Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence.
In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
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Today's Topics:
- Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Hannu Saarenmaa)
Message: 1 Date: Sat, 28 Sep 2013 08:25:55 +0300 From: Hannu Saarenmaa hannu@bioshare.com Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: 'TDWG Content Mailing List' tdwg-content@lists.tdwg.org Message-ID: 52466863.8050703@bioshare.com Content-Type: text/plain; charset="iso-8859-1"
Basically I support the views of Aaike and Donald. Keep the quantity and unit separate. No need for special term for AbundanceAsPercentage, then.
However, I am a bit uncertain whether "Abundance" is the right term. How about "Quantity"? It is more generic, and can be applied for example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters of timber. "Abundance" is semantically not right for those measures.
I also think that a range for the quantity is needed, to express uncertainty about the quantity. I saw about 1000 geese this morning, certainly more than 500 but less than 2000. Uncertainty is so common in sightings.
Are we also going to deprecate "IndividualCount"? I hope so.
Hannu
--
Hannu Saarenmaa, Research Director hannu.saarenmaa@helsinki.fi Mobile +358-50-4479668
University of Eastern Finland School of Computing, SIB Labs, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FIN-80101 Joensuu
www.digitarium.fi - Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland www.biovel.eu - Workflows for Scientific Research www.eubon.eu - EU BON - GEO BON - Data Integration and Interoperability
On 2013-09-26 18:07, Donald Hobern [GBIF] wrote:
Hi Rob.
I understand your concern, but my concern is with the opportunities we are currently missing to enable our occurrence mobilisation processes to offer significantly more value in many contexts.
Some of the problem may be in the use of the word "abundance". If we understand "abundance" to refer to the size and density of a population or species, then a survey may give us a workable measure we can use to represent this. I am thinking of mobilisation of less ambitious measurements of relative abundance of a taxon in any sampling event or set of associated observations. I visit a reservoir and follow some standard protocol and count 30 mallards and a single gadwall. Today that might be exposed in simple Darwin Core as two occurrence records, each of which might somehow include an individualCount. In the absence of any other information, this count information cannot be seen as much more than an anecdotal annotation. If we understood that these two observations were part of a single survey event associated with a protocol also used for some number of other survey events for which we have observations, we could (in principle) find more ways to explore the significance of the count and use it to help to fine-tune distribution models and to enhance them to indicate patterns of abundance. If we can find a way to do this consistently for all types of biodiversity observation (malaise traps, transects, expression of ITS or CO1 from environmental samples), a large number of databases already contributing to GBIF and other networks could immediately offer a richer view to users and analysts.
I believe we could readily handle this with three properties that are available for use with any occurrence -- a sampling event id, a sampling protocol identifier (ideally a URL leading to information on the protocol) and a relative abundance value within that sample. Any occurrence record could include these fields if appropriate. Of course more normalisation is possible, but DwC has never been about full normalisation.
We can debate which DwC classes ought to include support for such elements. I personally think we've tied ourselves in unnecessary knots with our use of Occurrences, Events, Material Samples, etc. I wish we just had an agreed meta-model/ontology which provides a graph of classes of interest to our domain (specimen, collection, taxon concept, taxon name, locality, collector, etc.) and a set of uniquely named properties each of which is associated with one of these classes or links instances of these classes. Darwin Core should then allow for the denormalised representation of any view corresponding to a subgraph of that model. Occurrence, Event, etc. should then be names for popularly-used subgraphs and should represent the logic for unpacking those denormalised DwC records back into a graph of meta-model objects (in other words they should express something like what SPARQL query might be able to extract this kind of record from data organised using the meta-model/ontology).
Best wishes,
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org mailto: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
*From:*robgur@gmail.com [mailto:robgur@gmail.com] *On Behalf Of *Robert Guralnick *Sent:* Thursday, September 26, 2013 4:37 PM *To:* Donald Hobern [GBIF] *Cc:* John Wieczorek; TDWG Content Mailing List *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
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 mailto: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 <mailto:
dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480 tel:%2B45%202875%201480
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From: gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com [mailto: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 mailto: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 mailto: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
mailto:dhobern@gbif.org Global Biodiversity
Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480 tel:%2B45%202875%201480
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[mailto: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 mailto: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/ <
http://rs.tdwg.org/dwc/terms/%3E
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/ <
http://rs.tdwg.org/dwc/terms/%3E
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 mailto: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 tel:%2B32%280%292%20627%2043%2090 mobile.: +32(0)486 28 05 93 tel:%2B32%280%29486%2028%2005%2093 email: <aaike.dewever@naturalsciences.be
mailto: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 mailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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Hi everyone --- Respectful, minor disagreement with Ramona on one point. A "survey" is defined as a "examin[ation] and record[ing] [of] the area and features of (an area of land) so as to construct a map, plan, or description." So I a not sure I think Hannu spottiing ~1000 geese (which is a nice image) is a survey, per se -- there is no assessment of the area recorded or a process described about doing "survery things", which seems critical to me. It is what might be called a "sighting" by an ecologist. I think these terms do matter in the discussion at hand.
