[tdwg-content] [External] Re: Proposed changes to Darwin Core

Richard Pyle deepreef at bishopmuseum.org
Wed Jul 23 18:00:40 CEST 2014

Yeah.  What he said.





P.S. I was going to write a detailed response myself, but Steve has obviated that need by capturing the main points I had planned to make (and more) – and much more clearly and effectively than I could have achieved.


From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Steve Baskauf
Sent: Wednesday, July 23, 2014 5:34 AM
To: Robert Guralnick
Cc: TDWG Content Mailing List
Subject: Re: [tdwg-content] [External] Re: Proposed changes to Darwin Core


This is beginning to resemble responses to a request for comments.  Is that what we are doing?  If so, can we have an official declaration of that?

With respect to Rob's point 1: we already have an organism/individual class.  Its existence is implied by the existing term dwc:individualID.  What the proposal does is to try to describe clearly what kinds of things could reasonably have their identifier be the value of dwc:individualID.  The proposal is not really about creating "new" classes, but rather about cleaning up the mess that we currently have with unclear definitions and having two terms in different namespaces (dwc: and dwctype:) that are apparently the same thing.  I won't say more here because the rationale for the proposal is given as clearly and succinctly as possible at https://code.google.com/p/darwincore/issues/detail?id=204

There are basically three separate issues that we are dealing with in this thread.  

The first issue is dealing with the proposed changes.  There is an existing process for adding and changing DwC terms.  It's a bit clunky and inefficient, but it has worked in the past.  At least nine people have expended considerable effort to organize the Documenting Darwin Core session, hammer out a consensus definitions, and get them into the issue tracker.  Let the system as it exists proceed, and if the proposals are inadequate, then revise or reject them.  There is no reason to delay that process, however imperfect it is.  

The second issue is about the function of TDWG, which includes revising the DwC "Namespace Policy" for dealing with term additions and changes, and which includes the role and function of the TAG.  Again there has been significant legwork already done to make concrete recommendations on how to deal with this.  Let the TDWG Chair and Executive take action on these recommendations, either by fiat or creation of a task group.  There is a process for this kind of thing: http://www.tdwg.org/about-tdwg/process/ .  Use it.

The third issue involves the mixing of DwC and BCO.  I have indicated in the past that I support BCO development because it has the potential to bring clarity to murky definitions.  However, it is not clear that directly linking the Darwin Core vocabulary semantically to an ontology like BCO is a good idea.  We've already done that with the RDF definition of Material Sample.  At the time, I thought that was OK, but after hearing Joel's talk at the TDWG meeting [1] I've changed my mind.  After considerable reflection, I don't think that a clear case has been made for what tangible benefits will be gained by tying a general purpose vocabulary like Darwin Core directly in RDF to an OBO ontology like BCO.  By "tangible benefits", I mean showing what semantic reasoning will be facilitated by that linkage.  What are the use cases? Give actual examples (i.e. via SPARQL or using an OWL reasoner) of how that reasoning will be accomplished?  I will write no more about this here, since I've blogged in detail about this elsewhere [2].  I think TDWG has already made a mistake once by setting out to construct the TDWG Ontology without a clear understanding of what concrete things would be accomplished by the effort.  Rob is now suggesting tying the management of a ratified TDWG standard to the maintenance of an Ontology that is being developed independently of the TDWG standards process.  I don't know if that would even be allowable under the rules of TDWG and even if it is, I think it's unwise without first having a discussion within TDWG about what such a linkage would facilitate.

We really should not be mixing up these three issues.  That's my fault for bringing up the process question in the same email as comments about the concrete proposals.  But they really need to be dealt with separately, by means that are appropriate for each of them.


[1] http://www.tdwg.org/fileadmin/2013conference/slides/Sachs_DwC_as_a_Model.pptx
[2] http://baskauf.blogspot.com/2014/05/confessions-of-rdf-agnostic-part-6.html in the section "Linking and the Biocollections Ontology" and those that follow.

Robert Guralnick wrote: 


  Hi everyone --- Excuse the brevity, but I am headed out for an annual vacation and will attempt (and likely fail) to ignore email for the next week.  However, the topics raised by Joel and Steve are important and I do have some quick comments, separated by topic (one on term issues and one on governance).

