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retog opened this issue Jun 23, 2021 · 2 comments
Open

Create single RDF representation #22

retog opened this issue Jun 23, 2021 · 2 comments

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@retog
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retog commented Jun 23, 2021

Currently, we are having two different RDF representations of treatments.

For example for the treatment 03CB87C52324FFE6FCDE9030FA24F97E we provide the following two representations (in RDF Turtle for readability).

@prefix ns0: <http://plazi.org/vocab/treatment#> .
@prefix dc11: <http://purl.org/dc/elements/1.1/> .
@prefix bibo: <http://purl.org/ontology/bibo/> .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:treatsTaxonName <http://taxon-name.plazi.org/id/Animalia/Galearis_spectabilis> ;
  dc11:creator "Jarvis, Charlie" ;
  ns0:publishedIn <http://dx.doi.org/10.5281/zenodo.250878> ;
  ns0:citesTaxonName <http://tb.plazi.org/GgServer/lodRdf/Orchis_spectabilis> .

<http://dx.doi.org/10.5281/zenodo.250878>
  dc11:title "pp 705 - 708 in: Order out of Chaos" ;
  dc11:creator "Jarvis, Charlie" ;
  a <http://purl.org/spar/fabio/BookSection> ;
  dc11:date "2007" ;
  bibo:startPage "705" ;
  bibo:endPage "708" .

@prefix ns0: <http://plazi.org/vocab/treatment#> .
@prefix ns1: <http://purl.org/spar/cito/> .
@prefix ns2: <http://rs.tdwg.org/ontology/voc/> .
@prefix dc11: <http://purl.org/dc/elements/1.1/> .
@prefix ns3: <http://rs.tdwg.org/dwc/terms/> .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E> ;
  ns0:publishedIn <http://dx.doi.org/10.5281/zenodo.250878> ;
  ns1:cites "Orchis spectabilis Linnaeus" ;
  ns2:SpeciesProfileModelhasInformation <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_1>, <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_2>, <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_3> .

<http://dx.doi.org/10.5281/zenodo.250878>
  dc11:title "pp 705 - 708 in: Order out of Chaos" ;
  dc11:creator "Jarvis, Charlie" .

<http://taxon-concept.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://filteredpush.org/ontologies/oa/dwcFP#Taxon> ;
  ns3:LSID-IPNI "urn:lsid:ipni.org:names:1009442-2" ;
  ns3:authorityName "(L.) Raf." ;
  ns3:authorityPageNumber "1837" ;
  ns3:box "[1030,1313,1719,1741]" ;
  ns3:class "Liliopsida" ;
  ns3:family "Orchidaceae" ;
  ns3:genus "Galearis" ;
  ns3:kingdom "Plantae" ;
  ns3:order "Asparagales" ;
  ns3:pageId "2" ;
  ns3:pageNumber "707" ;
  ns3:phylum "Tracheophyta" ;
  ns3:rank "species" ;
  ns3:species "spectabilis" .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_1>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent "   Orchis spectabilisLinnaeus, Species Plantarum2: 943- 1753." .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_2>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent " “ Habitatin Virginia. D. Gronovius.” RCN: 6832." .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_3>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent " Lectotype (Sheviak in Cafferty & Jarvis in Taxon48: 49. 1999): Clayton s.n.,Herb. Linn. No. 1054.44 (LINN)." .

The first graph is available when dereferencing http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E with an appropriate accept-header as well when dereferencing http://tb.plazi.org/GgServer/lodRdf/03CB87C52324FFE6FCDE9030FA24F97E. The second Graph is available at http://tb.plazi.org/GgServer/rdf/03CB87C52324FFE6FCDE9030FA24F97E.

I suggest serving a unified RDF representation describing all the information we have about a treatment in a way that is accessible to all users of our RDF data and which aims for wide compliance with Data on the Web Best Practices.

Differences in the expressed content

One version contains more literal content of the treatment in the form of "InfoItems" the other version contains more explicit information about synonymity.

example

Treatment 03ACBF18FFD61B34FF31FB52FD04ED5B "deprecates" Sadayoshia_acroporae_Macpherson_2010 and defines adayoshia_aludra_Macpherson_2012 according to the lodRdf version:

<http://treatment.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/Animalia/Sadayoshia_aludra_Macpherson_2012> ;
  ns0:deprecates <http://taxon-concept.plazi.org/id/Animalia/Sadayoshia_acroporae_Macpherson_2010> ;
  ns1:cites <http://dx.doi.org/10.5281/zenodo.214647>, <http://dx.doi.org/10.5281/zenodo.214650> .
  ...

The other rdf version states in regard to these two names:


<http://treatment.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B> ;
  ns1:cites "Sadayoshia acroporae Macpherson & Baba 2010 : 418" ;
 ...

<http://taxon-concept.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://filteredpush.org/ontologies/oa/dwcFP#Taxon> ;
...
  ns4:rank "species" ;
  ns4:species "aludra" ;
  ns4:status "n. sp." .
retog added a commit that referenced this issue Jul 21, 2021
@retog
Trying a simple union of the two RDF #22
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retog commented Jul 21, 2021 •
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The ontology namespace http://rs.tdwg.org/ontology/voc/ and the terms therein don't dereference.

According to https://github.com/tdwg/rs.tdwg.org/blob/master/README.md the namespace for terms is: http://rs.tdwg.org/vvv/sss/ttt

I can't fid any reference to SpeciesProfileModelhasInformation within the tdwg GitHub organisation, nor anywhere else. @tcatapano, do you have a reference?

@retog
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retog commented Jul 21, 2021

cito:cites

In one RDF the objects are literals, in the other resources identified by URIs. What is the range of cito:cites? Potentially the definition of its superptoperty http://purl.org/spar/cito/citesAsAuthority could be helpful.

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