I think Matt hit the nail on the head. Although Darwin Core can be used to exchange survey data, it lacks the semantics and structure necessary to archive the data without loss of information. I think the biodiversity community would be better served devoting energy to harmonizing existing technologies such as OGC, OBOE, and BCO, not to mention the many database for storing plot or survey data. The goal should be to preserve the data in the most informative manner possible.

There is a strong a case for wanting to search across all evidence for occurences, including surveys and point occurences, so I can see possible demand for a tool that would extract occurences from survey data to a DwC archive. However, I am very concerned that making a DwC archive the primary exchange format for survey or plot data commits us to a path of losing information from the start, for all but the simplest sampling schemas.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Research Associate, Bio5 Institute, University of Arizona
Laboratory Research Associate, New York Botanical Garden


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Today's Topics:

   1. Re: Darwin Core: proposed news terms for expressing sample
      data (Matt Jones)
   2. Re: Darwin Core: proposed news terms for expressing       sample
      data (Donald Hobern [GBIF])


----------------------------------------------------------------------

Message: 1
Date: Thu, 21 Aug 2014 18:52:06 -0800
From: Matt Jones <jones@nceas.ucsb.edu>
Subject: Re: [tdwg-content] Darwin Core: proposed news terms for
        expressing sample data
To: ?amonn ? Tuama [GBIF] <eotuama@gbif.org>
Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.org>
Message-ID:
        <CAFSW8xkx7uRP9PC2g3=JT_VJanqujH8nPXoz8GXwh+JwKw5Ccw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

This proposal is treading on ground that is quite similar to other
observations and measurements standards for data exchange that are already
mature, in particular:

* OGC Observations and Measurements (
http://www.opengeospatial.org/standards/om)
* Extensible Observation Ontology (OBOE;
https://semtools.ecoinformatics.org/oboe)

The former is a standard and broadly deployed, whereas the latter is part
of a research program in the use of ontologies for measurements.  Through
collaboration between the two projects, they've been modified to be
reasonably isomorphic, but O&M uses an XML serialization while OBOE uses an
OWL-DL serialization. They largely express the same measurements and
sampling model once one gets beyond the terminology differences.

So, I'm wondering if it make much sense to extend Darwin Core, which is at
heart an Occurrence exchange syntax, into this measurements area that is
well represented by these other existing specifications?  I'm curious to
hear why people would even want to do this.  And if we do go down this
path, won't we just end up with a new syntax that does essentially what O&M
and OBOE do now?

Matt



On Thu, Aug 21, 2014 at 12:22 AM, ?amonn ? Tuama [GBIF] <eotuama@gbif.org>
wrote:

