1. List maps
List all (sub)maps in a project.
1.1. Path Parameters
Parameter | Description |
---|---|
|
project identifier |
1.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
2.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
name of the map |
|
|
description |
|
|
map id |
|
|
map width |
|
|
map height |
|
|
size of the png tile used to visualize in frontend |
|
|
default x center used in frontend visualization |
|
|
default y center used in frontend visualization |
|
|
default zoom level used in frontend visualization |
|
|
minimum zoom level availbale for the map |
|
|
maximum zoom level available for the map |
|
|
type of the submap |
|
|
list of authors |
|
|
list of references |
|
|
creation date |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
3.2. Request Fields
Path | Type | Description |
---|---|---|
|
|
default x center used in frontend visualization |
|
|
default y center used in frontend visualization |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
4.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
5.2. Request Parameters
Parameter | Description |
---|---|
|
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 |
|
polygon defining part of the model to be downloaded |
|
list of element ids that should be included in the output |
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
6.2. Request Parameters
Parameter | Description |
---|---|
|
class preparing image. Available options: lcsb.mapviewer.converter.graphics.PngImageGenerator, lcsb.mapviewer.converter.graphics.PdfImageGenerator, lcsb.mapviewer.converter.graphics.SvgImageGenerator |
|
polygon defining part of the map to be downloaded |
|
identifier of the overlay used as a background when creating image |
|
zoom level at which image should be generated (min value used by default) |
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
7.2. Request Parameters
Parameter | Description |
---|---|
|
set of database ids (all by default) |
|
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 |
|
set of database compartment ids (all by default) |
|
set of database compartment ids (none by default) |
|
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 |
---|---|---|
|
|
unique element identifier |
|
|
element identifier taken from source file |
|
|
name |
|
|
map identifier |
|
|
identifier of a complex in which element is located |
|
|
identifier of a compartment in which element is located |
|
|
identifier of a submap to which this element is an entry point (anchor) |
|
|
element type |
|
|
coordinates and the dimension of the element on the map |
|
|
at what zoom level this element becomes visible in hierarchical view |
|
|
at what zoom level this element becomes transparent in hierarchical view |
|
|
list of synonyms |
|
|
list of former symbols |
|
|
list of references |
|
|
notes and description |
|
|
symbol |
|
|
full name |
|
|
abbreviation |
|
|
formula |
|
|
SBML kinetics is boundary condition |
|
|
SBML kinetics is constant |
|
|
SBML kinetics initial amount |
|
|
SBML kinetics initial concentration |
|
|
image glyph associated with the element |
|
|
id of file associated with the glyph |
|
|
is the element active |
|
|
is the element hypothetical |
|
|
multimer value |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
8.2. Request Parameters
Parameter | Description |
---|---|
|
set of database ids (all by default) |
|
set of columns (all by default). Available options: id, reactionId, modelId, type, lines, kineticLaw, centerPoint, products, reactants, modifiers, hierarchyVisibilityLevel, references, notes |
|
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 |
---|---|---|
|
|
unique element identifier |
|
|
reaction identifier taken from source file |
|
|
map identifier |
|
|
reaction type |
|
|
center point |
|
|
list of lines used to draw reaction |
|
|
at what zoom level this element becomes visible in hierarchical view |
|
|
list of references |
|
|
list of modifiers |
|
|
list of reactants |
|
|
list of products |
|
|
notes and description |
|
|
SBML kinetics law |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
9.2. Request Parameters
Parameter | Description |
---|---|
|
search term identifying bioEntity |
|
coordinates where bioEntity should be located |
|
max number of bioEntities to return |
|
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 |
|
true when true query must be matched exactly, if false similar results are also acceptable |
9.3. Response Fields
Path | Type | Description |
---|---|---|
|
|
unique element identifier |
|
|
map identifier |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
10.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
11.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
list of functions |
|
|
unique function identifier |
|
|
name |
|
|
definition |
|
|
function identifier taken from source file |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
|
function identifier |
12.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
unique function identifier |
|
|
name |
|
|
definition |
|
|
function identifier taken from source file |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
13.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
list of parameters |
|
|
unique parameter identifier |
|
|
name |
|
|
value |
|
|
unit identifier |
|
|
is parameter global |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
|
parameter identifier |
14.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
unique parameter identifier |
|
|
name |
|
|
value |
|
|
unit identifier |
|
|
is parameter global |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
15.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
list of units |
|
|
unique unit identifier |
|
|
name |
|
|
in complex unit this define how specific unit types are associated |
|
|
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
Parameter | Description |
---|---|
|
project identifier |
|
map identifier |
|
unit identifier |
16.2. Response Fields
Path | Type | Description |
---|---|---|
|
|
unique unit identifier |
|
|
name |
|
|
in complex unit this define how specific unit types are associated |
|
|
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" : [ ]
}