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:
RamonaI 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 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.org> wrote:
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Today's Topics:
abundanceAsPercent (Hannu Saarenmaa)
----------------------------------------------------------------------
Message: 1
Date: Sat, 28 Sep 2013 08:25:55 +0300
From: Hannu Saarenmaa <hannu@bioshare.com>To: 'TDWG Content Mailing List' <tdwg-content@lists.tdwg.org>
Subject: Re: [tdwg-content] Proposed new Darwin Core terms -
abundance, abundanceAsPercent
Message-ID: <52466863.8050703@bioshare.com>
Content-Type: text/plain; charset="iso-8859-1"L?nsikatu 15 (P.O. Box 111)
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
> available for use with any occurrence -- a sampling event id, a
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
> <mailto:dhobern@gbif.org>
> 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
> *From:*robgur@gmail.com [mailto:robgur@gmail.com] *On Behalf Of
>
> 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
>
> ----------------------------------------------------------------------
>
> *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:> Donald Hobern - GBIF Director - dhobern@gbif.org <mailto:dhobern@gbif.org>
>
> 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
>
> ----------------------------------------------------------------------
> Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471
> Global Biodiversity Information Facility http://www.gbif.org/
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark
> ----------------------------------------------------------------------> [mailto:gtuco.btuco@gmail.com <mailto:gtuco.btuco@gmail.com>] On
>
>
> -----Original Message-----
>
> From: gtuco.btuco@gmail.com <mailto:gtuco.btuco@gmail.com>
> <mailto:aaike.dewever@naturalsciences.be>; TDWG Content Mailing List
> Behalf Of John
> Wieczorek
> Sent: Thursday, September 26, 2013 3:48 PM
> To: Donald Hobern [GBIF]
> Cc: aaike.dewever@naturalsciences.be
> <dhobern@gbif.org <mailto:dhobern@gbif.org>>
> 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]
> <mailto:dhobern@gbif.org> Global Biodiversity
> 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
> > Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471
> > Information Facility http://www.gbif.org/ GBIF Secretariat,
> > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark
> > ----------------------------------------------------------------------
> >
> >
> > -----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
> >> Namespace: http:/rs.tdwg.org/dwc/terms/ <http://rs.tdwg.org/dwc/terms/>> > 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/>
> >> 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
> >> tdwg-content@lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org>
> >> 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
> > tel.: +32(0)2 627 43 90 <tel:%2B32%280%292%20627%2043%2090>
> >> 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
> > mobile.: +32(0)486 28 05 93 <tel:%2B32%280%29486%2028%2005%2093>
> > email: <aaike.dewever@naturalsciences.be
> <mailto:aaike.dewever@naturalsciences.be>>> > tdwg-content@lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org>
> > 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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