Elements and reactions of a map, served from
/new_api/projects/{projectId}/maps/{mapId}/bio_entities.
1. Elements
Species/elements (proteins, genes, compartments, …) placed on the map.
See full documentation.
2. Reactions
A reaction links map elements as reactants, products, modifiers and operators; this lists the reactions defined in the map.
See full documentation.
3. Search for bio entities
Returns list of bio entities matching the query.
|
Note
|
The result is paged - use the page and size query parameters to
walk through it.
|
3.1. HTTP request
GET /minerva/new_api/projects/test_project/maps/*/bio_entities:search?query=GSTA&size=20&page=0&perfectMatch=false HTTP/1.13.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
3.3. Query Parameters
| Parameter | Description |
|---|---|
|
search term identifying bioEntity |
|
true when true query must be matched exactly, if false similar results are also acceptable |
|
index of the page to fetch, counted from 0; 0 by default |
|
number of entries on a page; 20 by default, 10000 at most |
3.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/*/bio_entities:search?query=GSTA&size=20&page=0&perfectMatch=false' -X GET3.5. HTTP response
HTTP/1.1 200 OK3.6. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of elements on the page |
|
|
element or reaction that matched the query |
|
|
is the bioEntity a perfect match to the search query |
|
|
link that should be opened immediately when element is clicked on the map |
|
|
unique bioEntity identifier |
|
|
name of the bioEntity displayed on the map |
|
|
element identifier taken from source file |
|
|
map identifier |
|
|
list of references |
|
|
z index (coordinate) of the element on the map |
|
|
notes and description |
|
|
at what zoom level this element becomes visible in hierarchical view |
|
|
multimer value |
|
|
SBO term identifying the type of the bioEntity |
|
|
short symbol identifying the element |
|
|
list of synonyms |
|
|
x coordinate of the element name on the map |
|
|
y coordinate of the element name on the map |
|
|
line type |
|
|
width of the box with element name |
|
|
height of the box with element name |
|
|
vertical align of the text inside the box with element name |
|
|
horizontal align of the text inside the box with element name |
|
|
font name used for element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA |
|
|
font weight for element label, one of: NORMAL, BOLD |
|
|
font style for element label, one of: NORMAL, ITALIC |
|
|
width of the element |
|
|
height of the element |
|
|
at what zoom level this element becomes transparent in hierarchical view |
|
|
list of former symbols |
|
|
unabbreviated name of the element |
|
|
image glyph associated with the element |
|
|
glyph id |
|
|
id of file associated with the glyph |
|
|
is the element active |
|
|
is the element hypothetical |
|
|
SBML kinetics is boundary condition |
|
|
SBML kinetics is constant |
|
|
SBML kinetics initial amount |
|
|
SBML kinetics initial concentration |
|
|
SBML charge |
|
|
SBML substance units |
|
|
SBML only substance units |
|
|
List of species modification residues |
|
|
Species structural state |
|
|
identifier of a complex in which element is located |
|
|
name of a complex in which element is located |
|
|
identifier of a compartment in which element is located |
|
|
identifier of a pathway in which element is located |
|
|
name of a compartment in which element is located |
|
|
submap to which this bioEntity is an entry point (anchor) |
|
|
submap id |
|
|
identifier of a submap to which this bioEntity is an entry point (anchor) |
|
|
type of submap connection |
|
|
x coordinate of the element on the map |
|
|
y coordinate of the element on the map |
|
|
border line width |
|
|
Species units |
|
|
color of the element label; |
|
|
size of the font used for the element label |
|
|
color used to fill the interior of the element; |
|
|
color used to draw the outline of the element; |
|
|
smiles identifier (for chemicals) |
|
|
inChI identifier (for chemicals) |
|
|
inChI key identifier (for chemicals) |
|
|
compartment membrane thickness |
|
|
compartment outer line width |
|
|
shape of a compartment |
|
|
compartment inner line width |
|
|
whether the element allows user interaction (e.g. clicking, hovering) |
|
|
