[IPT] update of Darwin Core Resource Relationship extension

Tue Jul 3 10:20:47 CEST 2018

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<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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