Elements of a map and their sub-resources, served from
/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements.
1. Element glyph
The image drawn for the element instead of its default shape.
See full documentation.
2. Element annotations
Annotations linking the element to external databases.
See full documentation.
3. Element modifications
Modification states (e.g. phosphorylation) of the element.
See full documentation.
4. Element synonyms
Alternative names known for the element.
See full documentation.
5. Element former symbols
Symbols the element was previously known by.
See full documentation.
6. Element children
Elements nested inside this element, such as members of a complex.
See full documentation.
7. Element compartment
The compartment element that this element is located in.
See full documentation.
8. Element complex
The complex element that this element is a part of.
See full documentation.
9. Element submap
The submap that this element links to, if the element is a link to another map.
See full documentation.
10. Element unit
The unit of quantity assigned to the element, chosen from the units already defined at the map level.
See full documentation.
11. List elements
Returns all elements belonging to a map.
|
Note
|
The result is paged - use the page and size query parameters to
walk through it.
|
11.1. HTTP request
GET /minerva/new_api/projects/test_project/maps/218/bio_entities/elements/ HTTP/1.111.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
11.3. Query Parameters
| Parameter | Description |
|---|---|
|
index of the page to fetch, counted from 0; 0 by default |
|
number of entries on a page; 20 by default, 10000 at most |
11.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/218/bio_entities/elements/' -X GET \
-H 'Authorization: Bearer xxxxxxxx'11.5. HTTP response
HTTP/1.1 200 OK11.6. Sample Response
{
"content" : [ {
"id" : 580,
"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" : 218,
"submap" : null,
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "SNCA",
"id" : 748,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000290"
}, {
"id" : 582,
"glyph" : null,
"compartment" : 580,
"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" : 218,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000253"
}, {
"id" : 583,
"glyph" : null,
"compartment" : 580,
"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" : 51520,
"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" : 583,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r4"
}, {
"id" : 51521,
"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" : 583,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
}, {
"id" : 51522,
"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" : 583,
"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" : 582,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : {
"id" : 192,
"unitId" : "u1",
"name" : "Weight",
"unitTypeFactors" : [ ]
},
"borderLineType" : "SOLID",
"map" : 218,
"submap" : {
"id" : 219
},
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "GSTA4",
"id" : 749,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252"
}, {
"id" : 584,
"glyph" : null,
"compartment" : 580,
"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" : 218,
"submap" : null,
"references" : [ {
"link" : null,
"type" : "CHEBI",
"resource" : "CHEBI:1234",
"id" : 750,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000247"
}, {
"id" : 585,
"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" : 218,
"submap" : null,
"references" : [ ],
"immediateLink" : null,
"sboTerm" : "SBO:0000247"
} ],
"totalPages" : 1,
"totalElements" : 5,
"numberOfElements" : 5,
"size" : 20,
"number" : 0
}12. Get element
Returns a single element by its identifier.
12.1. HTTP request
GET /minerva/new_api/projects/test_project/maps/216/bio_entities/elements/578 HTTP/1.112.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
|
unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file) |
12.3. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/216/bio_entities/elements/578' -X GET \
-H 'Authorization: Bearer xxxxxxxx'12.4. HTTP response
HTTP/1.1 200 OK12.5. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
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) |
12.6. Sample Response
{
"id" : 578,
"glyph" : null,
"compartment" : 575,
"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" : 51515,
"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" : 578,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r4"
}, {
"id" : 51516,
"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" : 578,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
}, {
"id" : 51517,
"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" : 578,
"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" : 576,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : {
"id" : 191,
"unitId" : "u1",
"name" : "Weight",
"unitTypeFactors" : [ ]
},
"borderLineType" : "SOLID",
"map" : 216,
"submap" : {
"id" : 217
},
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "GSTA4",
"id" : 742,
"annotator" : null
} ],
"immediateLink" : null,
"sboTerm" : "SBO:0000252"
}13. Add element
Creates a new element in the map. The fontName field accepts one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA (default: ARIAL).
