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

Thu Sep 26 17:10:28 CEST 2013

@Rob,

Do you think the ratification of a MaterialSample class (and the
associated property materialSampleID) would have any effect on the
viability or definition of an abundance term in Darwin Core?

On Thu, Sep 26, 2013 at 5:04 PM, John Wieczorek <tuco at berkeley.edu> wrote:
> Not that is is propoer justification, but abundance was recommended to
> be organized within Occurrence (no actual semantic link will be put
> into existence with this proposal) simply because individualCount,
> whose failings inspired the abundance term, was organized in
> Occurrence.
>
> On Thu, Sep 26, 2013 at 4:57 PM, Chuck Miller <Chuck.Miller at mobot.org> wrote:
>> Although abundance is not “evidence of an occurrence in nature” it is
>> “information pertaining to evidence”, isn’t it?
>>
>>
>>
>> Chuck
>>
>>
>>
>> From: tdwg-content-bounces at lists.tdwg.org
>> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Robert Guralnick
>> Sent: Thursday, September 26, 2013 9:37 AM
>> To: Donald Hobern [GBIF]
>> Cc: 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 at 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 at gbif.org
>> Global Biodiversity Information Facility http://www.gbif.org/
>> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>> Tel: +45 3532 1471  Mob: +45 2875 1471  Fax: +45 2875 1480
>> ----------------------------------------------------------------------
>>
>>
>> -----Original Message-----
>>
>> From: gtuco.btuco at gmail.com [mailto:gtuco.btuco at gmail.com] On Behalf Of John
>> Wieczorek
>> Sent: Thursday, September 26, 2013 3:48 PM
>> To: Donald Hobern [GBIF]
>> Cc: aaike.dewever at 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 at 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 at gbif.org Global Biodiversity
>>> Information Facility http://www.gbif.org/ GBIF Secretariat,
>>> Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>>> Tel: +45 3532 1471  Mob: +45 2875 1471  Fax: +45 2875 1480
>>> ----------------------------------------------------------------------
>>>
>>>
>>> -----Original Message-----
>>> From: tdwg-content-bounces at lists.tdwg.org
>>> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Aaike De
>>> Wever
>>> Sent: Thursday, September 26, 2013 8:44 AM
>>> To: tuco at berkeley.edu; TDWG Content Mailing List
>>> Subject: Re: [tdwg-content] Proposed new Darwin Core terms -
>>> abundance, abundanceAsPercent
>>>
>>> Dear all,
>>>
>>> As somewhat of an outsider I have another question with regards to the
>>> proposed terms abundance and abundanceAsPercent.
>>>
>>> Is there a specific reason for not adopting:
>>> * the abundance field as a field to store only the value and
>>> * a field abundanceUnit/abundanceType to specify whether the value is
>>> in % of species, % of biovolume, % of biomass, individuals/l,
>>> ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field
>> specific for %)?
>>>
>>> Maybe this has been discussed during the hackathon and I missed it in
>>> the report?
>>>
>>> Thanks for considering this question.
>>>
>>> With best regards,
>>> Aaike
>>>
>>> John Wieczorek wrote:
>>>> Dear all,
>>>>
>>>> GBIF has just published "Meeting Report: GBIF hackathon-workshop on
>>>> Darwin Core and sample data (22-24 May 2013)" at
>>>> http://www.gbif.org/orc/?doc_id=5424. Now that this document is
>>>> available for public reference, I would like to formally open the
>>>> minimum 30-day comment period on two related new terms proposed
>>>> during the workshop and defined in the referenced document.
>>>>
>>>> The formal proposal would add the following new terms:
>>>>
>>>> Term Name: abundance
>>>> Identifier: http://rs.tdwg.org/dwc/terms/abundance
>>>> Namespace: http:/rs.tdwg.org/dwc/terms/
>>>> Label: Abundance
>>>> Definition: The number of individuals of a taxon found in a sample.
>>>> This is typically expressed as number per unit of area or volume. In
>>>> the case of vegetation and colonial/encrusting species, percent cover
>>>> can be used.
>>>> Comment: Examples: "4 per square meter", "0.32 per cubic meter",
>>>> "24%". For discussion see
>>>> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no
>>>> further documentation here until the term is ratified) Type of Term:
>>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
>>>> Refines:
>>>> Status: proposed
>>>> Date Issued: 2012-03-01
>>>> Date Modified: 2013-09-25
>>>> Has Domain:
>>>> Has Range:
>>>> Refines:
>>>> Version: abundance-2013-09-25
>>>> Replaces:
>>>> IsReplaceBy:
>>>> Class: http://rs.tdwg.org/dwc/terms/Occurrence
>>>> ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
>>>>
>>>> Term Name: abundanceAsPercent
>>>> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent
>>>> Namespace: http:/rs.tdwg.org/dwc/terms/
>>>> Label: Abundance as Percent
>>>> Definition: 100 times the number of individuals of a taxon found in a
>>>> sample divided by the total number of individuals of all taxa in the
>>>> sample.
>>>> Comment: Examples: "2.4%". For discussion see
>>>> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no
>>>> further documentation here until the term is ratified) Type of Term:
>>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
>>>> Refines:
>>>> Status: proposed
>>>> Date Issued: 2012-08-01
>>>> Date Modified: 2013-09-25
>>>> Has Domain:
>>>> Has Range:
>>>> Refines:
>>>> Version: abundanceAsPercent-2013-09-25
>>>> Replaces:
>>>> IsReplaceBy:
>>>> Class: http://rs.tdwg.org/dwc/terms/Occurrence
>>>> ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
>>>>
>>>> The related issues in the Darwin Core issue tracker are
>>>> https://code.google.com/p/darwincore/issues/detail?id=142
>>>> and
>>>> https://code.google.com/p/darwincore/issues/detail?id=187
>>>>
>>>> If there are any objections to the changes proposed for these new
>>>> terms, or comments about their definitions, please respond to this
>>>> message. If there are no objections or if consensus can be reached on
>>>> any amendments put forward, the proposal will go before the Executive
>>>> Committee for authorization to put these additions into effect after
>>>> the public commentary period.
>>>>
>>>> Cheers,
>>>>
>>>> John
>>>> _______________________________________________
>>>> tdwg-content mailing list
>>>> tdwg-content at lists.tdwg.org
>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>>
>>> --
>>> Aaike De Wever
>>> BioFresh Science Officer
>>> Freshwater Laboratory, Royal Belgian Institute of Natural Sciences
>>> Vautierstraat 29, 1000 Brussels Belgium
>>> tel.: +32(0)2 627 43 90
>>> mobile.: +32(0)486 28 05 93
>>> email: <aaike.dewever at naturalsciences.be>
>>> skype: aaikew
>>> LinkedIn: <http://be.linkedin.com/in/aaikedewever>
>>> BioFresh: <http://www.freshwaterbiodiversity.eu/> and
>>> <http://data.freshwaterbiodiversity.eu/>
>>> Belgian Biodiversity Platform: <http://www.biodiversity.be>
>>> _______________________________________________
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>>>
>>>
>>
>>
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