1. List maps

List all (sub)maps in a project.

1.1. Path Parameters

Table 1. /projects/{projectId}/models/
Parameter Description

projectId

project identifier

1.2. Response Fields

Path Type Description

[]

array<Map>

list of maps

1.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/empty/models/' -i -X GET

1.4. Sample Response

[ {
  "name" : null,
  "idObject" : 3,
  "tileSize" : 256,
  "width" : 25195,
  "height" : 14285,
  "defaultCenterX" : null,
  "defaultCenterY" : null,
  "defaultZoomLevel" : null,
  "minZoom" : 2,
  "maxZoom" : 9,
  "submodelType" : "UNKNOWN",
  "references" : [ ],
  "authors" : [ ],
  "creationDate" : null,
  "modificationDates" : [ ],
  "description" : null
} ]

2. Get by id

Returns map identified by id.

2.1. Path Parameters

Table 2. /projects/{projectId}/models/{mapId}
Parameter Description

projectId

project identifier

mapId

map identifier

2.2. Response Fields

Path Type Description

name

string

name of the map

description

string

description

idObject

number

map id

width

number

map width

height

number

map height

tileSize

number

size of the png tile used to visualize in frontend

defaultCenterX

number

default x center used in frontend visualization

defaultCenterY

number

default y center used in frontend visualization

defaultZoomLevel

number

default zoom level used in frontend visualization

minZoom

number

minimum zoom level availbale for the map

maxZoom

number

maximum zoom level available for the map

submodelType

string

type of the submap

authors

array<Author>

list of authors

references

array<Reference>

list of references

creationDate

timestamp

creation date

modificationDates

array<timestamp>

modification dates

2.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/669' -i -X GET

2.4. Sample Response

{
  "name" : null,
  "idObject" : 669,
  "tileSize" : 256,
  "width" : 100,
  "height" : 100,
  "defaultCenterX" : null,
  "defaultCenterY" : null,
  "defaultZoomLevel" : null,
  "minZoom" : 2,
  "maxZoom" : 2,
  "submodelType" : "UNKNOWN",
  "references" : [ ],
  "authors" : [ ],
  "creationDate" : null,
  "modificationDates" : [ ],
  "description" : ""
}

3. Update map

Updates map data.

3.1. Path Parameters

Table 3. /projects/{projectId}/models/{mapId}
Parameter Description

projectId

project identifier

mapId

map identifier

3.2. Request Fields

Path Type Description

model.defaultCenterX

number

default x center used in frontend visualization

model.defaultCenterY

number

default y center used in frontend visualization

model.defaultZoomLevel

number

default zoom level used in frontend visualization

3.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/212' -i -X PATCH \
    -d '{"model":{"defaultCenterX":10, "defaultCenterY":20, "defaultZoomLevel":3}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

3.4. Sample Response

{
  "name" : "map_name",
  "idObject" : 212,
  "tileSize" : 256,
  "width" : 100,
  "height" : 100,
  "defaultCenterX" : 10.0,
  "defaultCenterY" : 20.0,
  "defaultZoomLevel" : 3,
  "minZoom" : 2,
  "maxZoom" : 2,
  "submodelType" : "UNKNOWN",
  "references" : [ ],
  "authors" : [ ],
  "creationDate" : null,
  "modificationDates" : [ ],
  "description" : ""
}

4. Get connections between maps

Returns list of connections between (sub)maps in a project.

4.1. Path Parameters

Table 4. /projects/{projectId}/submapConnections/
Parameter Description

projectId

project identifier

4.2. Response Fields

Path Type Description

[]

array

list of connections

4.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/empty/submapConnections/' -i -X GET

4.4. Sample Response

[ ]

5. Download map

Download map in a standard format.

5.1. Path Parameters

Table 5. /projects/{projectId}/models/{mapId}:downloadModel
Parameter Description

projectId

project identifier

mapId

map identifier

5.2. Request Parameters

Parameter Description

handlerClass

class preparing model file. Available options: lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser, lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter, lcsb.mapviewer.converter.model.sbml.SbmlParser, lcsb.mapviewer.wikipathway.GpmlParser

polygonString

polygon defining part of the model to be downloaded

elementIds

list of element ids that should be included in the output

reactionIds

list of reaction ids that should be included in the output

5.3. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/671:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser' -i -X GET

5.4. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/670:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&polygonString=0,0;100,0;0,100' -i -X GET

5.5. CURL sample 3

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/665:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&elementIds=1032' -i -X GET

6. Download map as image

Download map as image.

