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 dont 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 GBIFs 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@lists.tdwg.org [mailto:tdwg-content-bounces@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@gbif.org http://www.gbif.org
On 27 Aug 2014, at 18:57, Ramona Walls rlwalls2008@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@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@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@gbif.org
wrote:
Hi Ramona,
Those are good points, and Id 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 were 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@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@lists.tdwg.org
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Today's Topics:
- Re: Darwin Core: proposed news terms for expressing sample data (Matt Jones)
- 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]
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
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.
- 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?
- 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.
- 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
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 isthe 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]
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:
*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.
*quantityType*: : the entity being referred to by quantity,e.g., individuals, biomass, %species, scale type.
*samplingGeometry*: an indication of what kind of space wassampled; select from point, line, area or volume.
*samplingUnit*: the unit of measurement used for reporting thequantity 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.
*eventSeriesID*: an identifier for a set of events that areassociated 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
[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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