Update metadta + documentation

frmichel · Jul 30, 2024 · 644b75d · 644b75d
1 parent 61db58c
commit 644b75d
Show file tree

Hide file tree

Showing 7 changed files with 75 additions and 58 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,19 +1,19 @@
 # TAXREF-LD changelog
 
 
-## [17.0] 2024-04-30
+## [17.0] 2024-07-30
+
+### Added
+- New SKOS collections: [taxref:TaxonomicRankCollection](http://taxref.mnhn.fr/lod/taxrank/TaxonomicRankCollection), [taxreftl:TrophicLevelCollection](http://taxref.mnhn.fr/lod/trophicLevel/TrophicLevelCollection), and [taxref:TaxonomicNameCollection](http://taxref.mnhn.fr/lod/TaxonomicNameCollection)
+- Various properties in dataset metadata: `vann:changes`, `owl:deprecated`
+- Split vernacular names that contain a comma into multiple values (done with property `taxrefprop:vernacularName` but not with `taxrefprop:vernacularNameXL` as a `skosxl:Label` can have only one `skosxl:literalForm`)
 
 ### Changed
 - Update to TAXREF version 17
 - Change URIs of graphs to non-versioned URIs
 - Fixed issue in the generation of the interactions: some interactions involve the TAXREF ids of synonyms, not reference names. As a results, the process was generating wrong URIs of taxa with ids of synonyms. The fix is to refer always to the referenceId field of the interaction.
 - Fixed issue in the generation of the DBXRefs: all ids were used as taxa whereas some ids are not reference ids. That lead to generating wrong URIs of taxa with ids of synonyms.
-- Fixed bug in the generation of vernacular names: names were generated with 3-letter language tags that must be mapped to 2-letter tagsn e.g. @fra instead of @fr
-
-### Added
-- Various properties in dataset metadata: `vann:changes`, `owl:deprecated`, `owl:deprecated`
-- Split vernacular names that contain a comma into multiple values (done with property `taxrefprop:vernacularName` but not with `taxrefprop:vernacularNameXL` as a `skosxl:Label` can have only one `skosxl:literalForm`)
-
+- Fixed bug in the generation of vernacular names: names were generated with 3-letter language tags that must be mapped to 2-letter tags, e.g. @fra instead of @fr
 
 
 ## [15.2] 2022-07-29

diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ The modelling is exemplified in [dataset/examples](dataset/examples).
 
 ### URIs naming scheme
 
-TAXREF-LD namespace is `http://taxref.mnhn.fr/lod/`. All URIs are dereferenceable.
+TAXREF-LD namespace is `http://taxref.mnhn.fr/lod/`, registered as prefix `taxref` on prefix.cc. All URIs are dereferenceable.
 
 The dataset itslef is identified by URI [`http://taxref.mnhn.fr/lod/taxref-ld`](http://taxref.mnhn.fr/lod/taxref-ld). It comes with  descriptions in DCAT, VOID and SPARQL SD vocabularies.
 
@@ -67,22 +67,22 @@ As an example, you can look up taxon [http://taxref.mnhn.fr/lod/taxon/60878](htt
 
 The following **named graphs** can be queried from our SPARQL endpoint:
 
