update of Darwin Core Resource Relationship extension
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards, Markus
On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt> wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.orghttp://gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
-- ------------------
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
_______________________________________________ IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
It is good to have such type of communication in every aspect to have common good platform. I have one question, can i secure a resource which is found in GBIF? Assume i am a user in GBIF platform, so rather than accessing the whole document a few of them might be secured and should be communicated to the system manager. Can i?
On Thu, Jun 28, 2018, 8:21 PM Quentin Groom < quentin.groom@plantentuinmeise.be> wrote:
Hi Rui, if you're interested we also published a checklist of rust fungi recently using the resource relationship extension (https://www.gbif.org/dataset /b043c480-dd36-4f4f-aa82-e188753ff09d). I total agree with you about the importance of species interactions. I'm glad GBIF has some plans for this. We have an interactions workshop at this year's TDWG meeting and I hope we will hear more about approaches to this problem. 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 28 June 2018 at 16:07, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi Tim,
I am glad to hear that species interactions will be incorporated in the next data model and indexing. I agree that it is not an easy task, but it is getting more and more attention, so I would say that supporting it is very important for GBIF in the future.
Best regards,
Rui
Rui Figueira Coordenador do Nó Português do GBIFruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195http://www.gbif.pthttp://www.isa.ulisboa.pt
On 06/28/2018 02:52 PM, Tim Robertson wrote:
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing.
I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org ipt-bounces@lists.gbif.org on behalf of Rui Figueira ruifigueira@isa.ulisboa.pt ruifigueira@isa.ulisboa.pt *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring mdoering@gbif.org mdoering@gbif.org *Cc: *"ipt@lists.gbif.org" ipt@lists.gbif.org ipt@lists.gbif.org ipt@lists.gbif.org, helpdesk helpdesk@gbif.org helpdesk@gbif.org *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class":
http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though.
The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187:
https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus)
If I lookup this record in your dataset it is missing:
https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded?
https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards,
Markus
On 28. Jun 2018, at 12:14, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
--
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
------------------
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards, Markus
On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.pt mailto:ruifigueira@isa.ulisboa.pt> wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org http://gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292? https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
--
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt mailto:ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing. I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks, Tim
From: IPT ipt-bounces@lists.gbif.org on behalf of Rui Figueira ruifigueira@isa.ulisboa.pt Date: Thursday, 28 June 2018 at 15.45 To: Markus Döring mdoering@gbif.org Cc: "ipt@lists.gbif.org" ipt@lists.gbif.org, helpdesk helpdesk@gbif.org Subject: Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
------------------
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
http://www.isa.ulisboa.pt On 06/28/2018 11:38 AM, Markus Döring wrote: Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards, Markus
On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt> wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.orghttp://gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
-- ------------------
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
_______________________________________________ IPT mailing list IPT@lists.gbif.orgmailto:IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
Hi Tim,
I am glad to hear that species interactions will be incorporated in the next data model and indexing. I agree that it is not an easy task, but it is getting more and more attention, so I would say that supporting it is very important for GBIF in the future.
Best regards,
Rui
------------------
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
On 06/28/2018 02:52 PM, Tim Robertson wrote:
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing.
I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org on behalf of Rui Figueira ruifigueira@isa.ulisboa.pt *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring mdoering@gbif.org *Cc: *"ipt@lists.gbif.org" ipt@lists.gbif.org, helpdesk helpdesk@gbif.org *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt mailto:ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui, the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page. When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&occurrence_id=701c94f1-16eb-4c1e-8449-f3b046100187&advanced=1 If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&advanced=1 If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa With regards, Markus On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt>> wrote: Hi IPT list members, Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update? I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org <http://gbif.org>, for example, in this record: https://www.gbif.org/occurrence/1585354292. I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292? Best regards, Rui -- ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt _______________________________________________ IPT mailing list IPT@lists.gbif.org <mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt
Hi Rui, if you're interested we also published a checklist of rust fungi recently using the resource relationship extension (https://www.gbif.org/dataset /b043c480-dd36-4f4f-aa82-e188753ff09d). I total agree with you about the importance of species interactions. I'm glad GBIF has some plans for this. We have an interactions workshop at this year's TDWG meeting and I hope we will hear more about approaches to this problem. 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 28 June 2018 at 16:07, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi Tim,
I am glad to hear that species interactions will be incorporated in the next data model and indexing. I agree that it is not an easy task, but it is getting more and more attention, so I would say that supporting it is very important for GBIF in the future.
