[tdwg-content] tdwg-content Digest, Vol 63, Issue 6
Steve Baskauf
steve.baskauf at vanderbilt.edu
Thu Aug 28 21:46:27 CEST 2014
A couple of points of clarification on what Chuck said:
1. Audubon Core is more than an extension of Darwin Core - it's a
vocabulary that is a ratified TDWG technical specification standard
(despite what [1] says - nobody has managed to change its status from
"Draft" to "Current" on the website). So it stands on the same level as
Darwin Core even though it's terms describe different kinds of things
than DwC. All ratified TDWG standards have gone through peer review,
public comment, and approval by the TDWG Executive. That is not the
case with Plinian Core or GBIF extensions.
2. The Darwin Core text guide that Chuck mentions IS actually part of
the Darwin Core Standard. TDWG Standards are composed of normative
("Type 1") documents that define the standard and non-normative ("Type
2") documents that "explain and justify" the standard. For Darwin Core,
there is a single normative RDF document that defines the standard. It
can be viewed at
https://code.google.com/p/darwincore/source/browse/trunk/rdf/dwctermshistory.rdf
. There are 67 non-normative documents, which include the entire Darwin
Core website (including the text guide page). How do I know that these
documents comprise the standard? Because they are what I get when I
download and unzip the standard from http://www.tdwg.org/standards/450/
. It is one of TDWG's deficiencies that it is not a simple matter to
know what actually comprises a standard and to view clearly-identified
components of a standard without having to download a zip archive.
I'm not sure that I can articulate the difference between the Darwin
Core Text Guide component of the standard and a "Darwin Core Archive".
It might be correct to say that Darwin Core Archives are sets of files
that are compliant with the Darwin Core Text Guide.
Steve
[1] http://www.tdwg.org/standards/
Chuck Miller wrote:
>
> Rob,
>
> GBIF is hard at work solving a problem for them. It seems natural for
> them to do what works best for them, particularly dealing with the
> volume/scale they do. And, Markus, Tim, Eamonn and others have been
> deeply involved in Darwin Core standards implementation, inventing the
> DwCA and the IPT in the first place. But, in using DwCA to get actual
> work done for GBIF they have added a term here and there via their own
> extensions. See http://tools.gbif.org/dwca-validator/extensions.do.
> It’s a long list of Registered and Stable extensions. What about
> Audubon and Plinian Core? Aren’t they actually “extensions” to Darwin
> Core, particularly in the “universal biodiversity data “ sense Darwin
> Core seems to be evolving to? Maybe we need a “SampleCore” or
> “EventCore” that organizes these sampling/event-related terms?
>
>
>
> GBIF is creating a new “Event core” for DwCA to do what they need to
> do. But, I don’t understand the problem with this. Occurrence core,
> Taxon core, Event core – so what? The DwCA model allows anything to be
> the core (ignoring IPT) and it does not actually restrict the terms
> used to DwC only, certainly it already includes Dublin Core and EML.
> In fact, lots of DwCA exchanges are being used outside GBIF now with
> extended terms from Audubon Core, Plinian Core, and others. How is
> this bad? It shows how flexible the DwCA data exchange structure is.
> And, it is an exchange, not a data storage format. What’s the problem
> with an Event core?
>
>
>
> As an aside, I have said many times that the most confusing thing to
> our community about DwCA is that it’s called _Darwin Core_ Archive
> when the structure is in fact not limited to only Darwin Core terms.
> Any validatable XML term can be used – like
> http://rs.gbif.org/terms/1.0/verbatimLabel which is used in the How-To
> Guide Whales example. And I commonly hear people at conferences and
> meetings now referring to their plans to adopt “Darwin Core” and upon
> questioning discover they are talking about the DwCA format, not
> really knowing the details of it. So, the words “Darwin Core” have
> become ambiguous.
>
>
>
> And I want to note that Darwin Core Archive is not a TDWG standard.
> It is a guideline for implementing the Darwin Core standard in text
> files. http://rs.tdwg.org/dwc/terms/guides/text/. This is another
> point of confusion. GBIF describes DwCA as “an internationally
> recognized biodiversity informatics data standard”
> http://www.gbif.org/resources/2551, but it’s not a TDWG standard, just
> a guideline. I think DwCA deserves to be made a TDWG data exchange
> standard on its own, separate from Darwin Core, and perhaps expanded
> in scope to embrace the other “Cores” and relabeled to “Biodiversity
> Data Archive” or something.
