2.9.7
(any
= {}
)
Search for a specific natural or active compound using its ID
Load the DBrefs and create a new property data
for each DBRef
(any)
(object
= {}
)
Name | Description |
---|---|
options.collections Array<string>?
|
List of collections to include |
options.excludedCollections Array<string>?
|
List of collections to include |
options.force boolean
(default false )
|
Force the inclusion of the data even if it is already present |
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
This function normalizes the activities of an entry of ActivesOrNaturals collection.
(Object)
an entry of ActivesOrNaturals collection
any
:
ActiveOrNatural entry with normalized activities
Search for natural or active compounds using various criteria
(object
= {}
)
Name | Description |
---|---|
options.masses (number | string | Array<number>)?
|
Observed monoisotopic mass |
options.noStereoTautomerID string
(default '' )
|
ID of the compound to search from the results |
options.ionizations string
(default '' )
|
string containing a comma separated list of modifications |
options.ranges string
(default '' )
|
Allows to filter by a range of molecular formula |
options.mf string
(default '' )
|
Search by molecular formula |
options.precision number
(default 1000 )
|
Precision of the monoisotopic mass in ppm |
options.fields string?
|
List of fields to retrieve |
options.kwTaxonomies string
(default '' )
|
Comma separated list of taxonomies family, genus or species of the product source |
options.kwActiveAgainst string
(default '' )
|
Comma separated list of taxonomies family, genus or species of the bioactivity target |
options.kwBioassays string
(default '' )
|
Comma separated list of keyword from the description of the bioassay |
options.kwMeshTerms string
(default '' )
|
Comma separated list of keyword from the medline MeshTerms |
options.kwTitles string
(default '' )
|
Comma separated list of keyword from the compound title |
options.minNbMassSpectra string?
|
Minimal number of mass spectra |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.route string
(default 'activesOrNaturals/v1/search' )
|
Route to this specific webservice |
options.includes (Array<string> | undefined)?
|
Array of DBref collections to include |
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
Base URL of the webservice |
Search for natural or active compounds and group them by molecular formula
(object
= {}
)
Name | Description |
---|---|
options.masses (number | string | Array<number>)?
|
Observed monoisotopic mass |
options.ionizations string
(default '' )
|
string containing a comma separated list of modifications |
options.ranges string
(default '' )
|
Allows to filter by a range of molecular formula |
options.precision number
(default 1000 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.fields string
(default 'data.noStereoOcl,data.em,data.mf' )
|
List of fields to retrieve |
options.kwTaxonomies string
(default '' )
|
Comma separated list of taxonomies family, genus or species of the product source |
options.kwActiveAgainst string
(default '' )
|
Comma separated list of taxonomies family, genus or species of the bioactivity target |
options.kwBioassays string
(default '' )
|
Comma separated list of keyword from the description of the bioassay |
options.kwMeshTerms string
(default '' )
|
Comma separated list of keyword from the medline MeshTerms |
options.kwTitles string
(default '' )
|
Comma separated list of keyword from compound title |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.route string
(default 'activesOrNaturals/v1/search' )
|
URL of the webservice |
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
Retrieve a list of molecular formulas from one or many monoisotopic mass that are present in pubchem compound. in the database and a monoisotopic mass.
(string)
Observed monoisotopic mass
(object
= {}
)
Name | Description |
---|---|
options.fields string?
|
Fields to retrieve from the database |
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.route string
(default 'mfs/v1/fromMF' )
|
URL of the webservice |
options.titleCompoundsURL string
(default 'titleCompounds/v1/ids' )
|
URL of the webservice |
options.limit number
(default 50000 )
|
Maximal number of entries to return |
This method will retrieve similar mass spectra
(object
= {}
)
Name | Description |
---|---|
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.masses (number | string | Array<number>)?
|
Observed monoisotopic mass |
options.precision number
(default 1000 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.modifications string
(default '' )
|
Comma |
options.databases Array<(
(default ['massBank','gnps'] )
|
List of databases to search for mass spectra |
options.routes object?
|
Object that contains the routes to use for each database |
options.uniqueMolecules boolean
(default true )
|
If true, only one molecule per entry is returned |
options.similarity object
(default {} )
|
|
options.similarity.nbPeaks number
(default 5 )
|
Number of peaks to use for the similarity |
options.similarity.massPower number
(default 1 )
|
Power to use for the mass |
options.similarity.minSimilarity number
(default 0.2 )
|
Minimal similarity to return |
options.similarity.intensityPower number
(default 0.6 )
|
Power to use for the intensity |
options.similarity.minNbCommonPeaks number
(default 0 )
|
Minimal number of common peaks |
options.similarity.experimental {x: Array<number>, y: Array<number>}
(default [] )
|
Experimental mass spectra to compare to |
Retrieve a list of molecular formulas from one or many monoisotopic mass that are present in pubchem compound. in the database and a monoisotopic mass.
