Re: [IPT] update of Darwin Core Resource Relationship extension

28 Jun 2018

      Hi Quentin,
Thank you very much, this is an excellent example. Actually, we will 
also prepare a checklist dataset, so this is really helpful also for 
that exercise.
About interactions, I hope there is enough momentum to get it going. The 
TDWG is a good opportunity. Another workshop on the topic was the 
Globis-B workshop in Bari, last February, which feedback might be 
important also. The GBIF Secretariat (Dmitry) was also represented 
there, so he might have given feedback on how the support of species 
interaction is important.
Kind regards,
Rui
On 06/28/2018 03:42 PM, Quentin Groom wrote:
...
Hi Rui,
if you're interested we also published a checklist of rust fungi 
recently using the resource relationship extension 
(https://www.gbif.org/dataset/b043c480-dd36-4f4f-aa82-e188753ff09d).
I total agree with you about the importance of species interactions. 
I'm glad GBIF has some plans for this.
We have an interactions workshop at this year's TDWG meeting and I 
hope we will hear more about approaches to this problem.
Quentin
Dr. Quentin Groom
(Botany and Information Technology)
Botanic Garden Meise
Domein van Bouchout
B-1860 Meise
Belgium
ORCID: 0000-0002-0596-5376 http://orcid.org/0000-0002-0596-5376
Landline; +32 (0) 226 009 20 ext. 364
FAX:      +32 (0) 226 009 45
E-mail: quentin.groom@plantentuinmeise.be 
mailto:quentin.groom@plantentuinmeise.be
Skype name: qgroom
Website: www.botanicgarden.be http://www.botanicgarden.be
On 28 June 2018 at 16:07, Rui Figueira <ruifigueira@isa.ulisboa.pt 
mailto:ruifigueira@isa.ulisboa.pt> wrote:
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@isa.ulisboa.pt <mailto:ruifigueira@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@lists.gbif.org>
<mailto:ipt-bounces@lists.gbif.org> on behalf of Rui Figueira
<ruifigueira@isa.ulisboa.pt> <mailto:ruifigueira@isa.ulisboa.pt>
*Date: *Thursday, 28 June 2018 at 15.45
*To: *Markus Döring <mdoering@gbif.org> <mailto:mdoering@gbif.org>
*Cc: *"ipt@lists.gbif.org" <mailto:ipt@lists.gbif.org>
<ipt@lists.gbif.org> <mailto:ipt@lists.gbif.org>, helpdesk
<helpdesk@gbif.org> <mailto:helpdesk@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
<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@isa.ulisboa.pt <mailto:ruifigueira@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
    <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
        <ruifigueira@isa.ulisboa.pt
        <mailto:ruifigueira@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
        <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
        ruifigueira@isa.ulisboa.pt
        <mailto:ruifigueira@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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