitly state what is in them. There will be no definition to look up in Darwin Core to understand that the content is supposed to be an abundance, or what an abundance is.
With MeasurementOrFact in the Darwin Core Occurrence Core Type [3], data publishers using Darwin Core Archives would be tempted to use the terms to capture the measurement or fact from of most importance to them from their data set, and there would be no guidance to tell them not to do so. A consumer would have to look into the content of the measurementType field to understand what to do with the contents of the other two fields. I'd urge to keep such a mess out of the realm of Simple Darwin Core.
On Thu, Oct 24, 2013 at 1:30 PM, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Following all the excellent contributions on this list relating to expressing abundance data in Darwin Core, I think we may have uncovered a way that does not require any changes to the DwC standard. As has been pointed out, modelling sampling and abundance can be quite complex and challenging and is best done as an ontology (as in the work of the BCO).
From the GBIF perspective, our goal is to make it as simple as possible for
data providers to deliver abundance data (in Darwin Core Archive format) that can support the science for processes such as CBD and IPBES. Here, I am using the term abundance (specifically population abundance) in the sense defined by GEO BON: "Quantity of individuals or biomass of a given taxon or functional group at a given location" [1].
The challenge is to come up with a way for Simple Darwin Core to express abundance data. It looks like we can probably work within the restrictions imposed by Simple Darwin Core [2] and use properties from MeasurementOrFact because, for the use case in question here, we only need to share one MeasurementOrFact per record.
The model: A sample, associated with a sampling protocol has one or more taxon occurrence records each of which has an abundance measure which is expressed using MeasurementOrFact.
At a minimum, we would need the following three MeasurementOrFact properties listed below (with definition and examples):
measurementType The nature of the measurement, fact, characteristic, or assertion. Examples: "tail length", "temperature", "trap line length", "survey area", "trap type".
For abundances we would use: count, percentage
measurementValue The value of the measurement, fact, characteristic, or assertion. Examples: "45", "20", "1", "14.5", "UV-light".
For abundances we would use any numeric value.
measurementMethod A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation.
For abundances we would use: Count/sq metre, count/litre, % of biovolume, % of species, ...
To enable automated processing, we would need to develop a controlled list for measurementMethod and, ideally, there would also be a URI for the sampling protocol used which would be recorded in the dwc:samplingProtocol field.
[1] http://www.earthobservations.org/documents/meetings/201202_geobon_ebv/30_ebv... [2] http://rs.tdwg.org/dwc/terms/simple/index.htm#rules [3] http://rs.gbif.org/core/dwc_occurrence.xml
I think my use of the term "Simple Darwin Core" was misleading. I was not suggesting putting a MeasurementOrfact in an Occurrence core. Rather we would create a new core as discussed in the DwC sample workshop - let's call it samplingEvent for now. Its properties would be drawn from Simple DwC (mainly Event, Location classes). We would then create an abundance extension consisting of occurrence records each of which has a single MeasurementOrFact along the lines I indicated. The extension name would indicate the nature of the MeasurementOrFact to a consuming application.
-----Original Message----- From: gtuco.btuco@gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: 24 October 2013 14:26 To: Éamonn Ó Tuama [GBIF] Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
I see several problems with using MeasurementOrFact in this way.
What happens when someone wants to add the next MeasurementOrFact to "Simple" Darwin Core? They won't be able to. "Every field in the Simple Darwin Core may appear either once or not at all in a single record - otherwise how could you distinguish one scientificName field from another one? Think of a database table. It will not allow you to have the same name for two different fields. Because of this design restriction (lack of flexibility for the sake of simplicity), the auxiliary fields from the ResourceRelationship and MeasurementOrFact classes are of somewhat limited utility here - you could only share one MeasurementOrFact and one ResourceRelationship per record." [2].
Why should abundance take precedence over any other potential MeasurementOrFact?
Unlike all other terms in Simple Darwin Core, the labels for the MeasurementOrFact terms will not explicitly state what is in them. There will be no definition to look up in Darwin Core to understand that the content is supposed to be an abundance, or what an abundance is.
With MeasurementOrFact in the Darwin Core Occurrence Core Type [3], data publishers using Darwin Core Archives would be tempted to use the terms to capture the measurement or fact from of most importance to them from their data set, and there would be no guidance to tell them not to do so. A consumer would have to look into the content of the measurementType field to understand what to do with the contents of the other two fields. I'd urge to keep such a mess out of the realm of Simple Darwin Core.
On Thu, Oct 24, 2013 at 1:30 PM, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Following all the excellent contributions on this list relating to expressing abundance data in Darwin Core, I think we may have uncovered a way that does not require any changes to the DwC standard. As has been pointed out, modelling sampling and abundance can be quite complex and challenging and is best done as an ontology (as in the work of
the BCO).
From the GBIF perspective, our goal is to make it as simple as possible for
data providers to deliver abundance data (in Darwin Core Archive format) that can support the science for processes such as CBD and IPBES. Here, I am using the term abundance (specifically population abundance) in the sense defined by GEO BON: "Quantity of individuals or biomass of a given taxon or functional group at a given location" [1].
The challenge is to come up with a way for Simple Darwin Core to express abundance data. It looks like we can probably work within the restrictions imposed by Simple Darwin Core [2] and use properties from MeasurementOrFact because, for the use case in question here, we only need to share one MeasurementOrFact per record.
The model: A sample, associated with a sampling protocol has one or more taxon occurrence records each of which has an abundance measure which is expressed using MeasurementOrFact.
At a minimum, we would need the following three MeasurementOrFact properties listed below (with definition and examples):
measurementType The nature of the measurement, fact, characteristic, or assertion. Examples: "tail length", "temperature", "trap line length", "survey area", "trap type".
