Hi Quentin, John,

This is rather timely... Over last 2 months or so GBIF have again been working with the IUCN and GIASIP folks to massage some checklist datasets into a format which included a pathway vocabulary [1] and data structures to model distribution [2] and the pathway itself [3]. These are preliminary at this stage and exist in the sandbox repository so can be used with IPTs in the TEST mode. To demonstrate progress with the project partners, an IPT with some datasets is available on http://giasip.gbif.org/ and was recently presented at the CBD SBSTTA meeting by Tim Hirsch.

The vocabulary GBIF have thus far adopted was "developed under the leadership of the IUCN Species Survival Commission Invasive Species Specialist Group (IUCN SSC ISSG). The vocabulary was published as supplementary material in Pagad et al., 2015, IUCN SSC Invasive Species Specialist Group: invasive alien species information management supporting practitioners, policy makers and decision takers (http://dx.doi.org/10.3391/mbi.2015.6.2.03)."

I think it would be worthwhile exploring if these efforts can converge before progressing too much further - there seems to be a lot of overlap from first glance.

Thanks, Tim

[1] http://rs.gbif.org/sandbox/vocabulary/issg/pathway.xml [2] http://rs.gbif.org/sandbox/extension/issg-distribution.xml [3] http://rs.gbif.org/sandbox/extension/issg-pathway.xml

From: tdwg-content <tdwg-content-bounces@lists.tdwg.orgmailto:tdwg-content-bounces@lists.tdwg.org> on behalf of John Wieczorek <tuco@berkeley.edumailto:tuco@berkeley.edu> Reply-To: "tuco@berkeley.edumailto:tuco@berkeley.edu" <tuco@berkeley.edumailto:tuco@berkeley.edu> Date: Monday 23 May 2016 at 20:36 To: Quentin Groom <quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be> Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org> 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.bemailto: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 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: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

Hi Tim, I will have to look at your links in more detail, but I think there is overlap. One thing I have avoided doing with these proposals is suggesting terms or vocabularies for whole taxa. So I feel invasiveness and impact are out of my scope. There are difficulties defining these for several reasons from the invasive species community, but I also think Darwin Core is not best suited to describing whole taxa, though there are some grey areas. I don't know how active Plinian Core is, but that seems to be a good home for these terms.

I'm glad there is so much interest in this area at the moment as that increases the likelihood of change. 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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

On 23 May 2016 at 20:47, Tim Robertson trobertson@gbif.org wrote:

Hi Quentin, John,

This is rather timely… Over last 2 months or so GBIF have again been working with the IUCN and GIASIP folks to massage some checklist datasets into a format which included a pathway vocabulary [1] and data structures to model distribution [2] and the pathway itself [3]. These are preliminary at this stage and exist in the sandbox repository so can be used with IPTs in the TEST mode. To demonstrate progress with the project partners, an IPT with some datasets is available on http://giasip.gbif.org/ and was recently presented at the CBD SBSTTA meeting by Tim Hirsch.

The vocabulary GBIF have thus far adopted was "developed under the leadership of the IUCN Species Survival Commission Invasive Species Specialist Group (IUCN SSC ISSG). The vocabulary was published as supplementary material in Pagad et al., 2015, IUCN SSC Invasive Species Specialist Group: invasive alien species information management supporting practitioners, policy makers and decision takers ( http://dx.doi.org/10.3391/mbi.2015.6.2.03).%E2%80%9D

I think it would be worthwhile exploring if these efforts can converge before progressing too much further – there seems to be a lot of overlap from first glance.

Thanks, Tim

[1] http://rs.gbif.org/sandbox/vocabulary/issg/pathway.xml [2] http://rs.gbif.org/sandbox/extension/issg-distribution.xml [3] http://rs.gbif.org/sandbox/extension/issg-pathway.xml

From: tdwg-content tdwg-content-bounces@lists.tdwg.org on behalf of John Wieczorek tuco@berkeley.edu Reply-To: "tuco@berkeley.edu" tuco@berkeley.edu Date: Monday 23 May 2016 at 20:36 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 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 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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

---

tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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@plantentuinmeise.be 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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

---

tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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@plantentuinmeise.be 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

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@plantentuinmeise.be

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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