> Hi Rob, Anne, Rich,
>
>
>
> I think Markus has answered your question as to why we opted for an Event
> core which is being used in the sense described by Anne and Rich. For any
> event, you can have a list of species in an Occurrence extension and for
> each species, you can include quantity and quantityType, e.g., biomass,
> etc. The proposed term eventSeriesID was intended for linking together
> related events, although it now looks like parentEventID might be a better,
> more flexible term. The measurementOrFact extension is a good fit for
> capturing environmental information relating to an event. See, e.g., the
> Gialova Lagoon brackish water invertebrate test data set [1] where a set
> of 18 environmental variables, including temp, pH, Rdx, particulate organic
> matter, dissolved oxygen, salinity, chlorophyll-a were measured for each
> sampling station-sampling period combination. An example mapping is:
>
>
>
> Id            measurementType           measurementValue
> measurementUnit               measurementRemarks
>
> IA           Tmp (sed)                           21.5
>                               degree C                             Tmp
> (sed): temperature at the bottom surface
>
>
>
> **Controlled vocabularies**
>
> Ideally, the values for samplingUnit and quantityType would be selected
> from controlled vocabularies. This is, effectively, what we do by
> presenting a small list of values in a drop-down menu. The current values
> are what we derived for example data sets and discussion but they can
> undoubtedly be extended and improved.
>
>
>
> We capture ?bucket? type measures through a combination of samplingEffort,
> samplingGeometry and samplingUnit. For example, a pitfall trap (in a point
> location) left out for 16 days might have samplingEffort: 16,
> samplingGeometry: point and samplingUnit: day. Three m^2 quadrats in a
> shore survey might have samplingEffort: 3, samplingGeometry: area and
> samplingUnit: m^2.
>
>
>
> It would be very useful to see your compilation of scope, effort and
> completeness measures to see if we can express them in our model and/or if
> we need to reconsider our approach.
>
>
>
> ?amonn
>
>
>
> [1] http://eubon-ipt.gbif.org/resource.do?r=ionian-brackish-lagoon
>
>
>
> *From:* tdwg-content-bounces@lists.tdwg.org [mailto:
> tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Markus D?ring
> *Sent:* 20 August 2014 23:47
> *To:* Robert Guralnick
>
> *Cc:* TDWG Content Mailing List
> *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for
> expressing sample data
>
>
>
> Rob,
>
>
>
> this proposal if for monitoring surveys really, not to be confused with
> material samples like environmental or tissue samples which have a distinct
> new dwc class MaterialSample.
>
>
>
> We tend to overload the term sampling a lot and it helps treating material
> samples different from pure observational "sampling". That is why the
> existing Event class was used as the core and classic Occurrence records as
> extensions. A classic example is a vegetation survey where each plot
> represents an Event record and each recorded species in that plot will be
> an Occurrence extension record with a given quantity. Darwin Core already
> offers individualCount to specify quantity, but it is a very specific way
> of measuring "abundance" restricted to only some use cases. Abiotic
> measurements about the plot (e.g. soil type, pH, temperature) can be
> published using the measurements or facts extension linked to the Event
> core.
>
>
>
> Markus
>
>
>
>
>
>
>
> On 20 Aug 2014, at 20:08, Robert Guralnick <Robert.Guralnick@colorado.edu>
> wrote:
>
>
>
>
>
>   Anne -- I don't know the answers!  These are questions for Eamonn.  I
> would presume that a sample could be a jumble of species or even just water
> or soil samples, and biomass would refer to that sample - but maybe that
> isn't a use case being considered?  The examples given in the longer
> document all link an event_id to species name and some measure of quantity
> for that species (to the species, not an individual specimen), so I assume
> that is the prevailing (or only) case?
>
> Best, Rob
>
>
>
>
>
> On Wed, Aug 20, 2014 at 11:56 AM, Anne Thessen <annethessen@gmail.com>
> wrote:
>
> Hi Rob
> I would like to respond to your item number 2.
> From my perspective, I deal with lots of published descriptions of taxa.
> The text might say something like "I saw species A in the Chesapeake Bay,
> the Adriatic Sea and the Indian Ocean and the biomass is 5 - 9 grams". The
> biomass range obviously corresponds to at least three different
> occurrences, but how to divide the biomass data? I would love to be able to
> have an *event* to attach it all to. There is almost two different levels
> of events - a sampling event and a "study event". The "study event" would
> correspond to the type of event I would like to use in the above example.
> It may not be ideal, but for the old literature that might be the best we
> can do.
> I have to admit that I don't know enough about trawl data to understand
> why an event core would be a problem. It seems that the trawl would be an
> event and each biomass measure (of each fish) would be attached to a
> separate occurrence which is attached to that event. Am I understanding
> this wrong?
> btw - I found a workaround for the example I gave, so it's not impossible
> to model with the current structure....
> Anne
>
>
>
> On 8/20/2014 1:16 PM, Robert Guralnick wrote:
>
>
>
> ?amonn et al. --- Thanks for the clarifications.  I think these help a ton
> but it raises a couple more questions for me.
>
>
>
> 1)   I am surprised that you plan to use of MeasurementorFact extension in
> relation to the Event core, which seems like a novel (or perhaps awkward or
> unintended?) mechanism for capturing environmental data, but the same
> extension was not be seen as relevant for describing samples? Can you
