1. Get project

Returns meta data of the project.

1.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/' -i -X GET

1.2. Path Parameters

Table 1. /projects/{projectId}/
Parameter Description

projectId

project identifier

1.3. Response Fields

Path Type Description

projectId

string

project identifier

name

string

name

version

string

version

owner

string

login of the project creator

creationDate

string

when project was uploaded

disease

Reference

identifier of the disease

organism

Reference

identifier of the organism

directory

string

directory where files related to the project are located. Whole path looks like: /minerva/map_images/{directory}

status

string

status of the uploaded project; possible values: ANNOTATING, CACHING, CACHING_CHEMICAL, CACHING_DRUG, CACHING_MIRIAM, CACHING_MI_RNA, DONE, FAIL, GENERATING_IMAGES, PARSING_DATA, REMOVING, UNKNOWN, UPLOADING_TO_DB, VALIDATING_MIRIAM

progress

double

how much current stage progressed in percent

notifyEmail

string

email address connected to the project

mapCanvasType

string

type of the engine that should be used for project rendering; possible values: GOOGLE_MAPS_API, OPEN_LAYERS

logEntries

boolean

flag indicating that there are log entries attached to the project

overviewImageViews

array<OverviewImage>

list of overview images

topOverviewImage

OverviewImage

overview image that should be used as top level image

1.4. Sample Response

{
  "version" : "1.0",
  "disease" : {
    "annotatorClassName" : "",
    "id" : 697,
    "link" : "http://id.nlm.nih.gov/mesh/D010300",
    "resource" : "D010300",
    "type" : "MESH_2012"
  },
  "organism" : {
    "annotatorClassName" : "",
    "id" : 698,
    "link" : "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606",
    "resource" : "9606",
    "type" : "TAXONOMY"
  },
  "idObject" : 292,
  "status" : "uninitialized",
  "directory" : "289b78b436176091ad900020c933c544",
  "progress" : 0.0,
  "notifyEmail" : "minerva@uni.lu",
  "logEntries" : true,
  "name" : "Test Disease",
  "owner" : "admin",
  "projectId" : "test_project",
  "creationDate" : "2021-10-29 11:33:29",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ {
    "idObject" : 228,
    "filename" : "289b78b436176091ad900020c933c544/image.png",
    "width" : 200,
    "height" : 100,
    "links" : [ ]
  } ],
  "topOverviewImage" : {
    "idObject" : 228,
    "filename" : "289b78b436176091ad900020c933c544/image.png",
    "width" : 200,
    "height" : 100,
    "links" : [ ]
  }
}

2. List

List all projects.

2.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/' -i -X GET

2.2. Response Fields

Path Type Description

[]

array<Project>

list of projects

2.3. Sample Response

[ {
  "version" : "empty DISEASE MAP",
  "disease" : null,
  "organism" : null,
  "idObject" : 4,
  "status" : "Ok",
  "directory" : "a2e4822a98337283e39f7b60acf85ec9",
  "progress" : 100.0,
  "notifyEmail" : null,
  "logEntries" : false,
  "name" : null,
  "owner" : "admin",
  "projectId" : "empty",
  "creationDate" : "2014-03-27 15:59:31",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ ],
  "topOverviewImage" : null
} ]

3. Create project

Creates project from file that is already uploaded to minerva.

3.1. Path Parameters

Table 2. /projects/{projectId}/
Parameter Description

projectId

project identifier

3.2. Request Parameters

Parameter Description

projectId

project identifier

file-id

identifier of the file that should be used to create project

parser

class of the parser that should be used for parsing the file. Available options: lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser, lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter, lcsb.mapviewer.converter.model.sbml.SbmlParser, lcsb.mapviewer.wikipathway.GpmlParser

cache

should the data from external sources be cached after project was created

description

description of the project

notify-email

email address that should be when something change in the project

disease

disease associated with the project (MESH id)

name

name of the project

organism

organism associated with the project (TAXONOMY id)

sbgn

should the map be visualized in sbgn-like way

semantic-zoom

should custom semantic zooming be enabled

version

version of the project

mapCanvasType

type of map canvas engine to be used when visualizing map. Available options: GOOGLE_MAPS_API, OPEN_LAYERS

annotate

should the project be automatically annotated

verify-annotations

should the annotations be verified

zip-entries

array of parameters describing each file in the zipped input file, file-index is number starting from 0

zip-entries[{number}][_filename]

name of the file

zip-entries[{number}][_type]