---

tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

---

tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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.bemailto: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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 24 May 2016 at 19:08, Francisco Pando <pando@gbif.esmailto: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 172tel:%2B34%2091%20420%203017%20x%20172

From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.orgmailto: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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 23 May 2016 at 21:10, Chuck Miller <Chuck.Miller@mobot.orgmailto: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 314-577-9419tel:314-577-9419 From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.orgmailto: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.bemailto: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 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: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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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@plantentuinmeise.be 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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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 <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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

---

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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@usgs.gov asimpson@usgs.gov703.648.4281 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

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@plantentuinmeise.be 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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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 <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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

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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@plantentuinmeise.be 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 http://bison.usgs.ornl.gov)* *Core Science Analytics, Synthesis, & Libraries Program*

*U.S. Geological Survey, MS 30212201 Sunrise Valley DriveReston, Virginia 20192=================asimpson@usgs.gov asimpson@usgs.gov703.648.4281 <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

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@plantentuinmeise.be 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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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 <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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

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All,

I second, third, and fourth similar spirited support. John, you have inspired growth & have helped our community to lift ourselves up from drudgery. We've failed to see it, but collecting and depositing specimens is the highest form of academic and social responsibility.

What strikes me most from this dialogue is the implicit, unwritten word. Email signatures have included nicely structured, without-a-second-thought links to ORCID profiles. Can we please inspire to do the same for specimens as we've now very quickly done for ourselves? Failure to do so with its legacy of excuses is no longer an option.

David

On Thu, May 26, 2016 at 11:31 PM, Lee Belbin leebelbin@gmail.com wrote:

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

ORCID: 0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.be 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

ORCID: 0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.be 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 >> >> >> >> ORCID: 0000-0002-0596-5376 >> >> >> >> Landline; +32 (0) 226 009 20 ext. 364 >> >> FAX: +32 (0) 226 009 45 >> >> >> >> E-mail: quentin.groom@plantentuinmeise.be >> >> 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 >> >> >> >> ORCID: 0000-0002-0596-5376 >> >> >> >> Landline; +32 (0) 226 009 20 ext. 364 >> >> FAX: +32 (0) 226 009 45 >> >> >> >> E-mail: quentin.groom@plantentuinmeise.be >> >> 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 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 >> >> >> >> Landline; +32 (0) 226 009 20 ext. 364 >> >> FAX: +32 (0) 226 009 45 >> >> >> >> E-mail: quentin.groom@plantentuinmeise.be >> >> Skype name: qgroom >> >> Website: www.botanicgarden.be >> >> >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content@lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> >> >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content@lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content@lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> > >

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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.bemailto: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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 25 May 2016 at 17:57, John Wieczorek <tuco@berkeley.edumailto: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.govmailto: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.govmailto:asimpson@usgs.gov 703.648.4281tel:703.648.4281 desk

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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 25 May 2016 at 03:17, John Wieczorek <tuco@berkeley.edumailto: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.orgmailto: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.orgmailto: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.bemailto: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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 24 May 2016 at 19:08, Francisco Pando <pando@gbif.esmailto: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 172tel:%2B34%2091%20420%203017%20x%20172

From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.orgmailto: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

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 23 May 2016 at 21:10, Chuck Miller <Chuck.Miller@mobot.orgmailto: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 314-577-9419tel:314-577-9419 From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.orgmailto: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.bemailto: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 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: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

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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/ 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 http://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

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@plantentuinmeise.be 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

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@plantentuinmeise.be 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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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

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@plantentuinmeise.be

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 <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 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

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I serve on the invasive plant listing committee for the Florida Exotic Pest Plant Council. To list a plant species as invasive in Florida, our rules require at least one voucher from a natural area in which the plant has become established and is displacing native flora. The means by which populations of invasive plant species become established is important to us with regards to early detection and rapid response as well as expanding our understanding of the source of introduction (hurricanes, nursery industry, inadvertent introduction, escapes from gardens, etc.).

Gil

On 5/23/2016 2:36 PM, John Wieczorek wrote:

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


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http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Dear Steve, thanks for pointing out the previous discussion. The differences in usage context of these terms is highly relevant and perhaps these contexts should be spelled out in the definitions. My opinion is also that dwc:establishmentMeans is a property of an an organism at a particular place and time. However, DwC is used for checklists and observations so a compromise might be to allow semi-colon separated lists in the case of regional checklists. 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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

On 20 June 2016 at 01:44, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:

Getting caught up on this thread after a holiday.