Inherent in Ramona's email is something about which I agree and think is important. I think Ramona was pointing out that some quantities about numbers of "biological things" are tied to what we call samples, and some may fit under occurrences. Mostly, I agree that it is complex, and context dependence is particularly important.
Just a reminder about "Abundance" as it was proposed here. This is from John W's original email on this topic. The definition was "The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume". That was the definition. Not sightings. Not records of weight of a bunch of fishes caught in a net. Doesn't this definition rather imply that abundance is derived from a sample?
Unfortunately, looking through this conversation, I don't see clarity emerging. Donald's points are not the same as Aaike's point or Hannu's points. "Abundance" is not "quantity". Aaike wants to separate measurement quantity into one field and call it abundance, and have another for the unit type, when the ecological definition of abundance is basically number of individuals found in a sample, and thus separating units and sampling is not really possible given the definition of the quantity.
I need to ask again: Do we understand what we are doing with abundance well enough to model it in Darwin Core, and if we do it poorly, are we really helping to model ecologically relevant measurements for the scientific community?
Best, Rob
On Sat, Sep 28, 2013 at 8:45 AM, Ramona Walls rlwalls2008@gmail.com wrote:
I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence.
In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one.
Ramona
Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Sat, Sep 28, 2013 at 3:00 AM, tdwg-content-request@lists.tdwg.orgwrote:
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Today's Topics:
- Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Hannu Saarenmaa)
Message: 1 Date: Sat, 28 Sep 2013 08:25:55 +0300 From: Hannu Saarenmaa hannu@bioshare.com
Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: 'TDWG Content Mailing List' tdwg-content@lists.tdwg.org Message-ID: 52466863.8050703@bioshare.com Content-Type: text/plain; charset="iso-8859-1"
Basically I support the views of Aaike and Donald. Keep the quantity and unit separate. No need for special term for AbundanceAsPercentage, then.
However, I am a bit uncertain whether "Abundance" is the right term. How about "Quantity"? It is more generic, and can be applied for example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters of timber. "Abundance" is semantically not right for those measures.
I also think that a range for the quantity is needed, to express uncertainty about the quantity. I saw about 1000 geese this morning, certainly more than 500 but less than 2000. Uncertainty is so common in sightings.
Are we also going to deprecate "IndividualCount"? I hope so.
Hannu
--
Hannu Saarenmaa, Research Director hannu.saarenmaa@helsinki.fi Mobile +358-50-4479668
University of Eastern Finland School of Computing, SIB Labs, Joensuu Science Park L?nsikatu 15 (P.O. Box 111)
FIN-80101 Joensuu
www.digitarium.fi - Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland www.biovel.eu - Workflows for Scientific Research www.eubon.eu - EU BON - GEO BON - Data Integration and Interoperability
On 2013-09-26 18:07, Donald Hobern [GBIF] wrote:
Hi Rob.
I understand your concern, but my concern is with the opportunities we are currently missing to enable our occurrence mobilisation processes to offer significantly more value in many contexts.
Some of the problem may be in the use of the word "abundance". If we understand "abundance" to refer to the size and density of a population or species, then a survey may give us a workable measure we can use to represent this. I am thinking of mobilisation of less ambitious measurements of relative abundance of a taxon in any sampling event or set of associated observations. I visit a reservoir and follow some standard protocol and count 30 mallards and a single gadwall. Today that might be exposed in simple Darwin Core as two occurrence records, each of which might somehow include an individualCount. In the absence of any other information, this count information cannot be seen as much more than an anecdotal annotation. If we understood that these two observations were part of a single survey event associated with a protocol also used for some number of other survey events for which we have observations, we could (in principle) find more ways to explore the significance of the count and use it to help to fine-tune distribution models and to enhance them to indicate patterns of abundance. If we can find a way to do this consistently for all types of biodiversity observation (malaise traps, transects, expression of ITS or CO1 from environmental samples), a large number of databases already contributing to GBIF and other networks could immediately offer a richer view to users and analysts.
I believe we could readily handle this with three properties that are available for use with any occurrence -- a sampling event id, a
sampling protocol identifier (ideally a URL leading to information on the protocol) and a relative abundance value within that sample. Any occurrence record could include these fields if appropriate. Of course more normalisation is possible, but DwC has never been about full normalisation.