> explain more about the thinking there?
>
>
>
> 2)  There may be a subtle issue here extending "Event" to be more what you
> call a "Sampling Event Core".  My read of this is that Darwin Core serves
> as a way to deal with point occurrences and Event reflects the context of a
> single capture event (whether a single observation, or a bulk sample
> capture).  The changes recommended seem to dramatically extend and change
> that meaning?  Its simply a question that I don't have answer to, but is
> Darwin Core, the right vehicle to start capturing repeated measures of
> biomass values from trawls?   I don't have answer but man, terms like
> quantityType (as a property of occurrence?) give me pause.
>
>
>
> 3)  Is Sampling Unit a controlled vocabulary? For another project, I have
> looked through - and captured scope, effort and completeness measures from
> - a large number of published biotic area inventories.  The vast majorities
> of these are measured in units like bucket hours, or trap nights.  Is a
> "bucket" part of SamplingGeometry or Sampling Unit?  I'd be happy to send
> along all the many examples of how biotic inventories of an area are
> completed and perhaps it might be good to see how those might be
> represented using the terms you are proposing?
>
>
>
> Best, Rob
>
>
>
>
>
>
>
>
>
>
>
> On Wed, Aug 20, 2014 at 10:16 AM, Richard Pyle <deepreef@bishopmuseum.org>
> wrote:
>
> Same here ? Events are central to the work that we do.
>
>
>
> Aloha,
>
> Rich
>
>
>
> *From:* tdwg-content-bounces@lists.tdwg.org [mailto:
> tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Anne Thessen
> *Sent:* Wednesday, August 20, 2014 2:59 AM
> *To:* tdwg-content@lists.tdwg.org
>
>
> *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for
> expressing sample data
>
>
>
> Hello
> I would just like to comment on *event core*.
> I've been doing a lot of work translating published data into Darwin Core.
> During that process I've wished several times that I could use Event as
> core. I am happy to hear about that proposed change. It will make it easier
> to model the data I am working with.
> Anne
>
> On 8/20/2014 7:04 AM, ?amonn ? Tuama [GBIF] wrote:
>
> Hi Rob,
>
>
>
> Thank you for the feedback. I have tried to address the two main issues
> you raise below. At the outset, I would like to emphasise that much of this
> work is taking place in the context of the EU BON project which includes a
> task on developing/enhancing tools and standards for data sharing with a
> particular focus on the IPT for publishing sample-based data. So, we were
> constrained by the need to publish sample-based data sets in the Darwin
> Core Archive format and to demonstrate practical application using a
> working prototype. When the discussion on the TDWG list faded out, we took
> it to our EU BON partners whose requirements were essential input to
> further development. We recognise that these discussions took place away
> from TDWG (although the TDWG/EU BON contributors overlapped) and this is
> the reason we are presenting  the outcomes here for further consideration.
>
>
>
> **Event core**
>
> As the SIGS report indicated, sample data can be modelled in Darwin Core
> Archives using either Occurrence or Event as core. This was the starting
> point for our evaluation but as things progressed the data wrangling pushed
> the model back towards the Event core. We actually went through the
> exercise of mapping multiple test datasets in an iterative process spanning
> several months' work. In the end, we found that using an Event core better
> matched the typical sample data we were dealing with, allowing use of a
> measurement-or-fact extension to be included for the efficient expression
> of environmental information associated with the event. The choice comes
> down to an Occurrence core or an Event core + Occurrence extension. In both
> cases, the true observation records are Occurrences. The big difference is
> what type the core has and therefore to which kind of records you can
> attach further facts and extra information with DwC-A extensions. Many
> sampling datasets have very rich information about the site and event, so
> it is very natural to hang facts from an Event core. When picking the
> Occurrence core those facts would have to be repeated for each and every
> occurrence record. Moreover, our approach doesn?t stop anyone from using
> the Occurrence core if they so wish. This just provides a different option
> for datasets that better fit an Event core model.
>
>
>
> I want to stress that we are not building a ?specific IPT version? to
> support an Event core but, rather, we adapted the IPT so that it can be
> configured to support any generic ?core + extension? format to enable its
> use for exploration of more data formats.  This is part of the core
> codebase and there were no custom forks of the IPT for this work.  Our view
> at GBIF is that if there are significant numbers of data publishers who are
> keen to adopt, promote and use a (any) format, and the tools can be
> configured to do so, then we should support it, and, if necessary, use a
> custom namespace.
>
>
>
> **New terms around abundance**
>
> Yes, the discussion on TDWG did fade out but it was clear that the term
> ?abundance?  as recommended by the SIGS report (along with
> abundanceAsPercent) was confusing many when we were looking for term(s)
> that reported quantitative measures of organisms in a sample. It also
> became clear we would need to be able to state the type of quantity being
> measured. An alternative suggestion for using the MeasurementsOrFact class
> was immediately shot down.
>
> As some of our main use cases were coming from the EU BON project,
> discussion shifted to that forum and consensus formed about the currently
> proposed terms. It was within this group that the additional terms
> (samplingGeometry, samplingUnit, eventSeriesID) were proposed and where we
