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Projects
- Project data
- Privileges
- Maps
- List all maps in a project
- Get info about specific map
- Get info about connections between the maps
- Update specific map
- Download map as a model file (i.e. in CellDesigner format)
- Download map as an image
- Get list of elements:
- Get list of reactions
- Search for bio entities on the map
- Get list of suggested search queries
- Get list of kinetic functions
- Get information about specific kinetic functions
- Get list of kinetic parameters
- Get information about specific kinetic parameters
- Get list of kinetic units
- Get information about specific kinetic unit
- Chemicals
- Comments
- Drugs
- MiRNAs
- Data overlays
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 projectfile-id
- identifier of the file that should be used to create project. Information how to upload files can be found hereparser
- class of the parser that should be used for parsing the file. List of all available parser is included in configuration inmodelFormats
listcache
- should the data from external sources be cached after project was createddescription
- description of the projectnotify-email
- email address that should be when something change in the projectdisease
- disease associated with the project (MESH id)name
- name of the projectorganism
- organism associated with the project (TAXONOMY id)sbgn
- should the map be visualized in sbgn-like waysemantic-zoom
- should custom semantic zooming be enabled (true/false)version
- version of the projectmapCanvasType
- 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 inmapCanvasTypes
annotate
- should the project be automatically annotatedverify-annotations
- should the annotations be verifiedzip-entries
- array of parameters describing each file in the zipped input file, file-index is number starting from 0zip-entries[{file-index}][_filename]
- name of the filezip-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 mapzip-entries[{file-index}][_data][name]
- for overlays - name of the overlayzip-entries[{file-index}][_data][description]
- for overlays - description of the overlay
-
Example:
- 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"
- 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 submapzip-entries[1]
- depicts main map of the project
- Simple file
Update project
- URL:
/projects/{projectId}/
- Method: PATCH
- Parameters:
projectId
- identifier of the project- body - json object with changes to apply
version
- version of the projectname
- name of the projectnotifyEmail
- email address that should be when something change in the projectorganism
- 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 inmapCanvasTypes
- 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 projectstart
- 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ characterstart
(*) - 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/
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"
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 projectmodelId
- 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 projectmodelId
- identifier of the map in the project- body - json object with the changes
defaultCenterX
- default center x coordinate used during first opening of the mapdefaultCenterY
- default center y coordinate used during first opening of the mapdefaultZoomLevel
- 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 projectmodelId
- identifier of the (sub)map in the projecthandlerClass
- class preparing model file. For list of all possible values check/configuration/
response.polygonString
(*) - polygon defining part of the model for downloadingelementIds
(*) - list of element ids that should be included in the outputreactionIds
(*) - 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 projectmodelId
- identifier of the (sub)map in the projecthandlerClass
- 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 imageoverlayIds
(*) - comma separated list of overlay identifiers that should be included in the imagezoomLevel
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ charactercolumns
(*) - 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 projectmodelId
- 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, notesid
(*) - set of database idsparticipantId
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ characterquery
(*) - search term identifying bioEntitycoordinates
(*) - coordinates where bioEntity should be locatedcount
(*) - max number of bioEntities to returnperfectMatch
(*) - 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 projectmodelId
- 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 projectmodelId
- 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 projectmodelId
- identifier of the mapfunctionId
- 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 projectmodelId
- 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 projectmodelId
- identifier of the mapparamId
- 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 projectmodelId
- 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 projectmodelId
- identifier of the mapunitId
- identifier of the unit
- Example:
curl -X GET "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 "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 projectcolumns
(*) - set of columns for each result. Possible values are: name, references, description, directEvidenceReferences, directEvidence, synonyms, id, targets,query
(*) - chemical nametarget
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ charactercolumns
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ characterreactionId
- identifier of the reactioncolumns
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ characterelementId
- identifier of the elementcolumns
(*) - 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 projectmodelId
- identifier of the (sub)map in the project or wildcard ‘*’ charactercoordinates
- coordinates of the point on (sub)mapcolumns
(*) - 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 projectmodelId
- identifier of the (sub)map in the projectelementId
- identifier of the element to be commentedname
- name of the authoremail
- email of the authorcontent
- content of the commentpinned
(*) - when true comment will be visible for others, if false then nobody except of admin will see itcoordinates
- 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 projectmodelId
- identifier of the (sub)map in the projectreactionId
- identifier of the reactionname
- name of the authoremail
- email of the authorcontent
- content of the commentpinned
(*) - when true comment will be visible for others, if false then nobody except of admin will see itcoordinates
- 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 projectmodelId
- identifier of the (sub)map in the projectname
- name of the authoremail
- email of the authorcontent
- content of the commentpinned
(*) - when true comment will be visible for others, if false then nobody except of admin will see itcoordinates
- 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 projectcommentId
- 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 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 projectcolumns
(*) - set of columns for each result. Possible values are: name, references, description, bloodBrainBarrier, brandNames, synonyms, id, targets,query
(*) - drug name or synonymtarget
(*) - 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
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 projectcolumns
(*) - set of columns for each result. Possible values are: name, id, targets,query
(*) - miRNA idtarget
(*) - 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
Data overlays
List data overlays
- URL:
/projects/{projectId}/overlays/
- Method: GET
- Parameters:
projectId
- identifier of the projectcreator
- 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 projectname
- name of the data overlaycontent
- content of the file that is uploaded with definition what should be visible wheredescription
- short description of the data overlayfilename
- name of the file that should be used when downloading the sourcegoogleLicenseConsent
- 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 projectoverlayId
- 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 projectoverlayId
- 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 projectoverlayId
- 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 projectoverlayId
- 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 projectoverlayId
- 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 projectmodelId
- identifier of the (sub)map in the projectoverlayId
- identifier of data overlayreactionId
- 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 projectmodelId
- identifier of the (sub)map in the projectoverlayId
- identifier of data overlayelementId
- 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/