We can debate which DwC classes ought to include support for such elements. I personally think we've tied ourselves in unnecessary knots with our use of Occurrences, Events, Material Samples, etc. I wish we just had an agreed meta-model/ontology which provides a graph of classes of interest to our domain (specimen, collection, taxon concept, taxon name, locality, collector, etc.) and a set of uniquely named properties each of which is associated with one of these classes or links instances of these classes. Darwin Core should then allow for the denormalised representation of any view corresponding to a subgraph of that model. Occurrence, Event, etc. should then be names for popularly-used subgraphs and should represent the logic for unpacking those denormalised DwC records back into a graph of meta-model objects (in other words they should express something like what SPARQL query might be able to extract this kind of record from data organised using the meta-model/ontology).
Best wishes,
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org mailto: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
*From:*robgur@gmail.com [mailto:robgur@gmail.com] *On Behalf Of *Robert Guralnick *Sent:* Thursday, September 26, 2013 4:37 PM *To:* Donald Hobern [GBIF] *Cc:* John Wieczorek; TDWG Content Mailing List *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms -
abundance, abundanceAsPercent
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 mailto: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 <mailto:
dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480 tel:%2B45%202875%201480
-----Original Message-----
From: gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com [mailto: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 mailto: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 mailto: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
mailto:dhobern@gbif.org Global Biodiversity
Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480 tel:%2B45%202875%201480
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[mailto: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 mailto: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/ <
http://rs.tdwg.org/dwc/terms/%3E
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/ <
http://rs.tdwg.org/dwc/terms/%3E
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 mailto:tdwg-content@lists.tdwg.org
-- 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 tel:%2B32%280%292%20627%2043%2090 mobile.: +32(0)486 28 05 93 tel:%2B32%280%29486%2028%2005%2093 email: <aaike.dewever@naturalsciences.be
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Minor point, but I did not mean to imply that observing geese was a survey - it is an observation. My point was that both observations and surveys are NOT material samples.
I also now see Rob's point re. making abundance a property of material samples in that the original definition proposed was ""The number of individuals of a taxon found in a sample..." Sorry I missed that earlier (I hate long email threads). This definition has a much narrower scope than what people have been discussing on this list (which is a good thing - DwC goes astray sometimes in trying to write definitions that cover everything), but it also does not define what many ecologists are talking about when they use the term abundance. If DwC needs a term for the number of individuals in a sample, simply call it something like "number of individuals in a sample", not "abundance" or "quantity" or some other vague and ambiguous name. Of course, I think that property already exists with "individualCount".
Assuming that DwC is going to continue to be used to describe survey data (a separate debate), I feel that there is a place in DwC for the concept of abundance (as it is typically used to describe the absolute or relative numbers of a taxon in a specified area over a specified time, and typically determined by some kind of survey), but I think it makes more sense to spend some time modeling it in the BCO and PCO first, then -- once there is some consensus about what abundance means logically -- see how it can fit into DwC.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Sat, Sep 28, 2013 at 8:20 AM, Robert Guralnick < Robert.Guralnick@colorado.edu> wrote:
Hi everyone --- Respectful, minor disagreement with Ramona on one point. A "survey" is defined as a "examin[ation] and record[ing] [of] the area and features of (an area of land) so as to construct a map, plan, or description." So I a not sure I think Hannu spottiing ~1000 geese (which is a nice image) is a survey, per se -- there is no assessment of the area recorded or a process described about doing "survery things", which seems critical to me. It is what might be called a "sighting" by an ecologist. I think these terms do matter in the discussion at hand.
Inherent in Ramona's email is something about which I agree and think is important. I think Ramona was pointing out that some quantities about numbers of "biological things" are tied to what we call samples, and some may fit under occurrences. Mostly, I agree that it is complex, and context dependence is particularly important.
Just a reminder about "Abundance" as it was proposed here. This is from John W's original email on this topic. The definition was "The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume". That was the definition. Not sightings. Not records of weight of a bunch of fishes caught in a net. Doesn't this definition rather imply that abundance is derived from a sample?
Unfortunately, looking through this conversation, I don't see clarity emerging. Donald's points are not the same as Aaike's point or Hannu's points. "Abundance" is not "quantity". Aaike wants to separate measurement quantity into one field and call it abundance, and have another for the unit type, when the ecological definition of abundance is basically number of individuals found in a sample, and thus separating units and sampling is not really possible given the definition of the quantity.
I need to ask again: Do we understand what we are doing with abundance well enough to model it in Darwin Core, and if we do it poorly, are we really helping to model ecologically relevant measurements for the scientific community?
Best, Rob
On Sat, Sep 28, 2013 at 8:45 AM, Ramona Walls rlwalls2008@gmail.comwrote:
I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence.
In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one.
Ramona
Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Sat, Sep 28, 2013 at 3:00 AM, tdwg-content-request@lists.tdwg.orgwrote:
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Today's Topics:
- Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Hannu Saarenmaa)
Message: 1 Date: Sat, 28 Sep 2013 08:25:55 +0300 From: Hannu Saarenmaa hannu@bioshare.com
Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: 'TDWG Content Mailing List' tdwg-content@lists.tdwg.org Message-ID: 52466863.8050703@bioshare.com Content-Type: text/plain; charset="iso-8859-1"
Basically I support the views of Aaike and Donald. Keep the quantity and unit separate. No need for special term for AbundanceAsPercentage, then.