reaction identifier taken from source file |
|
|
is reaction reversible |
|
|
reaction SBML kinetics law |
|
|
list of reaction products |
|
|
identifier of the element for this product |
|
|
SBML stoichiometry |
|
|
line used to draw product connection |
|
|
list of reaction reactants |
|
|
identifier of the element for this reactant |
|
|
SBML stoichiometry |
|
|
line used to draw reactant connection |
|
|
list of reaction modifiers |
|
|
identifier of the element for this modifier |
|
|
SBML stoichiometry |
|
|
SBO term identifying the type of the modifier |
|
|
line used to draw modifier connection |
|
|
coordinates of process in the reaction if defined manually. If this value is not present then center of line should be taken. |
|
|
reaction central line |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
reaction operators |
|
|
operator identifier |
|
|
line for the operator |
|
|
SBO term identifying the type of the operator |
|
|
total number of pages |
|
|
total number of elements |
|
|
number of elements on this page |
|
|
page size |
|
|
page number |
3.7. Sample Response
{
"content" : [ {
"bioEntity" : {
"id" : 493,
"glyph" : null,
"compartment" : null,
"pathway" : null,
"elementId" : "p8",
"x" : 10.0,
"y" : 20.0,
"z" : 18,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "GSTA4",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "GSTA_XX", "GSTA_YY" ],
"formerSymbols" : [ ],
"modificationResidues" : [ {
"id" : 51443,
"idModificationResidue" : "r9",
"name" : "",
"x" : 10.0,
"y" : 20.0,
"z" : 19,
"width" : 15.0,
"height" : 15.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 15.0,
"nameHeight" : 15.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 493,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r9"
}, {
"id" : 51444,
"idModificationResidue" : "",
"name" : "X",
"x" : 10.0,
"y" : 20.0,
"z" : 20,
"width" : 10.0,
"height" : 10.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 493,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
} ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : null,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : null,
"borderLineType" : "SOLID",
"map" : 189,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252",
"compartmentName" : null,
"complexName" : null
},
"perfect" : false
}, {
"bioEntity" : {
"id" : 494,
"glyph" : null,
"compartment" : 491,
"pathway" : null,
"elementId" : "p3",
"x" : 10.0,
"y" : 20.0,
"z" : 12,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "GSTA4",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "GSTA_XX", "GSTA_YY" ],
"formerSymbols" : [ ],
"modificationResidues" : [ {
"id" : 51445,
"idModificationResidue" : "r4",
"name" : "",
"x" : 10.0,
"y" : 20.0,
"z" : 13,
"width" : 15.0,
"height" : 15.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 15.0,
"nameHeight" : 15.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 494,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r4"
}, {
"id" : 51446,
"idModificationResidue" : "",
"name" : "X",
"x" : 10.0,
"y" : 20.0,
"z" : 14,
"width" : 10.0,
"height" : 10.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 494,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
}, {
"id" : 51447,
"idModificationResidue" : "b5",
"name" : "",
"x" : 60.0,
"y" : 20.0,
"z" : 15,
"width" : 10.0,
"height" : 10.0,
"nameX" : 60.0,
"nameY" : 20.0,
"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 494,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000494",
"size" : 100.0,
"elementId" : "b5"
} ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : 492,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : {
"id" : 162,
"unitId" : "u1",
"name" : "Weight",
"unitTypeFactors" : [ ]
},
"borderLineType" : "SOLID",
"map" : 188,
"submap" : {
"id" : 189
},
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "GSTA4",
"id" : 628,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252",
"compartmentName" : "Comp",
"complexName" : "CP"
},
"perfect" : false
} ],
"totalPages" : 1,
"totalElements" : 2,
"numberOfElements" : 2,
"size" : 20,
"number" : 0
}4. Search for bio entities of any type
Returns list of bio entities matching the query across all bio entity types, using the special
* map identifier to search all maps in the project at once.
|
Note
|
The result is paged - use the page and size query parameters to
walk through it.
