Name	Name	Last commit message	Last commit date
parent directory ..
readme.md	readme.md

SPARQL Queries

Fetch all the data based on category, i.e., AmplifiedCdna

PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT (?s as ?ID) (?p as ?Property) (?o as ?Data)  
WHERE {
  ?s ?p ?o.
  { 
    SELECT ?entity 
    WHERE { ?entity biolink:category bican:AmplifiedCdna. }
  } FILTER (?s = ?entity)
}
GROUP BY ?s ?p ?o

Get property count based on category

PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT (?s as ?ID) (COUNT(?p) as ?PropertyCount)
WHERE {
  ?s ?p ?o.
  { 
    SELECT ?entity 
    WHERE { ?entity biolink:category bican:AmplifiedCdna. }
  } FILTER (?s = ?entity)
}
GROUP BY ?s

Select distinct classes properties filtered based on regex expressions.

SELECT DISTINCT ?s WHERE {
  ?s ?p ?o .
  FILTER regex(STR(?s), "bican|prov|biolink")
}

Get data filtered by NIMP ID.

PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX NIMP: <http://example.org/NIMP/>
select *  where {
    ?s ?p ?o.
   FILTER (?s = NIMP:LI-DDFMNG372245)
}

Get data where either subject, predicate or object match to BC-ABUEKB857169.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
SELECT ?subject ?predicate ?object
WHERE {
  { BIND(<http://example.org/NIMP/BC-ABUEKB857169> AS ?id)
    ?subject ?predicate ?id . }
  UNION
  { BIND(<http://example.org/NIMP/BC-ABUEKB857169> AS ?id)
    ?id ?predicate ?object . }
  UNION
  { BIND(<http://example.org/NIMP/BC-ABUEKB857169> AS ?id)
    ?subject ?id ?object . }
}

SPARQL query to get data of LibraryPool category

PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/> 
PREFIX biolink: <https://w3id.org/biolink/vocab/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 

SELECT ?id ?label ?local_tube_id
WHERE {
  ?id ?p ?o.
  { 
    SELECT DISTINCT ?entity ?label ?local_tube_id
    WHERE { ?entity biolink:category bican:LibraryPool. 			
            ?entity rdfs:label ?label.
            ?entity bican:local_tube_id ?local_tube_id
        }
  } FILTER (?id = ?entity)
}

Tissue Sample

PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/> 
PREFIX biolink: <https://w3id.org/biolink/vocab/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 

SELECT ?id ?label ?structure
WHERE {
  ?id ?p ?o.
  { 
    SELECT DISTINCT ?entity ?label ?structure
    WHERE { ?entity biolink:category bican:TissueSample.  
            ?entity rdfs:label ?label.
            ?entity bican:structure ?structure.
        }
  } FILTER (?id = ?entity)
}

GET doner and tissue sample as well as the intermediate hops count

PREFIX BICAN: <https://identifiers.org/brain-bican/vocab/>
PREFIX biolink: <https://w3id.org/biolink/vocab/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

SELECT ?entity ?target ?targetType ?intermediate ?hopCount
WHERE {
  {
    SELECT ?entity ?target ?targetType (COUNT(?mid) AS ?hopCount)
    WHERE {
      ?entity biolink:category BICAN:DissociatedCellSample.
      ?entity (prov:wasDerivedFrom)* ?mid.
      ?mid prov:wasDerivedFrom ?target.
      ?target biolink:category ?targetType.
      FILTER(?targetType IN (bican:Donor, bican:TissueSample))
    }
    GROUP BY ?entity ?target ?targetType
  }

  ?entity biolink:category BICAN:DissociatedCellSample.
  ?entity (prov:wasDerivedFrom)* ?intermediate.
  ?intermediate (prov:wasDerivedFrom)+ ?target.
  ?target biolink:category ?targetType.
  FILTER(?targetType IN (bican:Donor, bican:TissueSample))
}
ORDER BY ?entity ?hopCount

GET doner and tissue sample as well as species value from doner and structure from tissue sample to link to GARS and ANSRS

