Projects

Table of contents

Project data

List projects:

  • URL: /projects/
  • Method: GET
  • Parameters: NONE
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/
    

Get project meta data:

  • URL: /projects/{projectId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3:downloadSource
    

Create project:

  • URL: /projects/{projectId}/
  • Method: POST
  • Parameters:
    • projectId - identifier of the project
    • file-id - identifier of the file that should be used to create project. Information how to upload files can be found here
    • parser - class of the parser that should be used for parsing the file. List of all available parser is included in configuration in modelFormats list
    • cache- should the data from external sources be cached after project was created
    • description - description of the project
    • notify-email - email address that should be when something change in the project
    • disease - disease associated with the project (MESH id)
    • name - name of the project
    • organism - organism associated with the project (TAXONOMY id)
    • sbgn - should the map be visualized in SBGN-like way
    • semantic-zoom - should custom semantic zooming be enabled (true/false)
    • version - version of the project
    • mapCanvasType - type of map canvas engine to be used when visualizing map, for now there are only two options available: “GOOGLE_MAPS_API”, “OPEN_LAYERS”. By setting type to Google Maps API you agree to Google Maps APIs Terms of Service. List of possible values is available in configuration in mapCanvasTypes
    • annotate - should the project be automatically annotated
    • verify-annotations - should the annotations be verified
    • zip-entries - array of parameters describing each file in the zipped input file, file-index is number starting from 0
      • zip-entries[{file-index}][_filename] - name of the file
      • zip-entries[{file-index}][_type] - type of the file (possible values: “MAP”, “OVERLAY”, “IMAGE”)
      • zip-entries[{file-index}][_data][type][id] - for submaps defines type of the connection (possible values: “DOWNSTREAM_TARGETS”, “PATHWAY”, “UNKNOWN”)
      • zip-entries[{file-index}][_data][root] - for submaps - is this map a root map (true/false)
      • zip-entries[{file-index}][_data][mapping] - for submaps - is this map a mapping file (true/false)
      • zip-entries[{file-index}][_data][name] - for submaps - name of the map
      • zip-entries[{file-index}][_data][name] - for overlays - name of the overlay
      • zip-entries[{file-index}][_data][description] - for overlays - description of the overlay
  • Example:

    1. Simple file
      curl -X POST --data \
      'file-id=2052&mapCanvasType=OPEN_LAYERS&parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser' \
      --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
      "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/test_project"
      
    2. Uploading of zip file with a submap.
      curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
      --data "parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&mapCanvasType=OPEN_LAYERS&file-id=8506&zip-entries%5B0%5D%5B_type%5D=MAP&zip-entries%5B0%5D%5B_filename%5D=submaps%2Fs1.xml&zip-entries%5B0%5D%5B_data%5D%5Bname%5D=s1&zip-entries%5B0%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B0%5D%5B_data%5D%5Btype%5D%5Bname%5D=Unknown&zip-entries%5B1%5D%5B_type%5D=MAP&zip-entries%5B1%5D%5B_filename%5D=main.xml&zip-entries%5B1%5D%5B_data%5D%5Broot%5D=true&zip-entries%5B1%5D%5B_data%5D%5Bname%5D=main&zip-entries%5B1%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B1%5D%5B_data%5D%5Btype%5D%5Bname%5D=Unknown" \
      "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/test_project"
      

      For better understanding of the command above first let’s decode the data send to the server (here is online tool that can do it for you):

      parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&file-id=8506&zip-entries[0][_type]=MAP&zip-entries[0][_filename]=submaps/s1.xml&zip-entries[0][_data][name]=s1&zip-entries[0][_data][type][id]=UNKNOWN&zip-entries[0][_data][type][name]=Unknown&zip-entries[1][_type]=MAP&zip-entries[1][_filename]=main.xml&zip-entries[1][_data][root]=true&zip-entries[1][_data][name]=main&zip-entries[1][_data][type][id]=UNKNOWN&zip-entries[1][_data][type][name]=Unknown
      

      After separating it into parameters we obtain something like:

       parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser
       mapCanvasType=OPEN_LAYERS
       file-id=8506
       zip-entries[0][_type]=MAP
       zip-entries[0][_filename]=submaps/s1.xml
       zip-entries[0][_data][name]=s1
       zip-entries[0][_data][type][id]=UNKNOWN
       zip-entries[0][_data][type][name]=Unknown
       zip-entries[1][_type]=MAP
       zip-entries[1][_filename]=main.xml
       zip-entries[1][_data][root]=true
       zip-entries[1][_data][name]=main
       zip-entries[1][_data][type][id]=UNKNOWN
       zip-entries[1][_data][type][name]=Unknown
      