Some previous discussion on dwc:establishmentMeans in 2010 was at: http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html

The opinion expressed in that thread was that dwc:establishmentMeans was a property of an organism at a particular place and time (i.e. an Occurrence.): how did a particular organism come to be in that place at that time. In that view, an organism might be at a location because it was a representative of a native species, or because it was managed at that location by humans. In that perspective, it would not make sense to use the value "invasive" with dwc:establishmentMeans because that is more of a property of a species at a location rather than an individual organism at that location and time.

Steve

Quentin Groom 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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

-- 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.http://bioimages.vanderbilt.eduhttp://vanderbilt.edu/trees

Dear Rich, Thanks for taking a look at the proposal!

perhaps you could clarify your comment regarding the upper limit of "population". Is this what I would call the use of Darwin Core for observations verses checklists?

You can only tell if an organism is invasive if you monitor it over time therefore this term in inappropriate for a single observation. Also, whether something is invasive is a different concept to whether something is native or alien, both can be invasive. I seems to me that the currently suggested vocabulary for dwc:establishmentMeans is conflating two concepts. Also, none of these terms have much to do with how the organism became established.

Currently, there are no fields where nativeness can be properly described and all we need is 1. This is needed for calculating essential biodiversity variables, for horizon scanning and invasive species monitoring. This is in contrast to occurrenceStatus where we currently have three ways to declare absence.

I would have preferred to deprecate the term dwc:establishmentMeans, because its definition doesn't match its suggested vocabulary. However, I chose to retain it for the sake of stability. It has already been suggested that a better term would be introductionMeans.

I don't understand your way of indicating nativeness or how it would work. For many species nativeness is a concept based upon limited available evidence. It isn't something that can be pinned down to a particular event or location. If Darwin Core was only ever used for single observations I would agree that we don't need a term for nativeness, but as it is also used for checklists and we have to accommodate terms that relate to a taxon over a large area.

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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

On 25 June 2016 at 08:13, Richard Pyle deepreef@bishopmuseum.org wrote:

Hi All,

When we discussed the scope of the class “Organism”, I believe we considered the upper limit of “population” – but I can’t remember whether we accepted that upper limit. If so, then the “Organism” instance participating in an particular Occurrence instance could logically be qualified as “invasive” or “native” (or whatever), in which case it seems more appropriate to apply terms such as “native”, “introduced”, “invasive”, etc. to dwc:establishmentMeans

I realize this is squishy, but we don’t really have another class within DwC-space to which the property of “native”, “introduced”, “invasive”, etc. can be applied. Moreover, I don’t think there SHOULD be such a class, because it short-circuits the basis for the presence of Taxon X at Location Y (i.e., this should be established via Taxon-->Identification-->Organism-->Occurrence-->Event-->Location).

I realize this is an extraordinarily convoluted way of saying “Taxon X is native to Location Y”; but ultimately that’s what we want…. Right?

Aloha,

Rich

*From:* tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Steve Baskauf *Sent:* Sunday, June 19, 2016 1:45 PM *To:* Quentin Groom *Cc:* tdwg-content@lists.tdwg.org *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core for invasive species data

Getting caught up on this thread after a holiday.

Some previous discussion on dwc:establishmentMeans in 2010 was at: http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html

The opinion expressed in that thread was that dwc:establishmentMeans was a property of an organism at a particular place and time (i.e. an Occurrence.): how did a particular organism come to be in that place at that time. In that view, an organism might be at a location because it was a representative of a native species, or because it was managed at that location by humans. In that perspective, it would not make sense to use the value "invasive" with dwc:establishmentMeans because that is more of a property of a species at a location rather than an individual organism at that location and time.

Steve

Quentin Groom 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

--

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.

http://bioimages.vanderbilt.edu

http://vanderbilt.edu/trees

Dear Steve, just to be clear, I was not suggesting dwc:establishmentMeans should be deprecated nor its name changed, just that the controlled vocabulary fits the definition. I understand your point regarding filtering, but it doesn't work due to the conflation of concepts and the need to accommodate observations and checklists. The solution I propose would still allow filtering, but would avoid them being mixed up if they were a planted native species, for example.

