ontology.setl.ttl

@prefix rdf:           <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:          <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:           <http://www.w3.org/2001/XMLSchema#> .
@prefix owl:           <http://www.w3.org/2002/07/owl#> .
@prefix skos:          <http://www.w3.org/2004/02/skos/core#> .
@prefix prov:          <http://www.w3.org/ns/prov#> .
@prefix sio:           <http://semanticscience.org/resource/> .
@prefix dcat:          <http://www.w3.org/ns/dcat#> .
@prefix dcterms:       <http://purl.org/dc/terms/> .
@prefix void:          <http://rdfs.org/ns/void#> .
@prefix foaf:          <http://xmlns.com/foaf/0.1/> .
@prefix ov:            <http://open.vocab.org/terms/> .
@prefix setl:          <http://purl.org/twc/vocab/setl/> .
@prefix csvw:          <http://www.w3.org/ns/csvw#> .
@prefix pv:            <http://purl.org/net/provenance/ns#>.
@prefix prv:           <http://hadatac.org/ont/prov#>.

@prefix :              <https://hadatac.org/setl/> .

@prefix chear:    <http://hadatac.org/ont/chear#> .


:analytes_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=0>;
  ].
  
:attributes_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=99342435>;
  ].

:instrument_perspectives_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=2136275427>;
  ].

:instruments_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=1602379898>;
  ].

:methods_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=1751401330>;
  ].

:objects_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=901041093>;
  ].

:roles_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=96467471>;
  ].

:samples_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=487418460>;
  ].

:indicators_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=1372995492>;
  ].

:studies_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=2079819994>;
  ].

:time_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=2119994014>;
  ].

:units_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=1938457669>;
  ].

:cogat_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=106241699>;
  ].

:labels_table a csvw:Table, setl:Table;
  prov:wasGeneratedBy [
    a setl:Extract;
    prov:used <https://docs.google.com/spreadsheets/d/1ZSIl_4XTa78ZIqWJaKr-dFUNEChdU_5OScNdP4ALkxQ/export?exportFormat=csv&gid=196531008>;
  ].