  PREFIX BICAN: <https://identifiers.org/brain-bican/vocab/>
  PREFIX biolink: <https://w3id.org/biolink/vocab/> 
  PREFIX prov: <http://www.w3.org/ns/prov#> 
  PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
  
  SELECT ?entity ?target ?targetType ?intermediate ?species_value_for_taxon_match ?structure_value_for_tissue_sample
  WHERE {
    {
      SELECT ?entity ?target ?targetType (COUNT(?mid) AS ?hopCount)
      WHERE {
        ?entity biolink:category BICAN:DissociatedCellSample.
        ?entity (prov:wasDerivedFrom)* ?mid.
        ?mid prov:wasDerivedFrom ?target.
        ?target biolink:category ?targetType.
        FILTER(?targetType IN (bican:Donor, bican:TissueSample))
      }
      GROUP BY ?entity ?target ?targetType
    }
  
    ?entity biolink:category BICAN:DissociatedCellSample.
    ?entity (prov:wasDerivedFrom)* ?intermediate.
    ?intermediate (prov:wasDerivedFrom)+ ?target.
    ?target biolink:category ?targetType.
    FILTER(?targetType IN (bican:Donor, bican:TissueSample))
  
    OPTIONAL {
      ?target bican:species ?species_value_for_taxon_match.
      FILTER(?targetType = bican:Donor)
    }
  
    OPTIONAL {
      ?target bican:structure ?structure_value_for_tissue_sample.
      FILTER(?targetType = bican:TissueSample)
    }
  }
  ORDER BY ?entity ?hopCount

Get GARS detail
Use ?species_value_for_taxon_match

PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

SELECT *
WHERE { 
    ?gar_id biolink:in_taxon ?gar_obj.
  	?gar_obj biolink:iri ?biriiri.
  	FILTER(CONTAINS(STR(?biriiri), "NCBITaxon_9544"))
}

Filter by NIMP ID + Category

PREFIX biolink: <https://w3id.org/biolink/vocab/>
  PREFIX prov: <http://www.w3.org/ns/prov#>
  PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

  PREFIX NIMP: <http://example.org/NIMP/>
SELECT DISTINCT ?entity (?targetType AS ?targets) ?species_value_for_taxon_match ?structure_value_for_tissue_sample
  WHERE {
    {
      SELECT ?entity ?target ?targetType (COUNT(?mid) AS ?hopCount)
      WHERE {
        ?entity biolink:category <https://identifiers.org/brain-bican/vocab/LibraryPool>.
        ?entity (prov:wasDerivedFrom)+ ?mid.
        ?mid prov:wasDerivedFrom ?target.
        ?target biolink:category ?targetType.
        FILTER(?targetType IN (bican:Donor, bican:TissueSample)) 
      }
      GROUP BY ?entity ?target ?targetType
    }
    ?entity biolink:category <https://identifiers.org/brain-bican/vocab/LibraryPool>.
    ?entity (prov:wasDerivedFrom)+ ?intermediate.
    ?intermediate (prov:wasDerivedFrom)+ ?target.
    ?target biolink:category ?targetType.
    FILTER(?targetType IN (bican:Donor, bican:TissueSample))  

    OPTIONAL {
      ?target bican:species ?species_value_for_taxon_match.
      FILTER(?targetType = bican:Donor)
    }
    OPTIONAL {
      ?target bican:structure ?structure_value_for_tissue_sample.
    }
    
             FILTER(?entity = <http://example.org/NIMP/LP-BIDMJM675091>) 
  }
  ORDER BY ?entity ?hopCount

Filter by ID

PREFIX biolink: <https://w3id.org/biolink/vocab/>
  PREFIX prov: <http://www.w3.org/ns/prov#>
  PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

  PREFIX NIMP: <http://example.org/NIMP/>
SELECT DISTINCT ?entity (?targetType AS ?targets) ?hopCount ?species_value_for_taxon_match ?structure_value_for_tissue_sample
  WHERE {
    {
      SELECT ?entity ?target ?targetType (COUNT(?mid) AS ?hopCount)
      WHERE { 
        ?entity (prov:wasDerivedFrom)+ ?mid.
        ?mid prov:wasDerivedFrom ?target.
        ?target biolink:category ?targetType.
        FILTER(?targetType IN (bican:Donor, bican:TissueSample)) 
      }
      GROUP BY ?entity ?target ?targetType
    } 
    ?entity (prov:wasDerivedFrom)+ ?intermediate.
    ?intermediate (prov:wasDerivedFrom)+ ?target.
    ?target biolink:category ?targetType.
    FILTER(?targetType IN (bican:Donor, bican:TissueSample))  