For abundances we would use: count, percentage
measurementValue The value of the measurement, fact, characteristic, or assertion. Examples: "45", "20", "1", "14.5", "UV-light".
For abundances we would use any numeric value.
measurementMethod A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or
assertion.
Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation.
For abundances we would use: Count/sq metre, count/litre, % of biovolume, % of species, ...
To enable automated processing, we would need to develop a controlled list for measurementMethod and, ideally, there would also be a URI for the sampling protocol used which would be recorded in the dwc:samplingProtocol field.
[1] http://www.earthobservations.org/documents/meetings/201202_geobon_ebv/30_ebv _species_table_v2.pdf [2] http://rs.tdwg.org/dwc/terms/simple/index.htm#rules [3] http://rs.gbif.org/core/dwc_occurrence.xml
I see what you are proposing, but I think there some things that have to be thought through carefully. First, why would a new core type be needed? In the Darwin Core Workshop we concluded that we could cast almost every use case with an Occurrence Core in a star schema. For the abundance case, we could construct records with a normal Occurrence Core and MeasurementOrFact extension. Or even with an abundance extension, where the abundance terms were defined outside of Darwin Core.
If we had a MeasurementOrFact extension specifically for abundance, what are the technical implications when somebody sees how you've done that and says, "Hey, I could do that for body mass too?" Now we would have another extension based on MeasurementOrFact. If you try to flatten the results, which would be reasonable since the relationships between the Core and each extension are logically one-to-one, you'll end up with duplication of column names again.
So, whereas I see that you could do this, I'm not convinced it is a good idea. I'm willing to be convinced though, because it could be brilliant and I am just being incapable of seeing it.
On Thursday, October 24, 2013, Éamonn Ó Tuama [GBIF] wrote:
I think my use of the term "Simple Darwin Core" was misleading. I was not suggesting putting a MeasurementOrfact in an Occurrence core. Rather we would create a new core as discussed in the DwC sample workshop - let's call it samplingEvent for now. Its properties would be drawn from Simple DwC (mainly Event, Location classes). We would then create an abundance extension consisting of occurrence records each of which has a single MeasurementOrFact along the lines I indicated. The extension name would indicate the nature of the MeasurementOrFact to a consuming application.
-----Original Message----- From: gtuco.btuco@gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: 24 October 2013 14:26 To: Éamonn Ó Tuama [GBIF] Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
I see several problems with using MeasurementOrFact in this way.
What happens when someone wants to add the next MeasurementOrFact to "Simple" Darwin Core? They won't be able to. "Every field in the Simple Darwin Core may appear either once or not at all in a single record - otherwise how could you distinguish one scientificName field from another one? Think of a database table. It will not allow you to have the same name for two different fields. Because of this design restriction (lack of flexibility for the sake of simplicity), the auxiliary fields from the ResourceRelationship and MeasurementOrFact classes are of somewhat limited utility here - you could only share one MeasurementOrFact and one ResourceRelationship per record." [2].
Why should abundance take precedence over any other potential MeasurementOrFact?
Unlike all other terms in Simple Darwin Core, the labels for the MeasurementOrFact terms will not explicitly state what is in them. There will be no definition to look up in Darwin Core to understand that the content is supposed to be an abundance, or what an abundance is.
With MeasurementOrFact in the Darwin Core Occurrence Core Type [3], data publishers using Darwin Core Archives would be tempted to use the terms to capture the measurement or fact from of most importance to them from their data set, and there would be no guidance to tell them not to do so. A consumer would have to look into the content of the measurementType field to understand what to do with the contents of the other two fields. I'd urge to keep such a mess out of the realm of Simple Darwin Core.
On Thu, Oct 24, 2013 at 1:30 PM, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Following all the excellent contributions on this list relating to expressing abundance data in Darwin Core, I think we may have uncovered a way that does not require any changes to the DwC standard. As has been pointed out, modelling sampling and abundance can be quite complex and challenging and is best done as an ontology (as in the work
of the BCO).
From the GBIF perspective, our goal is to make it as simple as possible for
data providers to deliver abundance data (in Darwin Core Archive format) that can support the science for processes such as CBD and IPBES. Here, I am using the term abundance (specifically population abundance) in the sense defined by GEO BON: "Quantity of individuals or biomass of a given taxon or functional group at a given location" [1].
The challenge is to come up with a way for Simple Darwin Core to express abundance data. It looks like we can probably work within the restrictions imposed by Simple Darwin Core [2] and use properties from MeasurementOrFact because, for the use case in question here, we only need to share one MeasurementOrFact per record.
The model: A sample, associated with a sampling protocol has one or more taxon occurrence records each of which has an abundance measure which is expressed using MeasurementOrFact.
At a minimum, we would need the following three MeasurementOrFact properties listed below (with definition and examples):
measurementType The nature of the measurement, fact, characteristic, or assertion. Examples: "tail length", "temperature", "trap line length", "survey area", "trap type".
For abundances we would use: count, percentage
measurementValue The value of the measurement, fact, characteristic, or assertion. Examples: "45", "20", "1", "14.5", "UV-light".
For abundances we would use any numeric value.
measurementMethod A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or
assertion.
Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation.
For abundances we would use: Count/sq metre, count/litre, % of biovolume, % of species, ...
To enable automated processing, we would need to develop a controlled list for measurementMethod and, ideally, there would also be a URI for the sampling protocol used which would be recorded in the dwc:samplingProtocol field.
[1]
participants (2)
-
John Wieczorek -
Éamonn Ó Tuama [GBIF]