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SABIO-RK Web Service Reference Manual This reference manual describes the methods of the SABIO-RK Web service in detail. |
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Important Guideline Since the release of version 2.0, there are two important guidelines that we'd like to mention here. Firstly, we have introduced the concept of "Reaction Instance ID". A SABIO Reaction ID is the ID associated with a general reaction, whereas a Reaction Instance ID is an instance of a SABIO reaction ID in a particular organism, in a certain tissue, having associated kinetic data, with a kinetic law and so forth. As is evident from the schematic overview below, all the kinetic information, organism, species, tissue, enzyme variant, protein, reaction equation etc. are now associated with the Reaction Instance IDs. The pathway and enzyme information is still, however, connected to the SABIO Reaction IDs. Secondly, The method getKinLawIDs returns an array containing a single kinetic law ID, and this ID will be identical to the input reaction instance ID. In essence, what this means is that you CAN treat reaction instance IDs as kinetic law IDs, thereby negating the need for the method getKinLawIDs. But the reason this method is being kept is that we would like to keep the two concepts (reaction instance IDs and kinetic law IDs) separate. Additionally, these two concepts have seperate entries in the SABIO-RK database. Keeping this method guarantees that there wont be any inconsitencies or erreneous output in the future, should the identical entries ever change. Therefore, we recommend you follow the schematic description and separate your reaction instance IDs from your kinetic law IDs. Lastly, if you were a user of the 1.x web service, please take a moment to review the method descriptions below. Quite a few new methods have been added, some have been removed, while others have been slightly modified to provide consistent input/output formats. Methods Following is a list of currently available methods. The figure below gives an overview of the functionality. Scroll down to see the list of methods and their descriptions.  Schematic Overview of SABIO-RK Web Service Functionality Click on a particular method to see it's detail. |
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Response classes: GetReactionEquationResponse GetGeneralReactionEquationResponse GetCompoundIDFromSpeciesIDResponse GetMultipleCompoundIDsResponse GetCompoundNameResponse GetKineticLawResponse GetOrganismFromKLIDResponse GetPubmedResponse GetParametersXMLResponse GetNormalizedParametersXMLResponse GetExpConditionsResponse GetLocationIDResponse GetLocationNameResponse GetTissueResponse GetEnzymeProteinResponse GetEnzymeVariantResponse GetSBMLResponse | |
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getPathwayNames Input: Pathway Name/Substring (String) Returned Value: Matching pathway names (String[]) Description: Accepts a sample pathway name and returns an array of recommended Pathway names matching the input substring. Back to top | |
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getReactionIDs Input: Recommended Pathway Name (String) Returned Value: Array of SABIO Reaction IDs (int[]) Description: Accepts a recommended pathway name and returns the SABIO reaction IDs belonging to this pathway. Back to top | |
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getKEGGReactionIDs Input: SABIO Reaction ID (int) Returned Value: KEGG Reaction IDs (String[]) Description: Accepts a SABIO Reaction ID and returns the corresponding KEGG reaction IDs as an array. Returns an empty string as the first and only entry of the array if no matches are found. Back to top | |
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getReactionIDsByKEGG Input: KEGG Reaction ID (String) Returned Value: SABIO Reaction IDs (int[]) Description: Accepts a KEGG Reaction ID and returns the corresponding SABIO reaction IDs as an array. Back to top | |
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searchCompounds Input: Compound Name/Substring (String) Returned Value: Array of Compund Names (String[]) Description: Accepts a sample compund name/substring and returns an array of recommended compound names. Back to top | |
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getReactionIDFromCompound Input: Recommended Compound Name (String) Returned Value: SABIO Reaction IDs (int[]) Description: Accepts a recommended compound name and returns all the SABIO reaction IDs in which this compound participates (as Substrate or Product). Back to top | |
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getReactionInstanceIDs Input: SABIO Reaction ID (int) Returned Value: Reaction Instance IDs (int[]) Description: Accepts a SABIO reaction ID and returns all the corresponding reaction instance IDs. Back to top | |
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getReactionEquation Input: Reaction Instance ID (int) Returned Value: GetReactionEquationResponse Description: Accepts a reaction instance ID and returns it's stoichiometric equation. Back to top | |
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getGeneralReactionEquation Input: Reaction ID (int) Returned Value: GetGeneralReactionEquationResponse Description: Accepts a reaction ID and returns it's stoichiometric equation. Back to top | |
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searchEnzymesByName Input: Enzyme Name/Substring (String) Returned Value: Array of Enzyme Names (String[]) Description: Accepts a sample enzyme name/substring and returns the names of matching enzymes. This is a double wildcard search at the beginning and end of the search string. Returns an empty array if no matching enzyme is found. Back to top | |
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searchEnzymesByECNumber Input: Enzyme Classification Number (String) Returned Value: Array of Enzyme Names (String[]) Description: Accepts an enzyme classification number and returns the matching enzyme name(s). Back to top | |