6.1. Path Parameters

Table 6. /projects/{projectId}/models/{mapId}:downloadImage
Parameter Description

projectId

project identifier

mapId

map identifier

6.2. Request Parameters

Parameter Description

handlerClass

class preparing image. Available options: lcsb.mapviewer.converter.graphics.PngImageGenerator, lcsb.mapviewer.converter.graphics.PdfImageGenerator, lcsb.mapviewer.converter.graphics.SvgImageGenerator

polygonString

polygon defining part of the map to be downloaded

backgroundOverlayId

identifier of the overlay used as a background when creating image

zoomLevel

zoom level at which image should be generated (min value used by default)

overlayIds

comma separated list of overlay identifiers that should be included in the image

6.3. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/250:downloadImage?handlerClass=lcsb.mapviewer.converter.graphics.PngImageGenerator' -i -X GET

6.4. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/242:downloadImage?handlerClass=lcsb.mapviewer.converter.graphics.PdfImageGenerator&polygonString=0,0;100,0;100,100;0,100' -i -X GET

7. Get elements

Get list of elements.

7.1. Path Parameters

Table 7. /projects/{projectId}/models/{mapId}/bioEntities/elements/
Parameter Description

projectId

project identifier

mapId

map identifier

7.2. Request Parameters

Parameter Description

id

set of database ids (all by default)

columns

set of columns (all by default). Available options: id, elementId, modelId, name, type, notes, symbol, complexId, compartmentId, fullName, abbreviation, formula, synonyms, formerSymbols, references, bounds, hierarchyVisibilityLevel, transparencyLevel, linkedSubmodel, other, initialConcentration, boundaryCondition, constant, hypothetical, activity, initialAmount, glyph, homomultimer

includedCompartmentIds

set of database compartment ids (all by default)

excludedCompartmentIds

set of database compartment ids (none by default)

type

element type (all by default). Available options: Antisense RNA, Compartment, Complex, Degraded, Drug, Gene, Ion, Pathway, Phenotype, Protein, RNA, Simple molecule, Unknown

7.3. Response Fields

Path Type Description

[].id

number

unique element identifier

[].elementId

string

element identifier taken from source file

[].name

string

name

[].modelId

number

map identifier

[].complexId

number

identifier of a complex in which element is located

[].compartmentId

number

identifier of a compartment in which element is located

[].linkedSubmodel

number

identifier of a submap to which this element is an entry point (anchor)

[].type

string

element type

[].bounds

object

coordinates and the dimension of the element on the map

[].hierarchyVisibilityLevel

string

at what zoom level this element becomes visible in hierarchical view

[].transparencyLevel

string

at what zoom level this element becomes transparent in hierarchical view

[].synonyms

array<string>

list of synonyms

[].formerSymbols

array<string>

list of former symbols

[].references

array<Reference>

list of references

[].notes

string

notes and description

[].symbol

string

symbol

[].fullName

string

full name

[].abbreviation

string

abbreviation

[].formula

string

formula

[].boundaryCondition

boolean

SBML kinetics is boundary condition

[].constant

boolean

SBML kinetics is constant

[].initialAmount

number

SBML kinetics initial amount

[].initialConcentration

boolean

SBML kinetics initial concentration

[].glyph

Glyph

image glyph associated with the element

[].glyph.fileId

Glyph

id of file associated with the glyph

[].activity

boolean

is the element active

[].hypothetical

boolean

is the element hypothetical

[].homomultimer

int

multimer value

[].other

object

list of oher properties

7.4. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities/elements/' -i -X GET

7.5. Sample Response 1

[ {
  "abbreviation" : null,
  "activity" : false,
  "boundaryCondition" : false,
  "bounds" : {
    "height" : 20.0,
    "width" : 100.0,
    "x" : 10.0,
    "y" : 20.0,
    "z" : 10
  },
  "compartmentId" : null,
  "complexId" : null,
  "constant" : false,
  "elementId" : "p1",
  "formerSymbols" : [ ],
  "formula" : null,
  "fullName" : null,
  "glyph" : {
    "fileId" : 511
  },
  "hierarchyVisibilityLevel" : "",
  "homomultimer" : 1,
  "hypothetical" : false,
  "id" : 1033,
  "initialAmount" : null,
  "initialConcentration" : 0.0,
  "linkedSubmodel" : null,
  "modelId" : 666,
  "name" : "GSTA4",
  "notes" : "",
  "other" : {
    "modifications" : [ ],
    "structuralState" : null,
    "structures" : { }
  },
  "references" : [ ],
  "symbol" : null,
  "synonyms" : [ ],
  "transparencyLevel" : "",
  "type" : "Protein"
} ]

7.6. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities/elements/?columns=name,complexId&type=Protein' -i -X GET

8. Get reactions

Get list of reactions.

