@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix biolink: <https://w3id.org/biolink/vocab/> .
@prefix this: <http://purl.org/np/RAAdEyxoy0xW37qmApBFwIdMX1a3qDJOigUSluB1DgF4c> .
@prefix sub: <http://purl.org/np/RAAdEyxoy0xW37qmApBFwIdMX1a3qDJOigUSluB1DgF4c#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix orcid: <https://orcid.org/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .

sub:Head {
  this: np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo;
    a np:Nanopublication .
}

sub:assertion {
  sub:assertion a nt:AssertionTemplate;
    rdfs:label "Defining a biomedical association with its context";
    nt:hasStatement sub:st00, sub:st01, sub:st02, sub:st03, sub:st04, sub:st05, sub:st06,
      sub:st07, sub:st08, sub:st09, sub:st10, sub:st11, sub:st12, sub:st13, sub:st14, sub:st15,
      sub:st16 .
  
  sub:association a nt:LocalResource;
    rdfs:label "This association" .
  
  sub:associationPredicate a nt:GuidedChoicePlaceholder;
    rdfs:label "search for the association predicate in the BioLink model";
    nt:possibleValue biolink:affects, biolink:correlated_with, biolink:interacts_with,
      biolink:treated_by, biolink:treats;
    nt:possibleValuesFromApi "http://data.bioontology.org/search?pagesize=20&apikey=fd451bec-eacd-4519-b972-90fb6c7007cb&ontologies=BLM&include_properties=true&q=" .
  
  sub:associationRelation a nt:GuidedChoicePlaceholder;
    rdfs:label "provide the relation between the 2 concepts of the association";
    nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols/api/select?q=" .
  
  sub:associationType a nt:GuidedChoicePlaceholder;
    rdfs:label "provide the association class from the BioLink model";
    nt:possibleValue biolink:Association, biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation,
      biolink:ChemicalToGeneAssociation, biolink:ChemicalToPathwayAssociation, biolink:GeneToDiseaseAssociation,
      biolink:PairwiseGeneToGeneInteraction;
    nt:possibleValuesFromApi "http://data.bioontology.org/search?pagesize=20&apikey=fd451bec-eacd-4519-b972-90fb6c7007cb&ontologies=BLM&include_properties=true&q=" .
  
  sub:hasDrug1 a nt:GuidedChoicePlaceholder;
    rdfs:label "provide the drugs used by this target group";
    nt:possibleValue sub:object, sub:subject;
    nt:possibleValuesFromApi "https://name-resolution-sri.renci.org/lookup?limit=10&string=" .
  
  sub:hasDrug2 a nt:GuidedChoicePlaceholder;
    rdfs:label "provide the drugs used by this target group";
    nt:possibleValuesFromApi "https://name-resolution-sri.renci.org/lookup?limit=10&string=" .
  
  sub:hasPhenotype a nt:GuidedChoicePlaceholder;
    rdfs:label "provide a URI for the specific phenotype of the target group";
    nt:possibleValuesFromApi "https://name-resolution-sri.renci.org/lookup?limit=10&string=" .
  
  sub:lifeStage a nt:LocalResource;
    rdfs:label "The target group life stage" .
  
  sub:lifeStageName a nt:LiteralPlaceholder;
    rdfs:label "describe the life stage or age of the target group" .
  
  sub:lifeStageType a nt:GuidedChoicePlaceholder;
    rdfs:label "provide the life stage of the target group class";
    nt:possibleValue biolink:LifeStage;
    nt:possibleValuesFromApi "http://data.bioontology.org/search?pagesize=20&apikey=fd451bec-eacd-4519-b972-90fb6c7007cb&ontologies=BLM&include_properties=true&q=" .
  
  sub:negated a nt:RestrictedChoicePlaceholder;
    nt:possibleValue xsd:false, xsd:true .
  
  sub:object a nt:GuidedChoicePlaceholder;
    rdfs:label "target biomedical entity";
    nt:possibleValuesFromApi "https://name-resolution-sri.renci.org/lookup?limit=10&string=" .
  
  sub:objectType a nt:GuidedChoicePlaceholder;
    rdfs:label "search for the object class in the BioLink model";
    nt:possibleValue biolink:ChemicalSubstance, biolink:Disease, biolink:Drug, biolink:Gene,
      biolink:PhenotypicFeature, biolink:Protein;
    nt:possibleValuesFromApi "http://data.bioontology.org/search?pagesize=20&apikey=fd451bec-eacd-4519-b972-90fb6c7007cb&ontologies=BLM&include_properties=true&q=" .
  
  sub:providedBy a nt:LiteralPlaceholder;
    rdfs:label "add the URI of the dataset or agent providing the associations" .
  
  sub:publication a nt:UriPlaceholder;
    rdfs:label "add the URI of a publication supporting this association (doi, PubMed, article URL, etc)" .
  
  sub:readableassertion a nt:LiteralPlaceholder;
    rdfs:label "describe the assertion concisely (e.g. tylenol treats pain in adults patients)" .
  
  sub:st00 rdf:object sub:readableassertion;
    rdf:predicate rdfs:label;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "1"^^xsd:integer .
  
  sub:st01 rdf:object sub:subject;
    rdf:predicate rdf:subject;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "2"^^xsd:integer .
  
  sub:st02 rdf:object sub:subjectType;
    rdf:predicate biolink:category;
    rdf:subject sub:subject;
    a rdf:Statement;
    nt:statementOrder "2"^^xsd:integer .
  