13.1. HTTP request
POST /minerva/new_api/projects/test_project/maps/222/bio_entities/elements/ HTTP/1.113.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
13.3. Request Fields
| Path | Type | Description |
|---|---|---|
|
|
SBO term defining the element type |
|
|
element identifier within the map |
|
|
element name |
|
|
x coordinate (top-left corner) |
|
|
y coordinate (top-left corner) |
|
|
z-index |
|
|
whether the element allows user interaction (e.g. clicking, hovering) |
|
|
element width |
|
|
element height |
|
|
x coordinate of the label box |
|
|
y coordinate of the label box |
|
|
width of the label box |
|
|
height of the label box |
|
|
vertical alignment of text in label box, one of: TOP, MIDDLE, BOTTOM |
|
|
horizontal alignment of text in label box, one of: LEFT, RIGHT, CENTER |
|
|
font size for the element label |
|
|
font used for the element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA (default: ARIAL) |
|
|
font weight for the element label, one of: NORMAL, BOLD (default: NORMAL) |
|
|
font style for the element label, one of: NORMAL, ITALIC (default: NORMAL) |
|
|
font colour; |
|
|
fill colour; |
|
|
border colour; |
|
|
notes and description |
|
|
zoom level at which the element becomes visible in hierarchical view |
|
|
zoom level at which the element becomes transparent in hierarchical view |
|
|
URL opened immediately when the element is clicked |
|
|
short symbol identifying the element |
|
|
unabbreviated name of the element |
|
|
line width (species only) |
|
|
multimer value (species only) |
|
|
border thickness (compartment only) |
|
|
outer border width (compartment only) |
|
|
inner border width (compartment only) |
|
|
is the element active (species only) |
|
|
is the element hypothetical (species only) |
|
|
SBML boundary condition (species only) |
|
|
SBML constant flag (species only) |
|
|
SBML initial amount (species only) |
|
|
SBML initial concentration (species only) |
|
|
SBML charge (species only) |
|
|
SBML only substance units flag (species only) |
13.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/222/bio_entities/elements/' -X POST \
-H 'Authorization: Bearer xxxxxxxx' \
-d '{"sboTerm":"SBO:0000243","elementId":"id11","x":10.0,"y":20.0,"z":30,"allowUiInteraction":true,"width":40.0,"height":50.0,"fontSize":12.0,"fontName":"ARIAL","fontWeight":"NORMAL","fontStyle":"NORMAL","fontColor":"#0000ffff","fillColor":"#ffff00ff","borderColor":"#404040ff","visibilityLevel":"","transparencyLevel":"","notes":"hello gene","symbol":"SNCA","fullName":"SNCA gene","name":"SNCA","nameX":10.0,"nameY":20.0,"nameWidth":40.0,"nameHeight":50.0,"nameVerticalAlign":"MIDDLE","nameHorizontalAlign":"CENTER","thickness":3.0,"outerWidth":5.0,"innerWidth":4.0,"activity":null,"lineWidth":1.0,"initialAmount":null,"charge":null,"initialConcentration":null,"onlySubstanceUnits":null,"homodimer":1,"hypothetical":null,"boundaryCondition":null,"constant":null,"immediateLink":"www.jerrold-botsford.io"}' \
-H 'Content-Type: application/json'13.5. HTTP response
HTTP/1.1 201 Created13.6. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
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) |
13.7. Sample Response
{
"id" : 598,
"glyph" : null,
"compartment" : null,
"pathway" : null,
"elementId" : "id11",
"x" : 10.0,
"y" : 20.0,
"z" : 30,
"allowUiInteraction" : true,
"width" : 40.0,
"height" : 50.0,
"fontSize" : 12.0,
"fontColor" : "#0000ffff",
"fillColor" : "#ffff00ff",
"borderColor" : "#404040ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "hello gene",
"symbol" : "SNCA",
"fullName" : "SNCA gene",
"name" : "SNCA",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 40.0,
"nameHeight" : 50.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ ],
"formerSymbols" : [ ],
"modificationResidues" : [ ],
"activity" : null,
"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" : 222,
"submap" : null,
"references" : [ ],
"immediateLink" : "www.jerrold-botsford.io",
"sboTerm" : "SBO:0000243"
}14. Update element
Updates an existing element. All fields from the request body replace the current values.