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getReactionIDFromEnzyme Input: Enzyme Name (String) Returned Value: Array of SABIO reaction IDs (int[]) Description: Accepts an enzyme name and returns all corresponding SABIO reaction IDs. Returns an empty string if there are no matches. Back to top | |
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getECByName Input: Enzyme Name (String) Returned Value: Enzyme Classification Number (String) Description: Accepts an enzyme name and returns the corresponding EC number. Returns an empty string if there are no matches. Back to top | |
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getReactionIDFromEC Input: Enzyme Classification Number (String) Returned Value: Array of SABIO Reaction IDs (int[]) Description: Accepts an EC Number and returns the corresponding SABIO reaction IDs. Back to top | |
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getECFromReactionID Input: SABIO Reaction ID (int) Returned Value: EC Numbers (String[]) Description: Accepts a SABIO reaction ID and returns the corresponding String array of EC numbers. Back to top | |
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getSubstratesSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Substrates Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the substrates of that reaction. Back to top | |
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getProductsSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Products Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the products of that reaction. Back to top | |
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getActivatorsSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Activators Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the activators of that reaction. Back to top | |
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getInhibitorsSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Inhibitors Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the inhibitors of that reaction. Back to top | |
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getCatalystsSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Catalysts Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the catalysts of that reaction. Back to top | |
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getCofactorsSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Cofactors Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for the cofactors of that reaction. Back to top | |
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getUnknownModifiersSpeciesIDs Input: Reaction Instance ID (int) Returned Value: Unknown Modifiers Species IDs (int[]) Description: Accepts a reaction instance ID and returns the corresponding array of species IDs for unknown modifiers of that reaction. (In some publications, the exact role for the modifier is not defined. We group such modifiers into the "Unknown Modifier" category) Back to top | |
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getCompoundIDFromSpeciesID Input: Species ID (int) Returned Value: GetCompoundIDFromSpeciesIDResponse Description: Accepts a reaction SABIO species ID and returns the corresponding SABIO compound ID. Returns 0 when no compound ID is found. (This should never happen if the species ID is correct) Back to top | |
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getCompoundID Input: Recommended Compound Name (String) Returned Value: SABIO Compound ID (int) Description: Accepts a recommended compound name and returns the corresponding SABIO compound ID. Returns 0 if the given name is not found. Back to top | |
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getMultipleCompoundIDs Input: Recommended Compound Names (String[]) Returned Value: GetMultipleCompoundIDsResponse Description: Accepts recommended compound names as an array of String and returns the corresponding SABIO compound IDs in the same order. Back to top | |
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getCompoundName Input: SABIO Compound ID (int) Returned Value: GetCompoundNameResponse Description: Accepts a SABIO compound ID and returns the corresponding recommended compound name. Returns an empty string if the given compound ID is not found. (This should never happen if the compound ID is correct) Back to top | |
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getKEGGID Input: SABIO Compound ID (int) Returned Value: KEGG Compound ID (String[]) Description: Accepts a SABIO compound ID and returns the corresponding KEGG compound ID as a string array. Back to top | |
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getCHEBIID Input: SABIO Compound ID (int) Returned Value: CHEBI Compound ID (String[]) Description: Accepts a SABIO compound ID and returns the corresponding CHEBI compound ID as a string array. Back to top | |
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getCompoundIDsFromKEGGID Input: KEGG Compound ID (String) Returned Value: SABIO Compound IDs (int[]) Description: Accepts a KEGG compound ID and returns the corresponding SABIO compound IDs as an array. Back to top | |
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getCompoundIDsFromCHEBIID Input: CHEBI Compound ID (String) Returned Value: SABIO Compound IDs (int[]) Description: Accepts a CHEBI compound ID and returns the corresponding SABIO compound IDs as an array. Back to top | |
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getKinLawIDs Input: Reaction Instance ID (int) Returned Value: Kinetic Law IDs (int[]) Description: Accepts a reaction instance ID and returns all the kinetic law IDs associated with this reaction. (From version 2.0 onwards, this function will return an array containing only one entry for a kinetic law ID. In addition, the kinetic law ID will be the same as the reaction instance ID. Refer to the Web service general description at the top of the page) Back to top | |