Two data elements that the invasive species researchers want, and are not provided currently, are the pathway of introduction and the nativeness (unconflated). If we don't do this using dwc:establishmentMeans, what else do you propose? The third elements "occurrenceStatus" is needed for conservation assessments and for invasive species researchers. There is currently no way in a checklist to say something is extinct. No one has yet questioned this suggested change, presumably because dwc:occurrenceStatus has been rather orphaned by dwc:individualCount. I'm a little surprised that no one has mentioned this, but dwc:occurrenceStatus currently can be used for occurrences (present or absent). However, this proposal would only make it suitable for checklists (e.g. extinct).

Much of the controversy of these proposals comes down to the use of DwC for checklists verses observations. I think I've said it before, but it would help is the DwC definitions would distinguish between terms used in these different contexts.

Before the TDWG meeting in December I hope to find the time to analyse the current usage of dwc:establishmentMeans and dwc:occurrenceStatus. That should make interesting reading.

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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

On 25 June 2016 at 16:16, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:

I don't think that dwc:establishmentMeans should be deprecated. It's possible that the definition or list of recommended values should be changed, but I think it satisfies an important use case as it is currently defined (or at least the way that I understand its definition). My understanding of the use case (based on previous discussion on this list from years ago) is as a filter for occurrence records - to allow the searcher to exclude occurrence records based on the amount of human intervention that was involved in the organism being established at the particular location where it was found in the occurrence. There is a sort of gradient of intervention:

*native*: no human intervention was ever involved in causing the organism's species to occur at that location. Example: http://bioimages.vanderbilt.edu/ind-baskauf/10897 where an *Acer negundo* individual was found in a forest with no apparent human intervention to cause that individual to be there.

*naturalised:* human intervention was involved in causing the species to occur at that location, but the population persists at that location without human intervention. Example: http://bioimages.vanderbilt.edu/ind-baskauf/12179 where a *Taraxacum officinale* individual was found in a lawn. *Taraxacum officinale* arrived in Cheatham County, Tennessee as a result of human intervention, but no human did anything to make that individual be at that location. In fact, humans are probably trying to get rid of its population, but it still persists.

*adventitive*: human intervention was involved in causing the species to occur at that location, but no intentional effort was made to cause that particular individual to be there and the population is not likely to persist. Example: http://bioimages.vanderbilt.edu/ind-baskauf/33559 where a *Triticum aestivum* individual was found growing in a construction site. *Triticum aestivum* is not native to Cheatham County, Tennessee and as far as I know, populations of it do not persist in the area without human intervention. This individual was not managed in an agricultural field; rather it appeared to have gotten started accidentally from straw used as mulch to protect planted grass seed.

*managed:* human intervention was involved in causing the species to occur at that location, and intentional efforts cause the organism to be at that location and to persist there. Example: http://bioimages.vanderbilt.edu/vanderbilt/12-43 where an *Acer negundo* was present as part of landscaping on a college campus.

Maintaining a "gradient" of values like this allows a user to perform a variety of screens on occurrence data. Users may only want native occurrences, perhaps because they want to collect DNA from native populations or want to see what the organism looks like when it grows in its native habitat. Users may search for native+naturalised occurrences in order to develop a checklist of species that are likely to be found over a long period of time in natural areas. Users may search for native+naturalised+adventive occurrences to develop a list of organisms that might be found in an area, including incidental occurrences. Users may search for managed occurrences to find locations (which would include zoos and botanical gardens) where they might be able to easily obtain samples of the organism from a contact person.

Using dwc:establishmentMeans as a value for occurrence records of a particular organism at a very precise location and a particular time is a very different use case that using it to assess populations of organisms in a broader area over a broader time to find out things such as whether a species is invading an area or not. In the examples above, *Acer negundo* is a native species to Tennessee, but http://bioimages.vanderbilt.edu/vanderbilt/12-43 is not a native occurrence of *Acer negundo* since it was planted and managed by humans at that location.

I agree that the two (or more) uses of dwc:establishmentMeans probably should be separated. My guess would be that using dwc:establishmentMeans the way that I described it above is more common, but I may just be biased because that's the way that I use it. The way I've described its use seems to be very much in keeping with the definition that is given for the term. If I had my way, I'd get rid of the value "invasive" and add the value "adventive" to the list of recommended values. "Invasive" is the value that doesn't really fit, because it's really difficult to assess that status based on a single occurrence record. The GBIF Establishment Means controlled vocabulary at http://rs.gbif.org/vocabulary/gbif/establishment_means.xml indicates that "introduced" is a superclass for naturalised, invasive, and managed, which I suppose could have some utility if that were made clear.

