Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent - tdwg-content

27 Sep 2013

      Aaike's suggestion of using the abundance field to store just the numeric
value and then provide another field called abundanceUnit/abundanceType to
specify what the value is does look like it might be a more workable,
machine processable solution. It would, of course, require that the value be
selected from a controlled list. At a guess, I do not think that list would
be very long but we would need to define it in association with the property
abundanceUnit/abundanceType.

Eamonn
...
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 %)?
...
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)
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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:
-
...
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
...
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)
------------------------------

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:
-
...
...
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.org>wrote:
...
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
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--
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>
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Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent

Éamonn Ó Tuama [GBIF]

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