An overlay entry describes how a single bioEntity should be rendered by the overlay: which bioEntity it matches, and the value, colour and line width used when drawing it. Entries are served from /new_api/projects/{projectId}/overlays/{overlayId}/entries.

An entry matches a bioEntity by any combination of its name, elementId, annotations, compartments and bioEntity types. A bioEntity type is identified by its SBO term, for instance SBO:0000252 for a protein. Annotations, compartments and types are managed as separate sub-resources, documented at the end of this page.

Note
 Entries should only be modified for overlays that were created manually through the API. When an overlay was created from a source file, its entries come from that file, and the file is what is returned by Download overlay source file - editing the entries makes the two disagree. Reading entries is fine for any overlay.

1. List overlay entries

Returns a page of entries of the given overlay.

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/1000018/entries/ HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

1.3. Query Parameters

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

1.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000018/entries/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

1.5. HTTP response

HTTP/1.1 200 OK

1.6. Response Fields

Path Type Description

content

Array

list of overlay entries on the page

content[].id

Number

identifier

content[].name

String

bioEntity name that should match

content[].sourceData

String

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

content[].mapName

String

map name that should match

content[].customLabel

String

custom label defined for the entry

content[].elementId

String

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

content[].lineWidth

Number

line width used when drawing overlay entry

content[].value

Number

normalized value ←1,1> assigned to this entry

content[].color

String

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

content[].description

String

free text description of the entry

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" : [ {
    "id" : 24,
    "name" : "",
    "sourceData" : null,
    "elementId" : null,
    "customLabel" : null,
    "lineWidth" : null,
    "value" : -1.0,
    "color" : null,
    "description" : null,
    "mapName" : null
  } ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "size" : 20,
  "number" : 0
}

2. Get overlay entry

Returns a single overlay entry by id.

2.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000019/entries/25 HTTP/1.1

2.2. Path Parameters

Table 2. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

2.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000019/entries/25' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

2.4. HTTP response

HTTP/1.1 200 OK

2.5. Response Fields

Path Type Description

id

Number

identifier

name

String

bioEntity name that should match

sourceData

String

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

mapName

String

map name that should match

customLabel

String

custom label defined for the entry

elementId

String

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

lineWidth

Number

line width used when drawing overlay entry

value

Number

normalized value ←1,1> assigned to this entry

color

String

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

description

String

free text description of the entry

2.6. Sample Response

{
  "id" : 25,
  "name" : "",
  "sourceData" : null,
  "elementId" : null,
  "customLabel" : null,
  "lineWidth" : null,
  "value" : -1.0,
  "color" : null,
  "description" : null,
  "mapName" : null
}

3. Add overlay entry

Adds a new entry to the overlay.

3.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000020/entries/ HTTP/1.1

3.2. Path Parameters

Table 3. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

3.3. Request Fields

Path Type Description

name

String

bioEntity name that should match

mapName

String

map name that should match

elementId

String

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

lineWidth

Number

line width used when drawing overlay entry

value

Number

normalized value ←1,1> assigned to this entry

color

String

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

description

String

free text description of the entry

3.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000020/entries/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"name":"John","mapName":"Abram Wolf","elementId":null,"lineWidth":83.6832100303,"value":-0.1766024212,"color":"#bc8ca1ff","description":"acutvftmldleoooocdzetelkelanckdtlcherlubksmhjlyaqiddtrafbuaisjstkfxcalgio"}' \
    -H 'Content-Type: application/json'

3.5. HTTP response

HTTP/1.1 201 Created

3.6. Response Fields

Path Type Description

id

Number

identifier

name

String

bioEntity name that should match

sourceData

String

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

mapName

String

map name that should match

customLabel

String

custom label defined for the entry

elementId

String

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

lineWidth

Number

line width used when drawing overlay entry

value

Number

normalized value ←1,1> assigned to this entry

color

String

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

description

String

free text description of the entry

3.7. Sample Response

{
  "id" : 27,
  "name" : "John",
  "sourceData" : null,
  "elementId" : null,
  "customLabel" : null,
  "lineWidth" : 83.6832100303,
  "value" : -0.1766024212,
  "color" : "#bc8ca1ff",
  "description" : "acutvftmldleoooocdzetelkelanckdtlcherlubksmhjlyaqiddtrafbuaisjstkfxcalgio",
  "mapName" : "Abram Wolf"
}

4. Update overlay entry

Updates an existing entry.