type of the file. Possible values: GLYPH, IMAGE, MAP, OVERLAY

zip-entries[{number}][_data][name]

name of the map/name of the overlay

zip-entries[{number}][_data][mapping]

for submaps - is this map a mapping file (true/false)

zip-entries[{number}][_data][root]

for submaps - is this map a root map (true/false)

zip-entries[{number}][_data][type][id]

for submaps defines type of the connection. Possible values: DOWNSTREAM_TARGETS, PATHWAY, UNKNOWN

zip-entries[{number}][_data][description]

for overlays - description of the overlay

3.3. Example 1.

Upload of project from simple file

3.3.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/' -i -X POST \
    -H 'Content-Type: application/x-www-form-urlencoded' \
    -d 'projectId=test_project&name=New+Disease+Map&file-id=335&mapCanvasType=OPEN_LAYERS&cache=false&description=this+is+my+awesome+project&notify-email=notify.me%40uni.lu&disease=D010300&organism=9606&sbgn=false&semantic-zoom=false&version=0.0.1&annotate=false&verify-annotations=false&parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

3.3.2. Sample Response

{
  "version" : "0.0.1",
  "disease" : {
    "annotatorClassName" : "",
    "id" : 689,
    "link" : "http://id.nlm.nih.gov/mesh/D010300",
    "resource" : "D010300",
    "type" : "MESH_2012"
  },
  "organism" : {
    "annotatorClassName" : "",
    "id" : 690,
    "link" : "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606",
    "resource" : "9606",
    "type" : "TAXONOMY"
  },
  "idObject" : 289,
  "status" : "uninitialized",
  "directory" : "97c4abf08dd8fb41b06631509e584601",
  "progress" : 0.0,
  "notifyEmail" : null,
  "logEntries" : false,
  "name" : "New Disease Map",
  "owner" : "admin",
  "projectId" : "test_project",
  "creationDate" : "2021-10-29 11:33:28",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ ],
  "topOverviewImage" : null
}

3.4. Example 2.

Upload of project from complex zip file

3.4.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/' -i -X POST \
    -H 'Content-Type: application/x-www-form-urlencoded' \
    -d 'projectId=test_project&file-id=339&mapCanvasType=OPEN_LAYERS&parser=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&zip-entries%5B0%5D%5B_type%5D=MAP&zip-entries%5B0%5D%5B_filename%5D=main.xml&zip-entries%5B0%5D%5B_data%5D%5Broot%5D=true&zip-entries%5B0%5D%5B_data%5D%5Bname%5D=main&zip-entries%5B0%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B1%5D%5B_type%5D=MAP&zip-entries%5B1%5D%5B_filename%5D=submaps%2Fmapping.xml&zip-entries%5B1%5D%5B_data%5D%5Broot%5D=false&zip-entries%5B1%5D%5B_data%5D%5Bname%5D=mapping&zip-entries%5B1%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B2%5D%5B_type%5D=MAP&zip-entries%5B2%5D%5B_filename%5D=submaps%2Fs1.xml&zip-entries%5B2%5D%5B_data%5D%5Broot%5D=false&zip-entries%5B2%5D%5B_data%5D%5Bname%5D=s1&zip-entries%5B2%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B3%5D%5B_type%5D=MAP&zip-entries%5B3%5D%5B_filename%5D=submaps%2Fs2.xml&zip-entries%5B3%5D%5B_data%5D%5Broot%5D=false&zip-entries%5B3%5D%5B_data%5D%5Bname%5D=s2&zip-entries%5B3%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN&zip-entries%5B4%5D%5B_type%5D=MAP&zip-entries%5B4%5D%5B_filename%5D=submaps%2Fs3.xml&zip-entries%5B4%5D%5B_data%5D%5Broot%5D=false&zip-entries%5B4%5D%5B_data%5D%5Bname%5D=s3&zip-entries%5B4%5D%5B_data%5D%5Btype%5D%5Bid%5D=UNKNOWN' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

3.4.2. Sample Response

{
  "version" : null,
  "disease" : null,
  "organism" : null,
  "idObject" : 295,
  "status" : "uninitialized",
  "directory" : "335c1485db479b22f96cae1d92409d1f",
  "progress" : 0.0,
  "notifyEmail" : null,
  "logEntries" : false,
  "name" : null,
  "owner" : "admin",
  "projectId" : "test_project",
  "creationDate" : "2021-10-29 11:33:30",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ ],
  "topOverviewImage" : null
}

4. Update project

Updates project.

