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

-- Hannu Saarenmaa, Research Director hannu.saarenmaa@helsinki.fi Mobile +358-50-4479668 University of Eastern Finland School of Computing, SIB Labs, Joensuu Science Park Länsikatu 15 (P.O. Box 111) 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 > 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@gbif.org > mailto: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 > > ---------------------------------------------------------------------- > > *From:*robgur@gmail.com [mailto:robgur@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@gbif.org mailto: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 mailto:dhobern@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@gmail.com mailto:gtuco.btuco@gmail.com > [mailto: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 > mailto: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 mailto: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 > mailto:dhobern@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@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 > > 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 > >> 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@lists.tdwg.org mailto: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 tel:%2B32%280%292%20627%2043%2090 > > mobile.: +32(0)486 28 05 93 tel:%2B32%280%29486%2028%2005%2093 > > email: <aaike.dewever@naturalsciences.be > mailto: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 mailto:tdwg-content@lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > _______________________________________________ > tdwg-content mailing list > tdwg-content@lists.tdwg.org mailto:tdwg-content@lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > _______________________________________________ > tdwg-content mailing list > tdwg-content@lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content