>
>
>
> Chuck
>
>
>
> *From:* tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] *On Behalf Of *Robert
> Guralnick
> *Sent:* Thursday, August 28, 2014 10:58 AM
> *To:* John Deck
> *Cc:* TDWG Content Mailing List; Ramona Walls
> *Subject:* Re: [tdwg-content] tdwg-content Digest, Vol 63, Issue 6
>
>
>
>
>
> Hi all --- Ok, I think the scope of the issue is quite clear. Let me
> summarize: 1) As Éamonn and the rest of GBIF has made quite clear,
> "GBIF is faced with the immediate task of making sample-based data
> discoverable and accessible using its current ecosystem of tools"
> given a funding mandate from EU-BON. 2) The solution for this
> problem is to develop an Event-core and to promote new terms to the
> Darwin Core to make this happen. I will note a small inconsistency
> here: the current ecosystem standards and tools of is Darwin Core (as
> it stands) and publishing systems such as IPT. That ecosystem of
> tools includes mechanisms to extend Darwin Core where needed, via
> extensions. The /current/ ecosystem of tools doesn't include new
> Cores or new DwC terms, does it?
>
>
>
> So this leads in nicely to the contentious issue(s) and places where
> there seems to be discussions --- these have to do with the nature of
> the changes suggested and the scope of those changes, both in terms of
> an Event core and DwC term additions. Leaving aside the Event-core
> for now, the key questions simply about term additions to the Darwin
> Core that seem to be at heart here are: 1) Is the intent of the
> Darwin Core to model surveys, which usually involve multiple kinds and
> types of sampling over multiple sites using multiple methods? 2) Is
> the solution to invent new terms for the Darwin Core if there are
> already terms from other efforts, wouldn't we work with those existing
> efforts to assure interoperability?
>
>
>
> I appreciate the efforts of GBIF here fully, and am personally torn
> because on the one hand, I fully agree with the goal of extending
> Darwin Core to better represent richer biodiversity data. On the
> other hand, I worry about process here and how to make that happen in
> a way that isn't too hasty or locks us into just the opposite of what
> I think many of us want with regards to sharing data more broadly than
> within just one ecosystem of tools.
>
>
>
> Best, Rob
>
>
>
>
>
>
>
>
>
> On Thu, Aug 28, 2014 at 6:30 AM, John Deck <jdeck at berkeley.edu
> <mailto:jdeck at berkeley.edu>> wrote:
>
> I see the rational for enabling this in Darwin Core Archives and
> adding the new terms. However, back to what Matt Jones brought up:
> "won't we just end up with a new syntax that does essentially
> what O&M and OBOE do now?".
>
>
>
> We should include explicit references to existing terms/definitions
> that encapsulate what we're talking about, e.g. in our MaterialSample
> proposal last year we linked the an existing term in OBI, which has a
> much richer description and context for MaterialSample than what we
> considered (https://code.google.com/p/darwincore/issues/detail?id=167)
>
> Have we explored the possibility of doing this with OBOE? I'm not
> suggesting we adopt OBOE wholesale, but it seems like we have a good
> opportunity to enable better semantic linking with that efforts.
>
>
>
> John
>
>
>
> On Thu, Aug 28, 2014 at 4:23 AM, Éamonn Ó Tuama [GBIF]
> <eotuama at gbif.org <mailto:eotuama at gbif.org>> wrote:
>
> Thanks, Ramona and Rob.
>
> I'd like to add a few points following on Markus's reply.
>
> I think your pressing of the need for a robust semantic model for
> biodiversity sample/survey data is incontestable – we do need one and it
> should enable rich data integration once it is defined and the tools and
> data standards to support it become available. However, GBIF is faced with
> the immediate task of making sample-based data discoverable and accessible
> using its current ecosystem of tools (IPT) and exchange standards (DwC;
> EML). Waiting for a functional, implementable semantic model and the tools
> and support services for it is just not an option for us right now.