4.1. Path Parameters

Table 3. /projects/{projectId}/
Parameter Description

projectId

project identifier

4.2. Request Fields

Path Type Description

project.version

string

version of the project

project.name

string

name of the project

project.notifyEmail

string

email address that should be when something change in the project

project.organism

Reference

organism associated with the project

project.disease

Reference

disease associated with the project

project.mapCanvasType

string

type of map canvas engine to be used when visualizing map, for now there are only two options available: GOOGLE_MAPS_API, OPEN_LAYERS

4.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/' -i -X PATCH \
    -d '{"project":{"version":"xxx", "name": "new name", "notifyEmail": "notify@uni.lu", "organism": {"type": "TAXONOMY", "resource": "9605"}, "disease": {"type": "MESH_2012", "resource": "D010300"}, "mapCanvasType": "OPEN_LAYERS" }}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

4.4. Sample Response

{
  "version" : "xxx",
  "disease" : {
    "annotatorClassName" : "",
    "id" : 712,
    "link" : "http://id.nlm.nih.gov/mesh/D010300",
    "resource" : "D010300",
    "type" : "MESH_2012"
  },
  "organism" : {
    "annotatorClassName" : "",
    "id" : 713,
    "link" : "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9605",
    "resource" : "9605",
    "type" : "TAXONOMY"
  },
  "idObject" : 307,
  "status" : "uninitialized",
  "directory" : "289b78b436176091ad900020c933c544",
  "progress" : 0.0,
  "notifyEmail" : "notify@uni.lu",
  "logEntries" : true,
  "name" : "new name",
  "owner" : "admin",
  "projectId" : "test_project",
  "creationDate" : "2021-10-29 11:33:35",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ {
    "idObject" : 233,
    "filename" : "289b78b436176091ad900020c933c544/image.png",
    "width" : 200,
    "height" : 100,
    "links" : [ ]
  } ],
  "topOverviewImage" : {
    "idObject" : 233,
    "filename" : "289b78b436176091ad900020c933c544/image.png",
    "width" : 200,
    "height" : 100,
    "links" : [ ]
  }
}

5. Delete project

5.1. Path Parameters

Table 4. /projects/{projectId}/
Parameter Description

projectId

project identifier

5.2. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project2/' -i -X DELETE

5.3. Sample Response

{
  "version" : null,
  "disease" : null,
  "organism" : null,
  "idObject" : 306,
  "status" : "Project removing",
  "directory" : "96c2ef8e36c05b7af9464f5a10b3e1ce",
  "progress" : 0.0,
  "notifyEmail" : null,
  "logEntries" : false,
  "name" : null,
  "owner" : "admin",
  "projectId" : "test_project2",
  "creationDate" : "2021-10-29 11:33:34",
  "mapCanvasType" : "OPEN_LAYERS",
  "overviewImageViews" : [ ],
  "topOverviewImage" : null
}

6. Get source

Gets source file used to create the project.

6.1. Path Parameters

Table 5. /projects/{projectId}:downloadSource
Parameter Description

projectId

project identifier

6.2. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project:downloadSource' -i -X GET