However, I am a bit uncertain whether "Abundance" is the right term. How about "Quantity"? It is more generic, and can be applied for example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters of timber. "Abundance" is semantically not right for those measures.
I also think that a range for the quantity is needed, to express uncertainty about the quantity. I saw about 1000 geese this morning, certainly more than 500 but less than 2000. Uncertainty is so common in sightings.
Are we also going to deprecate "IndividualCount"? I hope so.
Hannu
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University of Eastern Finland School of Computing, SIB Labs, Joensuu Science Park L?nsikatu 15 (P.O. Box 111)
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On 2013-09-26 18:07, Donald Hobern [GBIF] wrote:
Hi Rob.
I understand your concern, but my concern is with the opportunities we are currently missing to enable our occurrence mobilisation processes to offer significantly more value in many contexts.
Some of the problem may be in the use of the word "abundance". If we understand "abundance" to refer to the size and density of a population or species, then a survey may give us a workable measure we can use to represent this. I am thinking of mobilisation of less ambitious measurements of relative abundance of a taxon in any sampling event or set of associated observations. I visit a reservoir and follow some standard protocol and count 30 mallards and a single gadwall. Today that might be exposed in simple Darwin Core as two occurrence records, each of which might somehow include an individualCount. In the absence of any other information, this count information cannot be seen as much more than an anecdotal annotation. If we understood that these two observations were part of a single survey event associated with a protocol also used for some number of other survey events for which we have observations, we could (in principle) find more ways to explore the significance of the count and use it to help to fine-tune distribution models and to enhance them to indicate patterns of abundance. If we can find a way to do this consistently for all types of biodiversity observation (malaise traps, transects, expression of ITS or CO1 from environmental samples), a large number of databases already contributing to GBIF and other networks could immediately offer a richer view to users and analysts.
I believe we could readily handle this with three properties that are available for use with any occurrence -- a sampling event id, a
sampling protocol identifier (ideally a URL leading to information on the protocol) and a relative abundance value within that sample. Any occurrence record could include these fields if appropriate. Of course more normalisation is possible, but DwC has never been about full normalisation.
We can debate which DwC classes ought to include support for such elements. I personally think we've tied ourselves in unnecessary knots with our use of Occurrences, Events, Material Samples, etc. I wish we just had an agreed meta-model/ontology which provides a graph of classes of interest to our domain (specimen, collection, taxon concept, taxon name, locality, collector, etc.) and a set of uniquely named properties each of which is associated with one of these classes or links instances of these classes. Darwin Core should then allow for the denormalised representation of any view corresponding to a subgraph of that model. Occurrence, Event, etc. should then be names for popularly-used subgraphs and should represent the logic for unpacking those denormalised DwC records back into a graph of meta-model objects (in other words they should express something like what SPARQL query might be able to extract this kind of record from data organised using the meta-model/ontology).
Best wishes,
Donald
Donald Hobern - GBIF Director - dhobern@gbif.org mailto: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
*From:*robgur@gmail.com [mailto:robgur@gmail.com] *On Behalf Of *Robert Guralnick *Sent:* Thursday, September 26, 2013 4:37 PM *To:* Donald Hobern [GBIF] *Cc:* John Wieczorek; TDWG Content Mailing List *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms -
abundance, abundanceAsPercent
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 mailto: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 <mailto:
dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480tel:%2B45%202875%201480
-----Original Message-----
From: gtuco.btuco@gmail.com mailto:gtuco.btuco@gmail.com [mailto: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 mailto: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 mailto: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
mailto:dhobern@gbif.org Global Biodiversity
Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 tel:%2B45%203532%201471 Mob: +45 2875 1471
tel:%2B45%202875%201471 Fax: +45 2875 1480tel:%2B45%202875%201480
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org
mailto:tdwg-content-bounces@lists.tdwg.org
[mailto: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 mailto: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/ <
http://rs.tdwg.org/dwc/terms/%3E
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/ <
http://rs.tdwg.org/dwc/terms/%3E
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 mailto:tdwg-content@lists.tdwg.org
-- 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 tel:%2B32%280%292%20627%2043%2090 mobile.: +32(0)486 28 05 93 tel:%2B32%280%29486%2028%2005%2093 email: <aaike.dewever@naturalsciences.be
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I agree Rob that the discussion has gone somewhat astray (context is so critical!) And as a measure proportion or percentage in a material sample, I think "abundance" (unqualified) is not a good choice of concept name because its too easily confused with the meaning in survey or ecological data. But I would also note that the concept of proportion in a sample applies very well to sampling events where no material is collected. Are those concepts equivalent/same-as? They seem close. Let's think carefully before we apply this concept to the material sample class without thinking about how it applies to the occurrence class.
