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

Tue May 24 23:16:33 CEST 2016

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<mailto: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<mailto:quentin.groom at plantentuinmeise.be>
Skype name: qgroom
Website:    www.botanicgarden.be<http://www.botanicgarden.be>

On 24 May 2016 at 19:08, Francisco Pando <pando at gbif.es<mailto: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<tel:%2B34%2091%20420%203017%20x%20172>

From: tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org<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<mailto:quentin.groom at plantentuinmeise.be>
Skype name: qgroom
Website:    www.botanicgarden.be<http://www.botanicgarden.be>

On 23 May 2016 at 21:10, Chuck Miller <Chuck.Miller at mobot.org<mailto: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<tel:314-577-9419>
From: tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org<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<mailto: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<mailto:quentin.groom at plantentuinmeise.be>
Skype name: qgroom
Website:    www.botanicgarden.be<http://www.botanicgarden.be>

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