Dear All, 

regarding the proposal to improve Darwin Core for invasive species data. Melodie McGeoch (Monash University) gave me this response off-list to the proposal and has allowed me to share it with you.

"I come at this discussion as very much a non-expert on data basing, but from the viewpoint of data needs for indicator use, errors associated with alien listing, and more recently essential variables for invasion monitoring. I will leave the technical details in your highly capable hands, and rather comment on some of the points you have made that resonate with various other activities on the go.

The point about the need to identify/designate the native and introduced ranges is spot on, and is possibly the most important current gap in available and readily accessible information from my perspective. This applies at both the individual record level as well as the species level, i.e. knowing if a species is known to occur/have been introduced outside of its native range, as well as knowing if individual records of the species are within either the introduced or native range. We have a couple of publications that deal with this topic, as well as one in review.

It would be very valuable if we could try and align the vocabulary with the Essential Biodiversity Variable initiative (http://geobon.org/essential-biodiversity-variables/what-are-ebvs/), as well as our recent project under this umbrella on Essential Variables for Invasion Monitoring (www.invasionevs.com). The basic info is on the website, but we have a paper undergoing minor revision with further detail which I can circulate soon. The 3 variables we identified as 'essential' are alien species occurrence, species alien status (i.e. a designation for each record of whether the record lies inside or outside of the native range) and alien species impact (using the new EICAT scheme). The vocab for the EVs is not 100% fixed - although it would be useful not to change it now, we can still do so to maximize alignment across initiatives, or at very least cross-reference these. 

In terms of the pathways you discussed in your proposal Quentin - I strongly support your suggestion to align the vocabulary with the 'Standard Categorisation of Pathways' scheme developed and adopted by the IUCN/CBD etc. There have been some recent developments and updates on this, which you are probably aware of (I can send these on if not)."

Regards
Quentin



Dr. Quentin Groom
(Botany and Information Technology)

Botanic Garden Meise
Domein van Bouchout
B-1860 Meise
Belgium


Landline; +32 (0) 226 009 20 ext. 364
FAX:      +32 (0) 226 009 45

Skype name: qgroom
Website:    www.botanicgarden.be


On 29 May 2016 at 08:14, Quentin Groom <quentin.groom@plantentuinmeise.be> wrote:
Dear Donald,
that's a fantastic manifesto and challenge.

In discussions over DwC changes for invasive species the lack of understanding on the uses of DwC and its fields was evident. In this light, Donald's wishlist to find a balance between human and computer usability seems very sensible. The lack of knowledge in the community is not the fault of DwC, but if DwC field names and vocabularies were more adopted within collection databases and other software understanding would improve.

A common problem of understanding was DwC's usage for checklists, as opposed to observations and specimens. These different perspectives give different meanings to fields. For example, occurrenceStatus make sense from the perspective of a checklist, but one could easily imagine it being competed by a diligent researcher for a specimen where is has ambiguous meaning.

Regarding what workshops might be needed, I'll leave this to the TDWG people, but I'm certainly trying to get to the annual TDWG conference this year and I hope some of this can be discussed there.

Regards
Quentin



Dr. Quentin Groom
(Botany and Information Technology)

Botanic Garden Meise
Domein van Bouchout
B-1860 Meise
Belgium


Landline; +32 (0) 226 009 20 ext. 364
FAX:      +32 (0) 226 009 45

Skype name: qgroom
Website:    www.botanicgarden.be


On 27 May 2016 at 16:28, Donald Hobern <dhobern@gbif.org> wrote:

On behalf of the GBIF Secretariat, I’d like to emphasise our extreme interest in assisting with the next phase in developing Darwin Core and TDWG standards generally.

 

Many important points have already been made.  Flexibility to accommodate plain text and URIs in the same fields leaves some problems for data aggregators and users but is clearly the only workable way to enable data publishing from the widest possible range of sources.

 

However, I think it is essential that we use this opportunity to revisit the whole architecture of how we represent share, and use biodiversity data.  There are several interconnected aspects that should be included in this debate.

