@datafire/ideaconsult_nanoreg

Client library for eNanoMapper database

Installation and Usage

npm install --save @datafire/ideaconsult_nanoreg

let ideaconsult_nanoreg = require('@datafire/ideaconsult_nanoreg').create();

.then(data => {
  console.log(data);
});

Description

AMBIT REST web services [eNanoMapper profile] with free text & faceted search

Actions

getInvestigationResults

Multiple studies in tabular form

ideaconsult_nanoreg.getInvestigationResults({
  "db": "",
  "type": "",
  "search": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • type required string (values: byinvestigation, byassay, bysubstance, byprovider, bycitation, bystudytype, bystructure_inchikey, bystructure_smiles, bystructure_name, bysubstance_name, bysubstance_type): query type
  • search required string: Search parameter, UUID of the investigation or a substance
  • inchikey string: Search parameter, InChI key(s) of the substance component(s), comma delimited
  • id string: Search parameter, chemical structure or substance identifier(s), comma delimited
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Investigation

searchByIdentifier

Returns compounds found

ideaconsult_nanoreg.searchByIdentifier({
  "db": "",
  "term": "",
  "representation": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • term required string (values: search, url, inchikey): search term type
  • representation required string (values: all, smiles, reach, stdinchi, stdinchikey, names, iupac_name, synonym, cas, einecs)
  • search string: Compound identifier (SMILES, InChI, name, registry identifiers)
  • b64search string: Base64 encoded mol file; if included, will be used instead of the 'search' parameter
  • casesens boolean: Case sensitive search if yes
  • bundle_uri string: Bundle URI
  • sameas string: Ontology URI to define groups of columns
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Dataset

searchBySimilarity

Returns similar compounds

ideaconsult_nanoreg.searchBySimilarity({
  "db": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • search string: Compound identifier (SMILES, InChI, name, registry identifiers)
  • b64search string: Base64 encoded mol file; if included, will be used instead of the 'search' parameter
  • type string (values: smiles, mol, url): Defines the expected content of the search parameter
  • threshold number: Similarity threshold
  • dataset_uri string: Restrict the search within the AMBIT dataset specified with the URI
  • filterBySubstance boolean: Restrict the search within the set of structures with assigned substances
  • bundle_uri string: If the structure is used in the specified bundle URI, the selection tag will be returned
  • sameas string: Ontology URI to define groups of columns
  • mol boolean: Only for application/json; to include mol as JSON field
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Dataset

searchBySmarts

Returns compounds with the specified substructure

ideaconsult_nanoreg.searchBySmarts({
  "db": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • search string: Compound identifier (SMILES, InChI, name, registry identifiers)
  • b64search string: Base64 encoded mol file; if included, will be used instead of the 'search' parameter
  • type string (values: smiles, mol, url): Defines the expected content of the search parameter
  • dataset_uri string: Restrict the search within the AMBIT dataset specified with the URI
  • filterBySubstance boolean: Restrict the search within the set of structures with assigned substances
  • bundle_uri string: If the structure is used in the specified bundle URI, the selection tag will be returned
  • sameas string: Ontology URI to define groups of columns
  • mol boolean: Only for application/json; to include mol as JSON field
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Dataset

getEndpointSummary

Returns endpoint summary

ideaconsult_nanoreg.getEndpointSummary({
  "db": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • top string (values: P-CHEM, ECOTOX, ENV FATE, TOX, EXPOSURE): Top endpoint category
  • category string: Endpoint category (The value in the protocol.category.code field)

Output

• output Facet

getSubstances

Returns a list of substances, according to the search criteria

ideaconsult_nanoreg.getSubstances({
  "db": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • search string: Search parameter
  • type string (values: substancetype, name, like, regexp, uuif, CompTox, DOI, reliability, purposeFlag, studyResultType, isRobustStudy, citation, citationowner, topcategory, endpointcategory, params, owner_name, owner_uuid, related, reference, facet)
  • compound_uri string: If type=related finds all substances containing this compound; if typ =reference - finds all substances with this compound as reference structure
  • bundle_uri string: Retrieves if selected in this bundle
  • addDummySubstance boolean: Adds a compound record as substance in JSON; only if type=related
  • studysummary boolean: If true retrieves study summary for each substance
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Substance

