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WikiPathways Federated SPARQL queries

WikiPathways Federated SPARQL queries

ChEMBL

all ChEMBL assays for pathways

PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>

SELECT ?pathway ?ensembl ?assay WHERE {
  {
    SELECT DISTINCT
      ?pathway ?ensembl
    WHERE {
      VALUES ?ensembl { <https://identifiers.org/ensembl/ENSG00000150093> }
      ?s wp:bdbEnsembl ?ensembl ;
         dcterms:isPartOf ?pathway .
    }
  }
  SERVICE <https://chemblmirror.rdf.bigcat-bioinformatics.org/sparql>  {
    OPTIONAL { ?assay a chembl:Assay ;
      chembl:hasTarget/chembl:hasTargetComponent/chembl:targetCmptXref ?ensembl . }
  }
} limit 100

Open

all molecules targeting pathways

Here a limit is used too, as well as an IRI rewrite (from HTTPS to HTTP).

PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX sio:    <http://semanticscience.org/resource/>

SELECT ?pathway ?ensembl ?molecule ?smiles WHERE {
  {
    SELECT DISTINCT
      ?pathway ?ensembl
    WHERE {
      ?s wp:bdbEnsembl ?ensembl ;
         dcterms:isPartOf ?pathway .
      ?pathway dcterms:identifier "WP15".
      
      ##The IRI for Ensembl from WikiPathways starts with https:// , where the one from ChEMBL starts with http:// , so we need to rewrite the IRI
    BIND(                      # Bind the created IRI into a new variable (called ?newIRI)
        IRI(                   # Convert the string back to an IRI
          CONCAT(              # Concatenate item 1 and 2 together as one string
               "http",        # First item to concat (more items can be added with a comma
              #Second item to concat:
               SUBSTR(         # Obtain a substring
                 STR(?ensembl), # Convert the Ensembl IRI from WikiPathways to a string,
                 6)            # removing the first 6 characters (<https)
        )) AS ?newIRI          # Name for the new variable 
    )
    }
  }
  SERVICE <https://chemblmirror.rdf.bigcat-bioinformatics.org/sparql>  {
    SELECT DISTINCT ?newIRI ?molecule ?smiles WHERE {
      ?assay a chembl:Assay ; chembl:hasTarget/chembl:hasTargetComponent/chembl:targetCmptXref ?newIRI .
      ?activity chembl:hasAssay ?assay ;
                chembl:hasMolecule ?molecule .
      OPTIONAL { ?molecule sio:SIO_000008 ?attrib . ?attrib a sio:CHEMINF_000018 ; sio:SIO_000300 ?smiles . }
    } limit 100
  }
}

Wikidata

Metabolites in Wikipedia with InChIKeys from Wikidata

The corresponding query on Wikidata is here.

PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT ?metabolite ?wikidata ?inchikey WHERE {
  {
    SELECT ?metabolite ?wikidata WHERE {
      ?metabolite a wp:Metabolite ;
        wp:bdbWikidata ?wikidata .
    } LIMIT 50
  }
  SERVICE <https://query.wikidata.org/sparql> {
    ?wikidata wdt:P235 ?inchikey .
  }
} LIMIT 50

Open

MolMeDB

Find all pathways, which link out to one compound in MolMeDB database

Find all pathways, which link out to one compound in MolMeDB database (http://identifiers.org/molmedb/MM00431) through Pubchem mapping.

SELECT DISTINCT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) WHERE
{
  SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/molmedb> {
   <http://identifiers.org/molmedb/MM00431> skos:exactMatch ?COMPOUND.
   filter (strstarts(str(?COMPOUND), 'http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID'))
  }
  
  ?gene a wp:Metabolite ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbPubChem ?COMPOUND .
  
  ?pathwayRes a wp:Pathway ;
    wp:organismName "Homo sapiens" ;
    dcterms:identifier ?wpid ;
    dc:title ?title . 
}

Find which pathways out of a subset of pathway (in the VALUES clause), link out to one compound in MolMeDB database (http://identifiers.org/molmedb/MM00431) through PubChem mapping.

SELECT DISTINCT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) WHERE {
  SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/molmedb> {
    SERVICE <https://sparql.wikipathways.org/sparql> {
      VALUES ?wpid {"WP4224" "WP4225" "WP4571"}

    ?gene a wp:Metabolite ;
      dcterms:identifier ?id ;
      dcterms:isPartOf ?pathwayRes ;
      wp:bdbPubChem ?COMPOUND .

    ?pathwayRes a wp:Pathway ;
      wp:organismName "Homo sapiens" ;
      dcterms:identifier ?wpid ;
      dc:title ?title .
    }
    
    <http://identifiers.org/molmedb/MM00431> skos:exactMatch ?COMPOUND.
  }
}

LIPID MAPS

Pathways describing the biology of oxygenated hydrocarbons (LMFA12)

PREFIX chebi: <http://purl.obolibrary.org/obo/chebi/>

SELECT ?lipid ?name ?formula ?lmid (GROUP_CONCAT(?wpid_;separator=", ") AS ?pathway)
WHERE {
  SERVICE <https://lipidmaps.org/sparql> {
    VALUES ?category { <https://www.lipidmaps.org/rdf/category/112> <https://www.lipidmaps.org/rdf/category/11200> } 
    ?lipidmaps rdfs:label ?name ;
      rdfs:subClassOf* ?category ;
      chebi:formula ?formula .
  }
  BIND (IRI(CONCAT("https://identifiers.org/lipidmaps/",
               SUBSTR(STR(?lipidmaps), 31))) AS ?lmid)
  ?lipid wp:bdbLipidMaps ?lmid ;
         dcterms:isPartOf ?pathway .
  ?pathway a wp:Pathway ; dcterms:identifier ?wpid_ .
}

Open

MetaNetX

Find WikiPathways reactions with a Rhea ID in MetaNetX

# Prefixes for the MetaNetX RDF:
PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rhea: <http://rdf.rhea-db.org/>

#Variable selection
SELECT DISTINCT (str(?title) as ?pathwayName) ?PWID ?interactionID ?reac
WHERE {
  # Pathway Model IDs of interest
  VALUES ?PWID {"WP5275"}
  
  ?pathway a wp:Pathway . #Define what a pathway is
  ?pathway dcterms:identifier ?PWID. #Obtain the ID
  ?pathway dc:title ?title . #Obtain the title
  
  ?interaction wp:bdbRhea ?interactionID . #Find interactions with a Rhea ID
  ?interaction dcterms:isPartOf ?pathway . #Only those part of PW
  
  ## The IRI for Rhea-IDs from WikiPathways starts with https://identifiers.org/rhea/, where the one
  ## from MetaNetX starts with "http://rdf.rhea-db.org/ , so we need to rewrite the IRI
    BIND(                      # Bind the created IRI into a new variable (called ?newIRI)
        IRI(                   # Convert the string back to an IRI
          CONCAT(              # Concatenate item 1 and 2 together as one string
               "http://rdf.rhea-db.org/",        # First item to concat (more items can be added with a comma
              #Second item to concat:
               SUBSTR(         # Obtain a substring
                 STR(?interactionID), # Convert the Rhea IRI from WikiPathways to a string,
                 30)            # removing the first 29 charachters
        )) AS ?newIRI          # Name for the new variable 
    )
   SERVICE <https://rdf.metanetx.org/sparql/>  {
     SELECT DISTINCT ?reac
                           WHERE{
    ?reac mnx:reacXref rhea:17658 .}
     }
  
} ORDER BY ASC(?pathway)