-| Named graph    | Description | No. RDF triples |
-| -------------  | ---- | ----: |
-| `http://taxref.mnhn.fr/lod/graph/metadata` | DCAT, VOID and SPARQL SD dataset descriptions + definition of various classes, concepts, properties (content of files `dataset/Taxrefld_static*.ttl`) |1,740|
-| `http://taxref.mnhn.fr/lod/graph/biblio` | bibliographic resources |408,737|
-| `http://taxref.mnhn.fr/lod/graph/locations` | regions, departements, territories etc. |393,496|
-| `http://taxref.mnhn.fr/lod/graph/media` | media (photos) linked to taxa |690,508|
-| `http://taxref.mnhn.fr/lod/graph/statuscodes` | description of the status values of types international convention, european directive, protection and regulation. These are represented as instances of the class bibo:DocumentPart (e.g. http://taxref.mnhn.fr/lod/status/BONN/IBOAC) and related to the bibliographic source describing the document with property dct:isPartOf (content of files `statusCodes.ttl` and `statusBiblio.ttl`) |1,804|
-| `http://taxref.mnhn.fr/lod/graph/classes` | description of taxa as OWL classes |4,374,167|
-| `http://taxref.mnhn.fr/lod/graph/concepts` | description of scientific names as SKOS concepts |7,799,394|
-| `http://taxref.mnhn.fr/lod/graph/interactions` | species interactions |303,025|
-| `http://taxref.mnhn.fr/lod/graph/statuses` | all taxa statuses (legal, biogeographical, red list) |7,846,358|
-| `http://taxref.mnhn.fr/lod/graph/vernacular` | taxa vernacular names (direct and as SKOS-XL labels) |518,708|
-| `http://taxref.mnhn.fr/lod/graph/dbxref` | cross-references to identifiers of third-party data sources such as GBIF, WoRMS, the Plant List etc. |10,330,904|
-| `http://taxref.mnhn.fr/lod/graph/webpages` | `foaf:page` links to webpages |2,567,841|
-| `http://taxref.mnhn.fr/lod/graph/links-*` | interllinking to equivalent URIs from NCBI, Agrovoc, WoRMS |250,249|
-| Total | | 35,486,931 |
+| Named graph    | Description |
+| -------------  | ---- |
+| `http://taxref.mnhn.fr/lod/graph/metadata` | DCAT, VOID and SPARQL SD dataset descriptions + definition of various classes, concepts, properties (content of files `dataset/Taxrefld_static*.ttl`) |
+| `http://taxref.mnhn.fr/lod/graph/biblio` | bibliographic resources |
+| `http://taxref.mnhn.fr/lod/graph/locations` | regions, departements, territories etc. |
+| `http://taxref.mnhn.fr/lod/graph/media` | media (photos) linked to taxa |
+| `http://taxref.mnhn.fr/lod/graph/statuscodes` | description of the status values of types international convention, european directive, protection and regulation. These are represented as instances of the class bibo:DocumentPart (e.g. http://taxref.mnhn.fr/lod/status/BONN/IBOAC) and related to the bibliographic source describing the document with property dct:isPartOf (content of files `statusCodes.ttl` and `statusBiblio.ttl`) |
+| `http://taxref.mnhn.fr/lod/graph/classes` | description of taxa as OWL classes |
+| `http://taxref.mnhn.fr/lod/graph/concepts` | description of scientific names as SKOS concepts |
+| `http://taxref.mnhn.fr/lod/graph/interactions` | species interactions |
+| `http://taxref.mnhn.fr/lod/graph/statuses` | all taxa statuses (legal, biogeographical, red list) |
+| `http://taxref.mnhn.fr/lod/graph/vernacular` | taxa vernacular names (direct and as SKOS-XL labels) |
+| `http://taxref.mnhn.fr/lod/graph/dbxref` | cross-references to identifiers of third-party data sources such as GBIF, WoRMS, the Plant List etc. |
+| `http://taxref.mnhn.fr/lod/graph/webpages` | `foaf:page` links to webpages |
+| `http://taxref.mnhn.fr/lod/graph/links-*` | interllinking to equivalent URIs from NCBI, Agrovoc, WoRMS |
+
 