>
> We have already spend considerable time in analysing the merits of
> Occurrence core vs Event core and have opted for an Event core for reasons
> previously given. I don’t believe we are trying to reconfigure Event (“an
> action that occurs at a place and during a period of time”) and regardless
> of whether we use Occurrence or Event, the need for some additional terms
> arise (e.g., quantity, quantityType, samplingGeometry, samplingUnit). Once
> the BCO model is available for uptake, it should be possible to develop a
> mapping between it and the simple DwC sample model.
>
> So GBIF’s stance is that we need to take a two-pronged approach by
> exploring
> how the IPT and DwC-A can be adapted for publishing sample-based data
> in the
> near term while supporting the work of TDWG and groups such as the BCO in
> advancing biodiversity informatics. GBIF has already engaged in the
> work of
> the BCO and will continue to do so.
>
> Éamonn
>
>
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>] On Behalf Of Markus Döring
> Sent: 28 August 2014 12:44
> To: Ramona Walls
> Cc: TDWG Content Mailing List
>
> Subject: Re: [tdwg-content] tdwg-content Digest, Vol 63, Issue 6
>
> Hi Ramona & Rob,
>
> The Event proposal does not try to change the semantics of an Event,
> it just
> uses the existing Darwin Core Event "class" at the core in Darwin Core
> archives. The actual change proposed is simply adding 3 new terms to the
> Event "group" to better share information about sampling methods &
> efforts,
> extending the existing limited capabilities of Darwin Core which
> already has
> the terms dwc:samplingProtocol and dwc:samplingEffort. It also proposes 2
> new terms for dealing with quantity of Occurrences, something that has
> been
> discussed since 2012 now, when I had proposed a new abundance term [2].
>
>
> In general application of Darwin Core is not at all limited to
> specimens and
> observations. It is used for sharing taxonomic datasets already and it's
> definition and goal is broad. Let me cite some of the introduction to
> Darwin
> Core [1]:
>
> What is the Darwin Core?
> The Darwin Core is body of standards. It includes a glossary of terms (in
> other contexts these might be called properties, elements, fields,
> columns,
> attributes, or concepts) intended to facilitate the sharing of information
> about biological diversity by providing reference definitions,
> examples, and
> commentaries. The Darwin Core is primarily based on taxa, their occurrence
> in nature as documented by observations, specimens, samples, and related
> information.
>
> Motivation: The Darwin Core standard was originally conceived to
> facilitate
> the discovery, retrieval, and integration of information about modern
> biological specimens, their spatiotemporal occurrence, and their
> supporting
> evidence housed in collections (physical or digital). The Darwin Core
> today
> is broader in scope and more versatile. It is meant to provide a stable
> standard reference for sharing information on biological diversity. As a
> glossary of terms, the Darwin Core is meant to provide stable semantic
> definitions with the goal of being maximally reusable in a variety of
> contexts.
>
>
> Markus
>
>
> [1] http://rs.tdwg.org/dwc/index.htm
> [2] https://code.google.com/p/darwincore/issues/detail?id=142
>
>
> --
> Markus Döring
> Software Developer
> Global Biodiversity Information Facility (GBIF)
> mdoering at gbif.org <mailto:mdoering at gbif.org>
> http://www.gbif.org
>
>
>
>
>
> On 27 Aug 2014, at 18:57, Ramona Walls <rlwalls2008 at gmail.com
> <mailto:rlwalls2008 at gmail.com>> wrote:
>
> > I think it is important to consider the purpose of both Darwin Core and
> DwC archives in deciding whether or not to expand them, but we should use
> that consideration to address the question at hand, which is whether
> or not
> to add an Event core and additional properties to describe events.
> >
> > Describing the exchange format before the semantics is the wrong way to
> go, given that we now have a framework for developing semantics. Expanding
> Darwin Core before we adequately model survey data is bound to lead to
> problems later, when we try to retro-fit the semantics to Darwin Core
> Event
> archives. This is exactly the problem we are running into now with
> Occurance
> archives, and we have the opportunity to avoid it.
> >
> > I suggest we first use existing ontologies to model survey data,
> then deal
> with if and how to exchange that information in DwC-A. This is what I was
> hinting at in my first email, but should have said more explicitly.