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getKinLawIDsNotNull Input: Reaction Instance ID (int) Returned Value: Kinetic Law IDs (int[]) Description: Accepts a reaction instance ID and returns the kinetic law IDs associated with this reaction which have corresponding kinetic laws in the database (not null). (From version 2.0 onwards, this function will return an array containing only one entry for a kinetic law ID, if the associated kinetic law is not null, otherwise it will be an empty array. In addition, the kinetic law ID, if returned, will be the same as the reaction instance ID. Refer to the Web service general description at the top of the page) Back to top | |
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getKineticLaw Input: Kinetic Law ID (int) Returned Value: GetKineticLawResponse Description: Accept a SABIO kinetic law ID and returns the corresponding kinetic law (formula). Back to top | |
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getOrganismFromKLID Input: Kinetic Law ID (int)) Returned Value: GetOrganismFromKLIDResponse Description: Accepts a SABIO kinetic law ID and returns the corresponding organism name. Returns an empty string if no organism is found for the given kinetic law. Back to top | |
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getPubmed Input: Kinetic Law ID (int) Returned Value: GetPubmedResponse Description: Accepts a SABIO kinetic law ID and returns the PubMed ID of the original publication. Returns 0 if no PubMed ID was found. Back to top | |
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getKinLawIDFromPubmed Input: PubMed ID (int) Returned Value: Kinetic Law IDs (int[]) Description: Accepts a PubMed ID of the original publication and returns an array of corresponding SABIO kinetic law IDs. Back to top | |
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getParametersXML Input: SABIO Kinetic Law ID (int) Returned Value: GetParametersXMLResponse Description: Accepts a SABIO Kinetic Law ID and returns the corresponding SABIO Parameter ID, Name, Species, Parameter Type, Start and End values and Deviation and the Units in an XML file sent back as a string. Back to top | |
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getNormalizedParametersXML Input: SABIO Kinetic Law ID (int) Returned Value: GetNormalizedParametersXML Description: Accepts a SABIO Kinetic Law ID and returns the corresponding SABIO Parameter ID, Name, Species, Parameter Type, Normalized Start, End and Deviation values, and the Units in an XML file sent back as a string. Back to top | |
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getExpConditions Input: Kinetic Law ID (int) Returned Value: GetExpConditionsResponse Description: Accepts a SABIO kinetic law ID and returns the corresponding experimental conditions - pH, temperature, buffer and comments - formatted in xml as a String. Returns an empty String if no experimental conditions were found. Back to top | |
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getLocationID Input: Species ID (int) Returned Value: GetLocationIDResponse Description: Accepts a SABIO species ID and returns the corresponding location ID. Returns 0 if no location ID is found. Back to top | |
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getLocationName Input: Location ID (int) Returned Value: GetLocationNameResponse Description: Accepts a location ID and returns the corresponding location name. Returns an empty String if the location ID or location name is not found. Back to top | |
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getTissue Input: Reaction Instance ID (int) Returned Value: GetTissueResponse Description: Accepts a reaction instance ID and returns the corresponding Tissue name. Returns "unknown" if the tissue is not specified in SABIO-RK, and an empty String if the given reaction instance ID is not found. (The latter should not happen if the reaction instance ID is correct) Back to top | |
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getEnzymeVariant Input: Reaction Instance ID (int) Returned Value: GetEnzymeVariantResponse Description: Accepts a reaction instance ID and returns the corresponding enzyme variant. Returns an empty String if not found. Back to top | |
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getEnzymeProtein Input: Reaction Instance ID (int) Returned Value: GetEnzymeProteinResponse Description: Accepts a reaction instance ID and returns the corresponding protein (UniProtId or complex). Returns an empty String if not found. Back to top | |
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getEnzymeProteinList Input: Reaction Instance ID (int) Returned Value: Protein (String) Description: Accepts a reaction instance ID and returns the corresponding proteins (0,1 or many. UniProtId or complex). Returns an empty String if not found. Back to top | |
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getAllUniProtIDs Input: None Returned Value: Array of Proteins (UniProt IDs) (String[]) Description: Returns all (unique) proteins stored in SABIO-RK. Protein complexes are not returned (Individual proteins are parsed from complexes and returned.) Back to top | |
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getReactionInstancesFromUniprotID(String UniProtID) Input: UniProt ID (String) Returned Value: Array of Reaction Instance IDs (int[]) Description: Returns all reaction instance IDs stored in SABIO-RK for a given UniProt ID. Back to top | |
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getReactionInstanceIDsFromProtein Input: Protein (String) Returned Value: Reaction Instance IDs (int[]) Description: Accepts a protein string and returns the corresponding reaction instance IDs. Performs a wild-card search (If a search string matching against a protein complex, corresponding reaction instance IDs are also returned) Back to top | |
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getAllCompoundIDs Input: None Returned Value: Array of SABIO Compound IDs (int[]) Description: Returns all Compound IDs stored in SABIO-RK. Back to top | |
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getAllReactionIDs Input: None Returned Value: Array of SABIO Reaction ID (int[]) Description: Returns all Reaction IDs stored in SABIO-RK. Back to top | |
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getAllEnzymes Input: None Returned Value: Array of EC numbers (String[]) Description: Returns all EC class IDs stored in SABIO-RK. Back to top | |
