[tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Hannu Saarenmaa
hannu at bioshare.com
Sat Sep 28 07:25:55 CEST 2013
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 at helsinki.fi
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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 at gbif.org
> <mailto: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
>
> ----------------------------------------------------------------------
>
> *From:*robgur at gmail.com [mailto:robgur at 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 at gbif.org <mailto: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 <mailto: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 <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 at gmail.com <mailto:gtuco.btuco at gmail.com>
> [mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <tel:%2B45%203532%201471> Mob: +45 2875 1471
> <tel:%2B45%202875%201471> Fax: +45 2875 1480 <tel:%2B45%202875%201480>
> > ----------------------------------------------------------------------
> >
> >
> > -----Original Message-----
> > From: tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> > [mailto: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 <mailto: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/ <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/>
> >> 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 <mailto: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 <tel:%2B32%280%292%20627%2043%2090>
> > mobile.: +32(0)486 28 05 93 <tel:%2B32%280%29486%2028%2005%2093>
> > email: <aaike.dewever at naturalsciences.be
> <mailto: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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> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >
> >
>
>
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