The fontName field accepts one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA.
|
Note
|
Supports optimistic locking via the If-Match header.
|
14.1. HTTP request
PUT /minerva/new_api/projects/test_project/maps/224/bio_entities/elements/602 HTTP/1.114.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
|
unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file) |
14.3. Request Fields
| Path | Type | Description |
|---|---|---|
|
|
SBO term defining the element type |
|
|
element identifier within the map |
|
|
element name |
|
|
x coordinate (top-left corner) |
|
|
y coordinate (top-left corner) |
|
|
z-index |
|
|
whether the element allows user interaction (e.g. clicking, hovering) |
|
|
element width |
|
|
element height |
|
|
x coordinate of the label box |
|
|
y coordinate of the label box |
|
|
width of the label box |
|
|
height of the label box |
|
|
vertical alignment of text in label box, one of: TOP, MIDDLE, BOTTOM |
|
|
horizontal alignment of text in label box, one of: LEFT, RIGHT, CENTER |
|
|
font size for the element label |
|
|
font used for the element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA (default: ARIAL) |
|
|
font weight for the element label, one of: NORMAL, BOLD (default: NORMAL) |
|
|
font style for the element label, one of: NORMAL, ITALIC (default: NORMAL) |
|
|
font colour; |
|
|
fill colour; |
|
|
border colour; |
|
|
notes and description |
|
|
zoom level at which the element becomes visible in hierarchical view |
|
|
zoom level at which the element becomes transparent in hierarchical view |
|
|
URL opened immediately when the element is clicked |
|
|
short symbol identifying the element |
|
|
unabbreviated name of the element |
|
|
line width (species only) |
|
|
multimer value (species only) |
|
|
border thickness (compartment only) |
|
|
outer border width (compartment only) |
|
|
inner border width (compartment only) |
|
|
is the element active (species only) |
|
|
is the element hypothetical (species only) |
|
|
SBML boundary condition (species only) |
|
|
SBML constant flag (species only) |
|
|
SBML initial amount (species only) |
|
|
SBML initial concentration (species only) |
|
|
SBML charge (species only) |
|
|
SBML only substance units flag (species only) |
14.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/224/bio_entities/elements/602' -X PUT \
-H 'Authorization: Bearer xxxxxxxx' \
-d '{"sboTerm":"SBO:0000252","elementId":"p3","x":10.0,"y":20.0,"z":30,"allowUiInteraction":true,"width":40.0,"height":50.0,"fontSize":12.0,"fontName":"ARIAL","fontWeight":"NORMAL","fontStyle":"NORMAL","fontColor":"#0000ffff","fillColor":"#ffff00ff","borderColor":"#404040ff","visibilityLevel":"","transparencyLevel":"","notes":"hello gene","symbol":"SNCA","fullName":"SNCA gene","name":"SNCA","nameX":10.0,"nameY":20.0,"nameWidth":40.0,"nameHeight":50.0,"nameVerticalAlign":"MIDDLE","nameHorizontalAlign":"CENTER","thickness":3.0,"outerWidth":5.0,"innerWidth":4.0,"activity":null,"lineWidth":1.0,"initialAmount":null,"charge":null,"initialConcentration":null,"onlySubstanceUnits":null,"homodimer":1,"hypothetical":null,"boundaryCondition":null,"constant":null,"immediateLink":"www.bryan-haley.biz"}' \
-H 'Content-Type: application/json'14.5. HTTP response
HTTP/1.1 200 OK14.6. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
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) |
14.7. Sample Response
{
"id" : 602,
"glyph" : null,
"compartment" : 599,
"pathway" : null,
"elementId" : "p3",
"x" : 10.0,
"y" : 20.0,
"z" : 30,
"allowUiInteraction" : true,
"width" : 40.0,
"height" : 50.0,