1)  To my surprise, I am no longer in favor of a DwC:Organism addition and attendant other changes (if I ever was in favor).  I think this reflects a shift in my thinking -- I have come to see the Darwin Core as really about biocollections and material samples or observations, making the specification of "individuals" or "organisms" less a compelling need.  I feel that "individual/organism" is actually fraught with a fair amount of peril, when knowledge modeled.  What we really deal with are samples --- the individual/organism is there ephemerally within the context of the collecting event, and sometimes not even then (road kill).  I just can't see why we need it at this point.


2)  Steve has a very good point about TAG and decision making.  The larger question is "what to do".  Here is a thought.  A few of us have agreed to weekly (virtual) meetings about BCO and DwC integration (John Wieczorek, John Deck, Ramona Walls, myself and a couple others) --- we haven't always come through but setting aside the time is important and useful.  Why not reconstitute the TAG or at least a subgroup and bring BCO/DwC kinds of activities together more firmly.  We could open those meetings more broadly to deal with continuing issues with DwC, while also keeping our eye on BCO and its growth.  I also see a real opportunity here (and I am not the only one) for funding this kind of work, in the context of NSF's RCN (Research Coordination Network) framework.  We clearly have the need and such funding could allow us the chance to meet more regularly than once a year.  If there is interest, I am willing to consider the work needed to make this happen. 


Best, Rob




On Wed, Jul 23, 2014 at 6:10 AM, Steve Baskauf <steve.baskauf at vanderbilt.edu> wrote:

Thanks for bringing these issues up, Joel.

To clarify the situation, the changes that have been proposed should be
handled in accordance with the Darwin Core term change policy [1].  If
I'm interpreting that policy correctly, the changes would fall in
sections 3.3 or 3.4.  The proposed changes that redefine existing terms
(like dwc:Occurrence) would be "Semantic changes in Darwin Core terms"
(section 3.3) and the changes that create new terms (like
dwc:LivingSpecimen) would be "Addition of Darwin Core term declarations
to exisiting Darwin Core namespaces (section 3.4).   The exact procedure
in both sections is a bit murky because it presupposes a functioning
Technical Architecture Group (TAG) that judges the merit of the proposal
and (at least in the case of 3.4) calls for a request for comments
(RFC).  Historically, there has not been a functioning TAG, so John
Wiecorek (shepherd of Darwin Core) has traditionally made the call for a
30 day RFC on tdwg-content.  He hasn't done that yet, to my knowledge.
I don't think that the Term Change Policy actually requires action by
the Executive, but I think that in actuality it has made the final call
since there hasn't been any TAG to do the job.

I have to say that I'm puzzled by the lack of motion on this proposal.
The usual reason for failure of proposed changes is "lack of
consensus".  However, in this case, there seemed (to me) to be
widespread support for these changes at the Documenting Darwin Core
workshop at the TDWG meeting in November.  In the discussions held in
December by the ad hoc group (whose purpose was to hammer out the actual
proposed definitions), there was a shocking degree of consensus about
everything except for the name of the one class (organism/individual).
So I don't understand why the proposed changes haven't gone to public
comment months ago.

The DwC RDF Guide [3] (which Joel mentioned) has similarly languished
for a year now, having already undergone numerous revisions and having
been endorsed by the task group that created it.  The only reason I
haven't pushed harder on moving it forward is that it would need to be
revised if the proposed DwC class changes were adopted.  So lack of
progress on the proposed term changes is holding up progress on that as

The real problem here is that the TDWG standards maintenance process is
broken.  We need a clear and usable system that covers all of the TDWG
technical standard vocabularies (i.e. DwC, Audubon Core, and any future
ones).  This was discussed in detail in several sessions at the last
TDWG meeting with some concrete proposals put on the table [4]. It was
my impression that this issue was very high on the agenda of the
Executive.  However, we are now nine month past that meeting and I
haven't seen any visible signs that there has been any progress on this
front.  Is TDWG actually a standards organization or not?  I'm not sure


