Rest New API Documentation

Chemicals related to the disease annotated on a project, served from /new_api/projects/{projectId}/chemicals.

1. Chemical search

Looks up chemicals in the Comparative Toxicogenomics Database (CTD), restricted to the disease annotated on the project, and returns each chemical together with its MeSH description and the map elements it targets. Search either by query (chemical name) or by target (an element on the map given as TYPE:ID); the project must have a disease assigned, otherwise the call fails.

1.1. HTTP request

GET /minerva/new_api/projects/test_project/chemicals:search?query=stilbene%20oxide HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/chemicals:search
Parameter	Description
`projectId`	project identifier

1.3. Query Parameters

Parameter Description

Parameter	Description
`query`	name of chemical that we are searching for
`target`	target element that we are searching for in format TYPE:ID

query

name of chemical that we are searching for

target

target element that we are searching for in format TYPE:ID

1.4. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/chemicals:search?query=stilbene%20oxide' -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
`[].id`	`Object`	identifier of the chemical
`[].name`	`String`	name of the chemical
`[].description`	`String`	summary of the chemical taken from the source database
`[].synonyms`	`Array`	list of synonyms
`[].references`	`Array`	list of references that identify sources
`[].targets`	`Array`	list of targets
`[].targets[].name`	`String`	target name
`[].targets[].references`	`Array`	list of target references
`[].targets[].targetElements`	`Array`	list of elements on the map associated with this target
`[].targets[].targetParticipants`	`Array`	list of identifiers associated with this target