    OPTIONAL {
      ?target bican:species ?species_value_for_taxon_match.
      FILTER(?targetType = bican:Donor)
    }
    OPTIONAL {
      ?target bican:structure ?structure_value_for_tissue_sample.
    }
    
             FILTER(?entity = <http://example.org/NIMP/LP-BIDMJM675091>) 
  }

Simplified version, when hopcount is not used and result returend as list

PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>

SELECT DISTINCT ?entity (GROUP_CONCAT(DISTINCT ?targetType; separator=", ") AS ?tissuedonertype) (GROUP_CONCAT(DISTINCT ?species_value_for_taxon_match; separator=", ") AS ?species_value_match_in_gars) (GROUP_CONCAT(DISTINCT ?structure_value_for_tissue_sample; separator=", ") AS ?structure_value_match_in_ansrs)
WHERE {
  ?entity biolink:category <https://identifiers.org/brain-bican/vocab/LibraryPool>.
  ?entity (prov:wasDerivedFrom)+ ?intermediate.
  ?intermediate (prov:wasDerivedFrom)+ ?target.
  ?target biolink:category ?targetType.
  FILTER(?targetType IN (bican:Donor, bican:TissueSample))  

  OPTIONAL {
    ?target bican:species ?species_value_for_taxon_match.
    FILTER(?targetType = bican:Donor)
  }
  OPTIONAL {
    ?target bican:structure ?structure_value_for_tissue_sample.
  }
  
  FILTER(?entity = <http://example.org/NIMP/LP-BIDMJM675091>) 
}
GROUP BY ?entity
ORDER BY ?entity

Retrieve result as list

PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>

SELECT DISTINCT ?entity (GROUP_CONCAT(DISTINCT ?targetType; separator=", ") AS ?tissuedonertype) (GROUP_CONCAT(DISTINCT ?species_value_for_taxon_match; separator=", ") AS ?species_value_match_in_gars) (GROUP_CONCAT(DISTINCT ?structure_value_for_tissue_sample; separator=", ") AS ?structure_value_match_in_ansrs)
WHERE {
  ?entity biolink:category <https://identifiers.org/brain-bican/vocab/LibraryPool>.
  ?entity (prov:wasDerivedFrom)+ ?intermediate.
  ?intermediate (prov:wasDerivedFrom)+ ?target.
  ?target biolink:category ?targetType.
  FILTER(?targetType IN (bican:Donor, bican:TissueSample))  

  OPTIONAL {
    ?target bican:species ?species_value_for_taxon_match.
    FILTER(?targetType = bican:Donor)
  }
  OPTIONAL {
    ?target bican:structure ?structure_value_for_tissue_sample.
  }
  
  FILTER(?entity = <http://example.org/NIMP/LP-BIDMJM675091>) 
}
GROUP BY ?entity

Connect to GARS, i.e., NIMP-->GARS

PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

SELECT DISTINCT (?gar_obj as ?gars_id) ?sp ?po ?oo
WHERE { 
    {
        SELECT ?gar_obj WHERE {
            ?gar_id biolink:in_taxon ?gar_obj.
            ?gar_obj biolink:iri ?biriiri.
            FILTER(CONTAINS(STR(?biriiri), "NCBITaxon_9544"))
        }
    }
    OPTIONAL {
        ?gar_obj ?sp ?oo .
    }
}

as list

PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX NIMP: <http://example.org/NIMP/>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>

