Rest New API Documentation

Overlays of a project, served from /new_api/projects/{projectId}/overlays.

1. List overlays

Returns a page of overlays for the given project.

Note	The result is paged - use the `page` and `size` query parameters to walk through it.

1.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/ HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/overlays/
Parameter	Description
`projectId`	project identifier

1.3. Query Parameters

Parameter Description

Parameter	Description
`page`	index of the page to fetch, counted from 0; 0 by default
`size`	number of entries on a page; 20 by default, 10000 at most

page

index of the page to fetch, counted from 0; 0 by default

size

number of entries on a page; 20 by default, 10000 at most

1.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

1.5. HTTP response

HTTP/1.1 200 OK

1.6. Response Fields

Path Type Description

Path	Type	Description
`content`	`Array`	list of overlays on the page
`content[].name`	`String`	name of the overlay
`content[].description`	`String`	free text description of the overlay
`content[].genomeType`	`String`	reference genome against which the variants are expressed, one of: UCSC
`content[].type`	`String`	color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT
`content[].publicOverlay`	`Boolean`	is the overlay public
`content[].genomeVersion`	`String`	version of the reference genome
`content[].creator`	`Number`	identifier of the overlay owner
`content[].group`	`Number`	group identifier
`content[].notMatchingAlpha`	`Number`	alpha to be used for all not matching bioEntities when highlighting this overlay
`content[].id`	`Number`	unique overlay identifier
`content[].order`	`Number`	position of the overlay on the list of overlays
`totalPages`	`Number`	total number of pages
`totalElements`	`Number`	total number of elements
`numberOfElements`	`Number`	number of elements on this page
`size`	`Number`	page size
`number`	`Number`	page number

content

Array

list of overlays on the page

content[].name

String

name of the overlay

content[].description

String

free text description of the overlay

content[].genomeType

String

reference genome against which the variants are expressed, one of: UCSC

content[].type

String

color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT

content[].publicOverlay

Boolean

is the overlay public

content[].genomeVersion

String

version of the reference genome

content[].creator

Number

identifier of the overlay owner

content[].group

Number

group identifier

content[].notMatchingAlpha

Number

alpha to be used for all not matching bioEntities when highlighting this overlay

content[].id

Number

unique overlay identifier

content[].order

Number

position of the overlay on the list of overlays

totalPages

Number

total number of pages

totalElements

Number

total number of elements

numberOfElements

Number

number of elements on this page

size

Number

page size

number

Number

page number

1.7. Sample Response

{
  "content" : [ {
    "name" : "test title",
    "group" : null,
    "notMatchingAlpha" : null,
    "creator" : 1,
    "description" : "test description",
    "genomeType" : null,
    "genomeVersion" : null,
    "id" : 1000005,
    "idObject" : 1000005,
    "publicOverlay" : false,
    "type" : "GENERIC",
    "order" : 0
  } ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "size" : 20,
  "number" : 0
}

2. Add overlay

Creates a new overlay for the given project.

2.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/ HTTP/1.1

2.2. Path Parameters

Table 2. /minerva/new_api/projects/{projectId}/overlays/
Parameter	Description
`projectId`	project identifier

2.3. Request Fields

Path Type Description

Path	Type	Description
`name`	`String`	overlay name
`public`	`Boolean`	whether the overlay is visible to all project users
`colorSchemaType`	`String`	color schema type used for rendering
`orderIndex`	`Number`	display order index
`fileId`	`Number`	id of the previously uploaded source file
`description`	`String`	optional description
`genomeVersion`	`String`	reference genome version
`genomeType`	`String`	reference genome type
`group`	`Number`	id of the overlay group to assign; null for no group

name

String

overlay name

public

Boolean

whether the overlay is visible to all project users

colorSchemaType

String

color schema type used for rendering

orderIndex

Number

display order index

fileId

Number

id of the previously uploaded source file

description

String

optional description

genomeVersion

String

reference genome version

genomeType

String

reference genome type

group

Number

id of the overlay group to assign; null for no group

2.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"name":"Karole Hane","group":null,"colorSchemaType":"GENERIC","orderIndex":411295511,"fileId":null,"description":"tuggtpadbwfcnwuxclnqbpanipaawimfrduomqqplobfdwftjonelurhz","genomeVersion":"Ms.","genomeType":"UCSC","public":true}' \
    -H 'Content-Type: application/json'

