take a elton nanopub and translate into web annotation format

[jhpoelen]

In order to connect datasets with their associated interaction claims, we'd like to use elton nanopubs as a started point to create a dervied web annotation snippet.

The goal is to identify additional information needed in the nanopubs to make a workable web annotation for a the first record of the Carvalheiro 2023 dataset.

[jhpoelen]

@prefix this: <http://purl.org/np/RAq94DFJ6rV5_dI7lpJdAb5RJJOdMUkXBEQ8Wh54g7BDI> .
@prefix sub: <http://purl.org/np/RAq94DFJ6rV5_dI7lpJdAb5RJJOdMUkXBEQ8Wh54g7BDI#> . 
@prefix np: <http://www.nanopub.org/nschema#> . 
@prefix dcterms: <http://purl.org/dc/terms/> . 
@prefix prov: <http://www.w3.org/ns/prov#> . 
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> . 
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . 
@prefix obo: <http://purl.obolibrary.org/obo/> .  
sub:Head {   
  this: np:hasAssertion sub:Assertion;     
  np:hasProvenance sub:Provenance;   
  np:hasPublicationInfo sub:Pubinfo;     
  a np:Nanopublication . 
}  
sub:Assertion {
   sub:Interaction obo:RO_0000057 sub:Organism_1, sub:Organism_2;
   a obo:GO_0044419 .
   sub:Organism_1 
        obo:RO_0002623 sub:Organism_2;
        rdfs:label "Pilosella oficinarum" .      
   sub:Organism_2 rdfs:label "Andrena" . 
}  
sub:Provenance { 
  sub:Assertion prov:wasDerivedFrom sub:Study .
  sub:Study dcterms:bibliographicCitation "https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&amp;id=1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8&amp;gid=776329546" . 
}  
sub:Pubinfo {   
  this: dcterms:license <https://creativecommons.org/licenses/by/4.0/>;     
  pav:createdBy <https://doi.org/10.5281/zenodo.998263>;     
  prov:wasDerivedFrom <https://github.com/globalbioticinteractions/carvalheiro2023> .      
  <https://github.com/globalbioticinteractions/carvalheiro2023> dcterms:bibliographicCitation       "WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro." . 
} 

please also see recent discussion around possible expressions of species interaction data in nanopub format at https://github.com/globalbioticinteractions/globalbioticinteractions/issues/923 .

[jhpoelen]

Here's another example of how species interactions can be presented in @tkuhn 's knowledgepixel and their collaborators at Pensoft - https://github.com/globalbioticinteractions/globalbioticinteractions/issues/923

@prefix this: <http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc> .
@prefix sub: <http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .

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

sub:assertion {
  sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation>;
    rdfs:comment "The association was established by the amplicon metagenomic analysis of the gut content of the beetles, which revealed DNA of the object taxon.";
    <https://w3id.org/biolink/vocab/object> sub:objtaxon;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002438>;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon .

  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/6H9MK> .

  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/3K9T3> .
}

sub:provenance {
  sub:assertion prov:wasGeneratedBy sub:research-activity .

  sub:research-activity dct:description <https://doi.org/10.3897/zookeys.1181.107496> .

  <https://doi.org/10.3897/zookeys.1181.107496> a <http://purl.org/spar/fabio/ScholarlyWork> .
}

sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCIEo4TSFAp5pUug46M+PE3k+rauSFJ/s5jLCNmNL/4XyRjVJ3D8kVq27SCmUY3dY5YvvrpYDZHafJ/cCf3wr3fVcmMTfQJnnAo5t5bPm4Uz1fXRfaoJiUKuSa1P0G2AUBmYUk9WHFDqVUurIXxfLUYKedgnU+R9hQfGbV6SRXWuwIDAQAB";
    npx:hasSignature "JpSYqlrhfbEUA0QN+F99NfbLJPKjpHw+rW2ePjz8Y6ktFVcl18Z0oryo5WL0LAAtZCrquaJcJtzDDuZgsSDbFYyUKsMJJ0kHc1DcD+PPfKi74wy5jk+hCucLW6d+A3yKOJOn2zT1qPMGN2C7Mw7KBSlKYo3KN4e3LLwxEl2HIQo=";
    npx:hasSignatureTarget this: .

  this: dct:created "2023-10-02T10:06:51.209Z"^^xsd:dateTime;
    dct:creator orcid:0000-0002-6724-6828;
    dct:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:hasNanopubType <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub>;
    npx:introduces sub:association;
    rdfs:label "Helictopleurus giganteus (Harold, 1869) (species) - trophically interacts with - Eulemur fulvus (É.Geoffroy Saint-Hilaire, 1796) (species)";
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RALfxe37qzq5rEk6tLLcsSeKtKQZ1FcoHZdf2nYVfU66w>;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM>,
      <http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90>;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0> .

  <https://www.checklistbank.org/dataset/9880/taxon/3K9T3> nt:hasLabelFromApi "Helictopleurus giganteus (Harold, 1869) (species)" .

  <https://www.checklistbank.org/dataset/9880/taxon/6H9MK> nt:hasLabelFromApi "Eulemur fulvus (É.Geoffroy Saint-Hilaire, 1796) (species)" .
}