[IPT] update of Darwin Core Resource Relationship extension

Mon Jul 2 09:07:20 CEST 2018

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> 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
>
> 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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