2.5. HTTP response

HTTP/1.1 201 Created

2.6. Response Fields

Path Type Description

Path	Type	Description
`name`	`String`	name of the overlay
`description`	`String`	free text description of the overlay
`genomeType`	`String`	reference genome against which the variants are expressed, one of: UCSC
`type`	`String`	color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT
`publicOverlay`	`Boolean`	is the overlay public
`genomeVersion`	`String`	version of the reference genome
`creator`	`Number`	identifier of the overlay owner
`group`	`Number`	group identifier
`notMatchingAlpha`	`Number`	alpha to be used for all not matching bioEntities when highlighting this overlay
`id`	`Number`	unique overlay identifier
`order`	`Number`	position of the overlay on the list of overlays

name

String

name of the overlay

description

String

free text description of the overlay

genomeType

String

reference genome against which the variants are expressed, one of: UCSC

type

String

color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT

publicOverlay

Boolean

is the overlay public

genomeVersion

String

version of the reference genome

creator

Number

identifier of the overlay owner

group

Number

group identifier

notMatchingAlpha

Number

alpha to be used for all not matching bioEntities when highlighting this overlay

id

Number

unique overlay identifier

order

Number

position of the overlay on the list of overlays

2.7. Sample Response

{
  "name" : "Karole Hane",
  "group" : null,
  "notMatchingAlpha" : null,
  "creator" : 1,
  "description" : "tuggtpadbwfcnwuxclnqbpanipaawimfrduomqqplobfdwftjonelurhz",
  "genomeType" : "UCSC",
  "genomeVersion" : "Ms.",
  "id" : 1000009,
  "idObject" : 1000009,
  "publicOverlay" : true,
  "type" : "GENERIC",
  "order" : 411295511
}

3. Get overlay

Returns a single overlay by id.

3.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000003 HTTP/1.1

3.2. Path Parameters

Table 3. /minerva/new_api/projects/{projectId}/overlays/{overlayId}
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

3.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000003' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

3.4. HTTP response

HTTP/1.1 200 OK

3.5. Response Fields

Path Type Description

Path	Type	Description
`name`	`String`	name of the overlay
`description`	`String`	free text description of the overlay
`genomeType`	`String`	reference genome against which the variants are expressed, one of: UCSC
`type`	`String`	color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT
`publicOverlay`	`Boolean`	is the overlay public
`genomeVersion`	`String`	version of the reference genome
`creator`	`Number`	identifier of the overlay owner
`group`	`Number`	group identifier
`notMatchingAlpha`	`Number`	alpha to be used for all not matching bioEntities when highlighting this overlay
`id`	`Number`	unique overlay identifier
`order`	`Number`	position of the overlay on the list of overlays

name

String

name of the overlay

description

String

free text description of the overlay

genomeType

String

reference genome against which the variants are expressed, one of: UCSC

type

String

color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT

publicOverlay

Boolean

is the overlay public

genomeVersion

String

version of the reference genome

creator

Number

identifier of the overlay owner

group

Number

group identifier

notMatchingAlpha

Number

alpha to be used for all not matching bioEntities when highlighting this overlay

id

Number

unique overlay identifier

order

Number

position of the overlay on the list of overlays

3.6. Sample Response

{
  "name" : "test title",
  "group" : 3,
  "notMatchingAlpha" : null,
  "creator" : 1,
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "id" : 1000003,
  "idObject" : 1000003,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 0
}

4. Update overlay

Replaces the editable properties of an overlay - its name, description, type, visibility, order and the group it belongs to. The content of the overlay (the uploaded file) is not changed.

Note	Supports optimistic locking via the `If-Match` header.

4.1. HTTP request

PUT /minerva/new_api/projects/test_project/overlays/1000002 HTTP/1.1

4.2. Path Parameters

Table 4. /minerva/new_api/projects/{projectId}/overlays/{overlayId}
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

4.3. Request Fields

Path Type Description

Path	Type	Description
`name`	`String`	overlay name
`public`	`Boolean`	whether the overlay is visible to all project users
`colorSchemaType`	`String`	color schema type used for rendering
`orderIndex`	`Number`	display order index
`fileId`	`Number`	id of the previously uploaded source file
`description`	`String`	optional description
`genomeVersion`	`String`	reference genome version
`genomeType`	`String`	reference genome type
`group`	`Number`	id of the overlay group to assign; null for no group

name

String

overlay name

public

Boolean

whether the overlay is visible to all project users

colorSchemaType

String

color schema type used for rendering

orderIndex

Number

display order index

fileId

Number

id of the previously uploaded source file

description

String

optional description

genomeVersion

String

reference genome version

genomeType

String

reference genome type

group

Number

id of the overlay group to assign; null for no group

4.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000002' -X PUT \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"name":"Kary Cummings","group":1,"colorSchemaType":"GENERIC","orderIndex":1380953269,"fileId":null,"description":"cfwhpzyykefnhfsbtbilvstawrytusuqhpnctxyhueidezwpxkdgxduxdqxrmgeziskouy","genomeVersion":"Mrs.","genomeType":"UCSC","public":true}' \
    -H 'Content-Type: application/json'