|
4.1. HTTP request
GET /minerva/new_api/projects/test_project/maps/*/bio_entities:search?size=100 HTTP/1.14.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
4.3. Query Parameters
| Parameter | Description |
|---|---|
|
search term identifying bioEntity |
|
true when true query must be matched exactly, if false similar results are also acceptable |
|
index of the page to fetch, counted from 0; 0 by default |
|
number of entries on a page; 20 by default, 10000 at most |
4.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/*/bio_entities:search?size=100' -X GET4.5. HTTP response
HTTP/1.1 200 OK4.6. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of elements on the page |
|
|
element or reaction that matched the query |
|
|
is the bioEntity a perfect match to the search query |
|
|
link that should be opened immediately when element is clicked on the map |
|
|
unique bioEntity identifier |
|
|
name of the bioEntity displayed on the map |
|
|
element identifier taken from source file |
|
|
map identifier |
|
|
list of references |
|
|
z index (coordinate) of the element on the map |
|
|
notes and description |
|
|
at what zoom level this element becomes visible in hierarchical view |
|
|
multimer value |
|
|
SBO term identifying the type of the bioEntity |
|
|
short symbol identifying the element |
|
|
list of synonyms |
|
|
x coordinate of the element name on the map |
|
|
y coordinate of the element name on the map |
|
|
line type |
|
|
width of the box with element name |
|
|
height of the box with element name |
|
|
vertical align of the text inside the box with element name |
|
|
horizontal align of the text inside the box with element name |
|
|
font name used for element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA |
|
|
font weight for element label, one of: NORMAL, BOLD |
|
|
font style for element label, one of: NORMAL, ITALIC |
|
|
width of the element |
|
|
height of the element |
|
|
at what zoom level this element becomes transparent in hierarchical view |
|
|
list of former symbols |
|
|
unabbreviated name of the element |
|
|
image glyph associated with the element |
|
|
glyph id |
|
|
id of file associated with the glyph |
|
|
is the element active |
|
|
is the element hypothetical |
|
|
SBML kinetics is boundary condition |
|
|
SBML kinetics is constant |
|
|
SBML kinetics initial amount |
|
|
SBML kinetics initial concentration |
|
|
SBML charge |
|
|
SBML substance units |
|
|
SBML only substance units |
|
|
List of species modification residues |
|
|
Species structural state |
|
|
identifier of a complex in which element is located |
|
|
name of a complex in which element is located |
|
|
identifier of a compartment in which element is located |
|
|
identifier of a pathway in which element is located |
|
|
name of a compartment in which element is located |
|
|
submap to which this bioEntity is an entry point (anchor) |
|
|
submap id |
|
|
identifier of a submap to which this bioEntity is an entry point (anchor) |
|
|
type of submap connection |
|
|
x coordinate of the element on the map |
|
|
y coordinate of the element on the map |
|
|
border line width |
|
|
Species units |
|
|
color of the element label; |
|
|
size of the font used for the element label |
|
|
color used to fill the interior of the element; |
|
|
color used to draw the outline of the element; |
|
|
smiles identifier (for chemicals) |
|
|
inChI identifier (for chemicals) |
|
|
inChI key identifier (for chemicals) |
|
|
compartment membrane thickness |
|
|
compartment outer line width |
|
|
shape of a compartment |
|
|
compartment inner line width |
|
|
whether the element allows user interaction (e.g. clicking, hovering) |
|
|
reaction identifier taken from source file |
|
|
is reaction reversible |
|
|
reaction SBML kinetics law |
|
|
list of reaction products |
|
|
identifier of the element for this product |
|
|
SBML stoichiometry |
|
|
line used to draw product connection |
|
|
list of reaction reactants |
|
|
identifier of the element for this reactant |
|
|
SBML stoichiometry |
|
|
line used to draw reactant connection |
|
|
list of reaction modifiers |
|
|
identifier of the element for this modifier |
|
|
SBML stoichiometry |
|
|
SBO term identifying the type of the modifier |
|
|
line used to draw modifier connection |
|
|
coordinates of process in the reaction if defined manually. If this value is not present then center of line should be taken. |
|
|
reaction central line |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
line identifier |
|
|
line width |
|
|
line z coordinate (z-index) |
|
|
line segments |
|
|
arrow definition of the line beginning |
|
|
arrow definition of the line ending |
|
|
line pattern |
|
|
line color; |
|
|
reaction operators |
|
|
operator identifier |
|
|
line for the operator |
|
|
SBO term identifying the type of the operator |