6.3. Sample Response

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4"
      xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner"
      level="2"
      version="4">
   <model metaid="untitled" id="untitled">
      <annotation>
         <celldesigner:extension>
            <celldesigner:modelVersion>4.0</celldesigner:modelVersion>
            <celldesigner:modelDisplay sizeX="600" sizeY="400"/>
            <celldesigner:listOfCompartmentAliases/>
            <celldesigner:listOfComplexSpeciesAliases/>
            <celldesigner:listOfSpeciesAliases>
               <celldesigner:speciesAlias id="sa1" species="s1">
                  <celldesigner:activity>inactive</celldesigner:activity>
                  <celldesigner:bounds x="141.0" y="110.0" w="80.0" h="40.0"/>
                  <celldesigner:font size="12"/>
                  <celldesigner:view state="usual"/>
                  <celldesigner:usualView>
                     <celldesigner:innerPosition x="0.0" y="0.0"/>
                     <celldesigner:boxSize width="80.0" height="40.0"/>
                     <celldesigner:singleLine width="1.0"/>
                     <celldesigner:paint color="ffccffcc" scheme="Color"/>
                  </celldesigner:usualView>
                  <celldesigner:briefView>
                     <celldesigner:innerPosition x="0.0" y="0.0"/>
                     <celldesigner:boxSize width="80.0" height="60.0"/>
                     <celldesigner:singleLine width="0.0"/>
                     <celldesigner:paint color="3fff0000" scheme="Color"/>
                  </celldesigner:briefView>
                  <celldesigner:info state="empty" angle="-1.5707963267948966"/>
               </celldesigner:speciesAlias>
            </celldesigner:listOfSpeciesAliases>
            <celldesigner:listOfGroups/>
            <celldesigner:listOfProteins>
               <celldesigner:protein id="pr1" name="generic protein" type="GENERIC"/>
            </celldesigner:listOfProteins>
            <celldesigner:listOfGenes/>
            <celldesigner:listOfRNAs/>
            <celldesigner:listOfAntisenseRNAs/>
            <celldesigner:listOfLayers/>
            <celldesigner:listOfBlockDiagrams/>
         </celldesigner:extension>
      </annotation>
      <listOfUnitDefinitions>
         <unitDefinition metaid="substance" id="substance" name="substance">
            <listOfUnits>
               <unit metaid="CDMT00001" kind="mole"/>
            </listOfUnits>
         </unitDefinition>
         <unitDefinition metaid="volume" id="volume" name="volume">
            <listOfUnits>
               <unit metaid="CDMT00002" kind="litre"/>
            </listOfUnits>
         </unitDefinition>
         <unitDefinition metaid="area" id="area" name="area">
            <listOfUnits>
               <unit metaid="CDMT00003" kind="metre" exponent="2"/>
            </listOfUnits>
         </unitDefinition>
         <unitDefinition metaid="length" id="length" name="length">
            <listOfUnits>
               <unit metaid="CDMT00004" kind="metre"/>
            </listOfUnits>
         </unitDefinition>
         <unitDefinition metaid="time" id="time" name="time">
            <listOfUnits>
               <unit metaid="CDMT00005" kind="second"/>
            </listOfUnits>
         </unitDefinition>
      </listOfUnitDefinitions>
      <listOfCompartments>
         <compartment metaid="default" id="default" size="1" units="volume"/>
      </listOfCompartments>
      <listOfSpecies>
         <species metaid="s1"
                  id="s1"
                  name="generic protein"
                  compartment="default"
                  initialAmount="0">
            <annotation>
               <celldesigner:extension>
                  <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
                  <celldesigner:speciesIdentity>
                     <celldesigner:class>PROTEIN</celldesigner:class>
                     <celldesigner:proteinReference>pr1</celldesigner:proteinReference>
                  </celldesigner:speciesIdentity>
               </celldesigner:extension>
            </annotation>
         </species>
      </listOfSpecies>
   </model>
</sbml>

7. Get logs

Gets logs generated on project upload.

7.1. Path Parameters

Table 6. /projects/{projectId}/logs/
Parameter Description

projectId

project identifier

7.2. Request Parameters

Parameter Description

start

number of first entry in this response

sortColumn

log entry column that should be used for sorting (default: id)

sortOrder

log entry sort order (asc, desc)

level

level of log entry (warning, error)

length

number of log entres we want to obtain

search

search query used for filtering

7.3. Response Fields

Path Type Description

data

array<LogEntry>

list of log entries

filteredSize

number

number of entries that match filter criteria

length

number

number of entries in this response

start

number

number of first entry in this response

totalSize

number

number of all log entries

7.4. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/logs/?start=0&length=5&level=warning&sortColumn=id&sortOrder=asc&search=age' -i -X GET

7.5. Sample Response

{
  "data" : [ {
    "id" : 228,
    "content" : "This is warning message",
    "level" : "WARNING",
    "type" : "OTHER",
    "objectIdentifier" : null,
    "objectClass" : null,
    "mapName" : "map_name",
    "source" : null
  } ],
  "filteredSize" : 1,
  "length" : 1,
  "start" : 0,
  "totalSize" : 1
}

8. Get statistics

Gets set of statistics about the project.