 

I take it as a given that our shared vision should include enabling human users and machines to find all of the information and to traverse all of the data connections that a knowledgeable researcher can see in the biodiversity literature, collections and other resources. By this, I mean that we should be able to start from any point in the biodiversity data graph and find the meaningful links to associated data objects. From specimen to taxon concept to taxon name to publication; from sequence to associated sequences to taxon concepts to species occurrences; etc., etc. 

 

This means that our data architecture needs to pay attention to the following matters (quite independently of the challenges of delivering the infrastructures that underpin their successful implementation):

 

·       Agreement on the set of core data classes within the biodiversity domain which we consider important enough to standardise (specimen, collection, taxon name, taxon concept, sequence, gene, publication, taxon trait, … - or whatever we all agree).

·       Agreement on the set of core relationships between instances of these classes that we consider important enough to standardise (specimen identifiedAs taxon concept, taxon name publishedIn publication, etc.).

·       Making sure that our data publishing mechanisms (cores, extensions, etc.) align accurately with these classes and support these relationships – this mainly means reworking the current confused interplay between cores, DwC classes, use of dcterms:type and use of basisOfRecord – every record should be clearly identified as an instance of a class (or a view of several linked class instances) and (for the core data classes) this should form the basis for inference and interpretation.

·       An ongoing process of defining for each core class what properties are mandatory (maybe only: id, class), highly desirable (depending on the class, things like: decimal coordinates, scientific name, identifiedAs, publishedIn), generally agreed (many other properties for which we have working vocabularies and do not want unnecessary multiplication, e.g.: waterbody, maximumDepthInMeters) or optional/bespoke (anything else that any data publisher wishes to include). In other words, allow any properties to be shared but ensure that the contours of the data are clear to standard tools.

·       A set of good examples of datasets mapped into this model, using various serialisations.

 

It would be valuable to get a feeling for what workshops might be needed, when might be best to hold them, and how much funding would be required to ensure the right attendance.  GBIF may be able to contribute some of this.

 

Donald

 

----------------------------------------------------------------------

Donald Hobern - GBIF Executive Secretary - dhobern@gbif.org

Global Biodiversity Information Facility http://www.gbif.org/

GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark

Tel: +45 3532 1471  Mob: +45 2875 1471  Fax: +45 2875 1480

----------------------------------------------------------------------

 

From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Lee Belbin
Sent: Friday, 27 May 2016 5:31 AM
To: Quentin Groom <quentin.groom@plantentuinmeise.be>
Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.org>


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

 

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@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

 

 

Landline; +32 (0) 226 009 20 ext. 364

FAX:      +32 (0) 226 009 45

 

Skype name: qgroom

Website:    www.botanicgarden.be

 

 

On 25 May 2016 at 17:57, John Wieczorek <tuco@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@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)

Core Science Analytics, Synthesis, & Libraries Program

U.S. Geological Survey, MS 302
12201 Sunrise Valley Drive
Reston, Virginia  20192
=================
asimpson@usgs.gov
703.648.4281 desk

 

On Wed, May 25, 2016 at 7:26 AM, John Wieczorek <tuco@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@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

 

 

Landline; +32 (0) 226 009 20 ext. 364

FAX:      +32 (0) 226 009 45

 

Skype name: qgroom

Website:    www.botanicgarden.be

 

 

On 25 May 2016 at 03:17, John Wieczorek <tuco@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@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@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@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

 

 

Landline; +32 (0) 226 009 20 ext. 364

FAX:      +32 (0) 226 009 45

 

Skype name: qgroom

Website:    www.botanicgarden.be

 

 

On 24 May 2016 at 19:08, Francisco Pando <pando@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@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

 

 

Landline; +32 (0) 226 009 20 ext. 364

FAX:      +32 (0) 226 009 45

 

Skype name: qgroom

Website:    www.botanicgarden.be

 

 

On 23 May 2016 at 21:10, Chuck Miller <Chuck.Miller@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

From: tdwg-content [mailto:tdwg-content-bounces@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@plantentuinmeise.be> wrote:

I've been working on a proposal to improve Darwin Core for use with invasive species data.

 

 

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

 

 

Landline; +32 (0) 226 009 20 ext. 364

FAX:      +32 (0) 226 009 45

 

Skype name: qgroom

Website:    www.botanicgarden.be

 


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