[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
>
>         _______________________________________________
>         IPT mailing list
>         IPT at lists.gbif.org <mailto:IPT at lists.gbif.org>
>         https://lists.gbif.org/mailman/listinfo/ipt
>
>
>

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