diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e480d5..c5371aa 100644 --- 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 index bab8d25..1e1e319 100644 --- 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 index d56c3d7..118ccb5 100644 --- a/dataset/Taxrefld_static_dataset_description.ttl +++ b/dataset/Taxrefld_static_dataset_description.ttl @@ -205,7 +205,7 @@ taxref:taxref-ld a void:Dataset; void:uriSpace "http://taxref.mnhn.fr/lod/"; void:rootResource ; - void:triples "37400000"^^xsd:integer; + void:triples "37800000"^^xsd:integer; void:sparqlEndpoint ; void:dataDump ; void:exampleResource ; @@ -213,6 +213,13 @@ taxref:taxref-ld , , , , , , , ; . + +taxref:TaxonomicNameCollection + a skos:Collection; + rdfs:isDefinedBy ; + rdfs:label "Collection of taxonomic names"@en. + + # ------------------------------------------------------------------------------ # SPARQL Service Description and DCAT DataService @@ -381,11 +388,11 @@ taxref:hal01617708 taxref:taxrefmethodo a , ; - 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 ; + schema:url ; . diff --git a/dataset/Taxrefld_static_defs_properties.ttl b/dataset/Taxrefld_static_defs_properties.ttl index 024d970..4de54ae 100644 --- 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 index ef158ae..d10c9d5 100644 --- 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 ; 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 ; - skos:prefLabel "Top concept for types of taxon statuses"@en. +taxrefstatus:LegalStatusCollection + a skos:Collection; + rdfs:isDefinedBy ; + 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 ; skos:prefLabel "International Convention"@en; skos:prefLabel "Convention internationale"@fr. taxrefstatus:EuropeanDirective a skos:Concept; - skos:broader taxrefstatus:TaxonStatusType ; skos:inScheme ; skos:prefLabel "European Directive"@en; skos:prefLabel "Directive européenne"@fr. taxrefstatus:Regulation a skos:Concept; - skos:broader taxrefstatus:TaxonStatusType ; skos:inScheme ; skos:prefLabel "Regulation"@en; skos:prefLabel "Règlementation"@fr. taxrefstatus:Protection a skos:Concept; - skos:broader taxrefstatus:TaxonStatusType ; skos:inScheme ; 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 ; - 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 . + +# Deprecated + +taxrefbgs:BioGeographicalStatus + rdfs:subClassOf skos:Concept; + rdfs:isDefinedBy ; + 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 index cec5770..ab0df53 100644 --- 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 ; - owl:equivalentClass ; - 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 ; 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 ; skos:prefLabel "Abberatio"@en. + + +# Deprecated + +taxrefrk:TaxonomicRank + rdfs:subClassOf skos:Concept; + rdfs:isDefinedBy ; + owl:equivalentClass ; + 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 index 3990af1..29ada31 100644 --- a/dataset/Taxrefld_static_defs_trophic_levels.ttl +++ b/dataset/Taxrefld_static_defs_trophic_levels.ttl @@ -26,7 +26,7 @@ @prefix taxrefloc: . @prefix taxrefprop: . @prefix taxrefrk: . -@prefix taxreftl: . +@prefix taxreftl: . @prefix taxrefstatus: . 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