If a biologist uses "abundance" in reference to the occurrence of organisms in nature, it is most fundamentally about the intersection of taxon-place-time (all of which can be scoped wider or narrower in precision). Take away any of those elements of context and the "meaning" is lost. Also abundance can (should) be conceived in a statistical framework if additional metadata are provided. I would say that the additional metadata is what really distinguishes measures of abundance (density, etc.) from the typical natural history collection specimen's data about its origin.
Finally, the statistician in me compels me to say that it's better to report raw numbers (with metadata) than already partially computed statistics (like proportions).
-Stan
From: Ramona Walls <rlwalls2008@gmail.commailto:rlwalls2008@gmail.com> Date: Saturday, September 28, 2013 9:08 AM To: Robert Guralnick <Robert.Guralnick@colorado.edumailto:Robert.Guralnick@colorado.edu> Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Minor point, but I did not mean to imply that observing geese was a survey - it is an observation. My point was that both observations and surveys are NOT material samples.
I also now see Rob's point re. making abundance a property of material samples in that the original definition proposed was ""The number of individuals of a taxon found in a sample..." Sorry I missed that earlier (I hate long email threads). This definition has a much narrower scope than what people have been discussing on this list (which is a good thing - DwC goes astray sometimes in trying to write definitions that cover everything), but it also does not define what many ecologists are talking about when they use the term abundance. If DwC needs a term for the number of individuals in a sample, simply call it something like "number of individuals in a sample", not "abundance" or "quantity" or some other vague and ambiguous name. Of course, I think that property already exists with "individualCount".
Assuming that DwC is going to continue to be used to describe survey data (a separate debate), I feel that there is a place in DwC for the concept of abundance (as it is typically used to describe the absolute or relative numbers of a taxon in a specified area over a specified time, and typically determined by some kind of survey), but I think it makes more sense to spend some time modeling it in the BCO and PCO first, then -- once there is some consensus about what abundance means logically -- see how it can fit into DwC.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Sat, Sep 28, 2013 at 8:20 AM, Robert Guralnick <Robert.Guralnick@colorado.edumailto:Robert.Guralnick@colorado.edu> wrote:
Hi everyone --- Respectful, minor disagreement with Ramona on one point. A "survey" is defined as a "examin[ation] and record[ing] [of] the area and features of (an area of land) so as to construct a map, plan, or description." So I a not sure I think Hannu spottiing ~1000 geese (which is a nice image) is a survey, per se -- there is no assessment of the area recorded or a process described about doing "survery things", which seems critical to me. It is what might be called a "sighting" by an ecologist. I think these terms do matter in the discussion at hand.
Inherent in Ramona's email is something about which I agree and think is important. I think Ramona was pointing out that some quantities about numbers of "biological things" are tied to what we call samples, and some may fit under occurrences. Mostly, I agree that it is complex, and context dependence is particularly important.
Just a reminder about "Abundance" as it was proposed here. This is from John W's original email on this topic. The definition was "The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume". That was the definition. Not sightings. Not records of weight of a bunch of fishes caught in a net. Doesn't this definition rather imply that abundance is derived from a sample?
Unfortunately, looking through this conversation, I don't see clarity emerging. Donald's points are not the same as Aaike's point or Hannu's points. "Abundance" is not "quantity". Aaike wants to separate measurement quantity into one field and call it abundance, and have another for the unit type, when the ecological definition of abundance is basically number of individuals found in a sample, and thus separating units and sampling is not really possible given the definition of the quantity.
I need to ask again: Do we understand what we are doing with abundance well enough to model it in Darwin Core, and if we do it poorly, are we really helping to model ecologically relevant measurements for the scientific community?
Best, Rob
On Sat, Sep 28, 2013 at 8:45 AM, Ramona Walls <rlwalls2008@gmail.commailto:rlwalls2008@gmail.com> wrote: I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence.
In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
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Today's Topics:
1. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Hannu Saarenmaa)
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Message: 1 Date: Sat, 28 Sep 2013 08:25:55 +0300 From: Hannu Saarenmaa <hannu@bioshare.commailto:hannu@bioshare.com>
Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: 'TDWG Content Mailing List' <tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org> Message-ID: <52466863.8050703@bioshare.commailto:52466863.8050703@bioshare.com> Content-Type: text/plain; charset="iso-8859-1"
Basically I support the views of Aaike and Donald. Keep the quantity and unit separate. No need for special term for AbundanceAsPercentage, then.
However, I am a bit uncertain whether "Abundance" is the right term. How about "Quantity"? It is more generic, and can be applied for example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters of timber. "Abundance" is semantically not right for those measures.
I also think that a range for the quantity is needed, to express uncertainty about the quantity. I saw about 1000 geese this morning, certainly more than 500 but less than 2000. Uncertainty is so common in sightings.
Are we also going to deprecate "IndividualCount"? I hope so.
