Element a reactant points at, served from /new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/reactants/{reactantId}/element.

1. Get element

Returns the element the reactant points at.

1.1. HTTP request

GET /minerva/new_api/projects/test_project/maps/352/bio_entities/reactions/160/reactants/1112/element HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/reactants/{reactantId}/element
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

reactantId

reactant identifier

1.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/352/bio_entities/reactions/160/reactants/1112/element' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

1.4. HTTP response

HTTP/1.1 200 OK

1.5. Response Fields

Path Type Description

immediateLink

String

link that should be opened immediately when element is clicked on the map

id

Number

unique bioEntity identifier

name

String

name of the bioEntity displayed on the map

elementId

String

element identifier taken from source file

map

Number

map identifier

references

Array

list of references

z

Number

z index (coordinate) of the element on the map

notes

String

notes and description

visibilityLevel

String

at what zoom level this element becomes visible in hierarchical view

homodimer

Number

multimer value

sboTerm

String

SBO term identifying the type of the bioEntity

symbol

String

short symbol identifying the element

synonyms

Array

list of synonyms

nameX

Number

x coordinate of the element name on the map

nameY

Number

y coordinate of the element name on the map

borderLineType

String

line type

nameWidth

Number

width of the box with element name

nameHeight

Number

height of the box with element name

nameVerticalAlign

String

vertical align of the text inside the box with element name

nameHorizontalAlign

String

horizontal align of the text inside the box with element name

fontName

String

font name used for element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA

fontWeight

String

font weight for element label, one of: NORMAL, BOLD

fontStyle

String

font style for element label, one of: NORMAL, ITALIC

width

Number

width of the element

height

Number

height of the element

transparencyLevel

String

at what zoom level this element becomes transparent in hierarchical view

formerSymbols

Array

list of former symbols

fullName

String

unabbreviated name of the element

glyph

Object

image glyph associated with the element

glyph.id

Number

glyph id

glyph.file

Number

id of file associated with the glyph

activity

Boolean

is the element active

hypothetical

Boolean

is the element hypothetical

boundaryCondition

Boolean

SBML kinetics is boundary condition

constant

Boolean

SBML kinetics is constant

initialAmount

Number

SBML kinetics initial amount

initialConcentration

Number

SBML kinetics initial concentration

charge

Number

SBML charge

substanceUnits

Object

SBML substance units

onlySubstanceUnits

Boolean

SBML only substance units

modificationResidues

Array

List of species modification residues

structuralState

Object

Species structural state

complex

Number

identifier of a complex in which element is located

complexName

String

name of a complex in which element is located

compartment

Number

identifier of a compartment in which element is located

pathway

Number

identifier of a pathway in which element is located

compartmentName

String

name of a compartment in which element is located

submap

Object

submap to which this bioEntity is an entry point (anchor)

submap.id

Number

submap id

submap.mapId

Number

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

submap.type

String

type of submap connection

x

Number

x coordinate of the element on the map

y

Number

y coordinate of the element on the map

lineWidth

Number

border line width

substanceUnits

Object

Species units

fontColor

String

color of the element label; #RRGGBBAA string

fontSize

Number

size of the font used for the element label

fillColor

String

color used to fill the interior of the element; #RRGGBBAA string

borderColor

String

color used to draw the outline of the element; #RRGGBBAA string

smiles

String

smiles identifier (for chemicals)

inChI

String

inChI identifier (for chemicals)

inChIKey

String

inChI key identifier (for chemicals)

thickness

Number

compartment membrane thickness

outerWidth

Number

compartment outer line width

shape

String

shape of a compartment

innerWidth

Number

compartment inner line width

allowUiInteraction

Boolean

whether the element allows user interaction (e.g. clicking, hovering)

1.6. Sample Response

{
  "id" : 987,
  "glyph" : null,
  "compartment" : 983,
  "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" : 352,
  "submap" : null,
  "references" : [ {
    "link" : null,
    "type" : "CHEBI",
    "resource" : "CHEBI:1234",
    "id" : 1279,
    "annotator" : null
  } ],
  "immediateLink" : null,
  "sboTerm" : "SBO:0000247"
}

2. Set element

Points the reactant at another element of the map.

Note
 Supports optimistic locking via the If-Match header.

2.1. HTTP request

POST /minerva/new_api/projects/test_project/maps/354/bio_entities/reactions/161/reactants/1119/element HTTP/1.1

2.2. Path Parameters

Table 2. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/reactants/{reactantId}/element
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

reactantId

reactant identifier

2.3. Request Fields

Path Type Description

id

Number

identifier of the referenced entity

2.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/354/bio_entities/reactions/161/reactants/1119/element' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"id":991}' \
    -H 'Content-Type: application/json'

2.5. HTTP response

HTTP/1.1 200 OK

2.6. Sample Response

{
  "id" : 991,
  "glyph" : null,
  "compartment" : 993,
  "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" : 51856,
    "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" : 991,
    "borderColor" : "#000000ff",
    "fillColor" : "#ffffffff",
    "fontSize" : 10.0,
    "fontWeight" : "NORMAL",
    "fontStyle" : "NORMAL",
    "state" : null,
    "sboTerm" : "SBO:0000493",
    "stateAbbreviation" : null,
    "size" : 225.0,
    "elementId" : "r4"
  }, {
    "id" : 51857,
    "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" : 991,
    "borderColor" : "#000000ff",
    "fillColor" : "#ffffffff",
    "fontSize" : 12.0,
    "fontWeight" : "NORMAL",
    "fontStyle" : "NORMAL",
    "sboTerm" : "SBO:0000181",
    "size" : 100.0,
    "elementId" : ""
  }, {
    "id" : 51858,
    "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" : 991,
    "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" : 989,
  "initialAmount" : null,
  "charge" : null,
  "initialConcentration" : 0.0,
  "onlySubstanceUnits" : false,
  "homodimer" : 1,
  "hypothetical" : null,
  "boundaryCondition" : false,
  "constant" : false,
  "substanceUnits" : {
    "id" : 326,
    "unitId" : "u1",
    "name" : "Weight",
    "unitTypeFactors" : [ ]
  },
  "borderLineType" : "SOLID",
  "map" : 354,
  "submap" : {
    "id" : 355
  },
  "references" : [ {
    "link" : null,
    "type" : "HGNC_SYMBOL",
    "resource" : "GSTA4",
    "id" : 1285,
    "annotator" : null
  } ],
  "immediateLink" : null,
  "sboTerm" : "SBO:0000252"
}