|
|
total number of pages |
|
|
total number of elements |
|
|
number of elements on this page |
|
|
page size |
|
|
page number |
4.7. Sample Response
{
"content" : [ {
"bioEntity" : {
"id" : 496,
"glyph" : null,
"compartment" : 497,
"pathway" : null,
"elementId" : "s6",
"x" : 10.0,
"y" : 20.0,
"z" : 16,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "water",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ ],
"formerSymbols" : [ ],
"modificationResidues" : [ ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : null,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : null,
"borderLineType" : "SOLID",
"map" : 190,
"submap" : null,
"references" : [ {
"link" : null,
"type" : "CHEBI",
"resource" : "CHEBI:1234",
"id" : 634,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000247",
"compartmentName" : "Comp",
"complexName" : null
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 497,
"glyph" : null,
"compartment" : null,
"pathway" : null,
"elementId" : "p1",
"x" : 5.0,
"y" : 5.0,
"z" : 10,
"allowUiInteraction" : true,
"width" : 1000.0,
"height" : 1000.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#000000ff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "Comp",
"nameX" : 5.0,
"nameY" : 5.0,
"nameWidth" : 1000.0,
"nameHeight" : 1000.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "my synonym" ],
"formerSymbols" : [ "FFH" ],
"thickness" : 12.0,
"outerWidth" : 2.0,
"innerWidth" : 1.0,
"shape" : "SQUARE_COMPARTMENT",
"map" : 190,
"submap" : null,
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "SNCA",
"id" : 635,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000290",
"compartmentName" : null
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 498,
"glyph" : null,
"compartment" : 497,
"pathway" : null,
"elementId" : "p2",
"x" : 10.0,
"y" : 20.0,
"z" : 11,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "CP",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ ],
"formerSymbols" : [ ],
"modificationResidues" : [ ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : null,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : null,
"borderLineType" : "SOLID",
"map" : 190,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000253",
"compartmentName" : "Comp",
"complexName" : null
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 499,
"glyph" : null,
"compartment" : null,
"pathway" : null,
"elementId" : "p8",
"x" : 10.0,
"y" : 20.0,
"z" : 18,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "GSTA4",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "GSTA_XX", "GSTA_YY" ],
"formerSymbols" : [ ],
"modificationResidues" : [ {
"id" : 51448,
"idModificationResidue" : "r9",
"name" : "",
"x" : 10.0,
"y" : 20.0,
"z" : 19,
"width" : 15.0,
"height" : 15.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 15.0,
"nameHeight" : 15.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 499,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r9"
}, {
"id" : 51449,
"idModificationResidue" : "",
"name" : "X",
"x" : 10.0,
"y" : 20.0,
"z" : 20,
"width" : 10.0,
"height" : 10.0,
"nameX" : 10.0,
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"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 499,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
} ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : null,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : null,
"borderLineType" : "SOLID",
"map" : 191,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252",
"compartmentName" : null,
"complexName" : null
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 500,
"glyph" : null,
"compartment" : 497,
"pathway" : null,
"elementId" : "p3",
"x" : 10.0,
"y" : 20.0,
"z" : 12,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "GSTA4",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "GSTA_XX", "GSTA_YY" ],
"formerSymbols" : [ ],
"modificationResidues" : [ {
"id" : 51450,
"idModificationResidue" : "r4",
"name" : "",
"x" : 10.0,
"y" : 20.0,
"z" : 13,
"width" : 15.0,
"height" : 15.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 15.0,
"nameHeight" : 15.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 500,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r4"
}, {
"id" : 51451,
"idModificationResidue" : "",
"name" : "X",
"x" : 10.0,
"y" : 20.0,
"z" : 14,
"width" : 10.0,
"height" : 10.0,
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 500,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
}, {
"id" : 51452,
"idModificationResidue" : "b5",
"name" : "",
"x" : 60.0,
"y" : 20.0,
"z" : 15,
"width" : 10.0,
"height" : 10.0,
"nameX" : 60.0,
"nameY" : 20.0,
"nameWidth" : 10.0,
"nameHeight" : 10.0,
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"species" : 500,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000494",
"size" : 100.0,
"elementId" : "b5"
} ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : 498,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : {
