KeyPathwayMinerWeb API

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Tutorial of the Cytoscape App Tutorial of KeyPathwayMinerWeb Restful API KeyPathwayMinerWeb API Integrate de novo network enrichment into your application using KeyPathwayMinerWeb Version: 1.0 Example code for usage in R is found under downloads IMPORTANT NOTICE: For job submission, parameters need to be submitted as POST form with the content type 'application/x-www-form-urlencoded'. Other content types are not accepted. Table of Contents `post /requests/submit` `post /requests/submitAsync` `get /requests/results` `get /requests/runStatus` `get /rest/availableNetworks` `get /rest/network` `get /rest/questsInQueue` `get /rest/runParameters` Up `post /requests/submit` Submit a new job (requestSubmitPost) Submit a new job Request body job (required) Body Parameter — a job to be submitted Return type Result Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 200 An object containing the state of the analysis and the result if finished / an error message otherwise. 0 The result object with success false and a description of the problem in the comment field. Up `post /requests/submitAsync` Submit a new job asynchronously (requestSubmitAsyncPost) Submit a new job asynchronously. This method returns the same result object as the submit method. In contrast, however, it will return an empty result object with success false immediately. The API user is encouraged to use the runStatus method to check if the job is completed and to subsequently use the results method to retrieve an updated results object containing the solutions. Request body job (required) Body Parameter — a job to be submitted Return type Result Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 0 An object containing the state of the analysis and the result if finished / an error message otherwise. Up `get /requests/results` Get the results of a specific job (requestsResultsGet) After submitting a job asynchronously with submitAsync, this method can be used to retrieve an up-to-date version of the results object. If the job has been completed successfully, this object will contain the solutions. If the job failed, an error message will be included in the comment property. Note that this method should only be used after the runStatus method has returned an objected with the property completed set to true. Query parameters questID (optional) Query Parameter — The id of the job to be queried Return type Result Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 0 An object containing the state of the analysis and the result if finished / an error message otherwise. Up `get /requests/runStatus` Get an update about the progress of a specific job (requestsRunStatusGet) After submitting a job asynchronously with submitAsync, this method can be used to query KeyPathwayMinerWeb for the progress of the job. This is useful to create a progress bar and to inform the user when the job is finished. Query parameters questID (required) Query Parameter — The id of the job to be queried Return type RunStatus Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 0 The status of the queried job Up `get /rest/availableNetworks` List of available networks (restAvailableNetworksGet) Returns a list of networks currently available in KeyPathwayMinerWeb. Return type array[Network] Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 200 An array of graphs. 0 No networks found Up `get /rest/network` Get network id using the network name (restNetworkGet) Query parameters name (required) Query Parameter — Name of the network Return type Network Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 200 An object containing the network id and name 0 Network not found Up `get /rest/questsInQueue` Number of jobs currently in queue (restQuestsInQueueGet) Return type Integer Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 200 Number of jobs in queue Up `get /rest/runParameters` Parameters of a specific KeyPathwayMinerWeb run (restRunParametersGet) The parameters that were part of the KeyPathwayMinerWeb network enrichment request Query parameters id (required) Query Parameter — ID of KeyPathwayMinerWeb run Return type KpmRun Produces This API call produces the following media types according to the Accept request header; the media type will be conveyed by the Content-Type response header. `application/json` Responses 200 An object containing nested run parameters 0 No run parameters found Up Models `Network` `KpmRun` `RunParameters` `KValues` `LValues` `Perturbations` `Graph` `Dataset` `Job` `Error` `ResultNode` `ResultEdge` `ResultGraph` `Result` `RunStatus` Network Up graphId Integer The id of the network name String Human readable name of the network KpmRun Up withPerturbation Boolean If a perturbation technique was used (for robustness analysis in future versions of KeyPathwayMiner Web parameters RunParameters Detailed parameters RunParameters Up name String The name of the run. Defaults to the date and time the run was started algorithm Object The