8.1. Path Parameters

Table 8. /projects/{projectId}/models/{mapId}/bioEntities/reactions/
Parameter Description

projectId

project identifier

mapId

map identifier

8.2. Request Parameters

Parameter Description

id

set of database ids (all by default)

columns

set of columns (all by default). Available options: id, reactionId, modelId, type, lines, kineticLaw, centerPoint, products, reactants, modifiers, hierarchyVisibilityLevel, references, notes

participantId

set of element identifiers for which reaction we are looking for (only reactions with at least one participant will be returned)

8.3. Response Fields

Path Type Description

[].id

number

unique element identifier

[].reactionId

string

reaction identifier taken from source file

[].modelId

number

map identifier

[].type

string

reaction type

[].centerPoint

point

center point

[].lines

array<line>

list of lines used to draw reaction

[].hierarchyVisibilityLevel

string

at what zoom level this element becomes visible in hierarchical view

[].references

array<Reference>

list of references

[].modifiers

array<object>

list of modifiers

[].reactants

array<object>

list of reactants

[].products

array<object>

list of products

[].notes

string

notes and description

[].kineticLaw

object

SBML kinetics law

[].other

object

list of oher properties

8.4. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities/reactions/' -i -X GET

8.5. Sample Response 1

[ {
  "centerPoint" : {
    "x" : 5.0,
    "y" : 0.0
  },
  "hierarchyVisibilityLevel" : "",
  "id" : 120,
  "kineticLaw" : null,
  "lines" : [ {
    "start" : {
      "x" : 10.0,
      "y" : 0.0
    },
    "end" : {
      "x" : 0.0,
      "y" : 0.0
    },
    "type" : "START"
  }, {
    "start" : {
      "x" : 10.0,
      "y" : 0.0
    },
    "end" : {
      "x" : 20.0,
      "y" : 0.0
    },
    "type" : "END"
  } ],
  "modelId" : 244,
  "modifiers" : [ ],
  "notes" : "",
  "products" : [ {
    "aliasId" : 360,
    "stoichiometry" : null
  } ],
  "reactants" : [ {
    "aliasId" : 360,
    "stoichiometry" : null
  } ],
  "reactionId" : "re1",
  "references" : [ {
    "annotatorClassName" : "",
    "article" : {
      "id" : 0,
      "title" : "MINERVA-a platform for visualization and curation of molecular interaction networks.",
      "authors" : [ "Gawron P", " Ostaszewski M", " Satagopam V", " Gebel S", " Mazein A", " Kuzma M", " Zorzan S", " McGee F", " Otjacques B", " Balling R", " Schneider R." ],
      "journal" : "NPJ systems biology and applications",
      "year" : 2016,
      "link" : "https://www.ncbi.nlm.nih.gov/pubmed/28725475",
      "pubmedId" : "28725475",
      "citationCount" : 21,
      "stringAuthors" : "Gawron P,  Ostaszewski M,  Satagopam V,  Gebel S,  Mazein A,  Kuzma M,  Zorzan S,  McGee F,  Otjacques B,  Balling R,  Schneider R."
    },
    "id" : 368,
    "link" : "https://www.ncbi.nlm.nih.gov/pubmed/28725475",
    "resource" : "28725475",
    "type" : "PUBMED"
  } ],
  "type" : "Transport"
} ]

8.6. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities/reactions/?columns=id,notes' -i -X GET

9. Search for bio entities

Returns list of bio entities matching the query.

9.1. Path Parameters

Table 9. /projects/{projectId}/models/{mapId}/bioEntities:search
Parameter Description

projectId

project identifier

mapId

map identifier

9.2. Request Parameters

Parameter Description

query

search term identifying bioEntity

coordinates

coordinates where bioEntity should be located

count

max number of bioEntities to return

type

type of bioEntity, available values are: antisense rna, catalysis, compartment, complex, degraded, dissociation, drug, gene, heterodimer association, inhibition, ion, known transition omitted, modulation, negative influence, pathway, phenotype, physical stimulation, positive influence, protein, reduced modulation, reduced physical stimulation, reduced trigger, rna, simple molecule, state transition, transcription, translation, transport, trigger, truncation, unknown, unknown catalysis, unknown inhibition, unknown negative influence, unknown positive influence, unknown reduced modulation, unknown reduced physical stimulation, unknown reduced trigger, unknown transition

perfectMatch

true when true query must be matched exactly, if false similar results are also acceptable

9.3. Response Fields

Path Type Description

[].id

number

unique element identifier

[].modelId

number

map identifier

[].type

string

type of the bioEntity (available options: ALIAS, REACTION)

9.4. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities:search?query=p1' -i -X GET

9.5. Sample Response 1

[ {
  "id" : 345,
  "modelId" : 234,
  "type" : "ALIAS"
} ]

9.6. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/196/bioEntities:search?coordinates=104.36,182.81' -i -X GET

10. Get list of suggested search queries

10.1. Path Parameters

Table 10. /projects/{projectId}/models/{mapId}/bioEntities/suggestedQueryList
Parameter Description

projectId

project identifier

mapId

map identifier

10.2. Response Fields

Path Type Description

[]

array<string>

list of all full search queries that could be used for quering the map

10.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/bioEntities/suggestedQueryList' -i -X GET

10.4. Sample Response

[ "gsta4", "water" ]

11. Kinetic functions

Get list of kinetic functions.