8.1. Path Parameters

Table 7. /projects/{projectId}/statistics
Parameter Description

projectId

project identifier

8.2. Response Fields

Path Type Description

reactionAnnotations

map<type,number>

list of reaction annotation types

elementAnnotations

map<type,number>

list of element annotation types

publications

number

number of publications included in the project

8.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/statistics' -i -X GET

8.4. Sample Response

{
  "elementAnnotations" : {
    "_3DMET" : 0,
    "BiGG_COMPARTMENT" : 0,
    "BiGG_METABOLITE" : 0,
    "BiGG_REACTIONS" : 0,
    "BIOMODELS_DATABASE" : 0,
    "BRENDA" : 0,
    "CAS" : 0,
    "CAZY" : 0,
    "CCDS" : 0,
    "CHEBI" : 0,
    "CHEM_ID_PLUS" : 0,
    "CHEMSPIDER" : 0,
    "CHEMBL_COMPOUND" : 0,
    "CHEMBL_TARGET" : 0,
    "CLINICAL_TRIALS_GOV" : 0,
    "COG" : 0,
    "COMPLEX_PORTAL" : 0,
    "DB_SNP" : 0,
    "DOI" : 0,
    "DRUGBANK" : 0,
    "DRUGBANK_TARGET_V4" : 0,
    "EC" : 0,
    "ECO" : 0,
    "ECOGENE" : 0,
    "ENSEMBL" : 0,
    "ENSEMBL_PLANTS" : 0,
    "ENTREZ" : 0,
    "FLYBASE" : 0,
    "GENE_DB" : 0,
    "GO" : 0,
    "HGNC" : 0,
    "HGNC_SYMBOL" : 0,
    "HMDB" : 0,
    "HUMAN_DISEASE_ONTOLOGY" : 0,
    "IMGT_HLA" : 0,
    "INTACT" : 0,
    "INTERPRO" : 0,
    "IUPHAR_LIGAND" : 0,
    "KEGG_COMPOUND" : 0,
    "KEGG_DRUG" : 0,
    "KEGG_GENES" : 0,
    "KEGG_GLYCAN" : 0,
    "KEGG_ORTHOLOGY" : 0,
    "KEGG_PATHWAY" : 0,
    "KEGG_REACTION" : 0,
    "KNAPSACK" : 0,
    "LIPID_BANK" : 0,
    "LIPID_MAPS" : 0,
    "MESH_2012" : 0,
    "MI_R_BASE_SEQUENCE" : 0,
    "MI_R_BASE_MATURE_SEQUENCE" : 0,
    "MIR_TAR_BASE_MATURE_SEQUENCE" : 0,
    "MGD" : 0,
    "MOD" : 0,
    "NCBI_PROTEIN" : 0,
    "OBI" : 0,
    "OMIM" : 0,
    "PANTHER" : 0,
    "PATO" : 0,
    "PDB" : 0,
    "PDB_CCD" : 0,
    "PFAM" : 0,
    "PHARM" : 0,
    "PMC" : 0,
    "PUBCHEM" : 0,
    "PUBCHEM_SUBSTANCE" : 0,
    "PUBMED" : 0,
    "REACTOME" : 0,
    "REFSEQ" : 0,
    "RGD" : 0,
    "RHEA" : 0,
    "SBO_TERM" : 0,
    "SGD" : 0,
    "SPIKE" : 0,
    "STITCH" : 0,
    "STRING" : 0,
    "SWISS_MODEL" : 0,
    "TAIR_LOCUS" : 0,
    "TAXONOMY" : 0,
    "TOXICOGENOMIC_CHEMICAL" : 0,
    "TTD_Drug" : 0,
    "UNIGENE" : 0,
    "UNIPROT" : 0,
    "UNIPROT_ISOFORM" : 0,
    "UNKNOWN" : 0,
    "VMH_METABOLITE" : 0,
    "VMH_REACTION" : 0,
    "WIKIDATA" : 0,
    "WIKIPATHWAYS" : 0,
    "WIKIPEDIA" : 0,
    "WORM_BASE" : 0,
    "ZFIN" : 0
  },
  "publications" : 1,
  "reactionAnnotations" : {
    "_3DMET" : 0,
    "BiGG_COMPARTMENT" : 0,
    "BiGG_METABOLITE" : 0,
    "BiGG_REACTIONS" : 0,
    "BIOMODELS_DATABASE" : 0,
    "BRENDA" : 0,
    "CAS" : 0,
    "CAZY" : 0,
    "CCDS" : 0,
    "CHEBI" : 0,
    "CHEM_ID_PLUS" : 0,
    "CHEMSPIDER" : 0,
    "CHEMBL_COMPOUND" : 0,
    "CHEMBL_TARGET" : 0,
    "CLINICAL_TRIALS_GOV" : 0,
    "COG" : 0,
    "COMPLEX_PORTAL" : 0,
    "DB_SNP" : 0,
    "DOI" : 0,
    "DRUGBANK" : 0,
    "DRUGBANK_TARGET_V4" : 0,
    "EC" : 0,
    "ECO" : 0,
    "ECOGENE" : 0,
    "ENSEMBL" : 0,
    "ENSEMBL_PLANTS" : 0,
    "ENTREZ" : 0,
    "FLYBASE" : 0,
    "GENE_DB" : 0,
    "GO" : 0,
    "HGNC" : 0,
    "HGNC_SYMBOL" : 0,
    "HMDB" : 0,
    "HUMAN_DISEASE_ONTOLOGY" : 0,
    "IMGT_HLA" : 0,
    "INTACT" : 0,
    "INTERPRO" : 0,
    "IUPHAR_LIGAND" : 0,
    "KEGG_COMPOUND" : 0,
    "KEGG_DRUG" : 0,
    "KEGG_GENES" : 0,
    "KEGG_GLYCAN" : 0,
    "KEGG_ORTHOLOGY" : 0,
    "KEGG_PATHWAY" : 0,
    "KEGG_REACTION" : 0,
    "KNAPSACK" : 0,
    "LIPID_BANK" : 0,
    "LIPID_MAPS" : 0,
    "MESH_2012" : 0,
    "MI_R_BASE_SEQUENCE" : 0,
    "MI_R_BASE_MATURE_SEQUENCE" : 0,
    "MIR_TAR_BASE_MATURE_SEQUENCE" : 0,
    "MGD" : 0,
    "MOD" : 0,
    "NCBI_PROTEIN" : 0,
    "OBI" : 0,
    "OMIM" : 0,
    "PANTHER" : 0,
    "PATO" : 0,
    "PDB" : 0,
    "PDB_CCD" : 0,
    "PFAM" : 0,
    "PHARM" : 0,
    "PMC" : 0,
    "PUBCHEM" : 0,
    "PUBCHEM_SUBSTANCE" : 0,
    "PUBMED" : 1,
    "REACTOME" : 0,
    "REFSEQ" : 0,
    "RGD" : 0,
    "RHEA" : 0,
    "SBO_TERM" : 0,
    "SGD" : 0,
    "SPIKE" : 0,
    "STITCH" : 0,
    "STRING" : 0,
    "SWISS_MODEL" : 0,
    "TAIR_LOCUS" : 0,
    "TAXONOMY" : 0,
    "TOXICOGENOMIC_CHEMICAL" : 0,
    "TTD_Drug" : 0,
    "UNIGENE" : 0,
    "UNIPROT" : 0,
    "UNIPROT_ISOFORM" : 0,
    "UNKNOWN" : 0,
    "VMH_METABOLITE" : 0,
    "VMH_REACTION" : 0,
    "WIKIDATA" : 0,
    "WIKIPATHWAYS" : 0,
    "WIKIPEDIA" : 0,
    "WORM_BASE" : 0,
    "ZFIN" : 0
  }
}