<http://hadatac.org/ont/chear> a void:Dataset;
  prov:wasGeneratedBy [
    a setl:Transform, setl:JSLDT;
    prov:used
        :analytes_table,
        :attributes_table,
        :instrument_perspectives_table,
        :instruments_table,
        :methods_table,
        :objects_table,
        :roles_table,
        :samples_table,
        :indicators_table,
        :studies_table,
        :time_table,
        :units_table;
    setl:hasContext '''{
  "@vocab" :   "http://hadatac.org/ont/chear#",
  "owl": "http://www.w3.org/2002/07/owl#",
  "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
  "sio" :     "http://semanticscience.org/resource/",
  "foaf" : "http://xmlns.com/foaf/0.1/",
  "chear" :   "http://hadatac.org/ont/chear#",
  "skos" :    "http://www.w3.org/2004/02/skos/core#",
  "prov" :    "http://www.w3.org/ns/prov#",
  "uniprot" :   "http://www.uniprot.org/uniprot/",
  "chebi" :   "http://purl.obolibrary.org/obo/CHEBI_",
  "cl" :   "http://purl.obolibrary.org/obo/CL_",
  "stato" :   "http://purl.obolibrary.org/obo/STATO_",
  "hp" :   "http://purl.obolibrary.org/obo/HP_",
  "efo" :   "http://www.ebi.ac.uk/efo/EFO_",
  "obo" :   "http://purl.obolibrary.org/obo/",
  "phenx" : "http://purl.bioontology.org/ontology/phenX/",
  "pubchem" : "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/",
  "dc"   :    "http://purl.org/dc/terms/",
  "hasco" : "http://hadatac.org/ont/hasco/",
  "vstoi" : "http://hadatac.org/ont/vstoi#",
  "hasneto" : "http://hadatac.org/ont/hasneto#",
  "vivo": "http://vivoweb.org/ontology/core#",
  "uberon" : "http://purl.obolibrary.org/obo/UBERON_",
  "envo" : "http://purl.obolibrary.org/obo/ENVO_",
  "radlex" : "http://radlex.org/RID/RID",
  "do": "http://purl.obolibrary.org/obo/DOID_",
  "doid": "http://purl.obolibrary.org/obo/DOID_",
  "prv" : "http://hadatac.org/ont/prov#",
  "chear-kb" : "http://hadatac.org/kb/chear#",
  "CSEO" : "http://scai.fraunhofer.de/CSEO#",
  "cmo"  :    "http://purl.obolibrary.org/obo/CMO_"
}''';
  prov:value '''[{
    "@id": "http://hadatac.org/ont/chear",
    "@context": {
  "@context": {
    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "xsd": "http://www.w3.org/2001/XMLSchema#",
    "owl": "http://www.w3.org/2002/07/owl#",
    "comment": "rdfs:comment",
    "isa": {
      "@id":"rdfs:subClassOf",
      "@type":"@id"
    },
    "Property": "rdfs:Property",
    "Relation": "owl:ObjectProperty",
    "Attribute": "owl:DatatypeProperty",
    "AnnotationProperty": "owl:AnnotationProperty",
    "Transitive": "owl:TransitiveProperty",
    "Reflexive": "owl:ReflexiveProperty",
    "Irreflexive": "owl:IrreflexiveProperty",
    "Symmetric": "owl:SymmetricProperty",
    "Asymmetric": "owl:AsymmetricProperty",
    "Functional": "owl:FunctionalProperty",
    "InverseFunctional": "owl:InverseFunctionalProperty",
    "Class": "owl:Class",
    "Restriction": "owl:Restriction",
    "AllDifferent": "owl:AllDifferent",
    "Ontology": "owl:Ontology",
    "imports": {
      "@id": "owl:imports",
      "@type": "@id"
    },
    "value":"owl:hasValue",
    "distinct": {
      "@id": "owl:distinctMembers",
      "@type": "@id"
    },
    "distinct": {
      "@id": "owl:distinctMembers",
      "@type": "@id"
    },
    "definedBy": {
      "@id": "rdfs:isDefinedBy",
      "@type": "@id"
    },
    "subPropertyOf": {
      "@id": "rdfs:subPropertyOf",
      "@type": "@id"
    },
    "range": {
      "@id": "rdfs:range",
      "@type": "@id"
    },
    "domain": {
      "@id": "rdfs:domain",
      "@type": "@id"
    },
    "seeAlso": {
      "@id": "rdfs:seeAlso",
      "@type": "@id"
    },
    "label": {
      "@id": "rdfs:label"
    },
    "not" : {
      "@id":"owl:disjointWith",
      "@type":"@id"
    },
    "complement" : {
      "@id":"owl:complementOf",
      "@type":"@id"
    },
    "some" : {
      "@id":"owl:someValuesFrom",
      "@type":"@id"
    },
    "only" : {
      "@id":"owl:allValuesFrom",
      "@type":"@id"
    },
    "on" : {
      "@id":"owl:onProperty",
      "@type":"@id"
    },
    "inverse" : {
      "@id":"owl:inverseOf",
      "@type":"@id"
    },
    "equivalent" : {
      "@id":"owl:equivalentClass",
      "@type":"@id"
    },
    "and" : {
      "@id":"owl:intersectionOf",
      "@type":"@id",
      "@container":"@list"
    },
    "or" : {
      "@id":"owl:unionOf",
      "@type":"@id",
      "@container":"@list"
    },
    "key" : {
      "@id":"owl:hasKey",
      "@type":"@id",
      "@container":"@list"
    },
    "in": {
      "@id": "owl:oneOf",
      "@type": "@id",
      "@container": "@list"
    },
    "min": {
      "@id": "owl:minCardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "max": {
      "@id": "owl:maxCardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "minq": {
      "@id": "owl:minQualifiedCardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "maxq": {
      "@id": "owl:maxQualifiedCardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "exactq": {
      "@id": "owl:qualifiedCardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "exactly": {
      "@id": "owl:cardinality",
      "@type": "xsd:nonNegativeInteger"
    },
    "onClass": {
      "@id": "owl:onClass",
      "@type": "@id"
    },
    "hasSelf": {
      "@id": "owl:hasSelf",
      "@type": "xsd:boolean"
    }
  }
},
    "@graph": [{
        "@if" : "'owl:deprecated' not in row or isempty(row['owl:deprecated']) or not float(row['owl:deprecated']) < 1.2",
        "@id": "{{row['hasURI']}}",
        "@type": [
          { "@if" : "not isempty(row['rdfs:subClassOf'])", "@id" : "owl:Class"},
          {
            "@if" : "'rdf:type' in row and row['rdf:type'] is not None and len(row['rdf:type'].strip()) > 0",