 ## License
 

diff --git a/dataset/Taxrefld_static_dataset_description.ttl b/dataset/Taxrefld_static_dataset_description.ttl
@@ -205,14 +205,21 @@ taxref:taxref-ld
     a                       void:Dataset;
     void:uriSpace           "http://taxref.mnhn.fr/lod/";
     void:rootResource       <http://taxref.mnhn.fr/lod/name/349525>;
-    void:triples            "37400000"^^xsd:integer;
+    void:triples            "37800000"^^xsd:integer;
     void:sparqlEndpoint     <https://taxref.mnhn.fr/sparql>;
     void:dataDump           <https://zenodo.org/record/12733630/files/taxrefld17.0.zip>;
     void:exampleResource    <http://taxref.mnhn.fr/lod/taxon/60878>;
     void:vocabulary         skos:, skosxl:, dct:, foaf:, schema:, bibo:, <http://www.wikidata.org/>, <http://sws.geonames.org/>, ro:, dwc:, dwciri:,
         <http://aims.fao.org/aos/agrovoc/>, <http://lod.taxonconcept.org/ontology/txn.owl>, <http://purl.obolibrary.org/obo/ncbitaxon.owl>, <http://purl.obolibrary.org/obo/envo.owl>, <http://rdf.geospecies.org/ont/geospecies.owl>, <http://rs.tdwg.org/ontology/voc/TaxonRank>, <http://rs.tdwg.org/ontology/voc/TaxonName>, <http://rs.tdwg.org/dwc/terms/>;
     .
 
+
+taxref:TaxonomicNameCollection
+    a skos:Collection;
+    rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
+    rdfs:label "Collection of taxonomic names"@en.
+
+
 # ------------------------------------------------------------------------------
 
 # SPARQL Service Description and DCAT DataService
@@ -381,11 +388,11 @@ taxref:hal01617708
 
 taxref:taxrefmethodo
     a <https://data.archives-ouvertes.fr/doctype/Report>, <https://schema.org/Article>;
-    dct:title "TAXREF v17, référentiel taxonomique pour la France : méthodologie, mise en œuvre et diffusion";
-    schema:name "TAXREF v17, référentiel taxonomique pour la France : méthodologie, mise en œuvre et diffusion";
-    dct:issued "2024"^^xsd:gYear; schema:datePublished "2024"^^xsd:gYear;
+    dct:title "TAXREF, référentiel taxonomique pour la France : méthodologie, mise en œuvre et diffusion";
+    schema:name "TAXREF, référentiel taxonomique pour la France : méthodologie, mise en œuvre et diffusion";
+    dct:issued "2022"^^xsd:gYear; schema:datePublished "2022"^^xsd:gYear;
     dct:bibliographicCitation "Gargominy O., Tercerie S., Régnier C., Ramage T., Dupont P., Daszkiewicz P. & Poncet L. (2024). TAXREF v17, référentiel taxonomique pour la France: méthodologie, mise en œuvre et diffusion. Muséum national d’Histoire naturelle, Paris";
     dct:creator taxref:oliviergargominy, taxref:sandrinetercerie, "Régnier C.", "Ramage T.", "Dupont P.", "Daszkiewicz P.", "Poncet L";
     schema:author taxref:oliviergargominy, taxref:sandrinetercerie, "Régnier C.", "Ramage T.", "Dupont P.", "Daszkiewicz P.", "Poncet L";
-    schema:url <https://inpn.mnhn.fr/docs-web/docs/download/XXXXX>;
+    schema:url <https://inpn.mnhn.fr/docs-web/docs/download/413731>;
     .
diff --git a/dataset/Taxrefld_static_defs_properties.ttl b/dataset/Taxrefld_static_defs_properties.ttl
@@ -178,7 +178,7 @@ taxrefprop:hasTrophicLevel
 
 
 # ============================================================
-# ==== Properties associated with taxon names
+# ==== Properties associated to taxon names
 # ============================================================
 
 taxrefprop:hasAuthority

diff --git a/dataset/Taxrefld_static_defs_statuses.ttl b/dataset/Taxrefld_static_defs_statuses.ttl
@@ -54,40 +54,37 @@ taxrefstatus:LegalStatus
     rdfs:subClassOf taxrefstatus:TaxonStatus;
     rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
     rdfs:label "Status of a taxon attested by a legal document"@en;
-    rdfs:comment "To be used jointly with http://taxref.mnhn.fr/lod/status/TaxonStatusType whose narrower concepts represent directives, conventions, regulations or protections"@en.
+    rdfs:comment "To be used jointly with http://taxref.mnhn.fr/lod/status/LegalStatusCollection whose member concepts represent directives, conventions, regulations or protections"@en.
 