Hannu
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On 2013-09-26 18:07, Donald Hobern [GBIF] wrote:
Hi Rob.
I understand your concern, but my concern is with the opportunities we are currently missing to enable our occurrence mobilisation processes to offer significantly more value in many contexts.
Some of the problem may be in the use of the word "abundance". If we understand "abundance" to refer to the size and density of a population or species, then a survey may give us a workable measure we can use to represent this. I am thinking of mobilisation of less ambitious measurements of relative abundance of a taxon in any sampling event or set of associated observations. I visit a reservoir and follow some standard protocol and count 30 mallards and a single gadwall. Today that might be exposed in simple Darwin Core as two occurrence records, each of which might somehow include an individualCount. In the absence of any other information, this count information cannot be seen as much more than an anecdotal annotation. If we understood that these two observations were part of a single survey event associated with a protocol also used for some number of other survey events for which we have observations, we could (in principle) find more ways to explore the significance of the count and use it to help to fine-tune distribution models and to enhance them to indicate patterns of abundance. If we can find a way to do this consistently for all types of biodiversity observation (malaise traps, transects, expression of ITS or CO1 from environmental samples), a large number of databases already contributing to GBIF and other networks could immediately offer a richer view to users and analysts.
I believe we could readily handle this with three properties that are available for use with any occurrence -- a sampling event id, a
sampling protocol identifier (ideally a URL leading to information on the protocol) and a relative abundance value within that sample. Any occurrence record could include these fields if appropriate. Of course more normalisation is possible, but DwC has never been about full normalisation.
We can debate which DwC classes ought to include support for such elements. I personally think we've tied ourselves in unnecessary knots with our use of Occurrences, Events, Material Samples, etc. I wish we just had an agreed meta-model/ontology which provides a graph of classes of interest to our domain (specimen, collection, taxon concept, taxon name, locality, collector, etc.) and a set of uniquely named properties each of which is associated with one of these classes or links instances of these classes. Darwin Core should then allow for the denormalised representation of any view corresponding to a subgraph of that model. Occurrence, Event, etc. should then be names for popularly-used subgraphs and should represent the logic for unpacking those denormalised DwC records back into a graph of meta-model objects (in other words they should express something like what SPARQL query might be able to extract this kind of record from data organised using the meta-model/ontology).
Best wishes,
Donald
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*From:*robgur@gmail.commailto:robgur@gmail.com [mailto:robgur@gmail.commailto:robgur@gmail.com] *On Behalf Of *Robert Guralnick *Sent:* Thursday, September 26, 2013 4:37 PM *To:* Donald Hobern [GBIF] *Cc:* John Wieczorek; TDWG Content Mailing List *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms -
abundance, abundanceAsPercent
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.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto: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
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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.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto: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.orgmailto:dhobern@gbif.org
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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/http://rs.tdwg.org/dwc/terms/ 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/http://rs.tdwg.org/dwc/terms/ 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.orgmailto:tdwg-content@lists.tdwg.org <mailto:tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org>
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Some thoughts about usage of some of the terms under discussion and the ultimate goals
I often use the term "abundance" as a refinement of the term "occurrence".
I say "Species X occurs or does not occur at Location L. This kind of statement is refined with a statement such as "Females are rare in March" or "Juveniles are common or very abundant in July". The details of the life stage, timing and numbers of individuals or groups are more specific but still categorical.
I think of such statements as being derived from "expert opinion" or being summary statements based on enumerations from a series of samples taken during several field trips. I think these kinds of generalities are useful for policy making.
In terms of data, the simplest category is "presence only" data. Some times this is referred to as occurrence data - some number of individuals are seen at a particular time and location. Many museum records fall into this category as there is no other information associated with the specimen. Such records are equivalent to an incidental sighting by a field ecologist.
Today many biodiversity data are collect following a particular protocol. Here sampling effort is known. A specific number of individuals seen in a "given area" and during a known time interval. From this information one can compute population densities.
As several others have commented, the results are dependent on the particular protocols and it can be difficult to reconcile data from two different protocols. How are data from pitfall traps equivalent to data from baits.....? This is an important challenge because we know that usually one and often two protocols are insufficient to characterize the presence of all members of a taxon
If I am not mistaken, the goal is to establish terms that will let humans efficiently prepare data and write programs so that machines can reason with the data. If so, the key challenges seem to be
1) Distinguishing presence-only data from data collected using known protocols 2) Finding ways to reconcile data from different protocols
Rob Stevenson
Rob Stevenson Biology Department UMass Boston
On Sep 28, 2013, at 1:23 PM, "Blum, Stan" <SBlum@calacademy.orgmailto:SBlum@calacademy.org> wrote:
I agree Rob that the discussion has gone somewhat astray (context is so critical!) And as a measure proportion or percentage in a material sample, I think "abundance" (unqualified) is not a good choice of concept name because its too easily confused with the meaning in survey or ecological data. But I would also note that the concept of proportion in a sample applies very well to sampling events where no material is collected. Are those concepts equivalent/same-as? They seem close. Let's think carefully before we apply this concept to the material sample class without thinking about how it applies to the occurrence class.