      We can easily see now that there are two files in the uploaded zip:

      • zip-entries[0] - is a description of a submap
      • zip-entries[1] - depicts main map of the project

Update project:

  • URL: /projects/{projectId}/
  • Method: PATCH
  • Parameters:
    • projectId - identifier of the project
    • body - json object with changes to apply
      • version - version of the project
      • name - name of the project
      • notifyEmail - email address that should be when something change in the project
      • organism - organism associated with the project (TAXONOMY id)
      • disease - disease associated with the project (MESH id)
      • mapCanvasType - type of map canvas engine to be used when visualizing map, for now there are only two options available: “GOOGLE_MAPS_API”, “OPEN_LAYERS”. By setting type to Google Maps API you agree to Google Maps APIs Terms of Service. List of possible values is available in configuration in mapCanvasTypes
  • Example:
curl -X PATCH --data '{"project":{"name": "some empty project"}}' \
--cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
 "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/empty"

Delete project:

  • URL: /projects/{projectId}/
  • Method: DELETE
  • Parameters:
    • projectId - identifier of the project
  • Example:
curl -X DELETE --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
 "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/test_project"

Get source file of the project:

  • URL: /projects/{projectId}:downloadSource
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3_pdb:downloadSource --output some.file
    

Get project logs:

  • Description: List all project logs according to pagination parameters
  • URL: /projects/{projectId}/logs/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • start - first log entry to returned (default: 0)
    • length - how many log entries we want to get (default: 10)
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/logs/?start=2&length=5"
    

Get project statistics:

  • Description: List statistics about the project
  • URL: /projects/{projectId}/statistics/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/statistics"
    

Get publications associated with the project

  • URL: /projects/{projectId}/models/{modelId}/publications/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • start (*) - first element to be return when pagination is on (default 0)
    • length (*) - how many publication we want to retrieve (default 10)
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/*/publications/
    

Maps

List all maps in a project

  • URL: /projects/{projectId}/models/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/"
    

Get info about specific map

  • URL: /projects/{projectId}/models/{modelId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38/"
    

Get info about connections between the maps

  • URL: /projects/{projectId}/submapConnections
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/submapConnections"
    

Update specific map

  • URL: /projects/{projectId}/models/{modelId}/
  • Method: PATCH
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
    • body - json object with the changes
    • defaultCenterX - default center x coordinate used during first opening of the map
    • defaultCenterY - default center y coordinate used during first opening of the map
    • defaultZoomLevel - default zoom level used during first opening of the map
  • Example:
    curl -X PATCH --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38/"
    

Download map as a model file (i.e. in CellDesigner format)

  • URL: /projects/{projectId}/models/{modelId}:downloadModel
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • handlerClass - class preparing model file. For list of all possible values check /configuration/ response.
    • polygonString (*) - polygon defining part of the model for downloading
  • See also /configuration/ query to get list of possible formats
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38:downloalass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"
    

Download map as an image

  • URL: /projects/{projectId}/models/{modelId}:downloadImage
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • handlerClass - class preparing image file. For list of all possible values check /configuration/ response.
    • backgroundOverlayId (*) - identifier of the overlay used as a background overlay when creating image
    • overlayIds (*) - comma separated list of overlay identifiers that should be included in the image
    • zoomLevel (*) - zoom level at which image should be generated (min value used by default)
    • polygonString (*) - polygon defining part of the model for downloading
  • See also /configuration/ query to get list of possible formats
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38:downloadImage?handlerClass=lcsb.mapviewer.converter.graphics.PngImageGenerator" --output some.file
    

Get list of elements:

  • URL: /projects/{projectId}/models/{modelId}/bioEntities/elements/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • columns (*) - set of columns (optional). Possible values are: id, modelId, name, type, description, symbol, complexId, compartmentId, fullName, abbreviation, formula, name, synonyms, formerSymbols, references, bounds, hierarchyVisibilityLevel,
    • ids (*)- set of database ids (optional)
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38/bioEntities/elements/?columns=id,name,type"
    

Get list of reactions:

  • URL: /projects/{projectId}/models/{modelId}/bioEntities/reactions/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
      • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • columns (*) - set of columns. Possible values are: id, reactionId, modelId, type, lines, centerPoint, products, reactants, modifiers, hierarchyVisibilityLevel, notes
    • ids (*) - set of database ids
    • participantId (*) - identifier of the element that should be part of the reaction
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/example2/models/38/bioEntities/reactions/?columns=id,name,type"
    

Search for bio entities on the map:

