[IPT] update of Darwin Core Resource Relationship extension

Thu Jun 28 13:37:45 CEST 2018

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 at 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 at plantentuinmeise.be
> Skype name: qgroom
> Website:    www.botanicgarden.be
>
> On 28 June 2018 at 16:07, Rui Figueira <ruifigueira at 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 at 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 at lists.gbif.org> <ipt-bounces at lists.gbif.org> on
>> behalf of Rui Figueira <ruifigueira at isa.ulisboa.pt>
>> <ruifigueira at isa.ulisboa.pt>
>> *Date: *Thursday, 28 June 2018 at 15.45
>> *To: *Markus Döring <mdoering at gbif.org> <mdoering at gbif.org>
>> *Cc: *"ipt at lists.gbif.org" <ipt at lists.gbif.org> <ipt at lists.gbif.org>
>> <ipt at lists.gbif.org>, helpdesk <helpdesk at gbif.org> <helpdesk at 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 at 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 at 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 at 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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>>
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