[IPT] update of Darwin Core Resource Relationship extension
Nicolas Noé
n.noe at biodiversity.be
Tue Jul 3 09:35:59 CEST 2018
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 at gbif.org
> <mailto:trobertson at 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 at lists.gbif.org
> <mailto:ipt-bounces at lists.gbif.org>> on behalf of Rui Figueira
> <ruifigueira at isa.ulisboa.pt <mailto:ruifigueira at isa.ulisboa.pt>>
> *Date: *Thursday, 28 June 2018 at 15.45
> *To: *Markus Döring <mdoering at gbif.org <mailto:mdoering at gbif.org>>
> *Cc: *"ipt at lists.gbif.org <mailto:ipt at lists.gbif.org>"
> <ipt at lists.gbif.org <mailto:ipt at lists.gbif.org>>, helpdesk
> <helpdesk at gbif.org <mailto: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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