4.5. HTTP response

HTTP/1.1 200 OK

4.6. Response Fields

Path Type Description

Path	Type	Description
`name`	`String`	name of the overlay
`description`	`String`	free text description of the overlay
`genomeType`	`String`	reference genome against which the variants are expressed, one of: UCSC
`type`	`String`	color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT
`publicOverlay`	`Boolean`	is the overlay public
`genomeVersion`	`String`	version of the reference genome
`creator`	`Number`	identifier of the overlay owner
`group`	`Number`	group identifier
`notMatchingAlpha`	`Number`	alpha to be used for all not matching bioEntities when highlighting this overlay
`id`	`Number`	unique overlay identifier
`order`	`Number`	position of the overlay on the list of overlays

name

String

name of the overlay

description

String

free text description of the overlay

genomeType

String

reference genome against which the variants are expressed, one of: UCSC

type

String

color schema used when drawing the overlay, one of: GENERIC, GENETIC_VARIANT

publicOverlay

Boolean

is the overlay public

genomeVersion

String

version of the reference genome

creator

Number

identifier of the overlay owner

group

Number

group identifier

notMatchingAlpha

Number

alpha to be used for all not matching bioEntities when highlighting this overlay

id

Number

unique overlay identifier

order

Number

position of the overlay on the list of overlays

4.7. Sample Response

{
  "name" : "Kary Cummings",
  "group" : 1,
  "notMatchingAlpha" : null,
  "creator" : 1,
  "description" : "cfwhpzyykefnhfsbtbilvstawrytusuqhpnctxyhueidezwpxkdgxduxdqxrmgeziskouy",
  "genomeType" : "UCSC",
  "genomeVersion" : "Mrs.",
  "id" : 1000002,
  "idObject" : 1000002,
  "publicOverlay" : true,
  "type" : "GENERIC",
  "order" : 1380953269
}

5. Delete overlay

Removes the overlay together with its entries.

Note	Supports optimistic locking via the `If-Match` header.

5.1. HTTP request

DELETE /minerva/new_api/projects/test_project/overlays/1000008 HTTP/1.1

5.2. Path Parameters

Table 5. /minerva/new_api/projects/{projectId}/overlays/{overlayId}
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

5.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000008' -X DELETE \
    -H 'Authorization: Bearer xxxxxxxx'

5.4. HTTP response

HTTP/1.1 200 OK

6. Download overlay source file

Returns the file that was originally uploaded to create the overlay, unchanged, as an attachment under its original filename. The response is plain text for the tab-separated overlay files and XML for .xml sources; overlays that were not created from a file (for example ones defined directly through the API) have no source and the call fails.

6.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000007:download_source HTTP/1.1

6.2. Path Parameters

Table 6. /minerva/new_api/projects/{projectId}/overlays/{overlayId}:download_source
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

6.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000007:download_source' -X POST \
    -H 'Authorization: Bearer xxxxxxxx'

6.4. HTTP response

HTTP/1.1 200 OK

6.5. Sample Response

element_identifier	value
	-1

7. Download overlay legend

Generates a PNG image describing how the values of the overlay are mapped onto colours, and returns it as an attachment.

7.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000006:download_legend HTTP/1.1

7.2. Path Parameters

Table 7. /minerva/new_api/projects/{projectId}/overlays/{overlayId}:download_legend
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

7.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000006:download_legend' -X POST \
    -H 'Authorization: Bearer xxxxxxxx'

7.4. HTTP response

HTTP/1.1 200 OK

8. Get overlay owner

Returns the user that currently owns the overlay.

8.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000011/owner HTTP/1.1

8.2. Path Parameters

Table 8. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/owner
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

8.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000011/owner' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

8.4. HTTP response

HTTP/1.1 200 OK

8.5. Response Fields

Path Type Description

Path	Type	Description
`id`	`Number`	identifier
`login`	`String`	user login
`orcidId`	`String`	orcid identifier
`name`	`String`	first name
`surname`	`String`	last name
`email`	`String`	email address
`removed`	`Boolean`	is user removed
`active`	`Boolean`	is the account active
`confirmed`	`Boolean`	is the account email confirmed
`connectedToLdap`	`Boolean`	is user connected to ldap
`ldapAccountAvailable`	`Boolean`	is the ldap account available
`termsOfUseConsent`	`Boolean`	did user accept terms of consent
`lastActive`	`String`	last activity timestamp
`privileges`	`Array`	list of privileges
`privileges[].privilegeType`	`String`	privilege name
`privileges[].objectId`	`String`	associated object
`lastLoginDate`	`String`	timestamp of the last login

id

Number

identifier

login

String

user login

orcidId

String

orcid identifier

name

String

first name

surname

String

last name

email

String

email address

removed

Boolean

is user removed

active

Boolean

is the account active

confirmed

Boolean

is the account email confirmed

connectedToLdap

Boolean

is user connected to ldap

ldapAccountAvailable

Boolean

is the ldap account available

termsOfUseConsent

Boolean

did user accept terms of consent

lastActive

String

last activity timestamp

privileges

Array

list of privileges

privileges[].privilegeType

String

privilege name

privileges[].objectId

String

associated object

lastLoginDate

String

timestamp of the last login

8.6. Sample Response

{
  "id" : 1,
  "login" : "admin",
  "name" : "",
  "surname" : "",
  "email" : "",
  "orcidId" : null,
  "removed" : false,
  "connectedToLdap" : false,
  "termsOfUseConsent" : false,
  "privileges" : [ {
    "privilegeType" : "READ_PROJECT",
    "objectId" : "empty"
  }, {
    "privilegeType" : "IS_ADMIN",
    "objectId" : null
  }, {
    "privilegeType" : "IS_CURATOR",
    "objectId" : null
  } ],
  "active" : true,
  "confirmed" : true,
  "lastLoginDate" : "2026-09-23T23:13:10Z",
  "ldapAccountAvailable" : false,
  "lastActive" : "2026-09-23T23:13:10Z"
}

9. Set overlay owner

Transfers ownership of an overlay to the specified user and returns the new owner.

