#Retrieve cell lines with their accessions and recommended names

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT ?cell_line ?accession ?name
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?name .
}
ORDER BY ?accession
LIMIT 100

# Search cell lines by name or synonym

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?recommended_name
  ?matched_name
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?recommended_name ;
    cello:name ?matched_name .

  FILTER(
    CONTAINS(
      LCASE(STR(?matched_name)),
      LCASE("HeLa")
    )
  )
}
ORDER BY ?accession
LIMIT 100

# Retrieve human cancer cell lines

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?name
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    a cello:CancerCellLine ;
    cello:primaryAccession ?accession ;
    cello:recommendedName ?name ;
    cello:derivedFromIndividualBelongingToSpecies ?species .

  ?species
    cello:isIdentifiedByIRI
      <http://purl.obolibrary.org/obo/NCBITaxon_9606> .
}
ORDER BY ?name
LIMIT 100

# Retrieve cell lines derived from a disease or its subclasses

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>
PREFIX db:    <https://purl.expasy.org/cellosaurus/rdf/db/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?cell_line_name
  ?disease_name
  ?disease_accession
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?cell_line_name ;
    cello:derivedFromIndividualWithDisease ?disease .

  ?disease
    cello:name ?disease_name ;
    cello:isIdentifiedByXref ?disease_concept .

  ?disease_concept
    cello:more_specific_than* ?target_concept ;
    cello:accession ?disease_accession .

  ?target_concept
    cello:database db:NCIt ;
    cello:accession "C5105" .
}
ORDER BY ?cell_line_name
LIMIT 100

# Retrieve cell lines derived from a specific anatomical site

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?cell_line_name
  ?site_name
  ?site_type
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?cell_line_name ;
    cello:derivedFromSite ?site .

  ?site
    cello:name ?site_name ;
    cello:isIdentifiedByIRI
      <http://purl.obolibrary.org/obo/UBERON_0001155> .

  OPTIONAL {
    ?site cello:siteType ?site_type .
  }
}
ORDER BY ?cell_line_name
LIMIT 100

# Retrieve parent and derived cell line relationships

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?parent
  ?parent_accession
  ?parent_name
  ?child
  ?child_accession
  ?child_name
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?child
    cello:hasParentCellLine ?parent ;
    cello:primaryAccession ?child_accession ;
    cello:recommendedName ?child_name .

  ?parent
    cello:primaryAccession ?parent_accession ;
    cello:recommendedName ?parent_name .
}
ORDER BY ?parent_name ?child_name
LIMIT 100

# Retrieve cell lines with reported TP53 variants

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?cell_line_name
  ?gene_name
  ?hgvs
  ?zygosity
  ?variation_status
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?cell_line_name ;
    cello:hasSequenceVariationInfo ?variation_info .

  ?variation_info
    cello:hasTarget ?variant .

  OPTIONAL {
    ?variation_info cello:variationStatus ?variation_status .
  }

  ?variant
    a cello:GeneMutation ;
    cello:ofGene ?gene ;
    cello:hgvs ?hgvs .

  OPTIONAL {
    ?variant cello:zygosity ?zygosity .
  }

  ?gene cello:name ?gene_name .

  FILTER(STR(?gene_name) = "TP53")
}
ORDER BY ?cell_line_name ?hgvs
LIMIT 100

# Retrieve CRISPR-Cas9 knockout cell lines

PREFIX cello: <https://purl.expasy.org/cellosaurus/rdf/ontology/>

SELECT DISTINCT
  ?cell_line
  ?accession
  ?cell_line_name
  ?gene_name
FROM <http://rdfportal.org/dataset/cellosaurus>
WHERE {
  ?cell_line
    cello:primaryAccession ?accession ;
    cello:recommendedName ?cell_line_name ;
    cello:hasGeneKnockout ?knockout .

  ?knockout
    cello:hasGenomeModificationMethod cello:CrisprCas9 ;
    cello:ofGene ?gene .

  ?gene cello:name ?gene_name .
}
ORDER BY ?gene_name ?cell_line_name
LIMIT 100