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
ruifigue...@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-boun...@lists.gbif.org> on behalf of Rui Figueira
<ruifigue...@isa.ulisboa.pt>
*Date: *Thursday, 28 June 2018 at 15.45
*To: *Markus Döring <mdoer...@gbif.org>
*Cc: *"ipt@lists.gbif.org" <ipt@lists.gbif.org>, helpdesk
<helpd...@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
ruifigue...@isa.ulisboa.pt <mailto:ruifigue...@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
<ruifigue...@isa.ulisboa.pt
<mailto:ruifigue...@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
ruifigue...@isa.ulisboa.pt <mailto:ruifigue...@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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