Note	Supports optimistic locking via the `If-Match` header.

9.1. HTTP request

PUT /minerva/new_api/projects/test_project/overlays/1000010/owner HTTP/1.1

9.2. Path Parameters

Table 9. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/owner
Parameter	Description
`projectId`	project identifier
`overlayId`	overlay identifier

9.3. Request Fields

Path Type Description

Path	Type	Description
`id`	`Number`	identifier of the user to set as overlay owner

id

Number

identifier of the user to set as overlay owner

9.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000010/owner' -X PUT \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"id":3}' \
    -H 'Content-Type: application/json'

9.5. HTTP response

HTTP/1.1 200 OK

9.6. Response Fields

Path Type Description

Path	Type	Description
`id`	`Number`	identifier
`login`	`String`	user login
`orcidId`	`String`	orcid identifier
`name`	`String`	first name
`surname`	`String`	last name
`email`	`String`	email address
`removed`	`Boolean`	is user removed
`active`	`Boolean`	is the account active
`confirmed`	`Boolean`	is the account email confirmed
`connectedToLdap`	`Boolean`	is user connected to ldap
`ldapAccountAvailable`	`Boolean`	is the ldap account available
`termsOfUseConsent`	`Boolean`	did user accept terms of consent
`lastActive`	`String`	last activity timestamp
`privileges`	`Array`	list of privileges
`privileges[].privilegeType`	`String`	privilege name
`privileges[].objectId`	`String`	associated object
`lastLoginDate`	`String`	timestamp of the last login

id

Number

identifier

login

String

user login

orcidId

String

orcid identifier

name

String

first name

surname

String

last name

email

String

email address

removed

Boolean

is user removed

active

Boolean

is the account active

confirmed

Boolean

is the account email confirmed

connectedToLdap

Boolean

is user connected to ldap

ldapAccountAvailable

Boolean

is the ldap account available

termsOfUseConsent

Boolean

did user accept terms of consent

lastActive

String

last activity timestamp

privileges

Array

list of privileges

privileges[].privilegeType

String

privilege name

privileges[].objectId

String

associated object

lastLoginDate

String

timestamp of the last login

9.7. Sample Response

{
  "id" : 3,
  "login" : "anonymous",
  "name" : "",
  "surname" : "",
  "email" : null,
  "orcidId" : null,
  "removed" : false,
  "connectedToLdap" : false,
  "termsOfUseConsent" : false,
  "privileges" : [ {
    "privilegeType" : "READ_PROJECT",
    "objectId" : "empty"
  }, {
    "privilegeType" : "READ_PROJECT",
    "objectId" : "test_project"
  } ],
  "active" : true,
  "confirmed" : true,
  "lastLoginDate" : null,
  "ldapAccountAvailable" : false,
  "lastActive" : null
}

10. Get list of associated bioEntities in the overlay

Resolves the identifiers used in the overlay into the actual elements and reactions of the map, and returns them as pairs: left is the matched bioEntity with its full definition, right is the overlay entry (value, colour, description) that matched it. Pass * as the map identifier to search every map of the project, and set the includeIndirect query parameter to true to additionally return the elements that link to a submap in which the overlay matched something, so that a match hidden inside a submap is still visible on the parent map.

10.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000004/models/*/bio_entities/ HTTP/1.1

10.2. Path Parameters

Table 10. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bio_entities/
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`overlayId`	overlay identifier

10.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000004/models/*/bio_entities/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

