@datafire/ideaconsult_enanomapper NPM

@datafire/ideaconsult_enanomapper

Client library for eNanoMapper database

Installation and Usage

npm install --save @datafire/ideaconsult_enanomapper

let ideaconsult_enanomapper = require('@datafire/ideaconsult_enanomapper').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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.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_enanomapper.solrquery_get({}, context)

Input

input object
- q string: The query
- fq string: Filter query
- fl string: Field list
- start integer: Starting page
- rows integer: Page size
- wt string (values: json, xml, csv): Response format

Output

output SolrResponse

solrquery_post

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

ideaconsult_enanomapper.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

datafire

@infinitebrahmanuniverse/nolb-_datafire_i @everything-registry/sub-chunk-222

3.0.0

5 years ago