> began testing with sample data sets.
>
>
>
> Best regards,
>
> ?amonn
>
>
>
>
>
> *From:* robgur@gmail.com [mailto:robgur@gmail.com <robgur@gmail.com>] *On
> Behalf Of *Robert Guralnick
> *Sent:* 19 August 2014 16:56
> *To:* ?amonn ? Tuama [GBIF]
> *Cc:* TDWG Content Mailing List
> *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for
> expressing sample data
>
>
>
>
>
>   Hi ?amonn --- I am curious about the outcomes presented in the SIGS
> paper, in particular, this portion of the paper:
>
>
>
> "Solutions without introducing an event core in Darwin Core Archives:
>  During the review of the solutions for the uses cases, it became apparent
> that either model could be applied to every use case. The core and
> extensions bore a complementary relationship and between them could express
> all the required information. The core simply provided the central anchor
> in the star schema from which to join the additional information.
> Therefore, using the Occurrence core, well established in the GBIF network
> through uptake of the IPT, seemed more appropriate than inventing
> CollectingEvent as an additional core type."
>
>
>
>    That SIGS paper has John Wieczorek and you both as authors, including
> many luminaries across the biodiversity standards spectrum.  Given the
> above, its curious to see the EventCore come back again, along with a
> specific IPT version to support it.
>
>
>
>     So I see two issues, conflated, in this post you just made.  One is
> the need for an EventCore at all, and the nature of relating Event and
> Occurrence/Material Sample.  The second is the introduction of new terms,
> which seemingly have arrived after debate on similar terms - but framed
> around abundance - stalled a year ago.  To my mind, these both require some
> further discussion, because I don't (necessarily) see TDWG community
> coherence around either issue?
>
>
>
> Best, Rob
>
>
>
>
>
> On Tue, Aug 19, 2014 at 6:11 AM, ?amonn ? Tuama [GBIF] <eotuama@gbif.org>
> wrote:
>
> Dear All,
>
>
>
> GBIF is committed to exploring ways in which the IPT and Darwin Core
> Archive format can be extended for publishing sample-based data sets. In
> association with the EU BON project [1], a customised version of the IPT
> [2] has been deployed to test this using a special type of Darwin Core
> Archive in which the core is an ?Event? with associated taxon occurrences
> in an ?Occurrence? extension.
>
>
>
> The Darwin Core vocabulary already provides a rich set of terms with many
> relevant for describing sample-based data. Synthesising several sources of
> input (GBIF organised workshop on sample data, May 2013 [3], discussions on
> the TDWG mailing list in late 2013; internal discussion among EU BON
> project partners), five new terms relating to sample data were identified
> as essential. The complete model including these new terms are fully
> described with examples in the online document ?Publishing sample data
> using the GBIF IPT? [4].
>
>
>
> As a first step towards ratification, we would like to register the new
> terms in the DwC Google Code tracker [5] if there are no major objections
> on this list. The five terms are:
>
>
>
> 1.      *quantity*: the number or enumeration value of the quantityType
> (e.g., individuals, biomass, biovolume, BraunBlanquetScale) per
> samplingUnit or a percentage measure recorded for the sample.
>
>
>
> 2.      *quantityType*: :  the entity being referred to by quantity,
> e.g., individuals, biomass, %species, scale type.
>
>
>
> 3.      *samplingGeometry*: an indication of what kind of space was
> sampled; select from point, line, area or volume.
>
>
>
> 4.      *samplingUnit*: the unit of measurement used for reporting the
> quantity in the sample, e.g., minute, hour, day, metre, metre^2, metre^3.
> It is combined with quantity and quantityType to provide the complete
> measurement, e.g., 9 individuals per day,  4 biomass-gm per metre^2.
>
>
>
> 5.      *eventSeriesID*: an identifier for a set of events that are
> associated in some way, e.g., a monitoring series; may be a global unique
> identifier or an identifier specific to the series.
>
>
>
>
>
> Best regards,
>
>
>
> ?amonn
>
>
>
> [1] http://eubon.eu
>
> [2] http://eubon-ipt.gbif.org
>
> [3]
> http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4898640
>
> [4] http://links.gbif.org/sample_data_model
>
> [5] https://code.google.com/p/darwincore/issues/list
>
>
>
>
>
>
>
> ____________________________________________________
>
> *?amonn ? Tuama, M.Sc., Ph.D. (eotuama@gbif.org <eotuama@gbif.org>), *
>
> *Senior Programme Officer for Interoperability, *
>
> *Global Biodiversity Information Facility Secretariat, *
>
> *Universitetsparken 15, DK-2100, Copenhagen ?, DENMARK*
>
> *Phone:  +45 3532 1494 <%2B45%203532%201494>; Fax:  +45 3532 1480
> <%2B45%203532%201480>*
>
>
>
>
> _______________________________________________
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>
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>
> --
>
> Anne E. Thessen, Ph.D.
>
> The Data Detektiv, Owner and Founder
>
> Ronin Institute, Research Scholar
>
> 443.225.9185
>
>
> _______________________________________________
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> Anne E. Thessen, Ph.D.
>
> The Data Detektiv, Owner and Founder
>
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>
> 443.225.9185
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Message: 2
Date: Fri, 22 Aug 2014 08:54:07 +0200
From: "Donald Hobern [GBIF]" <dhobern@gbif.org>
Subject: Re: [tdwg-content] Darwin Core: proposed news terms for
        expressing      sample data
To: "'Matt Jones'" <jones@nceas.ucsb.edu>, '?amonn ? Tuama [GBIF]'
        <eotuama@gbif.org>
Cc: 'TDWG Content Mailing List' <tdwg-content@lists.tdwg.org>
Message-ID: <003401cfbdd5$de52b640$9af822c0$@gbif.org>
Content-Type: text/plain; charset="utf-8"