10.4. HTTP response

HTTP/1.1 200 OK

10.5. Response Fields

Path Type Description

Path	Type	Description
`[].left`	`Object`	bioEntity
`[].right`	`Object`	overlay entry matching bioEntity
`[].left.immediateLink`	`String`	link that should be opened immediately when element is clicked on the map
`[].left.id`	`Number`	unique bioEntity identifier
`[].left.name`	`String`	name of the bioEntity displayed on the map
`[].left.elementId`	`String`	element identifier taken from source file
`[].left.map`	`Number`	map identifier
`[].left.references`	`Array`	list of references
`[].left.z`	`Number`	z index (coordinate) of the element on the map
`[].left.notes`	`String`	notes and description
`[].left.visibilityLevel`	`String`	at what zoom level this element becomes visible in hierarchical view
`[].left.homodimer`	`Number`	multimer value
`[].left.sboTerm`	`String`	SBO term identifying the type of the bioEntity
`[].left.symbol`	`String`	short symbol identifying the element
`[].left.synonyms`	`Array`	list of synonyms
`[].left.nameX`	`Number`	x coordinate of the element name on the map
`[].left.nameY`	`Number`	y coordinate of the element name on the map
`[].left.borderLineType`	`String`	line type
`[].left.nameWidth`	`Number`	width of the box with element name
`[].left.nameHeight`	`Number`	height of the box with element name
`[].left.nameVerticalAlign`	`String`	vertical align of the text inside the box with element name
`[].left.nameHorizontalAlign`	`String`	horizontal align of the text inside the box with element name
`[].left.fontName`	`String`	font name used for element label, one of: ARIAL, HELVETICA, TIMES_NEW_ROMAN, COURIER_NEW, GEORGIA, VERDANA
`[].left.fontWeight`	`String`	font weight for element label, one of: NORMAL, BOLD
`[].left.fontStyle`	`String`	font style for element label, one of: NORMAL, ITALIC
`[].left.width`	`Number`	width of the element
`[].left.height`	`Number`	height of the element
`[].left.transparencyLevel`	`String`	at what zoom level this element becomes transparent in hierarchical view
`[].left.formerSymbols`	`Array`	list of former symbols
`[].left.fullName`	`String`	unabbreviated name of the element
`[].left.glyph`	`Object`	image glyph associated with the element
`[].left.glyph.id`	`Number`	glyph id
`[].left.glyph.file`	`Number`	id of file associated with the glyph
`[].left.activity`	`Boolean`	is the element active
`[].left.hypothetical`	`Boolean`	is the element hypothetical
`[].left.boundaryCondition`	`Boolean`	SBML kinetics is boundary condition
`[].left.constant`	`Boolean`	SBML kinetics is constant
`[].left.initialAmount`	`Number`	SBML kinetics initial amount
`[].left.initialConcentration`	`Number`	SBML kinetics initial concentration
`[].left.charge`	`Number`	SBML charge
`[].left.substanceUnits`	`Object`	SBML substance units
`[].left.onlySubstanceUnits`	`Boolean`	SBML only substance units
`[].left.modificationResidues`	`Array`	List of species modification residues
`[].left.structuralState`	`Object`	Species structural state
`[].left.complex`	`Number`	identifier of a complex in which element is located
`[].left.complexName`	`String`	name of a complex in which element is located
`[].left.compartment`	`Number`	identifier of a compartment in which element is located
`[].left.pathway`	`Number`	identifier of a pathway in which element is located
`[].left.compartmentName`	`String`	name of a compartment in which element is located
`[].left.submap`	`Object`	submap to which this bioEntity is an entry point (anchor)
`[].left.submap.id`	`Number`	submap id
`[].left.submap.mapId`	`Number`	identifier of a submap to which this bioEntity is an entry point (anchor)
`[].left.submap.type`	`String`	type of submap connection
`[].left.x`	`Number`	x coordinate of the element on the map
`[].left.y`	`Number`	y coordinate of the element on the map
`[].left.lineWidth`	`Number`	border line width
`[].left.substanceUnits`	`Object`	Species units
`[].left.fontColor`	`String`	color of the element label; `#RRGGBBAA` string
`[].left.fontSize`	`Number`	size of the font used for the element label
`[].left.fillColor`	`String`	color used to fill the interior of the element; `#RRGGBBAA` string
`[].left.borderColor`	`String`	color used to draw the outline of the element; `#RRGGBBAA` string
`[].left.smiles`	`String`	smiles identifier (for chemicals)
`[].left.inChI`	`String`	inChI identifier (for chemicals)
`[].left.inChIKey`	`String`	inChI key identifier (for chemicals)
`[].left.thickness`	`Number`	compartment membrane thickness
`[].left.outerWidth`	`Number`	compartment outer line width