"fontSize" : 12.0,
"fontColor" : "#0000ffff",
"fillColor" : "#ffff00ff",
"borderColor" : "#404040ff",
"visibilityLevel" : "",
"transparencyLevel" : "",
"notes" : "hello gene",
"symbol" : "SNCA",
"fullName" : "SNCA gene",
"name" : "SNCA",
"nameX" : 10.0,
"nameY" : 20.0,
"nameWidth" : 40.0,
"nameHeight" : 50.0,
"fontName" : "ARIAL",
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"nameVerticalAlign" : "MIDDLE",
"nameHorizontalAlign" : "CENTER",
"synonyms" : [ "GSTA_XX", "GSTA_YY" ],
"formerSymbols" : [ ],
"modificationResidues" : [ {
"id" : 51535,
"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" : 602,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"state" : null,
"sboTerm" : "SBO:0000493",
"stateAbbreviation" : null,
"size" : 225.0,
"elementId" : "r4"
}, {
"id" : 51536,
"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" : 602,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 12.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000181",
"size" : 100.0,
"elementId" : ""
}, {
"id" : 51537,
"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" : 602,
"borderColor" : "#000000ff",
"fillColor" : "#ffffffff",
"fontSize" : 10.0,
"fontWeight" : "NORMAL",
"fontStyle" : "NORMAL",
"sboTerm" : "SBO:0000494",
"size" : 100.0,
"elementId" : "b5"
} ],
"activity" : null,
"lineWidth" : 1.0,
"complex" : 600,
"initialAmount" : null,
"charge" : null,
"initialConcentration" : 0.0,
"onlySubstanceUnits" : false,
"homodimer" : 1,
"hypothetical" : null,
"boundaryCondition" : false,
"constant" : false,
"substanceUnits" : {
"id" : 198,
"unitId" : "u1",
"name" : "Weight",
"unitTypeFactors" : [ ]
},
"borderLineType" : "SOLID",
"map" : 224,
"submap" : {
"id" : 225
},
"references" : [ {
"link" : null,
"type" : "HGNC_SYMBOL",
"resource" : "GSTA4",
"id" : 773,
"annotator" : null
} ],
"immediateLink" : "www.bryan-haley.biz",
"sboTerm" : "SBO:0000252"
}15. Delete element
Deletes an element from the map. Returns 400 if the element is part of a reaction, compartment, or complex that cannot be left empty.
|
Note
|
Supports optimistic locking via the If-Match header.
|
15.1. HTTP request
DELETE /minerva/new_api/projects/test_project/maps/220/bio_entities/elements/590 HTTP/1.115.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
|
unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file) |
15.3. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/220/bio_entities/elements/590' -X DELETE \
-H 'Authorization: Bearer xxxxxxxx'15.4. HTTP response
HTTP/1.1 200 OK16. Export elements to CSV
Exports elements matching the request to a CSV file.
16.1. HTTP request
POST /minerva/new_api/projects/test_project/maps/*/bio_entities/elements:download_csv HTTP/1.116.2. Path Parameters
| Parameter | Description |
|---|---|
|
project identifier |
|
map identifier |
16.3. Request Fields
| Path | Type | Description |
|---|---|---|
|
|
list of element types |
|
|
list of map identifiers |
|
|
list of compartment identifiers where elements should be included |
|
|
list of columns that should be returned in csv |
|
|
list of annotations that should be returned in csv |
|
|
list of compartment identifiers from which elements should be excluded |
16.4. CURL sample
$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/*/bio_entities/elements:download_csv' -X POST \
-d '{"types":["Simple molecule"],"submaps":[246],"columns":["id","modelId"],"annotations":["CHEBI"],"includedCompartmentIds":[668],"excludedCompartmentIds":[]}' \
-H 'Content-Type: application/json'16.5. HTTP response
HTTP/1.1 200 OK16.6. Sample Response
id,modelId,CHEBI
669,246,CHEBI:1234