 
 #------------------ Types of taxon legal statuses -------------------
 
-taxrefstatus:TaxonStatusType
-    a skos:Concept;
-    skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
-    skos:prefLabel "Top concept for types of taxon statuses"@en.
+taxrefstatus:LegalStatusCollection
+    a skos:Collection;
+    rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
+    rdfs:label "Collection of types of legal statuses"@en;
+    skos:member taxrefstatus:InternationalConvention, taxrefstatus:EuropeanDirective, taxrefstatus:Regulation, taxrefstatus:Protection.
 
 taxrefstatus:InternationalConvention
     a skos:Concept;
-    skos:broader taxrefstatus:TaxonStatusType ;
     skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
     skos:prefLabel "International Convention"@en;
     skos:prefLabel "Convention internationale"@fr.
 
 taxrefstatus:EuropeanDirective
     a skos:Concept;
-    skos:broader taxrefstatus:TaxonStatusType ;
     skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
     skos:prefLabel "European Directive"@en;
     skos:prefLabel "Directive européenne"@fr.    
 
 taxrefstatus:Regulation
     a skos:Concept;
-    skos:broader taxrefstatus:TaxonStatusType ;
     skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
     skos:prefLabel "Regulation"@en;
     skos:prefLabel "Règlementation"@fr.
 
 taxrefstatus:Protection
     a skos:Concept;
-    skos:broader taxrefstatus:TaxonStatusType ;
     skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
     skos:prefLabel "Protection"@en;
     skos:prefLabel "Protection"@fr.    
@@ -125,13 +122,6 @@ taxrefstatus:Protection
 
 # --------------------------- Biogeographical status values -------------------------------
 
-taxrefbgs:BioGeographicalStatus
- rdfs:subClassOf skos:Concept;
- rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
- rdfs:label "Class of biogeographical status values"@en;
- dct:description "Class of biogeographical status values (subclass of skos:Concept)"@en;
- owl:deprecated "true"^^xsd:boolean.
-
 
 taxrefbgs:BioGeographicalStatusCollection
     a skos:Collection;
@@ -271,3 +261,13 @@ taxrefbgs:Q
  skos:definition "Taxon mentionné par erreur comme présent sur le territoire considéré."@fr;
  skos:exactMatch <http://rs.tdwg.org/ontology/voc/SPMInfoItems#AbsentButReportedInError>.
 
+
+# Deprecated
+
+taxrefbgs:BioGeographicalStatus
+ rdfs:subClassOf skos:Concept;
+ rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
+ rdfs:label "Class of biogeographical status values"@en;
+ dct:description "Class of biogeographical status values (subclass of skos:Concept)"@en;
+ owl:deprecated "true"^^xsd:boolean.
+
diff --git a/dataset/Taxrefld_static_defs_taxranks.ttl b/dataset/Taxrefld_static_defs_taxranks.ttl
@@ -31,20 +31,19 @@
 