`[].left.shape`	`String`	shape of a compartment
`[].left.innerWidth`	`Number`	compartment inner line width
`[].left.allowUiInteraction`	`Boolean`	whether the element allows user interaction (e.g. clicking, hovering)
`[].left.idReaction`	`String`	reaction identifier taken from source file
`[].left.reversible`	`Boolean`	is reaction reversible
`[].left.kinetics`	`Object`	reaction SBML kinetics law
`[].left.products`	`Array`	list of reaction products
`[].left.products[].element`	`Number`	identifier of the element for this product
`[].left.products[].stoichiometry`	`Number`	SBML stoichiometry
`[].left.products[].line`	`Object`	line used to draw product connection
`[].left.reactants`	`Array`	list of reaction reactants
`[].left.reactants[].element`	`Number`	identifier of the element for this reactant
`[].left.reactants[].stoichiometry`	`Number`	SBML stoichiometry
`[].left.reactants[].line`	`Object`	line used to draw reactant connection
`[].left.modifiers`	`Array`	list of reaction modifiers
`[].left.modifiers[].element`	`Number`	identifier of the element for this modifier
`[].left.modifiers[].stoichiometry`	`Number`	SBML stoichiometry
`[].left.modifiers[].sboTerm`	`String`	SBO term identifying the type of the modifier
`[].left.modifiers[].line`	`Object`	line used to draw modifier connection
`[].left.processCoordinates`	`Object`	coordinates of process in the reaction if defined manually. If this value is not present then center of line should be taken.
`[].left.[].left.line`	`Object`	reaction central line
`[].left.line.id`	`Number`	line identifier
`[].left.line.width`	`Number`	line width
`[].left.line.z`	`Number`	line z coordinate (z-index)
`[].left.line.segments`	`Array`	line segments
`[].left.line.startArrow`	`Object`	arrow definition of the line beginning
`[].left.line.endArrow`	`Object`	arrow definition of the line ending
`[].left.line.lineType`	`String`	line pattern
`[].left.line.color`	`String`	line color; `#RRGGBBAA` string
`[].left.products[].line.id`	`Number`	line identifier
`[].left.products[].line.width`	`Number`	line width
`[].left.products[].line.z`	`Number`	line z coordinate (z-index)
`[].left.products[].line.segments`	`Array`	line segments
`[].left.products[].line.startArrow`	`Object`	arrow definition of the line beginning
`[].left.products[].line.endArrow`	`Object`	arrow definition of the line ending
`[].left.products[].line.lineType`	`String`	line pattern
`[].left.products[].line.color`	`String`	line color; `#RRGGBBAA` string
`[].left.reactants[].line.id`	`Number`	line identifier
`[].left.reactants[].line.width`	`Number`	line width
`[].left.reactants[].line.z`	`Number`	line z coordinate (z-index)
`[].left.reactants[].line.segments`	`Array`	line segments
`[].left.reactants[].line.startArrow`	`Object`	arrow definition of the line beginning
`[].left.reactants[].line.endArrow`	`Object`	arrow definition of the line ending
`[].left.reactants[].line.lineType`	`String`	line pattern
`[].left.reactants[].line.color`	`String`	line color; `#RRGGBBAA` string
`[].left.modifiers[].line.id`	`Number`	line identifier
`[].left.modifiers[].line.width`	`Number`	line width
`[].left.modifiers[].line.z`	`Number`	line z coordinate (z-index)
`[].left.modifiers[].line.segments`	`Array`	line segments
`[].left.modifiers[].line.startArrow`	`Object`	arrow definition of the line beginning
`[].left.modifiers[].line.endArrow`	`Object`	arrow definition of the line ending
`[].left.modifiers[].line.lineType`	`String`	line pattern
`[].left.modifiers[].line.color`	`String`	line color; `#RRGGBBAA` string
`[].left.operators`	`Array`	reaction operators
`[].left.operators[].id`	`Number`	operator identifier
`[].left.operators[].line`	`Object`	line for the operator
`[].left.operators[].sboTerm`	`String`	SBO term identifying the type of the operator
`[].right.id`	`Number`	identifier
`[].right.name`	`String`	bioEntity name that should match
`[].right.sourceData`	`String`	value of the source data column taken from the uploaded overlay file
`[].right.mapName`	`String`	map name that should match
`[].right.customLabel`	`String`	custom label defined for the entry
`[].right.elementId`	`String`	bioEntity identifier from external resource (like CellDesigner file that was used for generating the map)
`[].right.lineWidth`	`Number`	line width used when drawing overlay entry
`[].right.value`	`Number`	normalized value ←1,1> assigned to this entry
`[].right.color`	`String`	color that should be used when drawing overlay entry; `#RRGGBBAA` string
`[].right.description`	`String`	free text description of the entry