  sub:st03 rdf:object sub:object;
    rdf:predicate rdf:object;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "4"^^xsd:integer .
  
  sub:st04 rdf:object sub:objectType;
    rdf:predicate biolink:category;
    rdf:subject sub:object;
    a rdf:Statement;
    nt:statementOrder "2"^^xsd:integer .
  
  sub:st05 rdf:object sub:associationType;
    rdf:predicate biolink:association_type;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "0"^^xsd:integer .
  
  sub:st06 rdf:object sub:associationRelation;
    rdf:predicate biolink:relation;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "1"^^xsd:integer .
  
  sub:st07 rdf:object sub:associationPredicate;
    rdf:predicate rdf:predicate;
    rdf:subject sub:association;
    a rdf:Statement;
    nt:statementOrder "1"^^xsd:integer .
  
  sub:st08 rdf:object sub:negated;
    rdf:predicate biolink:negated;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "6"^^xsd:integer .
  
  sub:st09 rdf:object sub:providedBy;
    rdf:predicate biolink:provided_by;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "7"^^xsd:integer .
  
  sub:st10 rdf:object sub:publication;
    rdf:predicate biolink:publications;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "8"^^xsd:integer .
  
  sub:st11 rdf:object sub:lifeStage;
    rdf:predicate biolink:stage_qualifier;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "13"^^xsd:integer .
  
  sub:st12 rdf:object sub:lifeStageType;
    rdf:predicate rdf:type;
    rdf:subject sub:lifeStage;
    a nt:OptionalStatement;
    nt:statementOrder "13"^^xsd:integer .
  
  sub:st13 rdf:object sub:lifeStageName;
    rdf:predicate rdfs:label;
    rdf:subject sub:lifeStage;
    a nt:OptionalStatement;
    nt:statementOrder "13"^^xsd:integer .
  
  sub:st14 rdf:object sub:hasPhenotype;
    rdf:predicate biolink:has_phenotype;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "12"^^xsd:integer .
  
  sub:st15 rdf:object sub:hasDrug1;
    rdf:predicate biolink:has_drug;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "15"^^xsd:integer .
  
  sub:st16 rdf:object sub:hasDrug2;
    rdf:predicate biolink:has_drug;
    rdf:subject sub:association;
    a nt:OptionalStatement;
    nt:statementOrder "16"^^xsd:integer .
  
  sub:subject a nt:GuidedChoicePlaceholder;
    rdfs:label "source biomedical entity";
    nt:possibleValuesFromApi "https://name-resolution-sri.renci.org/lookup?limit=10&string=" .
  
  sub:subjectType a nt:GuidedChoicePlaceholder;
    rdfs:label "search for the subject class in the BioLink model";
    nt:possibleValue biolink:ChemicalSubstance, biolink:Disease, biolink:Drug, biolink:Gene,
      biolink:PhenotypicFeature, biolink:Protein;
    nt:possibleValuesFromApi "http://data.bioontology.org/search?pagesize=20&apikey=fd451bec-eacd-4519-b972-90fb6c7007cb&ontologies=BLM&include_properties=true&q=" .
  
  rdf:object rdfs:label "has object" .
  
  rdf:predicate rdfs:label "has predicate" .
  
  rdf:subject rdfs:label "has subject" .
  
  rdf:type rdfs:label "has type" .
  
  rdfs:label rdfs:label "has label" .
  
  xsd:false rdfs:label "false" .
  
  xsd:true rdfs:label "true" .
  
  biolink:association_type rdfs:label "has type" .
  
  biolink:category rdfs:label "is a" .
  
  biolink:description rdfs:label "is described by" .
  
  biolink:has_drug rdfs:label "uses drug" .
  
  biolink:has_phenotype rdfs:label "has phenotype" .
  
  biolink:id rdfs:label "has id" .
  
  biolink:negated rdfs:label "is negated" .
  
  biolink:provided_by rdfs:label "is provided by" .
  
  biolink:publications rdfs:label "has publications" .
  
  biolink:qualifiers rdfs:label "is qualified by" .
  
  biolink:relation rdfs:label "has relation" .
  
  biolink:stage_qualifier rdfs:label "is qualified by life stage" .
}

sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0003-4727-9435 .
}

sub:pubinfo {
  npx:supersedes <http://purl.org/np/RAapknSKaEkcpmLmq5NTRC2L62IEox6U3O_aQVoHXdkLk>
      ""^^xsd:integer .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCR9fz0fKCdWOWC+pxhkQhEM/ppbdIYe5TLSdj+lJzSlv9mYBaPgrzVezSwwbmhlHBPDZa4/vHycU315BdmUGq+pXllp9+rWFfrb+kBJwhZjpG6BeyyXBsRFz4jmQVxl/ZYHilQTh/XalYzKkEAyTiEMPee4Kz61PaWOKH24CsnOQIDAQAB";
    npx:hasSignature "elRyYnLLUPMAtzUR0VJg2cNGEzQdGyOxCXWnR3S+gOl1SP1zyBb65zbeCWNbErz6ZhVexvDOZCKCqAWbYNchY6soyT+C6r3lKsrbYnenLJuqq8lTKBlZX493amka5Jt3QRJmVM1JoDMkU3cYh0wXT9JqiTQQyPHMlhgKu8bsJJ4=";
    npx:hasSignatureTarget this: .
  
  this: dcterms:created "2020-11-19T10:00:00+01:00"^^xsd:dateTime;
    dcterms:creator orcid:0000-0003-4727-9435 .
}