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getAllPathways Input: None Returned Value: Array of Pathway names (String[]) Description: Returns all Pathway names stored in SABIO-RK. Back to top | |
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getAllUnits Input: None Returned Value: Array of units (String[]) Description: Returns all units stored in SABIO-RK. Back to top | |
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getSBML Input 1: Array of SABIO Reaction IDs to be exported in the SBML file (int[]) Input 2: Array of kinetic law IDs (int[]) Input 3: SBML Level (int) Input 4: SBML Version (int) Input 5: Name of Model (String) Input 6: Choice for exporting normalized parameters (boolean) Returned Value: GetSBMLResponse Description: Accepts six inputs. The first input is an array of SABIO reaction IDs of all reactions (without kinetics data) that are to be included in the SBML file. The second input is an array of kinetic law IDs; the corresponding reaction data are included automatically into the model as well. These two arrays are independent; thus if you want to include only reactions containing kinetics data, the first array would be null and vice versa. For example, if you wish to export 2 reactions with SABIO reaction IDs 98, 107 respectively, and additionally wish to include kinetic information for kinetic law ID 5046 (reaction ID 88), then the input will be: int reactions[] = {98, 107}; The corresponding second argument will be: int kinlaws[] = {5046}; If you would like to export multiple kinetic laws (and no additional reactions without kinectics data), then this can be done as: int reactions[] = {null}; int kinlaws[] = {5361, 5046}; The third input is the SBML level number (2); The fourth input is the SBML version (3). The fifth input is the name that you wish to give to your model. The final argument is a boolean value (true or false) to indicate whether you would like to export the normalized parameter values. Back to top | |
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Response classes: GetReactionEquationResponse Returned by method: getReactionEquation Public method: get_return() Returned value: String Description: Returns the reaction stoichiometry Back to top | |
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GetGeneralReactionEquationResponse Returned by method: getGeneralReactionEquation Public method: get_return() Returned value: String Description: Returns the reaction stoichiometry Back to top | |
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GetCompoundIDFromSpeciesIDResponse Returned by method: getCompoundIDFromSpeciesID Public method: get_return() Returned value: int Description: Returns the compound ID Back to top | |
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GetMultipleCompoundIDsResponse Returned by method: getMultipleCompoundIDs Public method: get_return() Returned value: int[] Description: Returns SABIO compound IDs Back to top | |
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GetCompoundNameResponse Returned by method: getCompoundName Public method: get_return() Returned value: String Description: Returns the compound name Back to top | |
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GetKineticLawResponse Returned by method: getKineticLaw Public method: get_return() Returned value: String Description: Returns the corresponding kinetic law (formula) Back to top | |
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GetOrganismFromKLIDResponse Returned by method: getOrganismFromKLID Public method: get_return() Returned value: String Description: Returns the corresponding organism name Back to top | |
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GetPubmedResponse Returned by method: getPubmed Public method: get_return() Returned value: int Description: Returns the PubMed ID of the original publication Back to top | |
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GetParametersXMLResponse Returned by method: getParametersXML Public method: get_return() Returned value: String Description: Returns parameters in XML format. The XML schema can be found here Back to top | |
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GetNormalizedParametersXMLResponse Returned by method: getNormalizedParametersXML Public method: get_return() Returned value: String Description: Returns normalized parameters in XML format. The XML schema can be found here Back to top | |
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GetExpConditionsResponse Returned by method: getExpConditions Public method: get_return() Returned value: String Description: Returns experimental conditions in XML format. The XML schema can be found here Back to top | |
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GetLocationIDResponse Returned by method: getLocationID Public method: get_return() Returned value: int Description: Returns the location ID Back to top | |
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GetLocationNameResponse Returned by method: getLocationName Public method: get_return() Returned value: String Description: Returns the location name Back to top | |
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GetTissueResponse Returned by method: getTissue Public method: get_return() Returned value: String Description: Returns the tissue name Back to top | |
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GetEnzymeProteinResponse Returned by method: getEnzymeProtein Public method: get_return() Returned value: String Description: Returns the protein name Back to top | |
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GetEnzymeVariantResponse Returned by method: getEnzymeVariant Public method: get_return() Returned value: String Description: Returns the enzyme variant (wild type) Back to top | |
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GetSBMLResponse Returned by method: getSBML Public method: get_return() Returned value: String Description: Returns the generated SBML as a String Back to top | |
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