[].left

Object

bioEntity

[].right

Object

overlay entry matching bioEntity

[].left.immediateLink

String

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

[].left.id

Number

unique bioEntity identifier

[].left.name

String

name of the bioEntity displayed on the map

[].left.elementId

String

element identifier taken from source file

[].left.map

Number

map identifier

[].left.references

Array

list of references

[].left.z

Number

z index (coordinate) of the element on the map

[].left.notes

String

notes and description

[].left.visibilityLevel

String

at what zoom level this element becomes visible in hierarchical view

[].left.homodimer

Number

multimer value

[].left.sboTerm

String

SBO term identifying the type of the bioEntity

[].left.symbol

String

short symbol identifying the element

[].left.synonyms

Array

list of synonyms

[].left.nameX

Number

x coordinate of the element name on the map

[].left.nameY

Number

y coordinate of the element name on the map

[].left.borderLineType

String

line type

[].left.nameWidth

Number

width of the box with element name

[].left.nameHeight

Number

height of the box with element name

[].left.nameVerticalAlign

String

vertical align of the text inside the box with element name

[].left.nameHorizontalAlign

String

horizontal align of the text inside the box with element name

[].left.fontName

String

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

[].left.fontWeight

String

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

[].left.fontStyle

String

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

[].left.width

Number

width of the element

[].left.height

Number

height of the element

[].left.transparencyLevel

String

at what zoom level this element becomes transparent in hierarchical view

[].left.formerSymbols

Array

list of former symbols

[].left.fullName

String

unabbreviated name of the element

[].left.glyph

Object

image glyph associated with the element

[].left.glyph.id

Number

glyph id

[].left.glyph.file

Number

id of file associated with the glyph

[].left.activity

Boolean

is the element active

[].left.hypothetical

Boolean

is the element hypothetical

[].left.boundaryCondition

Boolean

SBML kinetics is boundary condition

[].left.constant

Boolean

SBML kinetics is constant

[].left.initialAmount

Number

SBML kinetics initial amount

[].left.initialConcentration

Number

SBML kinetics initial concentration

[].left.charge

Number

SBML charge

[].left.substanceUnits

Object

SBML substance units

[].left.onlySubstanceUnits

Boolean

SBML only substance units

[].left.modificationResidues

Array

List of species modification residues

[].left.structuralState

Object

Species structural state

[].left.complex

Number

identifier of a complex in which element is located

[].left.complexName

String

name of a complex in which element is located

[].left.compartment

Number

identifier of a compartment in which element is located

[].left.pathway

Number

identifier of a pathway in which element is located

[].left.compartmentName

String

name of a compartment in which element is located

[].left.submap

Object

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

[].left.submap.id

Number

submap id

[].left.submap.mapId

Number

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

[].left.submap.type

String

type of submap connection

[].left.x

Number

x coordinate of the element on the map

[].left.y

Number

y coordinate of the element on the map

[].left.lineWidth

Number

border line width

[].left.substanceUnits

Object

Species units

[].left.fontColor

String

color of the element label; #RRGGBBAA string

[].left.fontSize

Number

size of the font used for the element label

[].left.fillColor

String

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

[].left.borderColor

String

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

[].left.smiles

String

smiles identifier (for chemicals)

[].left.inChI

String

inChI identifier (for chemicals)

[].left.inChIKey

String

inChI key identifier (for chemicals)

[].left.thickness

Number

compartment membrane thickness

[].left.outerWidth

Number

compartment outer line width

[].left.shape

String

shape of a compartment

[].left.innerWidth

Number

compartment inner line width

[].left.allowUiInteraction

Boolean

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

[].left.idReaction

String

reaction identifier taken from source file

[].left.reversible

Boolean

is reaction reversible

[].left.kinetics

Object

reaction SBML kinetics law

[].left.products

Array

list of reaction products

[].left.products[].element

Number

identifier of the element for this product

[].left.products[].stoichiometry

Number

SBML stoichiometry

[].left.products[].line

Object

line used to draw product connection

[].left.reactants

Array

list of reaction reactants

[].left.reactants[].element

Number

identifier of the element for this reactant

[].left.reactants[].stoichiometry

Number

SBML stoichiometry

[].left.reactants[].line

Object

line used to draw reactant connection

[].left.modifiers

Array

list of reaction modifiers

[].left.modifiers[].element

Number

identifier of the element for this modifier

[].left.modifiers[].stoichiometry

Number

SBML stoichiometry

[].left.modifiers[].sboTerm

String

SBO term identifying the type of the modifier

[].left.modifiers[].line

Object

line used to draw modifier connection

[].left.processCoordinates

Object

coordinates of process in the reaction if defined manually. If this value is not present then center of line should be taken.

[].left.[].left.line

Object

reaction central line

[].left.line.id

Number

line identifier

[].left.line.width

Number

line width

[].left.line.z

Number

line z coordinate (z-index)

[].left.line.segments

Array

line segments

[].left.line.startArrow

Object

arrow definition of the line beginning

[].left.line.endArrow

Object

arrow definition of the line ending

[].left.line.lineType

String

line pattern

[].left.line.color

String

line color; #RRGGBBAA string

[].left.products[].line.id

Number

line identifier

[].left.products[].line.width

Number

line width

[].left.products[].line.z

Number

line z coordinate (z-index)

[].left.products[].line.segments

Array

line segments

[].left.products[].line.startArrow

Object

arrow definition of the line beginning

[].left.products[].line.endArrow

Object

arrow definition of the line ending

[].left.products[].line.lineType

String

line pattern

[].left.products[].line.color

String

line color; #RRGGBBAA string

[].left.reactants[].line.id

Number

line identifier

[].left.reactants[].line.width

Number

line width

[].left.reactants[].line.z

Number

line z coordinate (z-index)

[].left.reactants[].line.segments

Array

line segments

[].left.reactants[].line.startArrow

Object

arrow definition of the line beginning

[].left.reactants[].line.endArrow

Object

arrow definition of the line ending

[].left.reactants[].line.lineType

String

line pattern

[].left.reactants[].line.color

String

line color; #RRGGBBAA string

[].left.modifiers[].line.id

Number

line identifier

[].left.modifiers[].line.width

Number

line width

[].left.modifiers[].line.z

Number

line z coordinate (z-index)