Hi Matt,



I?ll take the chance to make a few quick comments here, because I believe that this work is of massive importance.



Clearly DwC should avoid trying to duplicate well-standardised models and protocols.  However at the same time, there is enormous value for producers and consumers of DwC to benefit from richer data on the events and methods associated with individual species occurrences.  I have never seen DwC as purely an Occurrence exchange syntax.  I see it (from GBIF?s standpoint) more closely as a mechanism for diverse parties to pool the evidence they have for the occurrence of any species including associated information and/or actionable links to associated information.  Users coming from this perspective certainly need (and are demanding) access to all the evidence that can be mobilized to serve as supporting evidence and they also need the ability to understand the significance of these records.  Abundance measures, levels of effort, use of consistent methods and redetection of individual organisms are all part of this.  DwC should be able to transmit as much data as publishers cho
 ose to share on such aspects as part of their publishing of DwC.  Users of DwC carrying out species modeling, threat assessment or community analyses will benefit from rapid ways to filter data for those which derive from standardized sampling events, to understand relative abundance within samples, etc.  Many publishers of DwC are currently sharing stripped-down subsets of data and wish to give more information on these points.  Users are certainly demanding it.



The challenge is finding the sweet spot, the achievable, non-destructive overlap between DwC and the proper domain of models better designed to handle the representation of complex systems outside DwC?s current domain.  If this is done correctly, there should be paths that enable us to generate O&E (and maybe OBOE) compatible data from data that publishers only serve as augmented DwC.



I?ll also note that this has been a prominent area of discussion now for several years.  Many of us believe strongly that this is one of the most important ways in which we need to close arbitrary gaps between data silos.  It?s a prominent part of the GBIF work programme for 2014-2016.



Very best wishes,



Donald



From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Matt Jones
Sent: Friday, August 22, 2014 4:52 AM
To: ?amonn ? Tuama [GBIF]
Cc: TDWG Content Mailing List
Subject: Re: [tdwg-content] Darwin Core: proposed news terms for expressing sample data



This proposal is treading on ground that is quite similar to other observations and measurements standards for data exchange that are already mature, in particular:



* OGC Observations and Measurements (http://www.opengeospatial.org/standards/om)

* Extensible Observation Ontology (OBOE; https://semtools.ecoinformatics.org/oboe)



The former is a standard and broadly deployed, whereas the latter is part of a research program in the use of ontologies for measurements.  Through collaboration between the two projects, they've been modified to be reasonably isomorphic, but O&M uses an XML serialization while OBOE uses an OWL-DL serialization. They largely express the same measurements and sampling model once one gets beyond the terminology differences.



So, I'm wondering if it make much sense to extend Darwin Core, which is at heart an Occurrence exchange syntax, into this measurements area that is well represented by these other existing specifications?  I'm curious to hear why people would even want to do this.  And if we do go down this path, won't we just end up with a new syntax that does essentially what O&M and OBOE do now?



