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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
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

  1. post /requests/submit
  2. post /requests/submitAsync
  3. get /requests/results
  4. get /requests/runStatus
  5. get /rest/availableNetworks
  6. get /rest/network
  7. get /rest/questsInQueue
  8. 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

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

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

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

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

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

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



Models

  1. Network
  2. KpmRun
  3. RunParameters
  4. KValues
  5. LValues
  6. Perturbations
  7. Graph
  8. Dataset
  9. Job
  10. Error
  11. ResultNode
  12. ResultEdge
  13. ResultGraph
  14. Result
  15. 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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