algorithm that was used. Either a heuristic (Greedy or ACO) or exact. strategy Object The search strategy that was used. Either individual node exceptions (INES) or global node exceptions (GLONE) k_values KValues Definition of the k parameter range in this run (node exceptions) removeBENs Boolean Whether border exception nodes should be removed. unmapped_nodes String What should be done with unmapped nodes, i.e. should they be added to the positive list (always included in solutions) or to the negative list (categorically ignored). computed_pathways Integer The number of solutions that should be computed graphID Integer The ID of the network that is used l_values LValues Definition of the l parameter range in this run (case exceptions) l_samePercentage Boolean If multiple datasets are defined, should the same l value be used for all of them (as a percentage?) samePercentageValue Integer The l percentage value that should be used for multiple datasets withPerturbation Boolean Whether to perform robustness analysis during the run or not. Available in future versions of KeyPathwayMinerWeb perturbation Perturbations Parameters for the perturbation of the network in case of a perturbation run (for future versions of KeyPathwayMinerWeb linkType String Either OR or AND to define how multiple datasets should be combined in the analysis. attachedToId String The quest id this job has been attached to. KValues Up val Integer Starting value of k range or k value if k is not ranged val_step Integer How k should be increased within the range val_max Integer The maximum k value, i.e. the upper limit of the range useRange Boolean If k should be ranged isPercentage Boolean Should the given values be interpreted as percentages? LValues Up val Integer Starting value of l range or l value if l is not ranged val_step Integer How l should be increased within the range val_max Integer The maximum l value, i.e. the upper limit of the range useRange Boolean If l should be ranged isPercentage Boolean Should the given values be interpreted as percentages? Perturbations Up technique String Perturbation technique, for example 'Node-removal' startPercent Integer Perturbation percentage range lower value stepPercent Integer Perturbation percentage step size maxPercent Integer Perturbation percentage range upper value graphsPerStep Integer Number of random graphs to be created (permutations) Graph Up name String Name of the network to be analyzed attachedToId String Name of the job where the network is supposed to be used contentBase64 String Base64 encoded representation of the network. The network file needs to be in Cytoscape SIF format Dataset Up name String Name of the dataset to be analyzed. attachedToId String Name of the job where the network is supposed to be used contentBase64 String The input dataset needs to an indicator matrix with a header. Row names are not allowed. The indicator matrix should contain 1s for active and 0s for inactive sample/case - gene/protein interactions. Note that quotes should not be included Job Up parameters RunParameters datasets array[Dataset] graph Graph Error Up message String error message ResultNode Up gID Integer The database ID of the solution (ResultGraph) id Integer The database ID of this node name String The name of this node, e.g. entrez gene id or gene symbol, ... overlapCount Integer Only useful for the union graph. How often is this node represented in all solutions? color String Only useful for the union graph. An internally used property to color nodes according to the overlapCount ResultEdge Up id Integer The database id of this edge source Integer The id of the source node of this edge target Integer The id of the target node of this edge value BigDecimal The edge weight if any relationshipType String The type of relationship as defined in the SIF file, e.g. pp for protein interaction ResultGraph Up edges array[ResultEdge] set of edges in this solution nodes array[ResultNode] set of nodes in this solutions k Integer the selected k value for this solution (node exceptions) l Integer the selected l value for this solution (case exceptions) isUnionSet Boolean Is this an ordinary solution (false) or the union of the solutions (true) nodeSetNr Integer This is solution no. x maxNodeCount Integer The size of the solution, i.e. the number of nodes Result Up runId Integer The id of the run. Used to look up results resultGraphs ResultGraph An array of solutions returned for the request comment String Comment on the outcome of the request. Contains error message in case success is false success Boolean Whether the request was successfully completed or not resultUrl String A URL to the web interface, where the progress and result of the network enrichment can be seen RunStatus Up runExists Boolean Is this actually a valid run/job id? completed Boolean Has this run/job been completed? cancelled Boolean Has this run/job been cancelled? progress BigDecimal The progress of this run/job as a percentage

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