Matt





On Thu, Aug 21, 2014 at 12:22 AM, ?amonn ? Tuama [GBIF] <eotuama@gbif.org> wrote:

Hi Rob, Anne, Rich,



I think Markus has answered your question as to why we opted for an Event core which is being used in the sense described by Anne and Rich. For any event, you can have a list of species in an Occurrence extension and for each species, you can include quantity and quantityType, e.g., biomass, etc. The proposed term eventSeriesID was intended for linking together related events, although it now looks like parentEventID might be a better, more flexible term. The measurementOrFact extension is a good fit for capturing environmental information relating to an event. See, e.g., the Gialova Lagoon brackish water invertebrate test data set [1] where a set of 18 environmental variables, including temp, pH, Rdx, particulate organic matter, dissolved oxygen, salinity, chlorophyll-a were measured for each sampling station-sampling period combination. An example mapping is:



Id            measurementType           measurementValue          measurementUnit               measurementRemarks

IA           Tmp (sed)                           21.5                                     degree C                             Tmp (sed): temperature at the bottom surface



*Controlled vocabularies*

Ideally, the values for samplingUnit and quantityType would be selected from controlled vocabularies. This is, effectively, what we do by presenting a small list of values in a drop-down menu. The current values are what we derived for example data sets and discussion but they can undoubtedly be extended and improved.



We capture ?bucket? type measures through a combination of samplingEffort, samplingGeometry and samplingUnit. For example, a pitfall trap (in a point location) left out for 16 days might have samplingEffort: 16, samplingGeometry: point and samplingUnit: day. Three m^2 quadrats in a shore survey might have samplingEffort: 3, samplingGeometry: area and samplingUnit: m^2.



It would be very useful to see your compilation of scope, effort and completeness measures to see if we can express them in our model and/or if we need to reconsider our approach.



?amonn



[1] http://eubon-ipt.gbif.org/resource.do?r=ionian-brackish-lagoon



From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Markus D?ring
Sent: 20 August 2014 23:47
To: Robert Guralnick


Cc: TDWG Content Mailing List
Subject: Re: [tdwg-content] Darwin Core: proposed news terms for expressing sample data



Rob,



this proposal if for monitoring surveys really, not to be confused with material samples like environmental or tissue samples which have a distinct new dwc class MaterialSample.



We tend to overload the term sampling a lot and it helps treating material samples different from pure observational "sampling". That is why the existing Event class was used as the core and classic Occurrence records as extensions. A classic example is a vegetation survey where each plot represents an Event record and each recorded species in that plot will be an Occurrence extension record with a given quantity. Darwin Core already offers individualCount to specify quantity, but it is a very specific way of measuring "abundance" restricted to only some use cases. Abiotic measurements about the plot (e.g. soil type, pH, temperature) can be published using the measurements or facts extension linked to the Event core.



Markus







On 20 Aug 2014, at 20:08, Robert Guralnick <Robert.Guralnick@colorado.edu> wrote:





  Anne -- I don't know the answers!  These are questions for Eamonn.  I would presume that a sample could be a jumble of species or even just water or soil samples, and biomass would refer to that sample - but maybe that isn't a use case being considered?  The examples given in the longer document all link an event_id to species name and some measure of quantity for that species (to the species, not an individual specimen), so I assume that is the prevailing (or only) case?

Best, Rob





On Wed, Aug 20, 2014 at 11:56 AM, Anne Thessen <annethessen@gmail.com> wrote:

Hi Rob
I would like to respond to your item number 2.
>From my perspective, I deal with lots of published descriptions of taxa. The text might say something like "I saw species A in the Chesapeake Bay, the Adriatic Sea and the Indian Ocean and the biomass is 5 - 9 grams". The biomass range obviously corresponds to at least three different occurrences, but how to divide the biomass data? I would love to be able to have an *event* to attach it all to. There is almost two different levels of events - a sampling event and a "study event". The "study event" would correspond to the type of event I would like to use in the above example. It may not be ideal, but for the old literature that might be the best we can do.
I have to admit that I don't know enough about trawl data to understand why an event core would be a problem. It seems that the trawl would be an event and each biomass measure (of each fish) would be attached to a separate occurrence which is attached to that event. Am I understanding this wrong?
btw - I found a workaround for the example I gave, so it's not impossible to model with the current structure....
Anne



On 8/20/2014 1:16 PM, Robert Guralnick wrote:



?amonn et al. --- Thanks for the clarifications.  I think these help a ton but it raises a couple more questions for me.



1)   I am surprised that you plan to use of MeasurementorFact extension in relation to the Event core, which seems like a novel (or perhaps awkward or unintended?) mechanism for capturing environmental data, but the same extension was not be seen as relevant for describing samples? Can you explain more about the thinking there?



