# Retrieve compounds reported in a given organism and their supporting references.

PREFIX lotus: <http://purl.jp/bio/lotus/ontology/>
PREFIX schema: <https://schema.org/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT
  ?organism ?compound ?compound_name ?inchikey ?reference ?doi
WHERE {
  VALUES ?scientific_name { "Annona muricata" }

  ?organism a dwc:Taxon ;
            dwc:scientificName ?scientific_name .

  ?occurrence a lotus:Occurrence ;
              lotus:organism ?organism ;
              lotus:structure ?compound ;
              dct:references ?reference .

  OPTIONAL { ?compound rdfs:label ?compound_name . }
  OPTIONAL { ?compound schema:inChIKey ?inchikey . }
  OPTIONAL { ?reference bibo:doi ?doi . }
}
ORDER BY ?compound ?reference
LIMIT 100

# Retrieve compounds classified as alkaloids by NPClassifier and reported in a given taxonomic family.

PREFIX lotus: <http://purl.jp/bio/lotus/ontology/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT
  ?compound ?compound_name ?organism ?scientific_name
WHERE {
  VALUES ?family { "Rutaceae" }

  ?organism a dwc:Taxon ;
            dwc:family ?family .

  ?occurrence a lotus:Occurrence ;
              lotus:organism ?organism ;
              lotus:structure ?compound .

  ?compound lotus:npclassifierPathway "Alkaloids" .

  OPTIONAL { ?compound rdfs:label ?compound_name . }
  OPTIONAL { ?organism dwc:scientificName ?scientific_name . }
}
ORDER BY ?compound_name ?scientific_name
LIMIT 100

# Retrieve organisms in which a compound identified by its InChIKey has been reported.

PREFIX lotus: <http://purl.jp/bio/lotus/ontology/>
PREFIX schema: <https://schema.org/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX bibo: <http://purl.org/ontology/bibo/>

SELECT DISTINCT
  ?compound ?organism ?scientific_name ?reference ?doi
WHERE {
  # Example InChIKey from the supplied RDF
  VALUES ?inchikey { "NMKSAYKQLCHXDK-UHFFFAOYSA-N" }

  ?compound a schema:MolecularEntity ;
            schema:inChIKey ?inchikey .

  ?occurrence a lotus:Occurrence ;
              lotus:structure ?compound ;
              lotus:organism ?organism ;
              dct:references ?reference .

  OPTIONAL { ?organism dwc:scientificName ?scientific_name . }
  OPTIONAL { ?reference bibo:doi ?doi . }
}
ORDER BY ?scientific_name ?reference
LIMIT 100

# Count distinct compounds, organisms, and references for each taxonomic family.

PREFIX lotus: <http://purl.jp/bio/lotus/ontology/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX dct: <http://purl.org/dc/terms/>

SELECT
  ?family
  (COUNT(DISTINCT ?compound) AS ?compound_count)
  (COUNT(DISTINCT ?organism) AS ?organism_count)
  (COUNT(DISTINCT ?reference) AS ?reference_count)
WHERE {
  ?occurrence a lotus:Occurrence ;
              lotus:structure ?compound ;
              lotus:organism ?organism ;
              dct:references ?reference .

  ?organism dwc:family ?family .
}
GROUP BY ?family
ORDER BY DESC(?compound_count) ?family
LIMIT 100

# Retrieve manually validated compound–organism occurrences and their supporting references.

PREFIX lotus: <http://purl.jp/bio/lotus/ontology/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT
  ?occurrence ?compound ?compound_name
  ?organism ?scientific_name ?reference ?doi
WHERE {
  ?occurrence a lotus:Occurrence ;
              lotus:manuallyValidated true ;
              lotus:structure ?compound ;
              lotus:organism ?organism ;
              dct:references ?reference .

  OPTIONAL { ?compound rdfs:label ?compound_name . }
  OPTIONAL { ?organism dwc:scientificName ?scientific_name . }
  OPTIONAL { ?reference bibo:doi ?doi . }
}
ORDER BY ?occurrence
LIMIT 100