Best regards,
Rui
Rui Figueira Coordenador do Nó Português do GBIFruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195http://www.gbif.pthttp://www.isa.ulisboa.pt
On 06/28/2018 02:52 PM, Tim Robertson wrote:
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing.
I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org ipt-bounces@lists.gbif.org on behalf of Rui Figueira ruifigueira@isa.ulisboa.pt ruifigueira@isa.ulisboa.pt *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring mdoering@gbif.org mdoering@gbif.org *Cc: *"ipt@lists.gbif.org" ipt@lists.gbif.org ipt@lists.gbif.org ipt@lists.gbif.org, helpdesk helpdesk@gbif.org helpdesk@gbif.org *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0- 5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class":
http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though.
The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187:
https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus)
If I lookup this record in your dataset it is missing:
https://www.gbif.org/occurrence/search?dataset_key= 85a3c886-3312-45c9-b040-4d7634653246&occurrence_id= 701c94f1-16eb-4c1e-8449-f3b046100187&advanced=1
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded?
https://www.gbif.org/occurrence/taxonomy?dataset_ key=85a3c886-3312-45c9-b040-4d7634653246&advanced=1
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards,
Markus
On 28. Jun 2018, at 12:14, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/ resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
--
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
Hi Quentin,
Thank you very much, this is an excellent example. Actually, we will also prepare a checklist dataset, so this is really helpful also for that exercise.
About interactions, I hope there is enough momentum to get it going. The TDWG is a good opportunity. Another workshop on the topic was the Globis-B workshop in Bari, last February, which feedback might be important also. The GBIF Secretariat (Dmitry) was also represented there, so he might have given feedback on how the support of species interaction is important.
Kind regards,
Rui
On 06/28/2018 03:42 PM, Quentin Groom wrote:
Hi Rui, if you're interested we also published a checklist of rust fungi recently using the resource relationship extension (https://www.gbif.org/dataset/b043c480-dd36-4f4f-aa82-e188753ff09d). I total agree with you about the importance of species interactions. I'm glad GBIF has some plans for this. We have an interactions workshop at this year's TDWG meeting and I hope we will hear more about approaches to this problem. 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
On 28 June 2018 at 16:07, Rui Figueira <ruifigueira@isa.ulisboa.pt mailto:ruifigueira@isa.ulisboa.pt> wrote:
Hi Tim, I am glad to hear that species interactions will be incorporated in the next data model and indexing. I agree that it is not an easy task, but it is getting more and more attention, so I would say that supporting it is very important for GBIF in the future. Best regards, Rui ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt On 06/28/2018 02:52 PM, Tim Robertson wrote:Thanks for raising this Rui This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing. I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model. Thanks, Tim *From: *IPT <ipt-bounces@lists.gbif.org> <mailto:ipt-bounces@lists.gbif.org> on behalf of Rui Figueira <ruifigueira@isa.ulisboa.pt> <mailto:ruifigueira@isa.ulisboa.pt> *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring <mdoering@gbif.org> <mailto:mdoering@gbif.org> *Cc: *"ipt@lists.gbif.org" <mailto:ipt@lists.gbif.org> <ipt@lists.gbif.org> <mailto:ipt@lists.gbif.org>, helpdesk <helpdesk@gbif.org> <mailto:helpdesk@gbif.org> *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension Hi Markus, Thank you for your quick reply. I understand the need to make the updated extension "correct", accordingly to the "class". However, the lack of implementation on GBIF in ingesting related resources is a point of concern. It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him! Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description. I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af <https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af>, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option. Best regards, Rui ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt On 06/28/2018 11:38 AM, Markus Döring wrote: Hi Rui, the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex <http://rs.tdwg.org/dwc/terms/index.htm#relindex> The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page. When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim <https://api.gbif.org/v1/occurrence/1585354292/verbatim> This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&occurrence_id=701c94f1-16eb-4c1e-8449-f3b046100187&advanced=1 <https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&occurrence_id=701c94f1-16eb-4c1e-8449-f3b046100187&advanced=1> If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&advanced=1 <https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&advanced=1> If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa <http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa> With regards, Markus On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt>> wrote: Hi IPT list members, Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update? I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia <http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia>, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org <http://gbif.org>, for example, in this record: https://www.gbif.org/occurrence/1585354292 <https://www.gbif.org/occurrence/1585354292>. I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292? <https://www.gbif.org/occurrence/1585354292?> Best regards, Rui -- ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt _______________________________________________ IPT mailing list IPT@lists.gbif.org <mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt <https://lists.gbif.org/mailman/listinfo/ipt>_______________________________________________ IPT mailing list IPT@lists.gbif.org <mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt <https://lists.gbif.org/mailman/listinfo/ipt>
Thanks Tim, Happy to see that you are designing a more expressive model for data exchange and indexing. Species interactions is a good example to start with, but I would rather see a more open model allowing relations between all possible entities we are dealing with: specimens, species, locations, events, people, materials, multimedia, projects...