2)  There may be a subtle issue here extending "Event" to be more what you call a "Sampling Event Core".  My read of this is that Darwin Core serves as a way to deal with point occurrences and Event reflects the context of a single capture event (whether a single observation, or a bulk sample capture).  The changes recommended seem to dramatically extend and change that meaning?  Its simply a question that I don't have answer to, but is Darwin Core, the right vehicle to start capturing repeated measures of biomass values from trawls?   I don't have answer but man, terms like quantityType (as a property of occurrence?) give me pause.



3)  Is Sampling Unit a controlled vocabulary? For another project, I have looked through - and captured scope, effort and completeness measures from - a large number of published biotic area inventories.  The vast majorities of these are measured in units like bucket hours, or trap nights.  Is a "bucket" part of SamplingGeometry or Sampling Unit?  I'd be happy to send along all the many examples of how biotic inventories of an area are completed and perhaps it might be good to see how those might be represented using the terms you are proposing?



Best, Rob











On Wed, Aug 20, 2014 at 10:16 AM, Richard Pyle <deepreef@bishopmuseum.org> wrote:

Same here ? Events are central to the work that we do.



Aloha,

Rich



From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Anne Thessen
Sent: Wednesday, August 20, 2014 2:59 AM
To: tdwg-content@lists.tdwg.org


Subject: Re: [tdwg-content] Darwin Core: proposed news terms for expressing sample data



Hello
I would just like to comment on *event core*.
I've been doing a lot of work translating published data into Darwin Core. During that process I've wished several times that I could use Event as core. I am happy to hear about that proposed change. It will make it easier to model the data I am working with.
Anne

On 8/20/2014 7:04 AM, ?amonn ? Tuama [GBIF] wrote:

Hi Rob,



Thank you for the feedback. I have tried to address the two main issues you raise below. At the outset, I would like to emphasise that much of this work is taking place in the context of the EU BON project which includes a task on developing/enhancing tools and standards for data sharing with a particular focus on the IPT for publishing sample-based data. So, we were constrained by the need to publish sample-based data sets in the Darwin Core Archive format and to demonstrate practical application using a working prototype. When the discussion on the TDWG list faded out, we took it to our EU BON partners whose requirements were essential input to further development. We recognise that these discussions took place away from TDWG (although the TDWG/EU BON contributors overlapped) and this is the reason we are presenting  the outcomes here for further consideration.



*Event core*

As the SIGS report indicated, sample data can be modelled in Darwin Core Archives using either Occurrence or Event as core. This was the starting point for our evaluation but as things progressed the data wrangling pushed the model back towards the Event core. We actually went through the exercise of mapping multiple test datasets in an iterative process spanning several months' work. In the end, we found that using an Event core better matched the typical sample data we were dealing with, allowing use of a measurement-or-fact extension to be included for the efficient expression of environmental information associated with the event. The choice comes down to an Occurrence core or an Event core + Occurrence extension. In both cases, the true observation records are Occurrences. The big difference is what type the core has and therefore to which kind of records you can attach further facts and extra information with DwC-A extensions. Many sampling datasets have very rich infor
 mation about the site and event, so it is very natural to hang facts from an Event core. When picking the Occurrence core those facts would have to be repeated for each and every occurrence record. Moreover, our approach doesn?t stop anyone from using the Occurrence core if they so wish. This just provides a different option for datasets that better fit an Event core model.



I want to stress that we are not building a ?specific IPT version? to support an Event core but, rather, we adapted the IPT so that it can be configured to support any generic ?core + extension? format to enable its use for exploration of more data formats.  This is part of the core codebase and there were no custom forks of the IPT for this work.  Our view at GBIF is that if there are significant numbers of data publishers who are keen to adopt, promote and use a (any) format, and the tools can be configured to do so, then we should support it, and, if necessary, use a custom namespace.



*New terms around abundance*

Yes, the discussion on TDWG did fade out but it was clear that the term ?abundance?  as recommended by the SIGS report (along with abundanceAsPercent) was confusing many when we were looking for term(s) that reported quantitative measures of organisms in a sample. It also became clear we would need to be able to state the type of quantity being measured. An alternative suggestion for using the MeasurementsOrFact class was immediately shot down.

As some of our main use cases were coming from the EU BON project, discussion shifted to that forum and consensus formed about the currently proposed terms. It was within this group that the additional terms (samplingGeometry, samplingUnit, eventSeriesID) were proposed and where we began testing with sample data sets.



