[tdwg-content] A proposal to improve Darwin Core for invasive species data

[Lee Belbin]

Hi John et al,

Ditto (to Annie's comment) from me.

As most of you know, I have been standing back from TDWG for a few years
now, but it has been hard to avoid interest in the development of TDWG's
most significant standard. I have been aware of at least three independent
suggestions that are relevant to my interests.

As from the beginning, the difficulty remains in getting wise heads
together (face-to-face) and getting consensus on recommendations in a
timely manner. The TDWG meetings are too busy without sufficient time to
achieve outcomes. Teleconferencing is great in theory but hopeless in
practice. The only alternative is to find time and $ for dedicated meetings
adjacent to, or separate from the TDWG Conference. It has been done before
to good effect.

I raise this as I believe that the time for such a meeting is well and
truly here.

Cheers

Lee

Lee Belbin
Blatant Fabrications Pty Ltd
Tasmania

On Thu, May 26, 2016 at 4:04 AM, Quentin Groom <
quentin.groom at plantentuinmeise.be> wrote:

> I second Annie, this is a real problem in Biodiversity Informatics in
> general. Unless you can turn maintenance tasks into peer reviewed papers
> then you get little credit for it.
> Quentin
>
>
>
> Dr. Quentin Groom
> (Botany and Information Technology)
>
> Botanic Garden Meise
> Domein van Bouchout
> B-1860 Meise
> Belgium
>
> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>
> Landline; +32 (0) 226 009 20 ext. 364
> FAX:      +32 (0) 226 009 45
>
> E-mail:     quentin.groom at plantentuinmeise.be
> Skype name: qgroom
> Website:    www.botanicgarden.be
>
>
> On 25 May 2016 at 17:57, John Wieczorek <tuco at berkeley.edu> wrote:
>
>> Thanks Annie. I don't plan to give up, it's just that I don't feel I have
>> been doing it justice for a while now.
>>
>> On Wed, May 25, 2016 at 12:52 PM, Simpson, Annie <asimpson at usgs.gov>
>> wrote:
>>
>>> Chiming in now, very briefly...
>>>
>>> John, you are the DwC champion who has kept it moving forward in a
>>> comprehensible and useful way. The TDWG community is very grateful for your
>>> work on this and I personally hope you don't give up the good fight.
>>>
>>> *Annie Simpson, biologist & information scientist*
>>> http://orcid.org/0000-0001-8338-5134
>>>
>>> *BISON project (http://bison.usgs.ornl.gov <http://bison.usgs.ornl.gov>)*
>>> *Core Science Analytics, Synthesis, & Libraries Program*
>>>
>>>
>>>
>>>
>>>
>>> *U.S. Geological Survey, MS 30212201 Sunrise Valley DriveReston,
>>> Virginia  20192=================asimpson at usgs.gov
>>> <asimpson at usgs.gov>703.648.4281 <703.648.4281> desk*
>>>
>>> On Wed, May 25, 2016 at 7:26 AM, John Wieczorek <tuco at berkeley.edu>
>>> wrote:
>>>
>>>> One primary idea behind the BCO is indeed as the proving ground you
>>>> mention. The challenge is having consistent available resources to do that
>>>> work. With BCO it could be a particular challenge, I think, since it can
>>>> cover so much semantic space. I would love to be in a position to be a
>>>> proper BCO caretaker, but I have not even been able to do a good job with
>>>> Darwin Core as it is.
>>>>
>>>> On Wed, May 25, 2016 at 2:00 AM, Quentin Groom <
>>>> quentin.groom at plantentuinmeise.be> wrote:
>>>>
>>>>> Interesting! I had not come across Apple Core before. Isn't this
>>>>> proving-ground role something that the Biological Collections Ontology
>>>>> can also do?
>>>>> I like the idea of a Darwin Core with different levels of adherence to
>>>>> rules. I agree that strict enforcement of rules will inhibit the flow of
>>>>> data, but in my own experience there are simple fields that I could have
>>>>> easily completed in a standardized way, if only I could have found a
>>>>> suitable recommendation to follow. Hierarchical vocabularies are
>>>>> particularly useful here, because they have built in flexibility.
>>>>> Regards
>>>>> Quentin
>>>>>
>>>>>
>>>>>
>>>>> Dr. Quentin Groom
>>>>> (Botany and Information Technology)
>>>>>
>>>>> Botanic Garden Meise
>>>>> Domein van Bouchout
>>>>> B-1860 Meise
>>>>> Belgium
>>>>>
>>>>> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>>>>>
>>>>> Landline; +32 (0) 226 009 20 ext. 364
>>>>> FAX:      +32 (0) 226 009 45
>>>>>
>>>>> E-mail:     quentin.groom at plantentuinmeise.be
>>>>> Skype name: qgroom
>>>>> Website:    www.botanicgarden.be
>>>>>
>>>>>
>>>>> On 25 May 2016 at 03:17, John Wieczorek <tuco at berkeley.edu> wrote:
>>>>>