I've recently experimented the Frictionless Data https://frictionlessdata.io/ that offers a truly entity relationship model for data publication. We have to go beyond the DwC star schema and present a well defined DarwinCore schema that supports all possible interactions (relations). I do hope nodes experience will be taken into account and GBIF + TDWG community will come with data model everyone can accept and use.
I'm looking forward to participate to this new data exchange model Best regards,
-- Ir Andre Heughebaert GBIF Node Manager at Belgian Biodiversity Platform http://www.biodiversity.be +32(0)2238 3796 Av. Louise 231 Louizalaan B-1050 Brussels ORCID 0000-0002-7839-5300 http://orcid.org/0000-0002-7839-5300
On Thu, 28 Jun 2018 at 15:52, Tim Robertson trobertson@gbif.org wrote:
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing.
I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org on behalf of Rui Figueira < ruifigueira@isa.ulisboa.pt> *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring mdoering@gbif.org *Cc: *"ipt@lists.gbif.org" ipt@lists.gbif.org, helpdesk < helpdesk@gbif.org> *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class":
http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though.
The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187:
https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus)
If I lookup this record in your dataset it is missing:
https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded?
https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards,
Markus
On 28. Jun 2018, at 12:14, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
--
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
Hi Tim,
Maybe it's slightly off-topic, but I was wondering if you already know how and where you plan to have the discussions and make progress on this topic ? Will it be a public process, happening online? I'm looking forward to bring my 2 cents, if possible :)
Cheers,
Nico
Le 2/07/18 à 09:07, André Heughebaert a écrit :
Thanks Tim, Happy to see that you are designing a more expressive model for data exchange and indexing. Species interactions is a good example to start with, but I would rather see a more open model allowing relations between all possible entities we are dealing with: specimens, species, locations, events, people, materials, multimedia, projects...
I've recently experimented the Frictionless Data https://frictionlessdata.io/ that offers a truly entity relationship model for data publication. We have to go beyond the DwC star schema and present a well defined DarwinCore schema that supports all possible interactions (relations). I do hope nodes experience will be taken into account and GBIF + TDWG community will come with data model everyone can accept and use.
I'm looking forward to participate to this new data exchange model Best regards,
-- Ir Andre Heughebaert GBIF Node Manager at Belgian Biodiversity Platform http://www.biodiversity.be +32(0)2238 3796 Av. Louise 231 Louizalaan B-1050 Brussels ORCID 0000-0002-7839-5300 http://orcid.org/0000-0002-7839-5300
On Thu, 28 Jun 2018 at 15:52, Tim Robertson <trobertson@gbif.org mailto:trobertson@gbif.org> wrote:
Thanks for raising this Rui This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing. I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model. Thanks, Tim *From: *IPT <ipt-bounces@lists.gbif.org <mailto:ipt-bounces@lists.gbif.org>> on behalf of Rui Figueira <ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt>> *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring <mdoering@gbif.org <mailto:mdoering@gbif.org>> *Cc: *"ipt@lists.gbif.org <mailto:ipt@lists.gbif.org>" <ipt@lists.gbif.org <mailto:ipt@lists.gbif.org>>, helpdesk <helpdesk@gbif.org <mailto:helpdesk@gbif.org>> *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension Hi Markus, Thank you for your quick reply. I understand the need to make the updated extension "correct", accordingly to the "class". However, the lack of implementation on GBIF in ingesting related resources is a point of concern. It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him! Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description. I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option. Best regards, Rui ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt On 06/28/2018 11:38 AM, Markus Döring wrote: Hi Rui, the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page. When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&occurrence_id=701c94f1-16eb-4c1e-8449-f3b046100187&advanced=1 If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040-4d7634653246&advanced=1 If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa With regards, Markus On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt>> wrote: Hi IPT list members, Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update? I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org <http://gbif.org>, for example, in this record: https://www.gbif.org/occurrence/1585354292. I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292? Best regards, Rui -- ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt <mailto:ruifigueira@isa.ulisboa.pt> Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt _______________________________________________ IPT mailing list IPT@lists.gbif.org <mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt _______________________________________________ IPT mailing list IPT@lists.gbif.org <mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt
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Hi Nicolas, André
You can be assured that this will all be done publicly, and needs to have opportunity for a lot of folk to contribute. Thank you for already expressing interest.
