[IPT] update of Darwin Core Resource Relationship extension

Quentin Groom quentin.groom at plantentuinmeise.be
Wed Jul 4 07:06:11 CEST 2018


There's a species interactions workshop at this year's TDWG and I think I'm
helping to chair it. Topics of conversation are likely to be wideranging,
but this would be an opportunity to hear ideas.
Quentin

On Tue, 3 Jul 2018, 10:21 Tim Robertson, <trobertson at gbif.org> wrote:

> Hi Nicolas, André
>
>
>
> You can be assured that this will all be done publicly, and needs to have
> opportunity for a lot of folk to contribute. Thank you for already
> expressing interest.
>
>
>
> At the moment I expect this process to kick off sometime after the
> European summer period. I’m afraid that beyond a few loose ideas it’s a bit
> premature at the moment to really comment.
>
>
>
> Thanks,
>
> Tim
>
>
>
>
>
> *From: *IPT <ipt-bounces at lists.gbif.org> on behalf of Nicolas Noé <
> n.noe at biodiversity.be>
> *Date: *Tuesday, 3 July 2018 at 09.44
> *To: *"ipt at lists.gbif.org" <ipt at lists.gbif.org>
> *Subject: *Re: [IPT] update of Darwin Core Resource Relationship extension
>
>
>
> 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> 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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