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
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