One might make the case that "establishmentMeans" is not a good "name" for what the term means, and that it should be changed. However, one should keep in mind that dwc:establishmentMeans is an abbreviation for the URI http://rs.tdwg.org/dwc/terms/establishmentMeans and as such, it's an identifier, not a descriptive label. Changing labels doesn't "break" anything; changing URIs does. If we don't like the definition of dwc:establishmentMeans, we should figure out how it is most commonly used and change the definition to match that use. That would be the approach that would provide the maximum stability for Darwin Core. I think that we made a mistake in the past when we changed dwc:individualID to dwc:organismID. I understand that there's a desire to make the local name parts of URIs "make sense" with respect to the meaning of the term, but that's only a convention, not a requirement. From an application or machine perspective, dwc:t03958 is just as good of an identifier as dwc:establishmentMeans. Get the human-readable label and definition right, but don't change or deprecate the URI unless absolutely necessary.

Steve

Quentin Groom wrote:

Dear Rich, Thanks for taking a look at the proposal!

perhaps you could clarify your comment regarding the upper limit of "population". Is this what I would call the use of Darwin Core for observations verses checklists?

You can only tell if an organism is invasive if you monitor it over time therefore this term in inappropriate for a single observation. Also, whether something is invasive is a different concept to whether something is native or alien, both can be invasive. I seems to me that the currently suggested vocabulary for dwc:establishmentMeans is conflating two concepts. Also, none of these terms have much to do with how the organism became established.

Currently, there are no fields where nativeness can be properly described and all we need is 1. This is needed for calculating essential biodiversity variables, for horizon scanning and invasive species monitoring. This is in contrast to occurrenceStatus where we currently have three ways to declare absence.

I would have preferred to deprecate the term dwc:establishmentMeans, because its definition doesn't match its suggested vocabulary. However, I chose to retain it for the sake of stability. It has already been suggested that a better term would be introductionMeans.

I don't understand your way of indicating nativeness or how it would work. For many species nativeness is a concept based upon limited available evidence. It isn't something that can be pinned down to a particular event or location. If Darwin Core was only ever used for single observations I would agree that we don't need a term for nativeness, but as it is also used for checklists and we have to accommodate terms that relate to a taxon over a large area.

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@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

On 25 June 2016 at 08:13, Richard Pyle deepreef@bishopmuseum.org wrote:

...

Hi All,

When we discussed the scope of the class “Organism”, I believe we considered the upper limit of “population” – but I can’t remember whether we accepted that upper limit. If so, then the “Organism” instance participating in an particular Occurrence instance could logically be qualified as “invasive” or “native” (or whatever), in which case it seems more appropriate to apply terms such as “native”, “introduced”, “invasive”, etc. to dwc:establishmentMeans

I realize this is squishy, but we don’t really have another class within DwC-space to which the property of “native”, “introduced”, “invasive”, etc. can be applied. Moreover, I don’t think there SHOULD be such a class, because it short-circuits the basis for the presence of Taxon X at Location Y (i.e., this should be established via Taxon-->Identification-->Organism-->Occurrence-->Event-->Location).

I realize this is an extraordinarily convoluted way of saying “Taxon X is native to Location Y”; but ultimately that’s what we want…. Right?

Aloha,

Rich

*From:* tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Steve Baskauf *Sent:* Sunday, June 19, 2016 1:45 PM *To:* Quentin Groom *Cc:* tdwg-content@lists.tdwg.org *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core for invasive species data

Getting caught up on this thread after a holiday.

Some previous discussion on dwc:establishmentMeans in 2010 was at: http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html

The opinion expressed in that thread was that dwc:establishmentMeans was a property of an organism at a particular place and time (i.e. an Occurrence.): how did a particular organism come to be in that place at that time. In that view, an organism might be at a location because it was a representative of a native species, or because it was managed at that location by humans. In that perspective, it would not make sense to use the value "invasive" with dwc:establishmentMeans because that is more of a property of a species at a location rather than an individual organism at that location and time.

