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 <[email protected]>
<mailto:[email protected]> on behalf of Rui Figueira
<[email protected]> <mailto:[email protected]>
*Date: *Thursday, 28 June 2018 at 15.45
*To: *Markus Döring <[email protected]> <mailto:[email protected]>
*Cc: *"[email protected]" <mailto:[email protected]>
<[email protected]> <mailto:[email protected]>, helpdesk
<[email protected]> <mailto:[email protected]>
*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
<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
[email protected] <mailto:[email protected]>
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
<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
<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
<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
<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
<http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa>
With regards,
Markus
On 28. Jun 2018, at 12:14, Rui Figueira
<[email protected]
<mailto:[email protected]>> 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
<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
<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?
<https://www.gbif.org/occurrence/1585354292?>
Best regards,
Rui
--
------------------
Rui Figueira
Coordenador do Nó Português do GBIF
[email protected]
<mailto:[email protected]>
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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