[1] http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges
[2] doesn't currently exist in the dwc: namespace; it's in the dwctype:
namespace, which we have proposed to deprecate
[3] https://code.google.com/p/tdwg-rdf/wiki/DwcRdf
[4] http://www.gbif.org/resources/2246 plus several in-person meetings

joel sachs wrote:
> Hi John,
> On Tue, 22 Jul 2014, John Wieczorek wrote:
>> Hi Joel,
>> Is this meant to call everyone's attention to the issues?
> Yes, that is the purpose of this email. My understaning of the process
> for changing the standard is that proposals are entered into the Issue
> Tracker, followed by a 30 day period of public comment, followed by
> the editor bringing the proposals to the executive for ratification.
> So, technically, tdwg-content does not need to be notified prior to
> ratification. (Is that correct?) Regardless, as much as I want to see
> our proposals ratified, I don't want it to happen under the radar, and
> so thought it made sense to inform the list.
>> To elicit further
>> commentary? Or to make a specific proposal for action?
>> I suspect it is to put forward your positions on issue 205. If that is
>> correct, I propose bringing those positions here for discussion.
> I don't mind airing my positions on Issue 205, but would prefer not to
> lead off with that. My questions and suggestions regarding the
> proposed dwc:Organism class are not as important as our proposal to
> deprecate the dwctype namespace, and to remove the phrase "The
> category of information pertaining to" from the definitions of the dwc
> classes.
> Cheers,
> Joel.
>> Cheers,
>> John
>> On Tue, Jul 22, 2014 at 5:16 PM, joel sachs <jsachs at csee.umbc.edu>
>> wrote:
>>       Hi Everyone,
>>       I’d like to direct everyone’s attention to issues 204 - 226 in
>>       the Darwin Core issue tracker [1]. These issues describe
>>       proposed changes to the Darwin Core standard, and were entered
>>       back in January in follow up to the Documenting Darwin Core
>>       workshop held at TDWG 2013. These proposals reflect what the
>>       organizers of that workshop believe to be the consensus that was
>>       reached during the workshop’s four sessions in Florence.
>>       The background for this is that, for some time, a number of
>>       TDWGers have been working towards an applicability statement to
>>       provide guidance on expressing Darwin Core data using RDF. In
>>       the course of this work, it became apparent that the semantics
>>       of Darwin Core itself needed a slight re-think, in order to be
>>       usable on the semantic web. The goal was to be
>>       backward-compatible, i.e. to introduce and re-define terms in a
>>       way that does not affect the meaning of existing Darwin Core
>>       spreadsheet data, but which provides the semantic grounding
>>       necessary for meaningful RDF. I think this goal has, for the
>>       most part, been realized. If you have examples to the contrary,
>>       please share them.
>>       Steve Baskauf provides a good overview of the proposals in Issue
>>       204. Of all of them, only Issue 205 (the introduction of a class
>>       to represent the taxonomically homogenous units that are
>>       described in Darwin Core occurrence data) was contentious,
>>       primarily because we disagreed on a good name for the class.
>>       (“We” refers to the ad-hoc group that worked on translating the
>>       notes from the workshop into concrete proposals - John
>>       Wieczorek, James Macklin, Markus Döring, Rich Pyle, Tim
>>       Robertson, Bob Morris, Hilmar Lapp, Steve Baskauf, Gregor
>>       Hagedorn, and myself.) I’ve mentioned my own concerns as a
>>       comment on that issue.
>>       There is one proposal that had the support of the group, but
>>       that is not yet entered into the Issue Tracker - the deprecation
>>       of dwc:basisOfRecord. The motivation for this proposal is that
>>       dwc:basisOfRecord is widely misunderstood and inconsistently
>>       used, coupled with the fact that GBIF currently uses
>>       basisOfRecord with the semantics of the (to be proposed)
>>       dwc:hasEvidence term. However, we have held back on proposing
>>       "hasEvidence", as there remain some unresolved issues regarding
>>       how it would be used. This will likely be left as future work,
>>       perhaps to be tackled at TDWG 2014.
>>       Many thanks to all who participated in the workshop, and to all
>>       who take the time to review its outcomes.
>>       Joel.
>>       1. https://code.google.com/p/darwincore/issues/list ["ID" ->
>>       "Sort Down" to see in order]
>>       _______________________________________________
>>       tdwg-content mailing list
>>       tdwg-content at lists.tdwg.org
>>       http://lists.tdwg.org/mailman/listinfo/tdwg-content

Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN  37235-1634,  U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
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