>>>>>> I think it is indeed worthwhile to have content standards to go with
>>>>>> the term definitions. Applce Core (now under renewed development at
>>>>>> https://github.com/tdwg/applecore) is a good example of this.
>>>>>>
>>>>>> On Tue, May 24, 2016 at 6:16 PM, Chuck Miller <Chuck.Miller at mobot.org
>>>>>> > wrote:
>>>>>>
>>>>>>> John,
>>>>>>>
>>>>>>> It’s interesting how long that text has been out there, and without
>>>>>>> much comment.  It seems to presume there is a binary situation: tightly
>>>>>>> controlled vocabulary that is exclusive or loosely controlled that is
>>>>>>> inclusive.   Maybe it’s time now to consider something additional in the
>>>>>>> middle.  We know a lot more about how the Darwin Core standard is being
>>>>>>> used, or at least have plenty of examples.  With the addition of use cases
>>>>>>> into the standards for terms, progress could be made on use-case-based
>>>>>>> standard vocabulary that could reduce the “garbage in/garbage out” problem
>>>>>>> that comes from being totally inclusive.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> TDWG standards in the 80s and 90s were a little more about
>>>>>>> controlled vocabulary and reducing garbage than they have been in the 00s
>>>>>>> and 10s.  Maybe we should spend some time on that aspect of data exchange
>>>>>>> again and use cases could be a method.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Chuck
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *From:* tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org] *On
>>>>>>> Behalf Of *John Wieczorek
>>>>>>> *Sent:* Tuesday, May 24, 2016 2:48 PM
>>>>>>>
>>>>>>> *To:* Quentin Groom
>>>>>>> *Cc:* TDWG Content Mailing List
>>>>>>> *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core for
>>>>>>> invasive species data
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I would say that the primary factor driving the philosophy for loose
>>>>>>> controlled vocabulary recommendations is a desire to promote the stability
>>>>>>> of Darwin Core term definitions, because changes can be disruptive. Section
>>>>>>> 1.4 on the Simple Darwin Core page (
>>>>>>> http://rs.tdwg.org/dwc/terms/simple/index.htm) gives further
>>>>>>> practical arguments for this stance. I have copied the relevant text here
>>>>>>> for convenience:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> "There is a difference between having data in a field and requiring
>>>>>>> that field to have a value from among a legal set of values. The Darwin
>>>>>>> Core is simple in that it has minimal restrictions on the contents of
>>>>>>> fields. The term comments give recommendations about the use of controlled
>>>>>>> vocabularies and how to structure content wherever appropriate. Data
>>>>>>> contributors are encouraged to follow these recommendations as well as
>>>>>>> possible. You might argue that having no restrictions will promote "dirty"
>>>>>>> data (data of low quality or dubious value). Consider the simple axiom
>>>>>>> "It's not what you have, but what you do with it that matters." If data
>>>>>>> restrictions were in place at the fundamental level, then a record having
>>>>>>> any non-compliant data in any of its fields could not be shared via the
>>>>>>> standard. Not only would there be a dearth of shared data in that case (or
>>>>>>> an unused standard), but also there would be no way to use the standard to
>>>>>>> build shared data cleaning tools to actually improve the situation, nor to
>>>>>>> use data services to look up alternative representations (language
>>>>>>> translations, for example) to serve a broader audience. The rest is up to
>>>>>>> how the records will be used - in other words, it is up to applications to
>>>>>>> enforce further restrictions if appropriate, and it is up to the
>>>>>>> stakeholders of those applications to decide what the restrictions will be
>>>>>>> for the purpose the application is trying to serve."
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, May 24, 2016 at 3:44 PM, Quentin Groom <
>>>>>>> quentin.groom at plantentuinmeise.be> wrote:
>>>>>>>
>>>>>>> Hi Paco,
>>>>>>>
>>>>>>> I'm glad to hear Plinian Core is active, I only recently discovered
>>>>>>> it and think it is a good initiative. The species data I've seen is in
>>>>>>> quite diverse and in unstandardised formats. It would be nice to see some
>>>>>>> of the big providers using Plinian Core.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'm not so worried about imposing limitations on users, because as
