Annotations (references to external databases) of a reaction, served from /new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations.

1. List annotations

Returns a page of annotations of the reaction.

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/maps/260/bio_entities/reactions/113/annotations/ HTTP/1.1

1.2. Path Parameters

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

projectId

project identifier

mapId

map identifier

reactionId

reaction 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/maps/260/bio_entities/reactions/113/annotations/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

1.5. HTTP response

HTTP/1.1 200 OK

1.6. Sample Response

{
  "content" : [ {
    "link" : null,
    "article" : null,
    "type" : "PUBMED",
    "resource" : "28725475",
    "id" : 912,
    "annotator" : null
  }, {
    "link" : null,
    "article" : null,
    "type" : "PUBMED",
    "resource" : "invalid123",
    "id" : 913,
    "annotator" : null
  } ],
  "totalPages" : 1,
  "totalElements" : 2,
  "numberOfElements" : 2,
  "size" : 20,
  "number" : 0
}

2. Get annotation

Returns a single annotation of the reaction.

2.1. HTTP request

GET /minerva/new_api/projects/test_project/maps/266/bio_entities/reactions/116/annotations/937 HTTP/1.1

2.2. Path Parameters

Table 2. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations/{annotationId}
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

annotationId

annotation identifier

2.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/266/bio_entities/reactions/116/annotations/937' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

2.4. HTTP response

HTTP/1.1 200 OK

2.5. Response Fields

Path Type Description

id

Number

unique annotation identifier

type

String

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

resource

String

resource identifier within the given type

link

String

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

article

Object

publication details; present only when type is PUBMED

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

2.6. Sample Response

{
  "link" : null,
  "article" : null,
  "type" : "PUBMED",
  "resource" : "28725475",
  "id" : 937,
  "annotator" : null
}

3. Add annotation

An annotation is a type/resource pair, for example type PUBMED with resource 11. type is an enum whose accepted values are the identifier types supported by the instance - see List identifiers.org types for the full list. The resource identifier itself is not checked against the external database; the response adds the assigned id and the link derived from the pair.

3.1. HTTP request

POST /minerva/new_api/projects/test_project/maps/264/bio_entities/reactions/115/annotations/ HTTP/1.1

3.2. Path Parameters

Table 3. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations/
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

3.3. 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

3.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/264/bio_entities/reactions/115/annotations/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"type":"PUBMED","resource":"11"}' \
    -H 'Content-Type: application/json'

3.5. HTTP response

HTTP/1.1 201 Created

3.6. Sample Response

{
  "link" : null,
  "article" : null,
  "type" : "PUBMED",
  "resource" : "11",
  "id" : 930,
  "annotator" : null
}

4. Update annotation

Replaces both the type and the resource of the annotation, so the request has to carry the complete pair even when only one of them changes. type accepts the same enum values as when creating one, listed by List identifiers.org types.

Note
 Supports optimistic locking via the If-Match header.

4.1. HTTP request

PUT /minerva/new_api/projects/test_project/maps/258/bio_entities/reactions/112/annotations/904 HTTP/1.1

4.2. Path Parameters

Table 4. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations/{annotationId}
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

annotationId

annotation identifier

4.3. 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

4.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/258/bio_entities/reactions/112/annotations/904' -X PUT \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"type":"PUBMED","resource":"11"}' \
    -H 'Content-Type: application/json'

4.5. HTTP response

HTTP/1.1 200 OK

4.6. Sample Response

{
  "link" : null,
  "article" : null,
  "type" : "PUBMED",
  "resource" : "11",
  "id" : 904,
  "annotator" : null
}

5. Delete annotation

Removes an annotation from the reaction.

Note
 Supports optimistic locking via the If-Match header.

5.1. HTTP request

DELETE /minerva/new_api/projects/test_project/maps/268/bio_entities/reactions/117/annotations/945 HTTP/1.1

5.2. Path Parameters

Table 5. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations/{annotationId}
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

annotationId

annotation identifier

5.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/268/bio_entities/reactions/117/annotations/945' -X DELETE \
    -H 'Authorization: Bearer xxxxxxxx'

5.4. HTTP response

HTTP/1.1 200 OK

6. Redirect to source

Redirects (HTTP 302) to the external page the annotation points at.

6.1. HTTP request

GET /minerva/new_api/projects/test_project/maps/262/bio_entities/reactions/114/annotations/920:redirect_to_source HTTP/1.1

6.2. Path Parameters

Table 6. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/reactions/{reactionId}/annotations/{annotationId}:redirect_to_source
Parameter Description

projectId

project identifier

mapId

map identifier

reactionId

reaction identifier

annotationId

annotation identifier

6.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/262/bio_entities/reactions/114/annotations/920:redirect_to_source' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

6.4. HTTP response

HTTP/1.1 302 Found