  • URL: /projects/{projectId}/models/{modelId}/bioEntities:search
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • query (*) - search term identifying bioEntity
    • coordinates (*) - coordinates where bioEntity should be located
    • count (*) - max number of bioEntities to return
    • perfectMatch (*) - true when true query must be matched exactly, if false similar results are also acceptable
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/*/bioEntities:search?query=SNCA"
    

Get list of suggested search queries:

  • URL: /projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList
  • Method: GET
  • Output: List of suggested queries for search mechanism.
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/*/bioEntities/suggestedQueryList"
    

Get list of kinetic functions:

  • URL: /projects/{projectId}/models/{modelId}/functions/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/functions/"
    

Get information about specific kinetic functions:

  • URL: /projects/{projectId}/models/{modelId}/functions/{functionId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map
    • functionId - identifier of the function
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/functions/312"
    

Get list of kinetic parameters:

  • URL: /projects/{projectId}/models/{modelId}/parameters/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/parameters/"
    

Get information about specific kinetic parameters:

  • URL: /projects/{projectId}/models/{modelId}/parameters/{paramId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map
    • paramId - identifier of the parameter
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/parameters/589"
    

Get list of kinetic units:

  • URL: /projects/{projectId}/models/{modelId}/units/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map in the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/units/"
    

Get information about specific kinetic unit:

  • URL: /projects/{projectId}/models/{modelId}/units/{unitId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the map
    • unitId - identifier of the unit
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/units/16"
    

Chemicals

Get list of suggested chemical queries in the context of the project

  • URL: /projects/{projectId}/chemicals/suggestedQueryList
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/chemicals/suggestedQueryList"
    

Search chemical in the context of the project

  • URL: /projects/{projectId}/chemicals:search
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • columns (*) - set of columns for each result. Possible values are: name, references, description, directEvidenceReferences, directEvidence, synonyms, id, targets,
    • query (*) - chemical name
    • target (*) - target for which we are looking for chemicals. Target is defined as TYPE:ID. For example “ALIAS:534” is searching for chemicals that target Alias with id=534.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/chemicals:search?query=rotenone"
    

Comments

Get list of comments

  • URL: /projects/{projectId}/comments/models/{modelId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • columns (*) - set of columns for each result. Possible values are: title, type, content, removed, coord, modelId, elementId, id, pinned, author, email,
    • removed (*) - if defined then removed parameter must match.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/comments/models/*/"
    

Get comments for specific reaction

  • URL: /projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • reactionId - identifier of the reaction
    • columns (*) - set of columns for each result. Possible values are: title, type, content, removed, coord, modelId, elementId, id, pinned, author, email,
    • removed (*) - if defined then removed parameter must match.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/comments/models/*/bioEntities/reactions/30614"
    

Get comments for specific element

  • URL: /projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
    • elementId - identifier of the element
    • columns (*) - set of columns for each result. Possible values are: title, type, content, removed, coord, modelId, elementId, id, pinned, author, email,
    • removed (*) - if defined then removed parameter must match.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva//api//projects/PD_150625_3/comments/models/*/bioEntities/elements/88232
    

Get comments for specific point

  • URL: /projects/{projectId}/comments/models/{modelId}/points/{coordinates}
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project or wildcard ‘*’ character
      • coordinates - coordinates of the point on (sub)map
      • columns (*) - set of columns for each result. Possible values are: title, type, content, removed, coord, modelId, elementId, id, pinned, author, email,
      • removed (*) - if defined then removed parameter must match.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    https://minerva-dev.lcsb.uni.lu/minerva//api//projects/PD_150625_3/comments/models/*/points/2488.78,2030.00
    

Create element comment

  • URL: /projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}
  • Method: POST
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • elementId - identifier of the element to be commented
    • name - name of the author
    • email - email of the author
    • content - content of the comment
    • pinned (*) - when true comment will be visible for others, if false then nobody except of admin will see it
    • coordinates - coordinates where comment is placed
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     --data "name=testComment&email=a@a.pl&content=someCont&coordinates=1,2" \
    https://minerva-dev.lcsb.uni.lu/minerva//api//projects/PD_150625_3/comments/models/70/bioEntities/elements/88232
    

Create reaction comment

  • URL: /projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}
  • Method: POST
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • reactionId - identifier of the reaction
    • name - name of the author
    • email - email of the author
    • content - content of the comment
    • pinned (*) - when true comment will be visible for others, if false then nobody except of admin will see it
    • coordinates - coordinates where comment is placed
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    --data "name=testComment&email=a@a.pl&content=someCont&coordinates=1,2" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/comments/models/70/bioEntities/reactions/30614"
    