> >
> > 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
> >
> >
> > On Wed, Aug 27, 2014 at 9:14 AM, Robert Guralnick
> <Robert.Guralnick at colorado.edu <mailto:Robert.Guralnick at colorado.edu>>
> wrote:
> >
> > It may be a sensible view for Darwin Core Archives and their intended
> use, but Tim's email suggests we should be putting the method of delivery
> ahead of the standard that delivers that content. If this was just about
> DwC-As, why not develop a survey extension that links each occurrence to
> information about the survey process using the existing star-schema
> methods
> we have in place? Why are we discussing adding terms to the Darwin
> Core or
> trying to fully reconfigure what we call an Event? That is what is on the
> table, not DwC-As and how we use them. Or am I missing something?
> >
> > Best, Rob
> >
> >
> >
> > On Wed, Aug 27, 2014 at 10:01 AM, Ramona Walls
> <rlwalls2008 at gmail.com <mailto:rlwalls2008 at gmail.com>>
> wrote:
> > Thanks, Tim, and yes, DwC-A as a view (but not necessarily the primary
> archive) of data seems like the right point of view.
> >
> > 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
> >
> >
> > On Wed, Aug 27, 2014 at 1:58 AM, Tim Robertson <trobertson at gbif.org
> <mailto:trobertson at gbif.org>>
> wrote:
> > Hi Ramona,
> >
> > Those are good points, and I’d like to come back to the original
> thinking
> behind the DwC-A.
> >
> > It was designed and intended to be a simple way of exposing a complete
> view of a dataset, primarily for building sophisticated indexes,
> inventories
> and allowing basic analytics (e.g. GBIF.org being one sophisticated
> index).
> We found that the star schema provided the flexibility to do a lot,
> and with
> the bundled metadata (e.g. EML) was enough to trace provenance and allow
> users to determine if the dataset might be fit for various uses. In many
> cases this represents the complete (e.g. lossless) view of a dataset.
> >
> > What we are discussing here are far richer datasets, where shoe-horning
> content into the star schema becomes lossy for some, although we’re
> finding
> other cases where it is indeed lossless. I believe we should be
> looking to
> harmonise ontologies / models etc as you mention but in parallel we should
> define one or more star schema views that can still be used for
> discovery /
> reporting / basic analytical purpose, and not long term archival of the
> dataset. The dataset would then have the canonical rich form and an
> additional DwC-A view. What I write here is applicable to all content
> types
> of course.
> >
> > Please also note that many people put supplementary files in the DwC-A
> which are ignored by DwC-A readers but could be a way of keeping the
> richer
> view in the bundle. If one wished you can describe those supplementary
> files in the EML document.
> >
> > Does this gel with the view of others as well?
> >
> > Cheers,
> > Tim
> >
> >
> >
> > On 27 Aug 2014, at 02:55, Ramona Walls <rlwalls2008 at gmail.com
> <mailto:rlwalls2008 at gmail.com>> wrote:
> >
> >> 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
> >>
> >>
> >> On Fri, Aug 22, 2014 at 3:00 AM,
> <tdwg-content-request at lists.tdwg.org
> <mailto:tdwg-content-request at lists.tdwg.org>>
> wrote:
> >> Send tdwg-content mailing list submissions to
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> >> than "Re: Contents of tdwg-content digest..."
> >>
> >>
> >> 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 at nceas.ucsb.edu <mailto:jones at nceas.ucsb.edu>>
> >> Subject: Re: [tdwg-content] Darwin Core: proposed news terms for
> >> expressing sample data
> >> To: ?amonn ? Tuama [GBIF] <eotuama at gbif.org <mailto:eotuama at gbif.org>>
> >> Cc: TDWG Content Mailing List <tdwg-content at lists.tdwg.org
> <mailto:tdwg-content at lists.tdwg.org>>
> >> Message-ID:
> >>
> <CAFSW8xkx7uRP9PC2g3=JT_VJanqujH8nPXoz8GXwh+JwKw5Ccw at mail.gmail.com
> <mailto:JT_VJanqujH8nPXoz8GXwh%2BJwKw5Ccw at 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 at gbif.org <mailto:eotuama at 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 at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org> [mailto:
> >> > tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at 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 at colorado.edu <mailto:Robert.Guralnick at 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 at gmail.com <mailto:annethessen at 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 at bishopmuseum.org <mailto:deepreef at bishopmuseum.org>>
> >> > wrote:
> >> >
> >> > Same here ? Events are central to the work that we do.