            "@for" : "t in re.split('\\\\s*[,&]\\\\s*', row['rdf:type'])",
            "@do" : "{{t}}"
          }
        ],
        "owl:deprecated": {
          "@if" : "not isempty(row['owl:deprecated']) and not float(row['owl:deprecated']) > 1.2",
          "@value" : true
        },
        "rdfs:label": {
          "@if" : "'rdfs:label' in row and row['rdfs:label'] is not None and len(row['rdfs:label'].strip()) > 0",
          "@value" : "{{row['rdfs:label']}}"
        },
        "dc:identifier": {
          "@if" : "'dcterms:identifier' in row and row['dcterms:identifier'] is not None and len(row['dcterms:identifier'].strip()) > 0",
          "@value" : "{{row['dcterms:identifier'].strip()}}"
        },
        "skos:editorialNote": {
          "@if" : "'skos:editorialNote' in row and row['skos:editorialNote'] is not None and len(row['skos:editorialNote'].strip()) > 0",
          "@value" : "{{row['skos:editorialNote']}}"
        },
        "skos:editorialNote": {
          "@if" : "'skos:editorialNote' in row and row['skos:editorialNote'] is not None and len(row['skos:editorialNote'].strip()) > 0",
          "@value" : "{{row['skos:editorialNote']}}"
        },
        "skos:definition": [
          {
            "@if" : "'rdfs:comment' in row and row['rdfs:comment'] is not None and len(row['rdfs:comment'].strip()) > 0",
            "@value" : "{{row['rdfs:comment']}}"
          },
          {
            "@if" : "'skos:definition' in row and row['skos:definition'] is not None and len(row['skos:definition'].strip()) > 0",
            "@value" : "{{row['skos:definition']}}"
          }
        ],
        "hasco:wasApprovedBy": [
          {
            "@if" : "'hasco:approvedBy' in row and row['hasco:approvedBy'] is not None and len(row['hasco:approvedBy'].strip()) > 0",
            "@value" : "{{row['hasco:approvedBy']}}"
          }
        ],
        "vivo:abbreviation": [
          {
            "@if" : "'vivo:abbreviation' in row and row['vivo:abbreviation'] is not None and len(row['vivo:abbreviation'].strip()) > 0",
            "@value" : "{{row['vivo:abbreviation']}}"
          }
        ],
        "skos:notation": [
          {
            "@if" : "'skos:notation' in row and row['skos:notation'] is not None and len(row['skos:notation'].strip()) > 0",
            "@value" : "{{row['skos:notation']}}"
          }
        ],
        "rdfs:subClassOf": [
          { "@if" : "'hasneto:hasUnit' in row and not isempty(row['hasneto:hasUnit'])",
            "@type" : "owl:Restriction",
            "owl:onProperty" : { "@id":"sio:hasUnit"},
            "owl:hasValue" : { "@id": "{{row['hasneto:hasUnit']}}" }
          },
          { "@if" : "'prov:wasGeneratedBy' in row and not isempty(row['prov:wasGeneratedBy'])",
            "@for" : "s in re.split('\\\\s*[,&]\\\\s*', row['prov:wasGeneratedBy'])",
            "@do" : {
              "@type" : "owl:Restriction",
              "owl:onProperty" : { "@id":"prov:wasDerivedFrom"},
              "owl:allValuesFrom" : { "@id": "{{s}}" }
            }
          },
          { "@if" : "'sio:isAttributeOf' in row and not isempty(row['sio:isAttributeOf'])",
            "@for" : "s in re.split('\\\\s*[,&]\\\\s*', row['sio:isAttributeOf'])",
            "@do" : { "@type" : "Restriction", "owl:onProperty" : "sio:isAttributeOf", "only" : "{{s}}" }
          },
          {
            "@if" : "'sio:hasUnit' in row and not isempty(row['sio:hasUnit'])",
            "@type" : "owl:Restriction", "owl:onProperty" : "sio:hasUnit", "value" : { "@id": "{{row['sio:hasUnit']}}" }
          },
          { "@if" : "'start' in row and not isempty(row.start)",
            "@type" : "Restriction", "owl:onProperty" : "sio:hasStartTime",
            "only" : {
              "@type" : "Class", "and" : [
                { "@id": "{{row['sio:hasUnit']}}" },
                { "@type" : "Restriction", "owl:onProperty" : "sio:hasValue", "value" : {"@value" : "{{r.start}}", "@type" : "xsd:integer"} }
              ]}
          },
          { "@if" : "'end' in row and not isempty(row.end)",
            "@type" : "Restriction", "on" : "sio:hasEndTime",
            "only" : {
              "@type" : "Class", "and" : [
                { "@id": "{{row['sio:hasUnit']}}" },
                { "@type" : "Restriction", "on" : "sio:hasValue", "value" : {"@value" : "{{r.end}}", "@type" : "xsd:integer"} }
              ]}
          },
          {
            "@if" : "'sio:inRelationTo' in row and not isempty(row['sio:inRelationTo'])",
            "@type" : "owl:Restriction", "on" : "sio:inRelationTo", "only" : {
              "@type" : "Class", "and" : [
                { "@id": "{{row['sio:inRelationTo']}}" },
                {
                  "@if" : "'sio:inRelationTo o sio:hasRole' in row and not isempty(row['sio:inRelationTo o sio:hasRole'])",
                  "@type" : "Restriction", "on" : "sio:hasRole", "only" : {"@id" : "{{row['sio:inRelationTo o sio:hasRole']}}"}
                }
              ]
            }
          },
          {
            "@if" : "'sio:isRoleOf o sio:hasAttribute' in row and not isempty(row['sio:isRoleOf o sio:hasAttribute'])",
            "@type" : "owl:Restriction", "on" : "sio:isRoleOf",
            "only" : {
              "@type" : "Restriction", "on" : "sio:hasAttribute", "some" : {"@id" : "{{row['sio:isRoleOf o sio:hasAttribute']}}"}
            }
          },
          {
            "@if" : "'rdfs:subClassOf' in row and row['rdfs:subClassOf'] is not None and len(row['rdfs:subClassOf'].strip()) > 0",
            "@for" : "s in re.split('\\\\s*[,&]\\\\s*', row['rdfs:subClassOf'])",
            "@do" : { "@id": "{{s}}", "@type": "owl:Class"}
          }
        ]
      }
    ]
  }
]''']
.