Create coordinates comment

  • URL: /projects/{projectId}/comments/models/{modelId}/points/{coordinates}
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • name - name of the author
    • email - email of the author
    • content - content of the comment
    • pinned (*) - when true comment will be visible for others, if false then nobody except of admin will see it
    • coordinates - coordinates where comment is placed
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    --data "name=testComment&email=a@a.pl&content=someCont" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/comments/models/70/points/1.00,2.00
    

Delete comment

  • URL: /projects/{projectId}/comments/{commentId}/
  • Method: DELETE
  • Parameters:
    • projectId - identifier of the project
    • commentId - identifier of the comment
  • Example:
    curl -X DELETE --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/comments/53/
    

Drugs

Get list of suggested drug queries in the context of the project

  • URL: /projects/{projectId}/drugs/suggestedQueryList
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/drugs/suggestedQueryList"
    

Search drug in the context of the project

  • URL: /projects/{projectId}/drugs:search
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • columns (*) - set of columns for each result. Possible values are: name, references, description, bloodBrainBarrier, brandNames, synonyms, id, targets,
    • query (*) - drug name or synonym
    • target (*) - target for which we are looking for drugs. Target is defined as TYPE:ID. For example “ALIAS:534” is searching for drugs that target Alias with id=534.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/drugs:search?query=aspirin
    

MiRNAs

Get list of suggested MiRNA queries in the context of the project

  • URL: /projects/{projectId}/miRnas/suggestedQueryList
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/miRnas/suggestedQueryList"
    

Search MiRNA in the context of the project

  • URL: /projects/{projectId}/miRnas:search
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • columns (*) - set of columns for each result. Possible values are: name, id, targets,
    • query (*) - miRNA id
    • target (*) - target for which we are looking for miRnas. Target is defined as TYPE:ID. For example “ALIAS:534” is searching for miRnas that target Alias with id=534.
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/miRnas:search?query=hsa-miR-125a-3p
    

Data overlays

List data overlays

  • URL: /projects/{projectId}/overlays/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • creator - login of the user who owns the data overlay (access to other user overlays is possible only when proper privileges are granted)
    • publicOverlay - true/false - are we interested in public overlays or private custom data sets
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/?publicOverlay=true"
    

Add overlay

  • URL: /projects/{projectId}/overlays/
  • Method: POST
  • Parameters:
    • projectId - identifier of the project
    • name - name of the data overlay
    • content - content of the file that is uploaded with definition what should be visible where
    • description - short description of the data overlay
    • filename - name of the file that should be used when downloading the source
    • googleLicenseConsent - true/false indicating if user agreed to the new Google Maps API license https://cloud.google.com/maps-platform/terms/
  • Example:
    curl -X POST --data "content=name%09color%0ACAPN1%09%2300FF00%0APARK7%09%23AC0000&description=test%20description&filename=test.txt&name=test%20name&googleLicenseConsent=true" \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/"
    

Update overlay

  • URL: /projects/{projectId}/overlays/{overlayId}/
  • Method: PATCH
  • Parameters:
    • projectId - identifier of the project
    • overlayId - identifier of data overlay
    • Body: json with updated overlay
    • name
    • description
  • Example:
    curl -X PATCH --data "{\"overlay\":{\"name\":\"test\", \"description\":\"test2\"}}" \
     --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/505/"
    

Remove overlay

  • URL: /projects/{projectId}/overlays/{overlayId}/
  • Method: DELETE
  • Parameters:
    • projectId - identifier of the project
    • overlayId - identifier of data overlay
  • Example:
    curl -X DELETE --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/505/"
    

Download source of data overlay

  • URL: /projects/{projectId}/overlays/{overlayId}:downloadSource
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • overlayId - identifier of data overlay
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504:downloadSource"
    

Data overlay details

  • URL: /projects/{projectId}/overlays/{overlayId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • overlayId - identifier of data overlay
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504/
    

bioEntities (Elements and reactions)

  • URL: /projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • overlayId - identifier of data overlay
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504/models/*/bioEntities/
    

Get reaction for data overlay

  • URL: /projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • overlayId - identifier of data overlay
      • reactionId - identifier of the reaction
    • Example:
      curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
       https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504/models/70/bioEntities/reactions/187811/
      

Get element for data overlay

  • URL: /projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/
  • Method: GET
  • Parameters:
    • projectId - identifier of the project
    • modelId - identifier of the (sub)map in the project
    • overlayId - identifier of data overlay
    • elementId - identifier of the element
  • Example:
    curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
     https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504/models/70/bioEntities/elements/89167/