@Tuco, if one agrees that abundance is a property of a materialSample and not an occurrence, yes. Donald's examples included "malaise traps, transects, expression of ITS or CO1 from environmental samples" --- to me those all represent sampling and samples. Yes we have event properties that link events to occurrences. But the point is that if it were just counts, fine. But its not. This is about counts over a specified area. To me this is a very important point and this pushes us out of "occurrence". Feel pretty strongly about it, actually.
@Donald, I resonate with Donald's perspective that what is needed is an ontology where we can represent relationships between classes and properties more effectively for graph traversal, and of course, there are efforts currently being developed to do just that (e.g. the Biocollections Ontology, where this would be a trivial use case).
Best, Rob
On Thu, Sep 26, 2013 at 9:10 AM, John Wieczorek tuco@berkeley.edu wrote:
@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@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@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@lists.tdwg.org [mailto:tdwg-content-bounces@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@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 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@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; 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>
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 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@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; 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@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@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 http://lists.tdwg.org/mailman/listinfo/tdwg-content
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