>>>>>>> far as I can see Darwin Core only recommends vocabularies, it doesn't
>>>>>>> enforce them. Having said that, it would be useful to know what is meant by
>>>>>>> "*Recommended best practice is to use a controlled vocabulary*",
>>>>>>> because if Darwin Core doesn't impose a vocabulary and there is no field to
>>>>>>> specify which vocabulary you are using then it doesn't help
>>>>>>> interoperability much.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'm happy to also discuss off list. Invasiveness and impact are
>>>>>>> difficult to standardize and so far I've chosen other fields that I
>>>>>>> consider easier to gain consensus on.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Quentin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dr. Quentin Groom
>>>>>>>
>>>>>>> (Botany and Information Technology)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Botanic Garden Meise
>>>>>>>
>>>>>>> Domein van Bouchout
>>>>>>>
>>>>>>> B-1860 Meise
>>>>>>>
>>>>>>> Belgium
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Landline; +32 (0) 226 009 20 ext. 364
>>>>>>>
>>>>>>> FAX:      +32 (0) 226 009 45
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> E-mail:     quentin.groom at plantentuinmeise.be
>>>>>>>
>>>>>>> Skype name: qgroom
>>>>>>>
>>>>>>> Website:    www.botanicgarden.be
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 24 May 2016 at 19:08, Francisco Pando <pando at gbif.es> wrote:
>>>>>>>
>>>>>>> Quentin et al.,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Plinian Core is active and backed up by an international group that
>>>>>>> seeks expansion. A session is planned in TDWG 2016 about it within the
>>>>>>> Species Information Interest Group slot.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> "Invasiveness" is a section within the Plinian Core schema:
>>>>>>> https://github.com/PlinianCore/Documentation/wiki/InvasivenessClass
>>>>>>>
>>>>>>> It is much based on the GISIN schema.   This can be revisited,
>>>>>>> updated and harmonized with current initiatives, some mentioned in this
>>>>>>> thread. Quentin, we may do a bit of exchange of-list
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Whereas shared vocabularies bring plenty of good things , I share
>>>>>>> Chuck’s concerns about imposing some unwanted limitations for some
>>>>>>> potential users of the schema.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Paco
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Francisco Pando
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Investigador
>>>>>>>
>>>>>>> Real Jardín Botánico - CSIC
>>>>>>>
>>>>>>> Plaza de Murillo, 2
>>>>>>>
>>>>>>> 28014 Madrid, Spain
>>>>>>>
>>>>>>> Tel.+34 91 420 3017 x 172
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *From:* tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org] *On
>>>>>>> Behalf Of *Quentin Groom
>>>>>>> *Sent:* Monday, May 23, 2016 10:10 PM
>>>>>>> *To:* Chuck Miller
>>>>>>>
>>>>>>>
>>>>>>> *Cc:* TDWG Content Mailing List
>>>>>>> *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core for
>>>>>>> invasive species data
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi Chuck,
>>>>>>>
>>>>>>> thanks for your point. The use cases I'm thinking of are
>>>>>>> conservation red-listing; horizon-scanning for potential new invasives;
>>>>>>> early warning of new aliens; impact assessment and invasion monitoring. We
>>>>>>> have recently be discussing the possibility of automating all of these
>>>>>>> process so that they can be repeated regularly, or as soon as new data
>>>>>>> becomes available. Obviously, for this we need observations, but we also
>>>>>>> need check-lists to tell us what is considered native or alien, present or
>>>>>>> extinct.
>>>>>>>
>>>>>>> I know more about invasive species research than red-listing, but I
>>>>>>> am aware that the current rate of red-listing is so slow that most things
>>>>>>> will become extinct before they are assessed. Given that the IUCN criteria
>>>>>>> are so clear, it should be possible to automate the whole process using
>>>>>>> GBIF. The only limitation with then be mobilizing the observations.
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Quentin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dr. Quentin Groom
>>>>>>>
>>>>>>> (Botany and Information Technology)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Botanic Garden Meise
>>>>>>>
>>>>>>> Domein van Bouchout
>>>>>>>
