Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core ( http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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
Hi Quentin Many thanks for this. I'll give it a careful read, but just based on your e-mail this seems to hit straight at the heart of the problem with alien species data as I see it. Will respond in further detail over the next week or so. Best Melodie On 27 April 2016 at 22:46, Quentin Groom <quentin.groom@plantentuinmeise.be> wrote:
Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core ( http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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
_______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias
-- Melodie A. McGeoch Associate Professor, School of Biological Sciences, Monash University, Clayton Campus (Bld 18, Innovation Walk, Rm 121), Melbourne, Victoria 3800, Australia. Tel: +61 3 99020464, Mobile: +61 (0) 499 954180, E-mail: melodie.mcgeoch@monash.edu, ISI Researcher ID F-8353-2011, Research Group website: http://melodiemcgeoch.com/ *ORCID *http://orcid.org/0000-0003-3388-2241
Fyi, updated link on suggested controlled vocabulary -----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 27 April 2016 02:47 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: [DFFU_IAS] Proposing Changes to Darwin Core Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core (http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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 The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer
Thanks John, I'll update the proposal ASAP. 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 8 June 2016 at 22:18, Wilson, John <jrwilson@sun.ac.za> < jrwilson@sun.ac.za> wrote:
Fyi, updated link on suggested controlled vocabulary
-----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 27 April 2016 02:47 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: [DFFU_IAS] Proposing Changes to Darwin Core
Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core ( http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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
The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer
_______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias
Dear John, the 2016 pathways standard seems to be same as the 2014 document I cited. So, I've added the 2016 document as an additional reference. Also, someone else asked if I could summerise the TDWG responses to the Darwin Core changes and I've done this at https://github.com/qgroom/ias-dwc-proposal/wiki/A-summary-of-key-points-from... 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 9 June 2016 at 20:02, Quentin Groom <quentin.groom@plantentuinmeise.be> wrote:
Thanks John, I'll update the proposal ASAP. 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 8 June 2016 at 22:18, Wilson, John <jrwilson@sun.ac.za> < jrwilson@sun.ac.za> wrote:
Fyi, updated link on suggested controlled vocabulary
-----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 27 April 2016 02:47 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: [DFFU_IAS] Proposing Changes to Darwin Core
Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core ( http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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
The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer
_______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias
Thanks Quentin, Apologies for the others if this is not the right place for this conversation, but I had some other thoughts. The term "establishmentMeans" is problematic in the sense that the word established is synonymous naturalised in invasion science, e.g. Richardson et al. 2000 doi: 10.1046/j.1472-4642.2000.00083.x, and Fig. 1 in Blackburn et al. 2011 doi: 10.1016/j.tree.2011.03.023. I appreciate it isn't a straightforward process, but it would seem to make more sense if it is actually talking about pathways to at least be: "*introduction*Means: The process by which the biological individual(s) represented in the Occurrence became *introduced to* the location. Recommended best practice is to use a controlled vocabulary." In many cases we would be dealing with species that might be transient or still reliant on cultivation, but as you discussed the invasion status of a population in the sense of progress along the introduction-naturalisation-invasion continuum is not (and should not be?) explicitly coded in the Darwin Core, though the current version of "establishmentMeans" does actually do this in some sense. As a finer point, the distinction of 1500, while useful, is quite Eurocentric. How would you deal with New Zealand and some other such islands? I'm sure there were some introductions between 1500 and when European visitors and colonists started introducing species. Separating movements of species by humans prior to the Age of Discovery is a bit of a fraught area and not just on islands. As I understand it, Ricinus communis might technically be a post-1500 archaeophyte in much of South Africa (there is possibly a nice biogeographical project to be done on this...). If it is to be made, rather than an arbitrary date can the distinction archaeobiota and neobiota be used? "introduced on or before 1500" can't technically be a synonym of archaeophyte as it isn't just plants. The term neobiota is used of course? Cheers, John -----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 11 June 2016 03:59 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: Re: [DFFU_IAS] Proposing Changes to Darwin Core Dear John, the 2016 pathways standard seems to be same as the 2014 document I cited. So, I've added the 2016 document as an additional reference. Also, someone else asked if I could summerise the TDWG responses to the Darwin Core changes and I've done this at https://github.com/qgroom/ias-dwc-proposal/wiki/A-summary-of-key-points-from... 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 9 June 2016 at 20:02, Quentin Groom <quentin.groom@plantentuinmeise.be> wrote: Thanks John, I'll update the proposal ASAP. 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 8 June 2016 at 22:18, Wilson, John <jrwilson@sun.ac.za> <jrwilson@sun.ac.za> wrote: Fyi, updated link on suggested controlled vocabulary -----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 27 April 2016 02:47 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: [DFFU_IAS] Proposing Changes to Darwin Core Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core (http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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 <tel:%2B32%20%280%29%20226%20009%2020%20ext.%20364> FAX: +32 (0) 226 009 45 <tel:%2B32%20%280%29%20226%20009%2045> E-mail: quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer _______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer
Hi John, my original preference for the proposal was to deprecate establishmentMeans so that some other term could be used for pathways, but I was advised by TDWG people that it would be better to impose the new vocabulary on establishmentMeans. I think this is to ensure back compatibility of software and is just simpler over all. It's not ideal, but it is something we can perhaps live with. Yes I agree that 1500 is Eurocentric. As you point out New Zealand is a particularly difficult case. Also it has no use in Darwin Core for the case of observations, as it is only relevant to checklists. In defense of the 1500 cut off, only Europe has sufficiently old documentation to make the distinction useful and European botanists do make considerable use of this distinction. 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 13 June 2016 at 12:05, Wilson, John <jrwilson@sun.ac.za> < jrwilson@sun.ac.za> wrote:
Thanks Quentin,
Apologies for the others if this is not the right place for this conversation, but I had some other thoughts.
