RESTful Web Services Search Keyword Vocabulary

The following vocabulary may be used to form queries to search for entries. These terms are identical to those used in the web interface for forming queries. An xml document containing all possible search fields is also accessible at Queries are formed using one or more of the fields below and should be passed as a request parameter named "q". Fields may be combined using the boolean AND operator to form complex queries.

Query syntax

It is highly recommended to encapsulate the query term within quotes. Any space character that is not inside quotes causes an error and subsequently no data will be returned (wrong: eg Organism:Homo sapiens; correct: Organism:"Homo sapiens"). This is especially important for queries that include organism, tissue, compound, pathway or enzyme name.

Only queries using Sabio-ID's should be performed without quoting (eg EntryID:123; SabioCompoundID:34; SabioReactionID:14).
The same applies for boolean values (eg HasKineticData:true).

Sabio-RK RESTful web services support both GET and POST requests.

Queries should be URL-encoded. A simple test can be performed using cURL or wget, eg for:

q=Substrate:"P1,P4-Bis(5'-guanosyl) tetraphosphate" AND CellularLocation:"cytosol" AND Tissue:"egg" AND Organism:"Artemia salina" AND temperature:[-10.0 TO 115.0]

curl --request POST

  • Entry
    • EntryID - SABIO-RK entry ID (eg EntryID:123)
  • Reaction/Pathway
    • Pathway - The name of the reaction pathway (eg, Pathway:"urea Cycle")
    • KeggReactionID - KEGG ID for the reaction (eg KeggReactionID:"R00782")
    • SabioReactionID - SABIO-RK ID for the reaction (eg SabioReactionID:14)
  • Compound
    • AnyRole - Compound found in any role in a reaction (eg AnyRole:"ATP")
    • Substrate - Compound acting as a substrate in a reaction (eg Substrate:"ATP")
    • Product - Compound acting as a product in a reaction (eg Product:"ATP")
    • Inhibitor - Compound acting as an inhibitor modifier in a reaction (eg Inhibitor:"ATP")
    • Catalyst - Compound acting as a catalyst modifier in a reaction (eg Catalyst:"ATP")
    • Cofactor - Compound acting as a cofactor in a reaction (eg Cofactor:"ATP")
    • Activator - Compound acting as an activator in a reaction (eg Activator:"ATP")
    • OtherModifier - Compound acting as a modifier not specified above, in a reaction (eg OtherModifier:"ATP")
    • PubChemID - PubChem ID number of a compound (eg PubChemID:"3304")
    • KeggID - KEGG ID number of a compound (eg KeggID:"C00002")
    • ChebiID - Chebi ID number of a compound (eg ChebiID:"15422")
    • SabioCompoundID - Sabio-RK compund ID (SabioCompoundID:34)
  • Enzyme
    • Enzymename - An enzyme may included in the search parameters by name. (eg Enzymename:"Acetoin dehydrogenase")
    • ECNumber - An enzyme may included in the search parameters by EC Class number (eg ECNumber:"")
    • UniProtKB_AC - Protein as listed in UniProtKB (eg UniProtKB_AC:"A1VCV2")
    • EnzymeType - Type of the Enzyme, only valid queries are EnzymeType:"mutant" or EnzymeType:"wildtype"
  • Biological Source
    • Tissue - The name of the tissue (eg. Tissue:"liver")
    • Organism - The name of the organism (eg. Organism:"homo sapiens")
    • CellularLocation - Location within the cell that a kinetic reaction takes place (eg. CellularLocation:"leucoplast")
  • Kinetic Data
    • Parametertype - Experimental parameter specified in the kinetic law entry (eg Parametertype:"Vmax")
    • KineticMechanismType - Mechanism for the kinetic data (eg KineticMechanismType:"rapid equilibrium")
    • AssociatedSpecies - Species which is associated with a parameter (eg AssociatedSpecies:"ATP")
  • Publication
    • Title - Publication within which the kinetic law data is published, by title (eg Title:"Ascaris suum hexokinase")
    • Author - Publication within which the kinetic law data is published, by author (eg Author:"Shelton E")
    • Year - Year of publication (eg Year:"2010")
    • PubMedID - Publication within which the kinetic law data is published, by PubMed ID (eg PubMedID:"13538975")
    • InfosourceType - Source of the data, valid queries are InfosourceType:"Journal" or InfosourceType:"direct submission"
    • DateSubmitted - Earliest possible date from which the entry exists in SABIO-RK (eg DateSubmitted:"27/10/2010")
  • Range options
    • TemperatureRange - Range of temperatures (eg TemperatureRange:[36.9 TO 37.1]
    • pHValueRange - Range of pH values (eg pHValueRange:[6.9 TO 7.1]
  • Boolean options
    • HasKineticData - Entry specifies a rate equation (eg HasKineticData:true)
    • IsRecombinant - Entry has recombinant data (eg IsRecombinant:false)