Best regards,

?amonn





From: robgur@gmail.com [mailto:robgur@gmail.com] On Behalf Of Robert Guralnick
Sent: 19 August 2014 16:56
To: ?amonn ? Tuama [GBIF]
Cc: TDWG Content Mailing List
Subject: Re: [tdwg-content] Darwin Core: proposed news terms for expressing sample data





  Hi ?amonn --- I am curious about the outcomes presented in the SIGS paper, in particular, this portion of the paper:



"Solutions without introducing an event core in Darwin Core Archives:  During the review of the solutions for the uses cases, it became apparent that either model could be applied to every use case. The core and extensions bore a complementary relationship and between them could express all the required information. The core simply provided the central anchor in the star schema from which to join the additional information. Therefore, using the Occurrence core, well established in the GBIF network through uptake of the IPT, seemed more appropriate than inventing CollectingEvent as an additional core type."



   That SIGS paper has John Wieczorek and you both as authors, including many luminaries across the biodiversity standards spectrum.  Given the above, its curious to see the EventCore come back again, along with a specific IPT version to support it.



    So I see two issues, conflated, in this post you just made.  One is the need for an EventCore at all, and the nature of relating Event and Occurrence/Material Sample.  The second is the introduction of new terms, which seemingly have arrived after debate on similar terms - but framed around abundance - stalled a year ago.  To my mind, these both require some further discussion, because I don't (necessarily) see TDWG community coherence around either issue?



Best, Rob





On Tue, Aug 19, 2014 at 6:11 AM, ?amonn ? Tuama [GBIF] <eotuama@gbif.org> wrote:

Dear All,



GBIF is committed to exploring ways in which the IPT and Darwin Core Archive format can be extended for publishing sample-based data sets. In association with the EU BON project [1], a customised version of the IPT [2] has been deployed to test this using a special type of Darwin Core Archive in which the core is an ?Event? with associated taxon occurrences in an ?Occurrence? extension.



The Darwin Core vocabulary already provides a rich set of terms with many relevant for describing sample-based data. Synthesising several sources of input (GBIF organised workshop on sample data, May 2013 [3], discussions on the TDWG mailing list in late 2013; internal discussion among EU BON project partners), five new terms relating to sample data were identified as essential. The complete model including these new terms are fully described with examples in the online document ?Publishing sample data using the GBIF IPT? [4].



As a first step towards ratification, we would like to register the new terms in the DwC Google Code tracker [5] if there are no major objections on this list. The five terms are:



1.      quantity: the number or enumeration value of the quantityType (e.g., individuals, biomass, biovolume, BraunBlanquetScale) per samplingUnit or a percentage measure recorded for the sample.



2.      quantityType: :  the entity being referred to by quantity, e.g., individuals, biomass, %species, scale type.



3.      samplingGeometry: an indication of what kind of space was sampled; select from point, line, area or volume.



4.      samplingUnit: the unit of measurement used for reporting the quantity in the sample, e.g., minute, hour, day, metre, metre^2, metre^3.  It is combined with quantity and quantityType to provide the complete measurement, e.g., 9 individuals per day,  4 biomass-gm per metre^2.



5.      eventSeriesID: an identifier for a set of events that are associated in some way, e.g., a monitoring series; may be a global unique identifier or an identifier specific to the series.





Best regards,



?amonn



[1] http://eubon.eu <http://eubon.eu/>

[2] http://eubon-ipt.gbif.org <http://eubon-ipt.gbif.org/>

[3] http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4898640

[4]  <http://links.gbif.org/sample_data_model> http://links.gbif.org/sample_data_model

[5] https://code.google.com/p/darwincore/issues/list







____________________________________________________

?amonn ? Tuama, M.Sc., Ph.D. (eotuama@gbif.org),

Senior Programme Officer for Interoperability,

Global Biodiversity Information Facility Secretariat,

Universitetsparken 15, DK-2100, Copenhagen ?, DENMARK

Phone:  +45 3532 1494 <tel:%2B45%203532%201494> ; Fax:  +45 3532 1480 <tel:%2B45%203532%201480>




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--
Anne E. Thessen, Ph.D.
The Data Detektiv, Owner and Founder
Ronin Institute, Research Scholar
443.225.9185


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Anne E. Thessen, Ph.D.
The Data Detektiv, Owner and Founder
Ronin Institute, Research Scholar
443.225.9185



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