9. Get publications

Gets publication list used in the project.

9.1. Path Parameters

Table 8. /projects/{projectId}/models/{mapId}/publications/
Parameter Description

projectId

project identifier

mapId

submap identifier (use '*' to indicate all maps)

9.2. Request Parameters

Parameter Description

start

number of first entry in this response

sortColumn

log entry column that should be used for sorting (default: id)

sortOrder

log entry sort order (asc, desc)

level

level of log entry (warning, error)

length

number of log entres we want to obtain

search

search query used for filtering

9.3. Response Fields

Path Type Description

data

array<Article>

list of publications

filteredSize

number

number of entries that match filter criteria

length

number

number of entries in this response

page

number

page number of result list

totalSize

number

number of all log entries

9.4. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/656/publications/' -i -X GET

9.5. Sample Response

{
  "data" : [ {
    "elements" : [ {
      "id" : 336,
      "modelId" : 656,
      "type" : "REACTION"
    } ],
    "publication" : {
      "article" : {
        "id" : 1,
        "title" : "MINERVA-a platform for visualization and curation of molecular interaction networks.",
        "authors" : [ "Gawron P", " Ostaszewski M", " Satagopam V", " Gebel S", " Mazein A", " Kuzma M", " Zorzan S", " McGee F", " Otjacques B", " Balling R", " Schneider R." ],
        "journal" : "NPJ systems biology and applications",
        "year" : 2016,
        "link" : "https://www.ncbi.nlm.nih.gov/pubmed/28725475",
        "pubmedId" : "28725475",
        "citationCount" : 21,
        "stringAuthors" : "Gawron P,  Ostaszewski M,  Satagopam V,  Gebel S,  Mazein A,  Kuzma M,  Zorzan S,  McGee F,  Otjacques B,  Balling R,  Schneider R."
      }
    }
  } ],
  "filteredSize" : 1,
  "length" : 1,
  "page" : 0,
  "totalSize" : 1
}