> >> >
> >> >
> >> >
> >> > Aloha,
> >> >
> >> > Rich
> >> >
> >> >
> >> >
> >> > *From:* tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org> [mailto:
> >> > tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>] *On Behalf Of *Anne Thessen
> >> > *Sent:* Wednesday, August 20, 2014 2:59 AM
> >> > *To:* tdwg-content at lists.tdwg.org
> <mailto:tdwg-content at 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 at gmail.com <mailto:robgur at gmail.com>
> [mailto:robgur at gmail.com <mailto:robgur at gmail.com> <robgur at gmail.com
> <mailto:robgur at 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 at gbif.org <mailto:eotuama at 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 at gbif.org
> <mailto:eotuama at gbif.org> <eotuama at gbif.org <mailto:eotuama at 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>
> <%2B45%203532%201494>; Fax: +45 3532 1480 <tel:%2B45%203532%201480>
> >> > <%2B45%203532%201480>*
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > tdwg-content mailing list
> >> > tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> >
> >> > tdwg-content mailing list
> >> >
> >> > tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> >
> >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> > Anne E. Thessen, Ph.D.
> >> >
> >> > The Data Detektiv, Owner and Founder
> >> >
> >> > Ronin Institute, Research Scholar
> >> >
> >> > 443.225.9185 <tel:443.225.9185>
> >> >
> >> >
> >> > _______________________________________________
> >> > tdwg-content mailing list
> >> > tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> > Anne E. Thessen, Ph.D.
> >> >
> >> > The Data Detektiv, Owner and Founder
> >> >
> >> > Ronin Institute, Research Scholar
> >> >
> >> > 443.225.9185 <tel:443.225.9185>
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > tdwg-content mailing list
> >> > tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > tdwg-content mailing list
> >> > tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >> >
> >> >
> >> -------------- next part --------------
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> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Fri, 22 Aug 2014 08:54:07 +0200
> >> From: "Donald Hobern [GBIF]" <dhobern at gbif.org
> <mailto:dhobern at gbif.org>>
> >> Subject: Re: [tdwg-content] Darwin Core: proposed news terms for
> >> expressing sample data
> >> To: "'Matt Jones'" <jones at nceas.ucsb.edu
> <mailto:jones at nceas.ucsb.edu>>, '?amonn ? Tuama [GBIF]'
> >> <eotuama at gbif.org <mailto:eotuama at gbif.org>>
> >> Cc: 'TDWG Content Mailing List' <tdwg-content at lists.tdwg.org
> <mailto:tdwg-content at lists.tdwg.org>>
> >> Message-ID: <003401cfbdd5$de52b640$9af822c0$@gbif.org
> <http://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 at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at 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 at gbif.org <mailto:eotuama at 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 at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at 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 at colorado.edu <mailto:Robert.Guralnick at 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 at gmail.com <mailto:annethessen at 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 at bishopmuseum.org <mailto:deepreef at bishopmuseum.org>> wrote:
> >>
> >> Same here ? Events are central to the work that we do.
> >>
> >>
> >>
> >> Aloha,
> >>
> >> Rich
> >>
> >>
> >>
> >> From: tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>] On Behalf Of Anne Thessen
> >> Sent: Wednesday, August 20, 2014 2:59 AM
> >> To: tdwg-content at lists.tdwg.org <mailto:tdwg-content at 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 at gmail.com <mailto:robgur at gmail.com>
> [mailto:robgur at gmail.com <mailto:robgur at 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 at gbif.org <mailto:eotuama at 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 at gbif.org
> <mailto:eotuama at 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>
> <tel:%2B45%203532%201494> ; Fax: +45 3532 1480 <tel:%2B45%203532%201480>
> <tel:%2B45%203532%201480>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> tdwg-content mailing list
> >> tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> tdwg-content mailing list
> >> tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> >>
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>
> >>
> >>
> >> --
> >> Anne E. Thessen, Ph.D.
> >> The Data Detektiv, Owner and Founder
> >> Ronin Institute, Research Scholar
> >> 443.225.9185 <tel:443.225.9185>
> >>
> >>
> >> _______________________________________________
> >> tdwg-content mailing list
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> >>
> >>
> >>
> >> --
> >> Anne E. Thessen, Ph.D.
> >> The Data Detektiv, Owner and Founder
> >> Ronin Institute, Research Scholar
> >> 443.225.9185 <tel:443.225.9185>
> >>
> >>
> >>
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