Steve

Quentin Groom 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@plantentuinmeise.be

Skype name: qgroom

Website: www.botanicgarden.be

--

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.

http://bioimages.vanderbilt.edu

http://vanderbilt.edu/trees

-- 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.http://bioimages.vanderbilt.eduhttp://vanderbilt.edu/trees

It's the problem of different uses cases again. The use cases need to be more explicit. Recording a taxonomic checklist and recording an occurrence of an organism are different use cases that happen to share some attributes but also differ. Without clear understanding of the use case, how can anyone know what the term being used means precisely.

Are some Darwin Core terms actually unique to particular use cases?

How about a binary term like IsInvasive (True, False or Null) - for checklists only?

Regards, Chuck

On Jun 25, 2016, at 8:25 PM, Richard Pyle <deepreef@bishopmuseum.orgmailto:deepreef@bishopmuseum.org> wrote:

I think we may be talking about different things; or maybe the same thing but from fundamentally different perspectives.

In the context of “checklist-style” dwc:Occurrence instances that represent direct associations of a dwc:Taxon instance to a dwc:Location instance, then all we really need to do is clarify the definitions of dwc:establishmentMeans and dwc:occurenceStatus in how they should be used to represent properties relevant to the presence of a Taxon at a Location; and also whether a new term is needed to represent properties that don’t really fit into either of those terms. If I understand correctly, this is the basis for your proposal; and I agree we at least need clarification of dwc:establishmentMeans, and perhaps also a new term.

My reply was in the context of moving away from such “checklist-style” instances of dwc:Occurrence, which I’ve always felt overloaded the concept. I think we should be more explicit about what we mean by Occurrence instances. Taxa don’t occur at locations. Organisms occur at locations, and their occurrence is fixed in 4-dimentional space (i.e., time being one of the dimensions); and hence via dwc:Events. Organisms are assigned to Taxa via dwc:Identification. My comment was based on how we can use this more explicit approach to capture information on Nativeness/etc.

When we were discussing the concept of an “Organism”, we all seemed to agree that it could apply to a single individual organism, or a colony of individuals (e.g., a coral head, or ant colony), or a defined group of multiple individuals (e.g., wolf pack or whale pod). We also discussed whether a “population” could be within the scope of an instance of “Organism”. I don’t recall where we ended up on that as the “upper limit” to an organism (i.e., some would argue that a population is the lower limit of a taxon, rather than the upper limit of an Organism). The basic problem is that there is a continuum from Organism to Taxon, and somewhere along that continuum we need to draw the line when assigning instances to one class or the other.

In any case, DwC currently does not have a class that represents the intersection of a Taxon and a Location – which is the logical thing one might want to apply the status of Native vs. Invasive, etc. The question is, can we meaningfully (and without stretching definitions of our existing classes and intended data representations too far) represent the native/invasive/etc. status of a Taxon at a Location using the existing Occurrence and other DwC classes. If we accept than dwc:Occurrence is an instance of dwc:Organism + an instance of dwc:Event, and dwc:Event is an instance of dwc:Location + Date/Time and other properties, and we also accept that an dwc:Organism is what dwc:Identification instances apply to, then we can logically apply the Native/Invasive/etc. status to such Occurrence instances.

For example, suppose I defined an Instance of “Organism” as the population of Aus bus within the state of Hawaii (i.e., the dwc:Organism instance has scope “population”, and an dwc:Identification instance applies the dwc:Taxon “Aus bus” to that population-level organism). We can create one or more dwc:Occurrence records to represent the presence of that Organism at one or more dwc:Event instances involving Hawaii as the dwc:Location, and whatever other dwc:Event properties that are relevant to the entire population of that Organism within Hawaii (such as a date when the population was first recorded from Hawaii via observation or representative specimens). If this is an acceptable instance of dwc:Occurrence (i.e., the population of Aus bus in Hawaii), then it seems appropriate to me to apply values of “Native” or “Invasive” or whatever via dwc:establishmentMeans as applied to that Occurrence.

Doing it this way allows you to monitor it (as a population) over time via multiple dwc:Occurrence instances associated with the same population-level dwc:Organism instance.

The problem isn’t a field for “Nativeness”, the problem is what dwc class should that field be applied to. It seems to me that dwc:Occurrence is appropriate, as long as the associated dwc:Organism can be defined as representing a population.