>>>>>>> B-1860 Meise
>>>>>>>
>>>>>>> Belgium
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Landline; +32 (0) 226 009 20 ext. 364
>>>>>>>
>>>>>>> FAX:      +32 (0) 226 009 45
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> E-mail:     quentin.groom at plantentuinmeise.be
>>>>>>>
>>>>>>> Skype name: qgroom
>>>>>>>
>>>>>>> Website:    www.botanicgarden.be
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 23 May 2016 at 21:10, Chuck Miller <Chuck.Miller at mobot.org>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Quentin,
>>>>>>>
>>>>>>> I think in addition to defining the community that needs the new
>>>>>>> Origin term, you also need to define the use cases to which the proposed
>>>>>>> controlled vocabularies for establishmentMeans and occurenceStatus apply.
>>>>>>> Darwin Core is used in multiple ways.  I think there may be use cases for
>>>>>>> these terms that don’t match the invasive species use cases. One controlled
>>>>>>> vocabulary may not work for all Darwin Core users.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Chuck
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Chuck Miller | VP-IT & CIO | Missouri Botanical Garden*
>>>>>>>
>>>>>>> *4344 Shaw Boulevard | Saint Louis, MO 63110 | Phone 314-577-9419
>>>>>>> <314-577-9419>*
>>>>>>>
>>>>>>> *From:* tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org] *On
>>>>>>> Behalf Of *John Wieczorek
>>>>>>> *Sent:* Monday, May 23, 2016 1:36 PM
>>>>>>> *To:* Quentin Groom
>>>>>>> *Cc:* TDWG Content Mailing List
>>>>>>> *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core for
>>>>>>> invasive species data
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi Quentin,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thank you for your effort in putting forth these welll thought out
>>>>>>> proposals. At various times I have heard discussions on the inadequecy of
>>>>>>> establishmentMeans. Your work encapsulates the problem well.
>>>>>>>
>>>>>>> One of the things that helps when proposing to add a Darwin Core
>>>>>>> term is demonstrating that there is a community that needs it. Can you tell
>>>>>>> us who has a demonstrated need to share this information? Anyone out there
>>>>>>> who has this interest is also welcome to share that here to provide
>>>>>>> evidence of demand from more than one group, project or individual.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> John
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, May 23, 2016 at 3:23 PM, Quentin Groom <
>>>>>>> quentin.groom at plantentuinmeise.be> wrote:
>>>>>>>
>>>>>>> I've been working on a proposal to improve Darwin Core for use with
>>>>>>> invasive species data.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The proposal is detailed on GitHub at
>>>>>>> https://github.com/qgroom/ias-dwc-proposal/blob/master/proposal.md.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The proposal is for a new term "origin" and suggested vocabularies
>>>>>>> for establishmentMeans and occurrenceStatus.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'd welcome your feedback on the proposal.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From my perspective it provides some needed clarity on
>>>>>>> the establishmentMeans and occurrenceStatus fields, but also adds the
>>>>>>> origin that is needed for invasive species research and for conservation
>>>>>>> assessments.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'm not sure of the best way to discuss this, but if you have
>>>>>>> concrete proposals for changes you might raise them as issues on GitHub, as
>>>>>>> well as mentioning them here.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Quentin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dr. Quentin Groom
>>>>>>>
>>>>>>> (Botany and Information Technology)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Botanic Garden Meise
>>>>>>>
>>>>>>> Domein van Bouchout
>>>>>>>
>>>>>>> B-1860 Meise
>>>>>>>
>>>>>>> Belgium
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Landline; +32 (0) 226 009 20 ext. 364
>>>>>>>
>>>>>>> FAX:      +32 (0) 226 009 45
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> E-mail:     quentin.groom at plantentuinmeise.be
>>>>>>>
>>>>>>> Skype name: qgroom
>>>>>>>
>>>>>>> Website:    www.botanicgarden.be
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>> tdwg-content at lists.tdwg.org
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
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