The term "establishmentMeans" is problematic in the sense that the word established is synonymous naturalised in invasion science, e.g. Richardson et al. 2000 doi: 10.1046/j.1472-4642.2000.00083.x, and Fig. 1 in Blackburn et al. 2011 doi: 10.1016/j.tree.2011.03.023.
I appreciate it isn't a straightforward process, but it would seem to make more sense if it is actually talking about pathways to at least be: "*introduction*Means: The process by which the biological individual(s) represented in the Occurrence became *introduced to* the location. Recommended best practice is to use a controlled vocabulary."
In many cases we would be dealing with species that might be transient or still reliant on cultivation, but as you discussed the invasion status of a population in the sense of progress along the introduction-naturalisation-invasion continuum is not (and should not be?) explicitly coded in the Darwin Core, though the current version of "establishmentMeans" does actually do this in some sense.
As a finer point, the distinction of 1500, while useful, is quite Eurocentric. How would you deal with New Zealand and some other such islands? I'm sure there were some introductions between 1500 and when European visitors and colonists started introducing species. Separating movements of species by humans prior to the Age of Discovery is a bit of a fraught area and not just on islands. As I understand it, Ricinus communis might technically be a post-1500 archaeophyte in much of South Africa (there is possibly a nice biogeographical project to be done on this...). If it is to be made, rather than an arbitrary date can the distinction archaeobiota and neobiota be used?
"introduced on or before 1500" can't technically be a synonym of archaeophyte as it isn't just plants. The term neobiota is used of course?
Cheers,
John
-----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 11 June 2016 03:59 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: Re: [DFFU_IAS] Proposing Changes to Darwin Core
Dear John, the 2016 pathways standard seems to be same as the 2014 document I cited. So, I've added the 2016 document as an additional reference.
Also, someone else asked if I could summerise the TDWG responses to the Darwin Core changes and I've done this at https://github.com/qgroom/ias-dwc-proposal/wiki/A-summary-of-key-points-from...
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 9 June 2016 at 20:02, Quentin Groom <quentin.groom@plantentuinmeise.be> wrote:
Thanks John, I'll update the proposal ASAP. 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 8 June 2016 at 22:18, Wilson, John <jrwilson@sun.ac.za> < jrwilson@sun.ac.za> wrote:
Fyi, updated link on suggested controlled vocabulary
-----Original Message----- From: DFFU_IAS [mailto:dffu_ias-bounces@lists.gbif.org] On Behalf Of Quentin Groom Sent: 27 April 2016 02:47 PM To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: [DFFU_IAS] Proposing Changes to Darwin Core
Dear All, I thought I'd introduce you to an initiative I've started to make changes to the Darwin Core Standard. This seems to be relevant to the Task Group and something we could point to as a concrete outcome. For a long time I have been bothered by the definition and suggested vocabulary for the establishmentMeans field in Darwin Core ( http://rs.tdwg.org/dwc/terms/). It doesn't seem fit for purpose and conflates various concepts. For this reason I've drafted a proposal for the TDWG organisation to change Darwin Core. This involved adding a new term "origin"; changing the definition of occurenceStatus and changing the controlled vocabulary of establishmentMeans. You can read the proposal on GitHub (https://github.com/qgroom/DwC_Proposal.git), but I've also attached a version here. I really welcome your comments and I'd be happy if you want to co-propose it with me. 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 <tel:%2B32%20%280%29%20226%20009%2020%20ext.%20364> FAX: +32 (0) 226 009 45 <tel:%2B32%20%280%29%20226%20009%2045>
E-mail: quentin.groom@plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be
The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer
_______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias
The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer _______________________________________________ DFFU_IAS mailing list DFFU_IAS@lists.gbif.org http://lists.gbif.org/mailman/listinfo/dffu_ias
participants (3)
-
Melodie McGeoch -
Quentin Groom -
Wilson, John <jrwilson＠sun.ac.za>