<chear.ttl> a pv:File;
    dcterms:format "text/turtle";
    setl:hasContext '''{
  "owl": "http://www.w3.org/2002/07/owl#",
  "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
  "sio" :     "http://semanticscience.org/resource/",
  "chear" :   "http://hadatac.org/ont/chear#",
  "skos" :    "http://www.w3.org/2004/02/skos/core#",
  "prov" :    "http://www.w3.org/ns/prov#",
  "obo" :   "http://purl.obolibrary.org/obo/",
  "pubchem" : "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/",
  "dc"   :    "http://purl.org/dc/terms/",
  "hasco" : "http://hadatac.org/ont/hasco#",
  "vstoi" : "http://hadatac.org/ont/vstoi#"
}''';
    prov:wasGeneratedBy [
      a setl:Load;
      prov:used <http://hadatac.org/ont/chear> ;
    ].
    
<chear.owl> a pv:File;
    setl:hasContext '''{
  "owl": "http://www.w3.org/2002/07/owl#",
  "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
  "sio" :     "http://semanticscience.org/resource/",
  "chear" :   "http://hadatac.org/ont/chear#",
  "skos" :    "http://www.w3.org/2004/02/skos/core#",
  "prov" :    "http://www.w3.org/ns/prov#",
  "obo" :   "http://purl.obolibrary.org/obo/",
  "pubchem" : "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/",
  "dc"   :    "http://purl.org/dc/terms/",
  "hasco" : "http://hadatac.org/ont/hasco#",
  "vstoi" : "http://hadatac.org/ont/vstoi#"
}''';
    dcterms:format "application/rdf+xml";
    prov:wasGeneratedBy [
      a setl:Load;
      prov:used <http://hadatac.org/ont/chear> ;
    ].

<chear.json> a pv:File;
    setl:hasContext '''{
  "owl": "http://www.w3.org/2002/07/owl#",
  "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
  "sio" :     "http://semanticscience.org/resource/",
  "chear" :   "http://hadatac.org/ont/chear#",
  "skos" :    "http://www.w3.org/2004/02/skos/core#",
  "prov" :    "http://www.w3.org/ns/prov#",
  "obo" :   "http://purl.obolibrary.org/obo/",
  "pubchem" : "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/",
  "dc"   :    "http://purl.org/dc/terms/",
  "hasco" : "http://hadatac.org/ont/hasco#",
  "vstoi" : "http://hadatac.org/ont/vstoi#"
}''';
    dcterms:format "application/json";
    prov:wasGeneratedBy [
      a setl:Load;
      prov:used <http://hadatac.org/ont/chear> ;
    ].