Rest New API Documentation

Publications referenced by the content of a map, served from /new_api/projects/{projectId}/maps/{mapId}/publications.

A publication is not stored on its own: it is derived from the PUBMED annotations of the elements and reactions of the map, and the bibliographic data (title, authors, journal, year, citation count) is fetched from PubMed and cached by the server. Every entry therefore comes with the list of bio entities that are annotated with it.

1. List publications

Returns a page of publications used in the map, each one together with the elements and reactions annotated with it. The search query filters by the text of the publication (title, authors, journal), and sort orders the result by one of the article columns, for example pubmedId,desc. mapId accepts * instead of an identifier to list the publications of all maps of the 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/maps/424/publications/ HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/maps/{mapId}/publications/
Parameter	Description
`projectId`	project identifier
`mapId`	map 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
`sort`	column used for sorting, for example `pubmedId,desc`
`search`	search query used for filtering

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

sort

column used for sorting, for example pubmedId,desc

search

search query used for filtering

1.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/424/publications/' -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 publications on the page
`content[].article.title`	`String`	title of the publication
`content[].article.authors`	`Array`	list of authors of the publication
`content[].article.journal`	`String`	journal where the publication appeared
`content[].article.year`	`Number`	year of the publication
`content[].article.link`	`String`	link to the publication
`content[].article.pubmedId`	`String`	pubmed identifier of the publication
`content[].article.citationCount`	`Number`	number of citations of the publication
`content[].elements`	`Array`	bio entities (elements and reactions) of the map annotated with the publication
`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
`filteredSize`	`Number`	number of elements matching the search query

content

Array

list of publications on the page

content[].article.title

String

title of the publication

content[].article.authors

Array

list of authors of the publication

content[].article.journal

String

journal where the publication appeared

content[].article.year

Number

year of the publication

content[].article.link

String

link to the publication

content[].article.pubmedId

String

pubmed identifier of the publication

content[].article.citationCount

Number

number of citations of the publication

content[].elements

Array

bio entities (elements and reactions) of the map annotated with the publication

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

filteredSize

Number

number of elements matching the search query

1.7. Sample Response

{
  "content" : [ {
    "elements" : [ {
      "id" : 189,
      "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" : 1691,
        "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" : 1320,
        "line" : {
          "id" : 1698,
          "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" : 1174,
        "sboTerm" : "SBO:0000013"
      } ],
      "elementId" : "path_0_re5933",
      "products" : [ {
        "id" : 1318,
        "line" : {
          "id" : 1697,
          "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" : 1172
      }, {
        "id" : 1319,
        "line" : {
          "id" : 1695,
          "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" : 1174
      } ],
      "reactants" : [ {
        "id" : 1315,
        "line" : {
          "id" : 1694,
          "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" : 1172
      }, {
        "id" : 1316,
        "line" : {
          "id" : 1692,
          "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" : 1174
      } ],
      "operators" : [ {
        "id" : 1314,
        "line" : {
          "id" : 1693,
          "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" : 1315
        }, {
          "id" : 1316
        } ],
        "outputs" : [ ],
        "operatorText" : "",
        "productOperator" : false,
        "modifierOperator" : false,
        "reactantOperator" : true,
        "sboTerm" : "SBO:0000173"
      }, {
        "id" : 1317,
        "line" : {
          "id" : 1696,
          "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" : 1318
        }, {
          "id" : 1319
        } ],
        "operatorText" : "",
        "productOperator" : true,
        "modifierOperator" : false,
        "reactantOperator" : false,
        "sboTerm" : "SBO:0000173"
      } ],
      "references" : [ {
        "link" : null,
        "article" : null,
        "type" : "PUBMED",
        "resource" : "28725475",
        "id" : 1513,
        "annotator" : null
      }, {
        "link" : null,
        "article" : null,
        "type" : "PUBMED",
        "resource" : "invalid123",
        "id" : 1514,
        "annotator" : null
      } ],
      "map" : 424,
      "sboTerm" : "SBO:0000185"
    } ],
    "article" : {
      "title" : "Mock article 28725475",
      "authors" : [ "Doe J.", "Smith A." ],
      "journal" : "Mock journal",
      "year" : 2020,
      "link" : "https://www.ncbi.nlm.nih.gov/pubmed/28725475",
      "pubmedId" : "28725475",
      "citationCount" : 7
    }
  } ],
  "totalPages" : 1,
  "totalElements" : 1,
  "numberOfElements" : 1,
  "filteredSize" : 1,
  "size" : 20,
  "number" : 0
}

Rest New API Documentation - Publications

1. List publications

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