"id" : 165,
"unitId" : "u1",
"name" : "Weight",
"unitTypeFactors" : [ ]
},
"borderLineType" : "SOLID",
"map" : 190,
"submap" : {
"id" : 191
},
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "GSTA4",
"id" : 636,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252",
"compartmentName" : "Comp",
"complexName" : "CP"
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 501,
"glyph" : null,
"compartment" : null,
"pathway" : null,
"elementId" : "s7",
"x" : 10.0,
"y" : 20.0,
"z" : 17,
"allowUiInteraction" : true,
"width" : 100.0,
"height" : 20.0,
"fontSize" : 12.0,
"fontColor" : "#000000ff",
"fillColor" : "#ffffffff",
"borderColor" : "#000000ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "",
"symbol" : null,
"fullName" : null,
"name" : "water",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 100.0,
"nameHeight" : 20.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ ],
"formerSymbols" : [ ],
"modificationResidues" : [ ],
"activity" : false,
"lineWidth" : 1.0,
"complex" : null,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : null,
"borderLineType" : "SOLID",
"map" : 190,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000247",
"compartmentName" : null,
"complexName" : null
},
"perfect" : true
}, {
"bioEntity" : {
"id" : 79,
"notes" : "",
"idReaction" : "path_0_re5933",
"name" : "",
"reversible" : false,
"visibilityLevel" : "",
"z" : 2,
"kinetics" : {
"parameters" : [ ],
"functions" : [ ],
"definition" : "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n</apply>\n</lambda></math>"
},
"line" : {
"id" : 704,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 0.0,
"y1" : 0.0,
"x2" : 10.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"processCoordinates" : null,
"modifiers" : [ {
"id" : 553,
"line" : {
"id" : 711,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 10.0,
"y1" : 0.0,
"x2" : 0.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"stoichiometry" : null,
"element" : 496,
"sboTerm" : "SBO:0000013"
} ],
"elementId" : "path_0_re5933",
"products" : [ {
"id" : 551,
"line" : {
"id" : 710,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 15.0,
"y1" : 0.0,
"x2" : 30.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"stoichiometry" : null,
"element" : 501
}, {
"id" : 552,
"line" : {
"id" : 708,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 15.0,
"y1" : 0.0,
"x2" : 20.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"stoichiometry" : null,
"element" : 496
} ],
"reactants" : [ {
"id" : 548,
"line" : {
"id" : 707,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 15.0,
"y1" : 0.0,
"x2" : 0.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"stoichiometry" : null,
"element" : 501
}, {
"id" : 549,
"line" : {
"id" : 705,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 10.0,
"y1" : 0.0,
"x2" : 0.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"stoichiometry" : null,
"element" : 496
} ],
"operators" : [ {
"id" : 547,
"line" : {
"id" : 706,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 10.0,
"y1" : 0.0,
"x2" : 15.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"inputs" : [ {
"id" : 548
}, {
"id" : 549
} ],
"outputs" : [ ],
"operatorText" : "",
"productOperator" : false,
"modifierOperator" : false,
"reactantOperator" : true,
"sboTerm" : "SBO:0000173"
}, {
"id" : 550,
"line" : {
"id" : 709,
"width" : 1.0,
"color" : "#000000ff",
"z" : 0,
"segments" : [ {
"x1" : 10.0,
"y1" : 0.0,
"x2" : 15.0,
"y2" : 0.0
} ],
"startArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"endArrow" : {
"arrowType" : "NONE",
"angle" : 2.748893571891069,
"lineType" : "SOLID",
"length" : 15.0
},
"lineType" : "SOLID"
},
"inputs" : [ ],
"outputs" : [ {
"id" : 551
}, {
"id" : 552
} ],
"operatorText" : "",
"productOperator" : true,
"modifierOperator" : false,
"reactantOperator" : false,
"sboTerm" : "SBO:0000173"
} ],
"references" : [ {
"link" : null,
"article" : null,
"type" : "PUBMED",
"resource" : "28725475",
"id" : 638,
"annotator" : null
}, {
"link" : null,
"article" : null,
"type" : "PUBMED",
"resource" : "invalid123",
"id" : 639,
"annotator" : null
} ],
"map" : 190,
"sboTerm" : "SBO:0000185"
},
"perfect" : false
} ],
"totalPages" : 1,
"totalElements" : 7,
"numberOfElements" : 7,
"size" : 100,
"number" : 0
}5. Suggested query list
Returns a list of suggested search queries for bio entities in the map.
5.1. HTTP request
GET /minerva/new_api/projects/test_project/maps/*/bio_entities/suggested_query_list HTTP/1.15.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
5.3. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/*/bio_entities/suggested_query_list' -X GET5.4. HTTP response
HTTP/1.1 200 OK5.5. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of suggested queries |
5.6. Sample Response
[ "comp", "cp", "ffh", "gsta4", "gsta_xx", "gsta_yy", "my synonym", "water" ]