SELECT DISTINCT (?gar_obj as ?gars_id) (GROUP_CONCAT(DISTINCT ?sp; separator=", ") AS ?property) (GROUP_CONCAT(DISTINCT ?oo; separator=", ") AS ?object)     
WHERE { 
    {
        SELECT ?gar_obj WHERE {
            ?gar_id biolink:in_taxon ?gar_obj.
            ?gar_obj biolink:iri ?biriiri.
            FILTER(CONTAINS(STR(?biriiri), "NCBITaxon_9544"))
        }
    }
    OPTIONAL {
        ?gar_obj ?sp ?oo .
    }
} GROUP BY ?gar_obj

NIMP-->ANSRS
Group results by ID, i.e., subject

PREFIX ansrs: <https://w3id.org/my-org/ansrs-schema/>
PREFIX biolink: <https://w3id.org/biolink/vocab/>
SELECT DISTINCT ?s (GROUP_CONCAT(DISTINCT ?property; separator=", ") AS ?property) (GROUP_CONCAT(DISTINCT ?object; separator=", ") AS ?object) 
WHERE { 
    {
        SELECT ?s ?o WHERE {
           ?s ansrs:has_parent_parcellation_term ?o.  
    		FILTER(CONTAINS(STR(?o), "MBA:1065"))
        }
    }
    OPTIONAL {
        ?s ?property ?object .
    }
} GROUP BY ?s

Fetch all results

PREFIX ansrs: <https://w3id.org/my-org/ansrs-schema/>
PREFIX biolink: <https://w3id.org/biolink/vocab/>
SELECT DISTINCT *
WHERE { 
    {
        SELECT ?s ?o WHERE {
           ?s ansrs:has_parent_parcellation_term ?o.  
    		FILTER(CONTAINS(STR(?o), "MBA:1065"))
        }
    }
    OPTIONAL {
        ?s ?property ?object .
    }
}

GET Doner by ID as list

select ?doner_id (GROUP_CONCAT (DISTINCT ?p; separator=", ") as ?property) (GROUP_CONCAT (DISTINCT ?o; separator=", ") as ?object) where {
    ?doner_id ?p ?o .
    FILTER(?doner_id = <http://example.org/NIMP/DO-CYPH5324>)
} GROUP BY ?doner_id

Tissue sample

select ?tissue_id (GROUP_CONCAT (DISTINCT ?p; separator=", ") as ?property) (GROUP_CONCAT (DISTINCT ?o; separator=", ") as ?object) where {
    ?tissue_id ?p ?o .
    FILTER(?tissue_id = <http://example.org/NIMP/TI-NMAZ561755>)
} GROUP BY ?tissue_id

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

sparql_queries

sparql_queries

readme.md

SPARQL Queries

Fetch all the data based on category, i.e., AmplifiedCdna

Get property count based on category

Select distinct classes properties filtered based on regex expressions.

Get data filtered by NIMP ID.

Get data where either subject, predicate or object match to BC-ABUEKB857169.

SPARQL query to get data of LibraryPool category

Tissue Sample

GET doner and tissue sample as well as the intermediate hops count

GET doner and tissue sample as well as species value from doner and structure from tissue sample to link to GARS and ANSRS

Get GARS detail

Filter by NIMP ID + Category

Filter by ID

Simplified version, when hopcount is not used and result returend as list

Retrieve result as list

Connect to GARS, i.e., NIMP-->GARS

NIMP-->ANSRS

GET Doner by ID as list

Files

sparql_queries

Directory actions

More options

Directory actions

More options

Latest commit

History

sparql_queries

Folders and files

parent directory

readme.md

SPARQL Queries

Fetch all the data based on category, i.e., AmplifiedCdna

Get property count based on category

Select distinct classes properties filtered based on regex expressions.

Get data filtered by NIMP ID.

Get data where either subject, predicate or object match to BC-ABUEKB857169.

SPARQL query to get data of LibraryPool category

Tissue Sample

GET doner and tissue sample as well as the intermediate hops count

GET doner and tissue sample as well as species value from doner and structure from tissue sample to link to GARS and ANSRS

Get GARS detail

Filter by NIMP ID + Category

Filter by ID

Simplified version, when hopcount is not used and result returend as list

Retrieve result as list

Connect to GARS, i.e., NIMP-->GARS

NIMP-->ANSRS

GET Doner by ID as list