Projects#

Project data#

List projects#

• URL: /projects/
• Method: GET
• Parameters: NONE
• Example:

curl -X GET 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3

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"

  1. 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 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 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/*/publications/

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Privileges#

Grant privilege#

• URL: /projects/{projectId}:grantPrivileges
• Method: PATCH
• Parameters:
  • projectId - identifier of the project
  • body - json object with list of privileges to grant
• Example:

curl -X PATCH --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
--data-binary '[{"login":"admin","privilegeType":"READ_PROJECT"}]' \
 "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3:grantPrivileges"

Revoke privilege#

• URL: /projects/{projectId}:revokePrivileges
• Method: PATCH
• Parameters:
  • projectId - identifier of the project
  • body - json object with list of privileges to revoke
• Example:

curl -X PATCH --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
--data-binary '[{"login":"admin","privilegeType":"READ_PROJECT"}]' \
 "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3:revokePrivileges"

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Maps#

List all maps in a project#

• URL: /projects/{projectId}/models/
• Method: GET
• Parameters:
  • projectId - identifier of the project
• Example:

curl -X GET 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/70/

Get info about connections between the maps#

• URL: /projects/{projectId}/submapConnections
• Method: GET
• Parameters:
  • projectId - identifier of the project
• Example:

curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/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/PD_150625_3/models/70/"

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

• URL: /projects/{projectId}/models/{modelId}:downloadModel
• Method: GET, POST
• 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
  • elementIds (*) - list of element ids that should be included in the output
  • reactionIds (*) - list of reaction ids that should be included in the output
• See also /configuration/ query to get list of possible formats
• Example:

curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/70:downloadModel?handlerClass=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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/70: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,
  • id (*)- set of database ids (optional)
• Example:

curl -X GET "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/70/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
  • id (*) - set of database ids
  • participantId (*) - identifier of the element that should be part of the reaction
• Example:

curl -X GET "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/models/70/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 "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 "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 "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 "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 "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 "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 "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 "https://minerva-dev.lcsb.uni.lu/minerva/api/projects/ASTHMA_V40_M06/models/*/units/16"

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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 "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 "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 "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 "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 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 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/

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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 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/drugs:search?query=aspirin

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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 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/miRnas:search?query=hsa-miR-125a-3p

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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 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 "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 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 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 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 https://minerva-dev.lcsb.uni.lu/minerva/api/projects/PD_150625_3/overlays/504/models/70/bioEntities/elements/89167/

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