[IPT] update of Darwin Core Resource Relationship extension
Rui Figueira
ruifigueira at isa.ulisboa.pt
Thu Jun 28 16:07:03 CEST 2018
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 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 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> on behalf of Rui Figueira
> <ruifigueira at isa.ulisboa.pt>
> *Date: *Thursday, 28 June 2018 at 15.45
> *To: *Markus Döring <mdoering at gbif.org>
> *Cc: *"ipt at lists.gbif.org" <ipt at lists.gbif.org>, helpdesk
> <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 <mailto: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
> <mailto: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
> <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 at isa.ulisboa.pt <mailto: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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