If a biologist uses "abundance" in reference to the occurrence of organisms in nature, it is most fundamentally about the intersection of taxon-place-time (all of which can be scoped wider or narrower in precision). Take away any of those elements of context and the "meaning" is lost. Also abundance can (should) be conceived in a statistical framework if additional metadata are provided. I would say that the additional metadata is what really distinguishes measures of abundance (density, etc.) from the typical natural history collection specimen's data about its origin.
Finally, the statistician in me compels me to say that it's better to report raw numbers (with metadata) than already partially computed statistics (like proportions).
-Stan
From: Ramona Walls <rlwalls2008@gmail.commailto:rlwalls2008@gmail.com> Date: Saturday, September 28, 2013 9:08 AM To: Robert Guralnick <Robert.Guralnick@colorado.edumailto:Robert.Guralnick@colorado.edu> Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Minor point, but I did not mean to imply that observing geese was a survey - it is an observation. My point was that both observations and surveys are NOT material samples.
I also now see Rob's point re. making abundance a property of material samples in that the original definition proposed was ""The number of individuals of a taxon found in a sample..." Sorry I missed that earlier (I hate long email threads). This definition has a much narrower scope than what people have been discussing on this list (which is a good thing - DwC goes astray sometimes in trying to write definitions that cover everything), but it also does not define what many ecologists are talking about when they use the term abundance. If DwC needs a term for the number of individuals in a sample, simply call it something like "number of individuals in a sample", not "abundance" or "quantity" or some other vague and ambiguous name. Of course, I think that property already exists with "individualCount".
Assuming that DwC is going to continue to be used to describe survey data (a separate debate), I feel that there is a place in DwC for the concept of abundance (as it is typically used to describe the absolute or relative numbers of a taxon in a specified area over a specified time, and typically determined by some kind of survey), but I think it makes more sense to spend some time modeling it in the BCO and PCO first, then -- once there is some consensus about what abundance means logically -- see how it can fit into DwC.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
On Sat, Sep 28, 2013 at 8:20 AM, Robert Guralnick <Robert.Guralnick@colorado.edumailto:Robert.Guralnick@colorado.edu> wrote:
Hi everyone --- Respectful, minor disagreement with Ramona on one point. A "survey" is defined as a "examin[ation] and record[ing] [of] the area and features of (an area of land) so as to construct a map, plan, or description." So I a not sure I think Hannu spottiing ~1000 geese (which is a nice image) is a survey, per se -- there is no assessment of the area recorded or a process described about doing "survery things", which seems critical to me. It is what might be called a "sighting" by an ecologist. I think these terms do matter in the discussion at hand.
Inherent in Ramona's email is something about which I agree and think is important. I think Ramona was pointing out that some quantities about numbers of "biological things" are tied to what we call samples, and some may fit under occurrences. Mostly, I agree that it is complex, and context dependence is particularly important.
Just a reminder about "Abundance" as it was proposed here. This is from John W's original email on this topic. The definition was "The number of individuals of a taxon found in a sample. This is typically expressed as number per unit of area or volume". That was the definition. Not sightings. Not records of weight of a bunch of fishes caught in a net. Doesn't this definition rather imply that abundance is derived from a sample?
Unfortunately, looking through this conversation, I don't see clarity emerging. Donald's points are not the same as Aaike's point or Hannu's points. "Abundance" is not "quantity". Aaike wants to separate measurement quantity into one field and call it abundance, and have another for the unit type, when the ecological definition of abundance is basically number of individuals found in a sample, and thus separating units and sampling is not really possible given the definition of the quantity.
I need to ask again: Do we understand what we are doing with abundance well enough to model it in Darwin Core, and if we do it poorly, are we really helping to model ecologically relevant measurements for the scientific community?
Best, Rob
On Sat, Sep 28, 2013 at 8:45 AM, Ramona Walls <rlwalls2008@gmail.commailto:rlwalls2008@gmail.com> wrote: I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence.
In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one.
Ramona
------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden
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Today's Topics:
1. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Hannu Saarenmaa)
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Message: 1 Date: Sat, 28 Sep 2013 08:25:55 +0300 From: Hannu Saarenmaa <hannu@bioshare.commailto:hannu@bioshare.com>
Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: 'TDWG Content Mailing List' <tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org> Message-ID: <52466863.8050703@bioshare.commailto:52466863.8050703@bioshare.com> Content-Type: text/plain; charset="iso-8859-1"
Basically I support the views of Aaike and Donald. Keep the quantity and unit separate. No need for special term for AbundanceAsPercentage, then.