 # --- Taxonomical ranks linked with equivalent ranks from other ontologies
 
-taxrefrk:TaxonomicRank
- rdfs:subClassOf skos:Concept;
- rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
- owl:equivalentClass <http://rs.tdwg.org/ontology/voc/TaxonRank#TaxonRankTerm>;
- rdfs:label "Class of taxonomical ranks"@en;
- dct:description "Class of taxonomical ranks, subclass of skos:Concept"@en;
- owl:deprecated "true"^^xsd:boolean.
-
-
 taxrefrk:TaxonomicRankCollection
  a skos:Collection;
  rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
  rdfs:label "Collection of taxonomical ranks"@en;
- skos:member taxrefrk:Domain.
+ skos:member 
+    taxrefrk:Domain, taxrefrk:Superkingdom, taxrefrk:Kingdom, taxrefrk:SubKingdom, taxrefrk:InfraKingdom,
+    taxrefrk:Phylum, taxrefrk:SubPhylum, taxrefrk:InfraPhylum, taxrefrk:Division, taxrefrk:SubDivision, taxrefrk:SuperClass, taxrefrk:Cladus, taxrefrk:Class, 
+    taxrefrk:SubClass, taxrefrk:InfraClass, taxrefrk:Legio, taxrefrk:SuperOrder, taxrefrk:Cohort, taxrefrk:Order, taxrefrk:SubOrder, taxrefrk:InfraOrder, 
+    taxrefrk:SuperFamily, taxrefrk:Family, taxrefrk:SubFamily, taxrefrk:Tribe, taxrefrk:SubTribe, taxrefrk:Genus, taxrefrk:SubGenus, taxrefrk:Section, 
+    taxrefrk:SubSection, taxrefrk:Series, taxrefrk:SubSeries, taxrefrk:Agregate, taxrefrk:Species, taxrefrk:SemiSpecies, taxrefrk:MicroSpecies, taxrefrk:SubSpecies, 
+    taxrefrk:Natio, taxrefrk:Varietas, taxrefrk:SubVarietas, taxrefrk:Forma, taxrefrk:SubForma, taxrefrk:FormaSpecies, taxrefrk:Linea, taxrefrk:Clone, 
+    taxrefrk:Race, taxrefrk:Cultivar, taxrefrk:Morpha, taxrefrk:Abberatio
+ .
 
 taxrefrk:Domain
  a skos:Concept;
@@ -468,3 +467,14 @@ taxrefrk:Abberatio
  a skos:Concept;
  skos:inScheme <http://taxref.mnhn.fr/lod/taxref-ld>;
  skos:prefLabel "Abberatio"@en.
+
+
+# Deprecated
+
+taxrefrk:TaxonomicRank
+ rdfs:subClassOf skos:Concept;
+ rdfs:isDefinedBy <http://taxref.mnhn.fr/lod/taxref-ld>;
+ owl:equivalentClass <http://rs.tdwg.org/ontology/voc/TaxonRank#TaxonRankTerm>;
+ rdfs:label "Class of taxonomical ranks"@en;
+ dct:description "Class of taxonomical ranks, subclass of skos:Concept"@en;
+ owl:deprecated "true"^^xsd:boolean.
diff --git a/dataset/Taxrefld_static_defs_trophic_levels.ttl b/dataset/Taxrefld_static_defs_trophic_levels.ttl
@@ -26,7 +26,7 @@
 @prefix taxrefloc:      <http://taxref.mnhn.fr/lod/loc/>.
 @prefix taxrefprop:     <http://taxref.mnhn.fr/lod/property/>.
 @prefix taxrefrk:       <http://taxref.mnhn.fr/lod/taxrank/>.
-@prefix taxreftl:      <http://taxref.mnhn.fr/lod/trophicLevel/>.
+@prefix taxreftl:       <http://taxref.mnhn.fr/lod/trophicLevel/>.
 @prefix taxrefstatus:   <http://taxref.mnhn.fr/lod/status/>.
 
 taxreftl:TrophicLevelCollection
@@ -44,7 +44,7 @@ taxreftl:Unknown
  rdfs:label "Unknown"@en;
  skos:prefLabel "Unknown"@en;
  skos:prefLabel "Inconnu"@fr;
- skos:definition "We don't know the species trophic level"@en;
+ skos:definition "The species trophic level is unknown"@en;
  skos:definition "On ne connait pas le niveau trophique de l'espèce"@fr.
 
 taxreftl:Autotroph