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PIERO Enzyme Reaction Ontology


RCLASS GenomeNet FTP

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

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.

  1. Get information about an EC number. ( EC 3.2.1.18 )


  2. Get information about a reaction. ( RN00004: ATP-hydrolyzing )


  3. Get information about a transformation. ( TR00216: phosphorylation )


  4. Get information about a KEGG Reaction entry. ( R00414: UDP-N-acetyl-D-glucosamine 2-epimerase )


  5. Get information about a KEGG Rpair entry. ( RP00020 )


  6. Get Transformations from a KEGG Reaction entry. ( R00001: polyphosphate polyphosphohydrolase )


  7. Get KEGG Reaction entries from a Transformation. ( `cyclization' )


  8. Get KEGG Reaction entries having the same Transformations of R02110


  9. Get KEGG Reaction entries from a KEGG Rpair entry. ( RP00020 )


  10. Get KEGG Reaction entries from multiple KEGG Rpair entries. ( RP00020 and RP00021 )


  11. Get EC numbers from a KEGG Rpair entry. ( RP00020 )


  12. Get EC numbers from a pair of KEGG Compound entries. ( C00015:UDP and C00043:UDP-N-acetyl-alpha-D-glucosamine )


Some more helpful SPARQL Queries

  1. Get KEGG Rpair entries that are included in EC2.7.


  2. Get common EC numbers from IUBMB terminologies. ( `acetyltransferase' and `alph-carboxylase' )


  3. Get KEGG Reaction, EC, and GO from a Transformation. ( `cyclization' )


  4. KEGG Rpair included in EC 1.2.3 or its subclasses.


  5. Get common KEGG Rpairs and their KEGG Reactions included in both EC 2.3.1.179 and EC 2.3.1.86.


  6. Get KEGG Reaction, EC, and GO from a compound pair. (C00003: NAD+, C00027: H2O2)


  7. Get KEGG Reactions including C00003(NAD+) but not C00004(NADH), with EC and GO.


  8. Get the hierarchical view of Transformations.


  9. Get the hierarchical view of Substructure Conversion.


Download turtle files

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