[tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
Donald Hobern [GBIF]
dhobern at gbif.org
Thu Sep 26 17:07:14 CEST 2013
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 - <mailto:dhobern at gbif.org> dhobern at gbif.org
Global Biodiversity Information Facility <http://www.gbif.org/>
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>
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 <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] 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 <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] 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 <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>
> 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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