However, I am a bit uncertain whether "Abundance" is the right term. How about "Quantity"? It is more generic, and can be applied for example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters of timber. "Abundance" is semantically not right for those measures.
I also think that a range for the quantity is needed, to express uncertainty about the quantity. I saw about 1000 geese this morning, certainly more than 500 but less than 2000. Uncertainty is so common in sightings.
Are we also going to deprecate "IndividualCount"? I hope so.
Hannu
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On 2013-09-26 18:07, Donald Hobern [GBIF] wrote:
Hi Rob.
I understand your concern, but my concern is with the opportunities we are currently missing to enable our occurrence mobilisation processes to offer significantly more value in many contexts.
Some of the problem may be in the use of the word "abundance". If we understand "abundance" to refer to the size and density of a population or species, then a survey may give us a workable measure we can use to represent this. I am thinking of mobilisation of less ambitious measurements of relative abundance of a taxon in any sampling event or set of associated observations. I visit a reservoir and follow some standard protocol and count 30 mallards and a single gadwall. Today that might be exposed in simple Darwin Core as two occurrence records, each of which might somehow include an individualCount. In the absence of any other information, this count information cannot be seen as much more than an anecdotal annotation. If we understood that these two observations were part of a single survey event associated with a protocol also used for some number of other survey events for which we have observations, we could (in principle) find more ways to explore the significance of the count and use it to help to fine-tune distribution models and to enhance them to indicate patterns of abundance. If we can find a way to do this consistently for all types of biodiversity observation (malaise traps, transects, expression of ITS or CO1 from environmental samples), a large number of databases already contributing to GBIF and other networks could immediately offer a richer view to users and analysts.
I believe we could readily handle this with three properties that are available for use with any occurrence -- a sampling event id, a
sampling protocol identifier (ideally a URL leading to information on the protocol) and a relative abundance value within that sample. Any occurrence record could include these fields if appropriate. Of course more normalisation is possible, but DwC has never been about full normalisation.
We can debate which DwC classes ought to include support for such elements. I personally think we've tied ourselves in unnecessary knots with our use of Occurrences, Events, Material Samples, etc. I wish we just had an agreed meta-model/ontology which provides a graph of classes of interest to our domain (specimen, collection, taxon concept, taxon name, locality, collector, etc.) and a set of uniquely named properties each of which is associated with one of these classes or links instances of these classes. Darwin Core should then allow for the denormalised representation of any view corresponding to a subgraph of that model. Occurrence, Event, etc. should then be names for popularly-used subgraphs and should represent the logic for unpacking those denormalised DwC records back into a graph of meta-model objects (in other words they should express something like what SPARQL query might be able to extract this kind of record from data organised using the meta-model/ontology).
Best wishes,
Donald
Donald Hobern - GBIF Director - dhobern@gbif.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto:dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/
GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark
Tel: +45 3532 1471tel:%2B45%203532%201471 Mob: +45 2875 1471tel:%2B45%202875%201471 Fax: +45 2875 1480tel:%2B45%202875%201480
*From:*robgur@gmail.commailto:robgur@gmail.com [mailto:robgur@gmail.commailto:robgur@gmail.com] *On Behalf Of *Robert Guralnick *Sent:* Thursday, September 26, 2013 4:37 PM *To:* Donald Hobern [GBIF] *Cc:* John Wieczorek; TDWG Content Mailing List *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms -
abundance, abundanceAsPercent
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.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto: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.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto:dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471tel:%2B45%203532%201471 tel:%2B45%203532%201471 Mob: +45 2875 1471tel:%2B45%202875%201471
tel:%2B45%202875%201471 Fax: +45 2875 1480tel:%2B45%202875%201480 tel:%2B45%202875%201480
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Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever@naturalsciences.bemailto:aaike.dewever@naturalsciences.be <mailto:aaike.dewever@naturalsciences.bemailto: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.orgmailto:dhobern@gbif.org <mailto:dhobern@gbif.orgmailto: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.orgmailto:dhobern@gbif.org
<mailto:dhobern@gbif.orgmailto:dhobern@gbif.org> Global Biodiversity
Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471tel:%2B45%203532%201471 tel:%2B45%203532%201471 Mob: +45 2875 1471tel:%2B45%202875%201471
tel:%2B45%202875%201471 Fax: +45 2875 1480tel:%2B45%202875%201480 tel:%2B45%202875%201480
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Wever Sent: Thursday, September 26, 2013 8:44 AM To: tuco@berkeley.edumailto:tuco@berkeley.edu <mailto:tuco@berkeley.edumailto: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/http://rs.tdwg.org/dwc/terms/ 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/http://rs.tdwg.org/dwc/terms/ 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.orgmailto:tdwg-content@lists.tdwg.org <mailto:tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org>
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participants (4)
-
Blum, Stan -
Ramona Walls -
Robert Guralnick -
Robert Stevenson