PIERO stands for "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation", which allows the extraction of partial reaction characteristics (or transformations) of the enzymatic reactions.

SPARQL is a query language that enables the search of the RDF data, which is a data format to exchange machine-understandable information on the Web. See the detail to learn the overview of SPARQL in the W3C Recommendation webpage. Recent years, RDF is gathering more attention in the bioinformatics community to describe various types of data, and some SPARQL endpoints are becoming available (such as those in Uniprot and in EBI)

Below are the list of examples of SPARQL queries using PIERO. Click "Run Query", and the search result will be shown. You can also edit the queries in the textbox.

Overview

• Visualized Schema (Large File)
• Schema in RDF/Turtle

SPARQL Endpoint

• Virtuoso SPARQL endpoint
• Web Query Interface ( powered by TOGOStanza )

Download

• Download turtle files (v0.4)

Step-by-step learning of easy SPARQL Queries using PIERO

1. Get information about an EC number. ( EC 3.2.1.18 )
   SELECT DISTINCT * WHERE { ec:3.2.1.18 ?p ?o . }
   


2. Get information about a reaction. ( RN00004: ATP-hydrolyzing )
   SELECT DISTINCT * WHERE { reaction:RN00004 ?p ?o . }
   


3. Get information about a transformation. ( TR00216: phosphorylation )
   # implove efficacy of queries by using the inference below DEFINE input:inference "http://reactionontology.org/inference" PREFIX transformation: <http://reactionontology.org/piero/transformation/> SELECT DISTINCT * WHERE { transformation:TR00216 ?p ?o . }
   


4. Get information about a KEGG Reaction entry. ( R00414: UDP-N-acetyl-D-glucosamine 2-epimerase )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT * WHERE { kegg:R00414 ?p ?o . }
   


5. Get information about a KEGG Rpair entry. ( RP00020 )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT * WHERE { kegg:RP00020 ?p ?o . }
   


6. Get Transformations from a KEGG Reaction entry. ( R00001: polyphosphate polyphosphohydrolase )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT * WHERE { kegg:R00001 piero:hasTransformation ?transformation . ?transformation rdfs:label ?transformation_name . }
   


7. Get KEGG Reaction entries from a Transformation. ( `cyclization' )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_reaction WHERE { ?transformation rdfs:label "cyclization" . ?kegg_reaction piero:hasTransformation ?transformation . }
   


8. Get KEGG Reaction entries having the same Transformations of R02110
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?transformation_label ?kegg_reaction WHERE { kegg:R02110 piero:hasTransformation ?transformation . ?transformation piero:hasKeggReaction ?kegg_reaction . ?transformation rdfs:label ?transformation_label . } ORDER BY ?transformation_label ?kegg_reaction
   


9. Get KEGG Reaction entries from a KEGG Rpair entry. ( RP00020 )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_reaction WHERE { kegg:RP00020 piero:inReaction ?kegg_reaction . ?kegg_reaction rdf:type kegg:reaction . } ORDER BY ?kegg_reaction
   


10. Get KEGG Reaction entries from multiple KEGG Rpair entries. ( RP00020 and RP00021 )
    DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_rpair, ?kegg_reaction WHERE { # get multiple RPAIRs VALUES ?kegg_rpair { kegg:RP00020 kegg:RP00021 } . ?kegg_rpair ?p ?kegg_reaction . ?kegg_reaction rdf:type kegg:reaction . } ORDER BY ?kegg_rpair ?kegg_reaction
    


11. Get EC numbers from a KEGG Rpair entry. ( RP00020 )
    DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_reaction, ?ec_number WHERE { kegg:RP00020 piero:inReaction ?kegg_reaction. ?kegg_reaction piero:catalyzedBy ?gene_product . ?gene_product piero:mediates ?ec . ?ec rdfs:label ?ec_number . } ORDER BY ?kegg_reaction ?ec_number
    


12. Get EC numbers from a pair of KEGG Compound entries. ( C00015:UDP and C00043:UDP-N-acetyl-alpha-D-glucosamine )
    DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_rpair, ?kegg_reaction, ?ec_number WHERE { kegg:C00015 piero:inRpair ?kegg_rpair . kegg:C00043 piero:inRpair ?kegg_rpair . ?kegg_rpair piero:inReaction ?kegg_reaction. ?kegg_reaction piero:catalyzedBy ?gene_product . ?gene_product piero:mediates ?ec . ?ec rdfs:label ?ec_number . } ORDER BY ?kegg_rpair ?kegg_reaction ?ec_number
    

Some more helpful SPARQL Queries

1. Get KEGG Rpair entries that are included in EC2.7.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?ec, ?kegg_reaction, ?kegg_rpair WHERE { ec:2.7 piero:hasChild/piero:hasChild ?ec . ?ec piero:mediatedBy ?gp . ?gp piero:catalyzes ?kegg_reaction . ?kegg_reaction piero:hasRpair ?kegg_rpair . } ORDER BY ?kegg_reaction ?kegg_rpair LIMIT 200
   


2. Get common EC numbers from IUBMB terminologies. ( `acetyltransferase' and `alph-carboxylase' )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT * WHERE { ?iubmb1 rdfs:label "acetyltransferase" . ?iubmb2 rdfs:label "alpha-carboxylase" . ?ec piero:hasIubmb ?iubmb1 . ?ec piero:hasIubmb ?iubmb2 . }
   