[].id

Object

identifier of the chemical

[].name

String

name of the chemical

[].description

String

summary of the chemical taken from the source database

[].synonyms

Array

list of synonyms

[].references

Array

list of references that identify sources

[].targets

Array

list of targets

[].targets[].name

String

target name

[].targets[].references

Array

list of target references

[].targets[].targetElements

Array

list of elements on the map associated with this target

[].targets[].targetParticipants

Array

list of identifiers associated with this target

1.7. Sample Response

[ {
  "name" : "stilbene oxide",
  "references" : [ {
    "link" : "https://identifiers.org/ctd.chemical:C025906",
    "type" : "TOXICOGENOMIC_CHEMICAL",
    "resource" : "C025906",
    "id" : 0,
    "annotator" : null
  }, {
    "link" : "www.patrick-gusikowski.org",
    "type" : "MESH_2012",
    "resource" : "C025906",
    "id" : 0,
    "annotator" : null
  } ],
  "description" : "Mesh term not available",
  "synonyms" : [ ],
  "id" : {
    "link" : "www.patrick-gusikowski.org",
    "type" : "MESH_2012",
    "resource" : "C025906",
    "id" : 0,
    "annotator" : null
  },
  "directEvidenceReferences" : "Unknown column",
  "directEvidence" : "Unknown column",
  "targets" : [ {
    "source" : null,
    "name" : "GSTA4",
    "targetParticipants" : [ {
      "link" : "www.patrick-gusikowski.org",
      "type" : "HGNC_SYMBOL",
      "resource" : "GSTA4",
      "id" : 0,
      "annotator" : null
    } ],
    "references" : [ {
      "link" : "www.patrick-gusikowski.org",
      "article" : null,
      "type" : "PUBMED",
      "resource" : "16510128",
      "id" : 0,
      "annotator" : null
    } ],
    "targetElements" : [ {
      "id" : 301,
      "glyph" : null,
      "compartment" : 302,
      "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" : 51281,
        "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" : 301,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 10.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "state" : null,
        "sboTerm" : "SBO:0000493",
        "stateAbbreviation" : null,
        "size" : 225.0,
        "elementId" : "r4"
      }, {
        "id" : 51282,
        "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" : 301,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 12.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "sboTerm" : "SBO:0000181",
        "size" : 100.0,
        "elementId" : ""
      }, {
        "id" : 51283,
        "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" : 301,
        "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" : 299,
      "initialAmount" : null,
      "charge" : null,
      "initialConcentration" : 0.0,
      "onlySubstanceUnits" : false,
      "homodimer" : 1,
      "hypothetical" : null,
      "boundaryCondition" : false,
      "constant" : false,
      "substanceUnits" : {
        "id" : 100,
        "unitId" : "u1",
        "name" : "Weight",
        "unitTypeFactors" : [ ]
      },
      "borderLineType" : "SOLID",
      "map" : 118,
      "submap" : {
        "id" : 119
      },
      "references" : [ {
        "link" : null,
        "type" : "HGNC_SYMBOL",
        "resource" : "GSTA4",
        "id" : 376,
        "annotator" : null
      } ],
      "immediateLink" : null,
      "sboTerm" : "SBO:0000252"
    }, {
      "id" : 300,
      "glyph" : null,
      "compartment" : null,
      "pathway" : null,
      "elementId" : "p8",
      "x" : 10.0,
      "y" : 20.0,
      "z" : 18,
      "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" : 51279,
        "idModificationResidue" : "r9",
        "name" : "",
        "x" : 10.0,
        "y" : 20.0,
        "z" : 19,
        "width" : 15.0,
        "height" : 15.0,
        "nameX" : 10.0,
        "nameY" : 20.0,
        "nameWidth" : 15.0,
        "nameHeight" : 15.0,
        "nameVerticalAlign" : "MIDDLE",
        "nameHorizontalAlign" : "CENTER",
        "species" : 300,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 10.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "state" : null,
        "sboTerm" : "SBO:0000493",
        "stateAbbreviation" : null,
        "size" : 225.0,
        "elementId" : "r9"
      }, {
        "id" : 51280,
        "idModificationResidue" : "",
        "name" : "X",
        "x" : 10.0,
        "y" : 20.0,
        "z" : 20,
        "width" : 10.0,
        "height" : 10.0,
        "nameX" : 10.0,
        "nameY" : 20.0,
        "nameWidth" : 10.0,
        "nameHeight" : 10.0,
        "nameVerticalAlign" : "MIDDLE",
        "nameHorizontalAlign" : "CENTER",
        "species" : 300,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 12.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "sboTerm" : "SBO:0000181",
        "size" : 100.0,
        "elementId" : ""
      } ],
      "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" : 119,
      "submap" : null,
      "references" : [ ],
      "immediateLink" : null,
      "sboTerm" : "SBO:0000252"
    }, {
      "id" : 301,
      "glyph" : null,
      "compartment" : 302,
      "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" : 51281,
        "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" : 301,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 10.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "state" : null,
        "sboTerm" : "SBO:0000493",
        "stateAbbreviation" : null,
        "size" : 225.0,
        "elementId" : "r4"
      }, {
        "id" : 51282,
        "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" : 301,
        "borderColor" : "#000000ff",
        "fillColor" : "#ffffffff",
        "fontSize" : 12.0,
        "fontWeight" : "NORMAL",
        "fontStyle" : "NORMAL",
        "sboTerm" : "SBO:0000181",
        "size" : 100.0,
        "elementId" : ""
      }, {
        "id" : 51283,
        "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" : 301,
        "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" : 299,
      "initialAmount" : null,
      "charge" : null,
      "initialConcentration" : 0.0,
      "onlySubstanceUnits" : false,
      "homodimer" : 1,
      "hypothetical" : null,
      "boundaryCondition" : false,
      "constant" : false,
      "substanceUnits" : {
        "id" : 100,
        "unitId" : "u1",
        "name" : "Weight",
        "unitTypeFactors" : [ ]
      },
      "borderLineType" : "SOLID",
      "map" : 118,
      "submap" : {
        "id" : 119
      },
      "references" : [ {
        "link" : null,
        "type" : "HGNC_SYMBOL",
        "resource" : "GSTA4",
        "id" : 376,
        "annotator" : null
      } ],
      "immediateLink" : null,
      "sboTerm" : "SBO:0000252"
    } ]
  }, {
    "source" : null,
    "name" : "GSTP1",
    "targetParticipants" : [ {
      "link" : "www.patrick-gusikowski.org",
      "type" : "HGNC_SYMBOL",
      "resource" : "GSTP1",
      "id" : 0,
      "annotator" : null
    } ],
    "references" : [ {
      "link" : "www.patrick-gusikowski.org",
      "article" : null,
      "type" : "PUBMED",
      "resource" : "17190945",
      "id" : 0,
      "annotator" : null
    }, {
      "link" : "www.patrick-gusikowski.org",
      "article" : null,
      "type" : "PUBMED",
      "resource" : "23721876",
      "id" : 0,
      "annotator" : null
    } ],
    "targetElements" : [ ]
  } ]
} ]

2. Suggested query list

Returns a list of suggested search queries for chemicals in the project.

2.1. HTTP request

GET /minerva/new_api/projects/test_project_2/chemicals/suggested_query_list HTTP/1.1

2.2. Path Parameters

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

2.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project_2/chemicals/suggested_query_list' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

2.4. HTTP response

HTTP/1.1 200 OK

2.5. Response Fields

Path Type Description

Path	Type	Description
`[]`	`Array`	list of suggested queries

[]

Array

list of suggested queries

2.6. Sample Response

[ ]

Rest New API Documentation - Chemicals

1. Chemical search

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. Suggested query list

2.1. HTTP request

2.2. Path Parameters

2.3. CURL sample

2.4. HTTP response

2.5. Response Fields

2.6. Sample Response