Note
 Supports optimistic locking via the If-Match header.

4.1. HTTP request

PUT /minerva/new_api/projects/test_project/overlays/1000022/entries/29 HTTP/1.1

4.2. Path Parameters

Table 4. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

4.3. Request Fields

Path Type Description

name

String

bioEntity name that should match

mapName

String

map name that should match

elementId

String

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

lineWidth

Number

line width used when drawing overlay entry

value

Number

normalized value ←1,1> assigned to this entry

color

String

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

description

String

free text description of the entry

4.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000022/entries/29' -X PUT \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"name":"Hae","mapName":"Mrs. Tamara Huels","elementId":null,"lineWidth":13.7107804339,"value":-0.5313494544,"color":"#d2d573ff","description":"ywcginouxqafydrsipfrgxzixhvritilbtirddddrvidhahuvnhbtwcfq"}' \
    -H 'Content-Type: application/json'

4.5. HTTP response

HTTP/1.1 200 OK

4.6. Response Fields

Path Type Description

id

Number

identifier

name

String

bioEntity name that should match

sourceData

String

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

mapName

String

map name that should match

customLabel

String

custom label defined for the entry

elementId

String

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

lineWidth

Number

line width used when drawing overlay entry

value

Number

normalized value ←1,1> assigned to this entry

color

String

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

description

String

free text description of the entry

4.7. Sample Response

{
  "id" : 29,
  "name" : "Hae",
  "sourceData" : null,
  "elementId" : null,
  "customLabel" : null,
  "lineWidth" : 13.7107804339,
  "value" : -0.5313494544,
  "color" : "#d2d573ff",
  "description" : "ywcginouxqafydrsipfrgxzixhvritilbtirddddrvidhahuvnhbtwcfq",
  "mapName" : "Mrs. Tamara Huels"
}

5. Delete overlay entry

Removes the entry from the overlay.

Note
 Supports optimistic locking via the If-Match header.

5.1. HTTP request

DELETE /minerva/new_api/projects/test_project/overlays/1000021/entries/28 HTTP/1.1

5.2. Path Parameters

Table 5. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

5.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000021/entries/28' -X DELETE \
    -H 'Authorization: Bearer xxxxxxxx'

5.4. HTTP response

HTTP/1.1 200 OK

6. List annotations

Returns a page of annotations that the entry should match.

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

6.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000013/entries/19/annotations/ HTTP/1.1

6.2. Path Parameters

Table 6. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/annotations/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

6.3. Query Parameters

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

6.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000013/entries/19/annotations/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

6.5. HTTP response

HTTP/1.1 200 OK

6.6. Response Fields

Path Type Description

content

Array

list of annotations on the page

content[].id

Number

unique annotation identifier

content[].type

String

type of the annotation (miriam data type, e.g. TAXONOMY, MESH_2012, PUBMED)

content[].resource

String

resource identifier within the given type

content[].link

String

URL computed from type and resource (identifiers.org link)

content[].article

Object

publication details; present only when type is PUBMED

content[].annotator

String

annotator that created this annotation, null when it was added manually; one of: BRENDA, CAZY, CHEBI, COPY_CELL_DESIGNER_ANNOTATIONS, ENSEMBL, ENTREZ, GO, HGNC, KEGG, PDB, TAIR, UNIPROT

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

6.7. Sample Response

{
  "content" : [ {
    "link" : null,
    "type" : "HGNC_SYMBOL",
    "resource" : "SNCA",
    "id" : 1612,
    "annotator" : null
  } ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "size" : 20,
  "number" : 0
}

7. Add annotation

Adds an annotation that the entry should match.

7.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000014/entries/20/annotations/ HTTP/1.1

7.2. Path Parameters

Table 7. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/annotations/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

7.3. Request Fields

Path Type Description

type

String

type of the annotation (miriam data type, e.g. TAXONOMY, MESH_2012, PUBMED)

resource

String

resource identifier within the given type

7.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000014/entries/20/annotations/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"type":"PUBMED","resource":"11"}' \
    -H 'Content-Type: application/json'

7.5. HTTP response

HTTP/1.1 201 Created

7.6. Sample Response

{
  "link" : null,
  "article" : null,
  "type" : "PUBMED",
  "resource" : "11",
  "id" : 1622,
  "annotator" : null
}

8. Delete annotation

Removes an annotation from the entry.