At the moment I expect this process to kick off sometime after the European summer period. I’m afraid that beyond a few loose ideas it’s a bit premature at the moment to really comment.
Thanks, Tim
From: IPT ipt-bounces@lists.gbif.org on behalf of Nicolas Noé n.noe@biodiversity.be Date: Tuesday, 3 July 2018 at 09.44 To: "ipt@lists.gbif.org" ipt@lists.gbif.org Subject: Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Tim,
Maybe it's slightly off-topic, but I was wondering if you already know how and where you plan to have the discussions and make progress on this topic ? Will it be a public process, happening online? I'm looking forward to bring my 2 cents, if possible :)
Cheers,
Nico
Le 2/07/18 à 09:07, André Heughebaert a écrit : Thanks Tim, Happy to see that you are designing a more expressive model for data exchange and indexing. Species interactions is a good example to start with, but I would rather see a more open model allowing relations between all possible entities we are dealing with: specimens, species, locations, events, people, materials, multimedia, projects...
I've recently experimented the Frictionless Datahttps://frictionlessdata.io/ that offers a truly entity relationship model for data publication. We have to go beyond the DwC star schema and present a well defined DarwinCore schema that supports all possible interactions (relations). I do hope nodes experience will be taken into account and GBIF + TDWG community will come with data model everyone can accept and use.
I'm looking forward to participate to this new data exchange model Best regards,
-- Ir Andre Heughebaert GBIF Node Manager at Belgian Biodiversity Platformhttp://www.biodiversity.be +32(0)2238 3796 Av. Louise 231 Louizalaan B-1050 Brussels ORCID 0000-0002-7839-5300http://orcid.org/0000-0002-7839-5300
On Thu, 28 Jun 2018 at 15:52, Tim Robertson <trobertson@gbif.orgmailto:trobertson@gbif.org> wrote: Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing. I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks, Tim
From: IPT <ipt-bounces@lists.gbif.orgmailto:ipt-bounces@lists.gbif.org> on behalf of Rui Figueira <ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt> Date: Thursday, 28 June 2018 at 15.45 To: Markus Döring <mdoering@gbif.orgmailto:mdoering@gbif.org> Cc: "ipt@lists.gbif.orgmailto:ipt@lists.gbif.org" <ipt@lists.gbif.orgmailto:ipt@lists.gbif.org>, helpdesk <helpdesk@gbif.orgmailto:helpdesk@gbif.org> Subject: Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
------------------
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
http://www.isa.ulisboa.pt On 06/28/2018 11:38 AM, Markus Döring wrote: Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class": http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though. The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187: https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus) If I lookup this record in your dataset it is missing: https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded? https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards, Markus
On 28. Jun 2018, at 12:14, Rui Figueira <ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt> wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.orghttp://gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
-- ------------------
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.ptmailto:ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
_______________________________________________ IPT mailing list IPT@lists.gbif.orgmailto:IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
_______________________________________________ IPT mailing list IPT@lists.gbif.orgmailto:IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
_______________________________________________
IPT mailing list
IPT@lists.gbif.orgmailto:IPT@lists.gbif.org
There's a species interactions workshop at this year's TDWG and I think I'm helping to chair it. Topics of conversation are likely to be wideranging, but this would be an opportunity to hear ideas. Quentin
On Tue, 3 Jul 2018, 10:21 Tim Robertson, trobertson@gbif.org wrote:
Hi Nicolas, André
You can be assured that this will all be done publicly, and needs to have opportunity for a lot of folk to contribute. Thank you for already expressing interest.
At the moment I expect this process to kick off sometime after the European summer period. I’m afraid that beyond a few loose ideas it’s a bit premature at the moment to really comment.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org on behalf of Nicolas Noé < n.noe@biodiversity.be> *Date: *Tuesday, 3 July 2018 at 09.44 *To: *"ipt@lists.gbif.org" ipt@lists.gbif.org *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Tim,
Maybe it's slightly off-topic, but I was wondering if you already know how and where you plan to have the discussions and make progress on this topic ? Will it be a public process, happening online? I'm looking forward to bring my 2 cents, if possible :)
Cheers,
Nico
Le 2/07/18 à 09:07, André Heughebaert a écrit :
Thanks Tim,
Happy to see that you are designing a more expressive model for data exchange and indexing.
Species interactions is a good example to start with, but I would rather see a more open model allowing relations between all possible entities we are dealing with: specimens, species, locations, events, people, materials, multimedia, projects...
I've recently experimented the Frictionless Data https://frictionlessdata.io/ that offers a truly entity relationship model for data publication.