[].left.modifiers[].line.segments

Array

line segments

[].left.modifiers[].line.startArrow

Object

arrow definition of the line beginning

[].left.modifiers[].line.endArrow

Object

arrow definition of the line ending

[].left.modifiers[].line.lineType

String

line pattern

[].left.modifiers[].line.color

String

line color; #RRGGBBAA string

[].left.operators

Array

reaction operators

[].left.operators[].id

Number

operator identifier

[].left.operators[].line

Object

line for the operator

[].left.operators[].sboTerm

String

SBO term identifying the type of the operator

[].right.id

Number

identifier

[].right.name

String

bioEntity name that should match

[].right.sourceData

String

value of the source data column taken from the uploaded overlay file

[].right.mapName

String

map name that should match

[].right.customLabel

String

custom label defined for the entry

[].right.elementId

String

bioEntity identifier from external resource (like CellDesigner file that was used for generating the map)

[].right.lineWidth

Number

line width used when drawing overlay entry

[].right.value

Number

normalized value ←1,1> assigned to this entry

[].right.color

String

color that should be used when drawing overlay entry; #RRGGBBAA string

[].right.description

String

free text description of the entry

10.6. Sample Response

[ {
  "left" : {
    "id" : 192,
    "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" : 1718,
      "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" : 1341,
      "line" : {
        "id" : 1725,
        "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" : 1192,
      "sboTerm" : "SBO:0000013"
    } ],
    "elementId" : "path_0_re5933",
    "products" : [ {
      "id" : 1339,
      "line" : {
        "id" : 1724,
        "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" : 1194
    }, {
      "id" : 1340,
      "line" : {
        "id" : 1722,
        "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" : 1192
    } ],
    "reactants" : [ {
      "id" : 1336,
      "line" : {
        "id" : 1721,
        "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" : 1194
    }, {
      "id" : 1337,
      "line" : {
        "id" : 1719,
        "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" : 1192
    } ],
    "operators" : [ {
      "id" : 1335,
      "line" : {
        "id" : 1720,
        "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" : 1336
      }, {
        "id" : 1337
      } ],
      "outputs" : [ ],
      "operatorText" : "",
      "productOperator" : false,
      "modifierOperator" : false,
      "reactantOperator" : true,
      "sboTerm" : "SBO:0000173"
    }, {
      "id" : 1338,
      "line" : {
        "id" : 1723,
        "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" : 1339
      }, {
        "id" : 1340
      } ],
      "operatorText" : "",
      "productOperator" : true,
      "modifierOperator" : false,
      "reactantOperator" : false,
      "sboTerm" : "SBO:0000173"
    } ],
    "references" : [ {
      "link" : null,
      "article" : null,
      "type" : "PUBMED",
      "resource" : "28725475",
      "id" : 1537,
      "annotator" : null
    }, {
      "link" : null,
      "article" : null,
      "type" : "PUBMED",
      "resource" : "invalid123",
      "id" : 1538,
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    "submap" : null,
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    "submap" : null,
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    "immediateLink" : null,
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    "visibilityLevel" : "",
    "transparencyLevel" : "",
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      "height" : 15.0,
      "nameX" : 10.0,
      "nameY" : 20.0,
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      "nameHeight" : 15.0,
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      "height" : 10.0,
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      "y" : 20.0,
      "z" : 15,
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      "height" : 10.0,
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Rest New API Documentation - Overlays

1. List overlays

1.1. HTTP request

1.2. Path Parameters

1.3. Query Parameters

1.4. CURL sample

1.5. HTTP response

1.6. Response Fields

1.7. Sample Response

2. Add overlay

2.1. HTTP request

2.2. Path Parameters

2.3. Request Fields

2.4. CURL sample

2.5. HTTP response

2.6. Response Fields

2.7. Sample Response

3. Get overlay

3.1. HTTP request

3.2. Path Parameters

3.3. CURL sample

3.4. HTTP response

3.5. Response Fields

3.6. Sample Response

4. Update overlay

4.1. HTTP request

4.2. Path Parameters

4.3. Request Fields

4.4. CURL sample

4.5. HTTP response

4.6. Response Fields

4.7. Sample Response

5. Delete overlay

5.1. HTTP request

5.2. Path Parameters

5.3. CURL sample

5.4. HTTP response

6. Download overlay source file

6.1. HTTP request

6.2. Path Parameters

6.3. CURL sample

6.4. HTTP response

6.5. Sample Response

7. Download overlay legend

7.1. HTTP request

7.2. Path Parameters

7.3. CURL sample

7.4. HTTP response

8. Get overlay owner

8.1. HTTP request

8.2. Path Parameters

8.3. CURL sample

8.4. HTTP response

8.5. Response Fields

8.6. Sample Response

9. Set overlay owner

9.1. HTTP request

9.2. Path Parameters

9.3. Request Fields

9.4. CURL sample

9.5. HTTP response

9.6. Response Fields

9.7. Sample Response

10. Get list of associated bioEntities in the overlay

10.1. HTTP request

10.2. Path Parameters

10.3. CURL sample

10.4. HTTP response

10.5. Response Fields

10.6. Sample Response