getSubstanceByUUID

Returns substance representation

ideaconsult_nanoreg.getSubstanceByUUID({
  "db": "",
  "uuid": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • uuid required string: Substance UUID
  • property_uris[] string: Property URIs
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Substance

getSubstanceComposition

Returns substance composition

ideaconsult_nanoreg.getSubstanceComposition({
  "db": "",
  "uuid": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • uuid required string: Substance UUID
  • all boolean: true (Show all compositions) false (do not show hidden compositions)
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output SubstanceComposition

getSubstanceStructures

Returns substance composition

ideaconsult_nanoreg.getSubstanceStructures({
  "db": "",
  "uuid": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • uuid required string: Substance UUID
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output Dataset

getSubstanceStudy

Returns substance study representation

ideaconsult_nanoreg.getSubstanceStudy({
  "db": "",
  "uuid": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • uuid required string: Substance UUID
  • top string (values: P-CHEM, ECOTOX, ENV FATE, TOX, EXPOSURE): Top endpoint category
  • category string: Endpoint category (The value in the protocol.category.code field)
  • property_uri string: Property URI https://data.enanomapper.net/property/{UUID} , see Property service
  • property string: Property UUID
  • investigation_uuid string: Investigation UUID, a code to link different studies
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output SubstanceStudy

getSubstanceStudySummary

Study summary

ideaconsult_nanoreg.getSubstanceStudySummary({
  "db": "",
  "uuid": ""
}, context)

Input

• input object
  • db required string (values: calibrate, enanomapper, enpra, marina, nanogenotox, nanoinformatix, nanoreg1, nanoreg2, nanotest): Database ID
  • uuid required string: Substance UUID
  • top string (values: P-CHEM, ECOTOX, ENV FATE, TOX, EXPOSURE): Top endpoint category
  • category string: Endpoint category (The value in the protocol.category.code field)
  • property_uri string: Property URI https://data.enanomapper.net/property/{UUID} , see Property service
  • property string: Property UUID, see Property service
  • result boolean: If true will group by topcategory,endpointcategory,interpretation result
  • page integer: Starting page
  • pagesize integer: Page size

Output

• output SubstanceStudySummary

solrquery_get

GET is simpler to use, but imposes restrictions on the complexity and the lenght of the parameters.

ideaconsult_nanoreg.solrquery_get({}, context)

Input

• input object
  • q string: The query
  • start integer: Starting page
  • rows integer: Page size
  • wt string (values: json, xml): Response format

Output

• output SolrResponse

solrquery_post

POST is more complex to use, but also allows for much for complex and lengthy queries.

ideaconsult_nanoreg.solrquery_post({}, context)

Input

• input object
  • wt string (values: json, xml): Response format
  • body object
    • facet object
    • params object
      • fl array
        • items string
      • rows integer

Output

• output SolrResponse

Definitions

Dataset

• Dataset object
  • dataEntry object
  • feature object
  • model_uri string
  • query object

Facet

• Facet object
  • facet object

Investigation

• Investigation object
  • childDocuments object
  • assay string
  • document_uuid string
  • effectendpoint string
  • endpoint string
  • endpointcategory string
  • err number
  • errQualifier string
  • guidance string
  • investigation string
  • loQualifier string
  • loValue number
  • name string
  • owner_name string
  • publicname string
  • reference string
  • reference_owner string
  • reference_year string
  • resulttype string
  • s_uuid string
  • studyResultType string
  • substanceType string
  • textValue string
  • topcategory string
  • type_s string
  • unit string
  • upQualifier string
  • upValue number
  • updated string

SolrQuery

• SolrQuery object
  • facet string
  • filter string
  • query string
  • rows integer
  • sort boolean
  • start integer

SolrResponse

• SolrResponse object
  • response object
    • docs array
      • items object
    • maxScore number
    • numFound integer
    • start integer
  • responseHeader object
    • QTime integer
    • params object
    • status integer
    • zkConnected boolean

Substance

• Substance object
  • substance object

SubstanceComposition

• SubstanceComposition object
  • composition object
  • feature object

SubstanceStudy

• SubstanceStudy object
  • study object

SubstanceStudySummary

• SubstanceStudySummary object
  • facet object