3. Get KEGG Reaction, EC, and GO from a Transformation. ( `cyclization' )
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_rclass, ?kegg_reaction, ?ec, ?go, ?go_id, ?go_name WHERE { ?transformation rdfs:label "cyclization" . ?transformation piero:hasRclass ?kegg_rclass . ?kegg_rclass piero:hasRpair ?kegg_rpair . ?kegg_rpair piero:inReaction ?kegg_reaction . OPTIONAL { ?kegg_reaction piero:catalyzedBy/piero:mediates ?ec . ?ec rdfs:label ?EC_Number . ?ec piero:hasGo ?go . ?go rdfs:label ?go_id . ?go rdfs:comment ?go_name . } }
   


4. KEGG Rpair included in EC 1.2.3 or its subclasses.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_rpair, (count(DISTINCT ?ec_id)) as ?ec_id_count, (sql:GROUP_DIGEST (?ec_id, " ", 1000000, 1)) as ?ec_numbers WHERE { ec:1.2.3 piero:hasChild* ?ec . ?ec piero:mediatedBy/piero:catalyzes ?kegg_reaction . ?ec rdfs:label ?ec_id . ?kegg_reaction piero:hasRpair ?kegg_rpair . } ORDER BY DESC(?ec_id_count)
   


5. Get common KEGG Rpairs and their KEGG Reactions included in both EC 2.3.1.179 and EC 2.3.1.86.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?common_kegg_rpair, (sql:GROUP_DIGEST (?reaction_id1, ",", 1000000, 1)) as ?kegg_reactions1, (sql:GROUP_DIGEST (?reaction_id2, ",", 1000000, 1)) as ?kegg_reactions2 WHERE { ec:2.3.1.179 piero:mediatedBy/piero:catalyzes ?kegg_reaction1 . ec:2.3.1.86 piero:mediatedBy/piero:catalyzes ?kegg_reaction2 . ?kegg_reaction1 piero:hasRpair ?common_kegg_rpair . ?kegg_reaction2 piero:hasRpair ?common_kegg_rpair . ?kegg_reaction1 rdfs:label ?reaction_id1 . ?kegg_reaction1 rdfs:label ?reaction_id2 . } ORDER BY ?kegg_rpair
   


6. Get KEGG Reaction, EC, and GO from a compound pair. (C00003: NAD+, C00027: H2O2)
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_reaction, ?ec_number, ?go_id, ?go_name WHERE { kegg:C00003 piero:inRpair/piero:inReaction ?kegg_reaction . kegg:C00027 piero:inRpair/piero:inReaction ?kegg_reaction . OPTIONAL { ?kegg_reaction piero:catalyzedBy/piero:mediates ?ec . ?ec rdfs:label ?ec_number . ?ec piero:hasGo ?go . ?go rdfs:label ?go_id . ?go rdfs:comment ?go_name . } }
   


7. Get KEGG Reactions including C00003(NAD+) but not C00004(NADH), with EC and GO.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?kegg_reaction, ?ec_number, ?go_id, ?go_name WHERE { kegg:C00003 piero:inRpair ?rpair . MINUS { kegg:C00004 piero:inRpair ?rpair . } ?rpair piero:inReaction ?kegg_reaction . OPTIONAL { ?kegg_reaction piero:catalyzedBy/piero:mediates ?ec . ?ec rdfs:label ?ec_number . ?ec piero:hasGo ?go . ?go rdfs:label ?go_id . ?go rdfs:comment ?go_name . } }
   


8. Get the hierarchical view of Transformations.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?l1, ?l2, ?l3, ?l4, ?l5 WHERE { transformation:TR00001 piero:hasChild ?tr1 . ?tr1 rdfs:label ?l1 . OPTIONAL { ?tr1 piero:hasChild ?tr2 } OPTIONAL { ?tr2 rdfs:label ?l2 } OPTIONAL { ?tr2 piero:hasChild ?tr3 } OPTIONAL { ?tr3 rdfs:label ?l3 } OPTIONAL { ?tr3 piero:hasChild ?tr4 } OPTIONAL { ?tr4 rdfs:label ?l4 } OPTIONAL { ?tr4 piero:hasChild ?tr5 } OPTIONAL { ?tr5 rdfs:label ?l5 } } ORDER BY ?l1 ?l2 ?l3 ?l4 ?l5
   


9. Get the hierarchical view of Substructure Conversion.
   DEFINE input:inference "http://reactionontology.org/inference" SELECT DISTINCT ?l1, ?l2, ?l3, ?l4, ?l5 WHERE { substructure_conversion:SC00001 piero:hasChild ?sc1 . ?sc1 rdfs:label ?l1 . OPTIONAL { ?sc1 piero:hasChild ?sc2 } OPTIONAL { ?sc2 rdfs:label ?l2 } OPTIONAL { ?sc2 piero:hasChild ?sc3 } OPTIONAL { ?sc3 rdfs:label ?l3 } OPTIONAL { ?sc3 piero:hasChild ?sc4 } OPTIONAL { ?sc4 rdfs:label ?l4 } OPTIONAL { ?sc4 piero:hasChild ?sc5 } OPTIONAL { ?sc5 rdfs:label ?l5 } } ORDER BY ?l1 ?l2 ?l3 ?l4 ?l5