SABIO-RK web services
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1
. Project information
Project information
Project
URL
Contact person
Email
2
. Which web services are you using or planning to use?
Which web services are you using or planning to use?
SOAP
RESTful (already in use)
RESTful (planned for the future)
3
. Which SOAP web services methods are you using?
(If you are not using SOAP web services please proceed with question 6!)
Which SOAP web services methods are you using? (If you are not using SOAP web services please proceed with question 6!)
getReactionIDs
getKEGGReactionIDs
getReactionIDsByKEGG
searchCompounds
getReactionIDFromCompound
getReactionInstanceIDs
getReactionEquation
getGeneralReactionEquation
searchEnzymesByName
searchEnzymesByECNumber
getReactionIDFromEnzyme
getECByName
getReactionIDFromEC
getECFromReactionID
getSubstratesSpeciesIDs
getProductsSpeciesIDs
getActivatorsSpeciesIDs
getInhibitorsSpeciesIDs
getCatalystsSpeciesIDs
getCofactorsSpeciesIDs
getUnknownModifiersSpeciesIDs
getCompoundIDFromSpeciesID
getCompoundID
getMultipleCompoundIDs
getCompoundName
getKEGGID
getCHEBIID
getCompoundIDsFromKEGGID
getCompoundIDsFromCHEBIID
getKinLawIDs
getKinLawIDsNotNull
getKineticLaw
getOrganismFromKLID
getPubmed
getKinLawIDFromPubmed
getParametersXML
getNormalizedParametersXML
getExpConditions
getLocationID
getLocationName
getTissue
getEnzymeVariant
getEnzymeProtein
getEnzymeProteinList
getReactionInstancesFromUniprotID
getAllUniProtIDs
getAllCompoundIDs
getAllReactionIDs
getAllEnzymes
getAllPathways
getAllUnits
getReactionInstanceIDsFromProtein
getSBML
GetReactionEquationResponse
GetGeneralReactionEquationResponse
GetCompoundIDFromSpeciesIDResponse
GetMultipleCompoundIDsResponse
GetCompoundNameResponse
GetKineticLawResponse
GetOrganismFromKLIDResponse
GetPubmedResponse
GetParametersXMLResponse
GetNormalizedParametersXMLResponse
GetExpConditionsResponse
GetLocationIDResponse
GetLocationNameResponse
GetTissueResponse
GetEnzymeProteinResponse
GetEnzymeVariantResponse
GetSBMLResponse
Other (please specify)
4
. How many SOAP service calls do you have to make to get from your starting point to the information you want? Please give examples of typical sequences of calls you use to get to your end point.
How many SOAP service calls do you have to make to get from your starting point to the information you want? Please give examples of typical sequences of calls you use to get to your end point.
1
2
3
4+
Typical sequence of calls (eg: getCompoundIDsFromKEGGID -> getReactionIDFromCompound -> getSBML )
5
. What kind of information are you attempting to retrieve from SABIO-RK through the current SOAP web services?
What kind of information are you attempting to retrieve from SABIO-RK through the current SOAP web services?
SABIO-RK entry IDs
SABIO-RK reaction IDs
SBML of SABIO-RK entries
Foreign IDs contained in SABIO-RK entries (eg which KEGG compound IDs are contained in entries) please specify below
Other (please specify)
6
. What URIs of the RESTful SABIO-RK API are you using or planning to use in the future?
What URIs of the RESTful SABIO-RK API are you using or planning to use in the future?
/status
/kineticLaws
/kineticLaws/{kinlawid}
/searchKineticLaws
/searchKineticLaws/sbml
/searchKineticLaws/kinlaws
/searchKineticLaws/biopax
/suggestions
/suggestions/{field}
/suggestions/{field}/count
Which URIs are missing that you would need?
7
. Which fields for /suggestions are you using or planning to use?
Which fields for /suggestions are you using or planning to use?
/suggestions/Enzymes
/suggestions/Tissues
/suggestions/Organisms
/suggestions/Compounds
/suggestions/Pathways
/suggestions/SABIOCompoundIDs
/suggestions/SABIOReactionIDs
/suggestions/UniprotIDs
/suggestions/KEGGReactionIDs
/suggestions/KEGGCompoundIDs
/suggestions/CHEBICompoundIDs
/suggestions/PUBCHEMCompoundIDs
/suggestions/PubmedIDs
Which fields are missing that you would need?
8
. Which keyword vocabulary are you using or planning to use with the RESTful API?
Which keyword vocabulary are you using or planning to use with the RESTful API?
ECNUMBER
ENZYMENAME
TISSUE
ORGANISM
PATHWAY
LOCATION
PUBMED
AUTHOR
TITLE
YEAR
UNIPROTID
PARAMETERTYPE
EVENTNAME
EVENTTYPE
REACTANT
REACTANTPUBCHEMID
REACTANTKEGGID
REACTANTCHEBIID
REACTANTCASID
REACTANTPRODUCT
REACTANTSUBSTRATE
REACTANTINHIBITOR
REACTANTCATALYST
REACTANTCOFACTOR
REACTANTACTIVATOR
REACTANTMODIFIER
MUTANT
WILDTYPE
RSABIO
RKEGG
Which keyword vocabulary is missing that you would need?
9
. For RESTful methods: Which output format do you prefer?
For RESTful methods: Which output format do you prefer?
SBML (for kinetic data entries)
BioPax/SBPAX (for kinetic data entries)
xml (for returning lists of IDs or names)
plain text, one ID per line (for returning lists of IDs or names)
Other (please specify)
10
. Are there other methods you would like to see in the RESTful services? Or are there any further comments or suggestions you want to make?
Are there other methods you would like to see in the RESTful services? Or are there any further comments or suggestions you want to make?
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