Of course, one can still simply use instances of dwc:Occurrence without any implied Organism or Event at all (ala the checklist approach of anchoring a Taxon to a Location, without implied Organism or Event instances), but I would like to think that our community is moving away from that approach towards a more explicit approach for documenting biodiversity.

Maybe I’m attacking this issue from the wrong angle, in which I apologize for cluttering the conversation.

Aloha, Rich

From: Quentin Groom [mailto:quentin.groom@plantentuinmeise.be] Sent: Friday, June 24, 2016 9:27 PM To: deepreef@bishopmuseum.orgmailto:deepreef@bishopmuseum.org Cc: Steve Baskauf; TDWG Content Mailing List Subject: Re: [tdwg-content] A proposal to improve Darwin Core for invasive species data

Dear Rich, Thanks for taking a look at the proposal!

perhaps you could clarify your comment regarding the upper limit of "population". Is this what I would call the use of Darwin Core for observations verses checklists?

You can only tell if an organism is invasive if you monitor it over time therefore this term in inappropriate for a single observation. Also, whether something is invasive is a different concept to whether something is native or alien, both can be invasive. I seems to me that the currently suggested vocabulary for dwc:establishmentMeans is conflating two concepts. Also, none of these terms have much to do with how the organism became established.

Currently, there are no fields where nativeness can be properly described and all we need is 1. This is needed for calculating essential biodiversity variables, for horizon scanning and invasive species monitoring. This is in contrast to occurrenceStatus where we currently have three ways to declare absence.

I would have preferred to deprecate the term dwc:establishmentMeans, because its definition doesn't match its suggested vocabulary. However, I chose to retain it for the sake of stability. It has already been suggested that a better term would be introductionMeans.

I don't understand your way of indicating nativeness or how it would work. For many species nativeness is a concept based upon limited available evidence. It isn't something that can be pinned down to a particular event or location. If Darwin Core was only ever used for single observations I would agree that we don't need a term for nativeness, but as it is also used for checklists and we have to accommodate terms that relate to a taxon over a large area.

Regards Quentin

Dr. Quentin Groom (Botany and Information Technology)

Botanic Garden Meise Domein van Bouchout B-1860 Meise Belgium

ORCID: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

On 25 June 2016 at 08:13, Richard Pyle <deepreef@bishopmuseum.orgmailto:deepreef@bishopmuseum.org> wrote: Hi All,

When we discussed the scope of the class “Organism”, I believe we considered the upper limit of “population” – but I can’t remember whether we accepted that upper limit. If so, then the “Organism” instance participating in an particular Occurrence instance could logically be qualified as “invasive” or “native” (or whatever), in which case it seems more appropriate to apply terms such as “native”, “introduced”, “invasive”, etc. to dwc:establishmentMeans

I realize this is squishy, but we don’t really have another class within DwC-space to which the property of “native”, “introduced”, “invasive”, etc. can be applied. Moreover, I don’t think there SHOULD be such a class, because it short-circuits the basis for the presence of Taxon X at Location Y (i.e., this should be established via Taxon-->Identification-->Organism-->Occurrence-->Event-->Location).

I realize this is an extraordinarily convoluted way of saying “Taxon X is native to Location Y”; but ultimately that’s what we want…. Right?

Aloha, Rich

From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.orgmailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Sunday, June 19, 2016 1:45 PM To: Quentin Groom Cc: tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] A proposal to improve Darwin Core for invasive species data

Getting caught up on this thread after a holiday.

Some previous discussion on dwc:establishmentMeans in 2010 was at: http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html

The opinion expressed in that thread was that dwc:establishmentMeans was a property of an organism at a particular place and time (i.e. an Occurrence.): how did a particular organism come to be in that place at that time. In that view, an organism might be at a location because it was a representative of a native species, or because it was managed at that location by humans. In that perspective, it would not make sense to use the value "invasive" with dwc:establishmentMeans because that is more of a property of a species at a location rather than an individual organism at that location and time.

Steve

Quentin Groom 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: 0000-0002-0596-5376http://orcid.org/0000-0002-0596-5376

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

E-mail: quentin.groom@plantentuinmeise.bemailto:quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.behttp://www.botanicgarden.be

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