Note
 Supports optimistic locking via the If-Match header.

8.1. HTTP request

DELETE /minerva/new_api/projects/test_project/overlays/1000012/entries/18/annotations/1603 HTTP/1.1

8.2. Path Parameters

Table 8. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/annotations/{annotationId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

annotationId

annotation identifier

8.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000012/entries/18/annotations/1603' -X DELETE \
    -H 'Authorization: Bearer xxxxxxxx'

8.4. HTTP response

HTTP/1.1 200 OK

9. List compartments

Returns a page of compartments that the entry should match.

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

9.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000016/entries/22/compartments/ HTTP/1.1

9.2. Path Parameters

Table 9. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/compartments/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

9.3. Query Parameters

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

9.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000016/entries/22/compartments/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

9.5. HTTP response

HTTP/1.1 200 OK

9.6. Response Fields

Path Type Description

content

array<string>

list of compartments defined for the overlay entry

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

9.7. Sample Response

{
  "content" : [ "comp" ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "size" : 20,
  "number" : 0
}

10. Add compartment

Adds a compartment that the entry should match.

10.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000017/entries/23/compartments/ HTTP/1.1

10.2. Path Parameters

Table 10. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/compartments/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

10.3. Request Fields

Path Type Description

compartment

String

name of the compartment that should match

10.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000017/entries/23/compartments/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"compartment":"Comp11"}' \
    -H 'Content-Type: application/json'

10.5. HTTP response

HTTP/1.1 201 Created

10.6. Sample Response

{
  "compartment" : "Comp11"
}

11. Delete compartment

Removes a compartment from the entry.

11.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000015/entries/21/compartments:delete HTTP/1.1

11.2. Path Parameters

Table 11. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/compartments:delete
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

11.3. Request Fields

Path Type Description

compartment

String

name of the compartment to remove

11.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000015/entries/21/compartments:delete' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"compartment":"comp"}' \
    -H 'Content-Type: application/json'

11.5. HTTP response

HTTP/1.1 200 OK

12. List bioEntity types

Returns a page of bioEntity types that the entry should match.

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

12.1. HTTP request

GET /minerva/new_api/projects/test_project/overlays/1000025/entries/32/types/ HTTP/1.1

12.2. Path Parameters

Table 12. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/types/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

12.3. Query Parameters

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

12.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000025/entries/32/types/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

12.5. HTTP response

HTTP/1.1 200 OK

12.6. Response Fields

Path Type Description

content

array<string>

list of SBO terms of the bioEntity types defined for the overlay entry

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

12.7. Sample Response

{
  "content" : [ "SBO:0000252" ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "size" : 20,
  "number" : 0
}

13. Add bioEntity type

Adds a bioEntity type that the entry should match.

13.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000023/entries/30/types/ HTTP/1.1

13.2. Path Parameters

Table 13. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/types/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

13.3. Request Fields

Path Type Description

sboTerm

String

SBO term of the bioEntity type that should match (for instance SBO:0000252 for a protein)

13.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000023/entries/30/types/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"sboTerm":"SBO:0000243"}' \
    -H 'Content-Type: application/json'

13.5. HTTP response

HTTP/1.1 201 Created

13.6. Sample Response

{
  "sboTerm" : "SBO:0000243"
}

14. Delete bioEntity type

Removes a bioEntity type from the entry.

14.1. HTTP request

POST /minerva/new_api/projects/test_project/overlays/1000024/entries/31/types:delete HTTP/1.1

14.2. Path Parameters

Table 14. /minerva/new_api/projects/{projectId}/overlays/{overlayId}/entries/{overlayEntryId}/types:delete
Parameter Description

projectId

project identifier

overlayId

overlay identifier

overlayEntryId

overlay entry identifier

14.3. Request Fields

Path Type Description

sboTerm

String

SBO term of the bioEntity type to remove (for instance SBO:0000252 for a protein)

14.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/overlays/1000024/entries/31/types:delete' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"sboTerm":"SBO:0000252"}' \
    -H 'Content-Type: application/json'

14.5. HTTP response

HTTP/1.1 200 OK