Back to SABIO-RK Home
          CONTACT | HELP | IMPRINTWeb Service Reference Manual


SABIO-RK Web Service Reference Manual

This reference manual describes the methods of the SABIO-RK Web service in detail.
Back to Web Service Home

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.
getPathwayNames
getReactionIDs
getKEGGReactionID     Deprecated
         Use getKEGGReactionIDs instead.
getReactionIDByKEGG     Deprecated
         Use getReactionIDsByKEGG instead.
searchCompounds
getReactionIDFromCompound
getReactionInstanceIDs
getReactionEquation
getGeneralReactionEquation
searchEnzymesByName
searchEnzymesByECNumber
getReactionIDFromEnzyme
getECByName
getReactionIDFromEC
getECFromReactionID
getSubstratesSpeciesIDs
getProductsSpeciesIDs
getActivatorsSpeciesIDs
getInhibitorsSpeciesIDs
getCatalystsSpeciesIDs
getCofactorsSpeciesIDs
getUnknownModifiersSpeciesIDs
getCompoundIDFromSpeciesID
getCompoundID
getMultipleCompoundIDs
getCompoundName
getKEGGID
getCHEBIID
getCompoundIDFromKEGGID     Deprecated
         Use getCompoundIDsFromKEGGID instead.
getCompoundIDFromCHEBIID     Deprecated
         Use getCompoundIDsFromCHEBIID instead.
getKinLawIDs
getKinLawIDsNotNull
getKineticLaw
getOrganismFromKLID
getPubmed
getKinLawIDFromPubmed
getParametersXML
getNormalizedParametersXML     -NEW-
getExpConditions
getLocationID
getLocationName
getTissue
getEnzymeVariant
getEnzymeProtein
getEnzymeProteinList
getReactionInstancesFromUniprotID
getAllUniProtIDs     -NEW-    (Not displayed In the figure)
getAllCompoundIDs     -NEW-    (Not displayed In the figure)
getAllReactionIDs     -NEW-    (Not displayed In the figure)
getAllEnzymes     -NEW-    (Not displayed In the figure)
getAllPathways     -NEW-    (Not displayed In the figure)
getAllUnits     -NEW-    (Not displayed In the figure)
getReactionInstanceIDsFromProtein     -NEW-
GenerateSBMLentities     Deprecated
         Use getSBML instead.
GenerateSBMLentities2     Deprecated
         Use getSBML instead.
getSBML     -NEW-



Response classes:
GetReactionEquationResponse
GetGeneralReactionEquationResponse
GetCompoundIDFromSpeciesIDResponse
GetMultipleCompoundIDsResponse
GetCompoundNameResponse
GetKineticLawResponse
GetOrganismFromKLIDResponse
GetPubmedResponse
GetParametersXMLResponse
GetNormalizedParametersXMLResponse
GetExpConditionsResponse
GetLocationIDResponse
GetLocationNameResponse
GetTissueResponse
GetEnzymeProteinResponse
GetEnzymeVariantResponse
GetSBMLResponse


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

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

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

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

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

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

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

getReactionEquation
Input: Reaction Instance ID (int)
Returned Value: GetReactionEquationResponse
Description: Accepts a reaction instance ID and returns it's stoichiometric equation.
Back to top

getGeneralReactionEquation
Input: Reaction ID (int)
Returned Value: GetGeneralReactionEquationResponse
Description: Accepts a reaction ID and returns it's stoichiometric equation.
Back to top

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getAllCompoundIDs
Input: None
Returned Value: Array of SABIO Compound IDs (int[])
Description: Returns all Compound IDs stored in SABIO-RK.
Back to top

getAllReactionIDs
Input: None
Returned Value: Array of SABIO Reaction ID (int[])
Description: Returns all Reaction IDs stored in SABIO-RK.
Back to top

getAllEnzymes
Input: None
Returned Value: Array of EC numbers (String[])
Description: Returns all EC class IDs stored in SABIO-RK.
Back to top

getAllPathways
Input: None
Returned Value: Array of Pathway names (String[])
Description: Returns all Pathway names stored in SABIO-RK.
Back to top

getAllUnits
Input: None
Returned Value: Array of units (String[])
Description: Returns all units stored in SABIO-RK.
Back to top

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


Response classes:
GetReactionEquationResponse
Returned by method: getReactionEquation
Public method: get_return()
Returned value: String
Description: Returns the reaction stoichiometry
Back to top

GetGeneralReactionEquationResponse
Returned by method: getGeneralReactionEquation
Public method: get_return()
Returned value: String
Description: Returns the reaction stoichiometry
Back to top

GetCompoundIDFromSpeciesIDResponse
Returned by method: getCompoundIDFromSpeciesID
Public method: get_return()
Returned value: int
Description: Returns the compound ID
Back to top

GetMultipleCompoundIDsResponse
Returned by method: getMultipleCompoundIDs
Public method: get_return()
Returned value: int[]
Description: Returns SABIO compound IDs
Back to top

GetCompoundNameResponse
Returned by method: getCompoundName
Public method: get_return()
Returned value: String
Description: Returns the compound name
Back to top

GetKineticLawResponse
Returned by method: getKineticLaw
Public method: get_return()
Returned value: String
Description: Returns the corresponding kinetic law (formula)
Back to top

GetOrganismFromKLIDResponse
Returned by method: getOrganismFromKLID
Public method: get_return()
Returned value: String
Description: Returns the corresponding organism name
Back to top

GetPubmedResponse
Returned by method: getPubmed
Public method: get_return()
Returned value: int
Description: Returns the PubMed ID of the original publication
Back to top

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

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

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

GetLocationIDResponse
Returned by method: getLocationID
Public method: get_return()
Returned value: int
Description: Returns the location ID
Back to top

GetLocationNameResponse
Returned by method: getLocationName
Public method: get_return()
Returned value: String
Description: Returns the location name
Back to top

GetTissueResponse
Returned by method: getTissue
Public method: get_return()
Returned value: String
Description: Returns the tissue name
Back to top

GetEnzymeProteinResponse
Returned by method: getEnzymeProtein
Public method: get_return()
Returned value: String
Description: Returns the protein name
Back to top

GetEnzymeVariantResponse
Returned by method: getEnzymeVariant
Public method: get_return()
Returned value: String
Description: Returns the enzyme variant (wild type)
Back to top

GetSBMLResponse
Returned by method: getSBML
Public method: get_return()
Returned value: String
Description: Returns the generated SBML as a String
Back to top




© HITS gGmbH (last updated Sept. 2010)