We have to go beyond the DwC star schema and present a well defined DarwinCore schema that supports all possible interactions (relations).
I do hope nodes experience will be taken into account and GBIF + TDWG community will come with data model everyone can accept and use.
I'm looking forward to participate to this new data exchange model
Best regards,
--
Ir Andre Heughebaert
GBIF Node Manager at Belgian Biodiversity Platform http://www.biodiversity.be +32(0)2238 3796 Av. Louise 231 Louizalaan B-1050 Brussels ORCID 0000-0002-7839-5300 http://orcid.org/0000-0002-7839-5300
On Thu, 28 Jun 2018 at 15:52, Tim Robertson trobertson@gbif.org wrote:
Thanks for raising this Rui
This is just a note to say that we are beginning to discuss starting the design of a more expressive model for data exchange, and indexing.
I am afraid that is not a short term task though, but it will of course cover interactions (species related and evidence of interactions). As things progress, your input would be very welcome, both on this topic and the broader model.
Thanks,
Tim
*From: *IPT ipt-bounces@lists.gbif.org on behalf of Rui Figueira < ruifigueira@isa.ulisboa.pt> *Date: *Thursday, 28 June 2018 at 15.45 *To: *Markus Döring mdoering@gbif.org *Cc: *"ipt@lists.gbif.org" ipt@lists.gbif.org, helpdesk < helpdesk@gbif.org> *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
Hi Markus,
Thank you for your quick reply.
I understand the need to make the updated extension "correct", accordingly to the "class".
However, the lack of implementation on GBIF in ingesting related resources is a point of concern.
It brings to my memory the XVII Congress of the European Mycological Association (EMA), in 2015, in Madeira. In that congress, Dmitry Schigel and myself, we were invited to organise a symposium on Biodiversity Informatics and Fungal Data, in the end of the first day. But, in the opening plenary session of the the conference, the President of EMA, David Minter, stated with emphasis that GBIF deliberately lacked support to all mycological researcher community. His main argument was that GBIF does not support interactions between species, which is critical data for many fungi species. Unfortunately, I think we have to agree with him!
Using associatedTaxa is a limited solution if we want to document the occurrence of the interaction. And using the extension will create problems when documenting interactions between different biological groups, namely in the metadata description.
I came across this problem precisely because I am preparing and update of a dataset of fungi https://www.gbif.org/dataset/651c0bec-bd78-4300-bbb0-5ed172fc82af, where all fungi are associated with a plant host. The use of the extension would allow us to define, for example, the establishment means of the host. But, if GBIF is not ingesting the resource relationship, we are only left with the option of using associatedTaxa and occurrenceRemarks to document interactions, which is not my preferred option.
Best regards,
Rui
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira@isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
On 06/28/2018 11:38 AM, Markus Döring wrote:
Hi Rui,
the scientificName term was dropped because it is not part of the regular DwC relation "class":
http://rs.tdwg.org/dwc/terms/index.htm#relindex
The resource relation can relate any kind of things and GBIF needs to lookup the ids to find the scientificName of the related resource in your case. Unfortunately this is not implemented right now, so by upgrading to the latest "correct" version of the extension you will lose the related scientific name on the GBIF occurrence page.
When I look at your example the data is a little unexpected though.
The relatedResourceID is given as 701c94f1-16eb-4c1e-8449-f3b046100187:
https://api.gbif.org/v1/occurrence/1585354292/verbatim
This should be the occurrenceID of the occurrence record for the plant it feeds on (Pistacia terebinthus)
If I lookup this record in your dataset it is missing:
https://www.gbif.org/occurrence/search?dataset_key=85a3c886-3312-45c9-b040-4...
If I look at the taxonomic overview of your dataset it is all Arthropoda, so the related food plants all seem to be excluded?
https://www.gbif.org/occurrence/taxonomy?dataset_key=85a3c886-3312-45c9-b040...
If you only want to annotate an occurrence record with the plant it feeds on you should not be using the relations extension but instead look into dwc:associatedTaxa: http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
With regards,
Markus
On 28. Jun 2018, at 12:14, Rui Figueira ruifigueira@isa.ulisboa.pt wrote:
Hi IPT list members,
Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update?
I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292.
I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292?
Best regards,
Rui
--
Rui Figueira Coordenador do Nó Português do GBIF ruifigueira@isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt
IPT mailing list IPT@lists.gbif.org https://lists.gbif.org/mailman/listinfo/ipt
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participants (7)
-
André Heughebaert -
Markus Döring -
Nicolas Noé -
Quentin Groom -
Rui Figueira -
Tadele Mulat -
Tim Robertson