11.1. Path Parameters

Table 11. /projects/{projectId}/models/{mapId}/functions/
Parameter Description

projectId

project identifier

mapId

map identifier

11.2. Response Fields

Path Type Description

[]

Array

list of functions

[].id

number

unique function identifier

[].name

string

name

[].definition

string

definition

[].functionId

string

function identifier taken from source file

[].arguments

array<object>

list of function parameters

11.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/780/functions/' -i -X GET

11.4. Sample Response

[ {
  "arguments" : [ ],
  "definition" : "test",
  "functionId" : "f1",
  "id" : 367,
  "name" : "name"
} ]

12. Kinetic function

Get information about specific kinetic function.

12.1. Path Parameters

Table 12. /projects/{projectId}/models/{mapId}/functions/{functionId}
Parameter Description

projectId

project identifier

mapId

map identifier

functionId

function identifier

12.2. Response Fields

Path Type Description

id

number

unique function identifier

name

string

name

definition

string

definition

functionId

string

function identifier taken from source file

arguments

array<object>

list of function parameters

12.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/778/functions/366' -i -X GET

12.4. Sample Response

{
  "arguments" : [ ],
  "definition" : "test",
  "functionId" : "f1",
  "id" : 366,
  "name" : "name"
}

13. Kinetic parameters

Get list of kinetic parameters.

13.1. Path Parameters

Table 13. /projects/{projectId}/models/{mapId}/parameters/
Parameter Description

projectId

project identifier

mapId

map identifier

13.2. Response Fields

Path Type Description

[]

Array

list of parameters

[].id

number

unique parameter identifier

[].name

string

name

[].value

number

value

[].unitsId

number

unit identifier

[].global

boolean

is parameter global

[].parameterId

string

parameter identifier taken from source file

13.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/parameters/' -i -X GET

13.4. Sample Response

[ {
  "global" : true,
  "id" : 364,
  "name" : "ppp",
  "parameterId" : "param1",
  "unitsId" : null,
  "value" : 1.0
} ]

14. Kinetic parameter

Get information about specific kinetic parameter.

14.1. Path Parameters

Table 14. /projects/{projectId}/models/{mapId}/parameters/{parameterId}
Parameter Description

projectId

project identifier

mapId

map identifier

parameterId

parameter identifier

14.2. Response Fields

Path Type Description

id

number

unique parameter identifier

name

string

name

value

number

value

unitsId

number

unit identifier

global

boolean

is parameter global

parameterId

string

parameter identifier taken from source file

14.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/parameters/362' -i -X GET

14.4. Sample Response

{
  "global" : true,
  "id" : 362,
  "name" : "ppp",
  "parameterId" : "param1",
  "unitsId" : null,
  "value" : 1.0
}

15. Get units

Get list of units.

15.1. Path Parameters

Table 15. /projects/{projectId}/models/{mapId}/units/
Parameter Description

projectId

project identifier

mapId

map identifier

15.2. Response Fields

Path Type Description

[]

Array

list of units

[].id

number

unique unit identifier

[].name

string

name

[].unitTypeFactors

array<object>

in complex unit this define how specific unit types are associated

[].unitId

string

unit identifier taken from source file

15.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/units/' -i -X GET

15.4. Sample Response

[ {
  "id" : 433,
  "name" : "uuu",
  "unitId" : "u1",
  "unitTypeFactors" : [ ]
} ]

16. Get unit

Get information about specific unit.

16.1. Path Parameters

Table 16. /projects/{projectId}/models/{mapId}/units/{unitId}
Parameter Description

projectId

project identifier

mapId

map identifier

unitId

unit identifier

16.2. Response Fields

Path Type Description

id

number

unique unit identifier

name

string

name

unitTypeFactors

array<object>

in complex unit this define how specific unit types are associated

unitId

string

unit identifier taken from source file

16.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/*/units/434' -i -X GET

16.4. Sample Response

{
  "id" : 434,
  "name" : "uuu",
  "unitId" : "u1",
  "unitTypeFactors" : [ ]
}