(object
= {}
)
Name | Description |
---|---|
options.ionizations string
(default '' )
|
string containing a comma separated list of modifications |
options.precision number
(default 1000 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.ranges string
(default '' )
|
Range of allowed molecular formula |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.minCount number
(default 5 )
|
Minimal number of molecules having a specific MF |
options.fields number?
|
Fields to retrieve from the database |
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.route string
(default 'mfs/v1/fromEM' )
|
URL of the webservice |
options.compoundsURL string
(default 'mfs/v1/fromMF' )
|
URL to retrieve corresponding compounds |
Retrieve the compounds from a pubmedID
(object)
The experimental spectrum to compare to
(string)
Molecular formula of the non ionized molecule
(object
= {}
)
Name | Description |
---|---|
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.mf string?
|
Molecular formula of the non ionized molecule (not available for inSilicoFragments) |
options.precision number
(default 100 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.massPower number
(default 1000 )
|
Maximal number of entries to return |
options.massPower number
(default 3 )
|
High power will give more weight to the mass. If you would prefer to observe fragments you should use a number less than 1 |
options.intensityPower number
(default 0.6 )
|
How important is the intensity. By default we don't give to much importance to it |
options.route string
(default 'inSilicoFragments/v1/search' )
|
Route to use |
(object)
The experimental spectrum to compare to
(object
= {}
)
Name | Description |
---|---|
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.mf string?
|
Molecular formula of the non ionized molecule (not available for inSilicoFragments) |
options.precision number
(default 100 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.ionizations string
(default "H+" )
|
Comma separated list of allowed ionizations |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.massPower number
(default 1000 )
|
Maximal number of entries to return |
options.massPower number
(default 3 )
|
High power will give more weight to the mass. If you would prefer to observe fragments you should use a number less than 1 |
options.intensityPower number
(default 0.6 )
|
How important is the intensity. By default we don't give to much importance to it |
options.route string
(default 'inSilicoFragments/v1/search' )
|
Route to use |
options.technique object
(default {} )
|
Technique used to generate the spectrum |
options.technique.mode string
(default "positive" )
|
Mode of the acquisition |
options.technique.ionization string
(default "esi" )
|
Ionization of the acquisition |
(object
= {}
)
Name | Description |
---|---|
options.baseURL string
(default 'https://octochemdb.cheminfo.org/' )
|
URL of the webservice |
options.masses (number | string | Array<number>)?
|
Observed fragment masses |
options.mf string?
|
Molecular formula of the non ionized molecule (not available for inSilicoFragments) |
options.precision number
(default 100 )
|
Precision (accuracy) of the monoisotopic mass in ppm |
options.limit number
(default 1000 )
|
Maximal number of entries to return |
options.modifications string
(default '' )
|
Comma separated list of allowed modifications |
options.route string
(default 'massBank/v1/search' )
|
Route to use |
options.link string
(default 'https://massbank.eu/MassBank/RecordDisplay?id=' )
|
Link to the database source |
Summarize the active or natural details with the given terms
(Object)
The active or natural details to summarize
(Object
= {}
)
The options to use for the search
Name | Description |
---|---|
options.activities Object
(default {} )
|
The options to use for the activities search |
options.activities.minScore number
(default 0.5 )
|
Minimum score for an entry to be returned |
options.activities.maxNbEntries number
(default 100 )
|
Maximum number of entries to return |
options.activities.relevance object
(default {k:1.2,b:0.75,d:0.5} )
|
BM25 algorithm {k: Term frequency saturation parameter, b: Length normalization parameter, d:Frequency normalization lower bound} |
options.activities.tolerance number
(default 1 )
|
-Typo Tolerance following the Levenshtein algorithm |
options.activities.queryFields Array<string>
(default ['assay'] )
|
Fields to query |
options.taxonomies Object
(default {} )
|
The options to use for the activities search |
options.taxonomies.minScore number
(default 0.5 )
|
Minimum score for an entry to be returned |
options.taxonomies.maxNbEntries number
(default 50 )
|
Maximum number of entries to return |
options.taxonomies.tolerance number
(default 1 )
|
-Typo Tolerance following the Levenshtein algorithm |
options.patents object
(default {} )
|
Options for patents |
options.patents.abstractsLimit number
(default 1000 )
|
If more than this number of abstracts, the search will be done on the without abstracts |
options.patents.maxNbEntries number
(default 100 )
|
Maximum number of entries to return |
options.patents.inScore number
(default 0.5 )
|
Minimum score for an entry to be returned |
options.patents.relevance object
(default {k:1.2,b:0.75,d:0.5} )
|
BM25 algorithm {k: Term frequency saturation parameter, b: Length normalization parameter, d:Frequency normalization lower bound} |
options.patents.tolerance number
(default 1 )
|
-Typo Tolerance following the Levenshtein algorithm |
options.patents.queryFields Array<string>
(default ['title','abstract'] )
|
Fields to query |
options.patents.boostFields object
(default {title:2,abstract:1} )
|
Fields weights, higher weight means higher importance |
options.pubmeds object
(default {} )
|
Options for pubmeds |
options.pubmeds.abstractsLimit number
(default 1000 )
|
If more than this number of abstracts, the search will be done on the without abstracts |
options.pubmeds.minScore number
(default 0.5 )
|
Minimum score for an entry to be returned |
options.pubmeds.maxNbEntries number
(default 100 )
|
Maximum number of entries to return |
options.pubmeds.relevance object
(default {k:1.2,b:0.75,d:0.5} )
|
BM25 algorithm {k: Term frequency saturation parameter, b: Length normalization parameter, d:Frequency normalization lower bound} |
options.pubmeds.tolerance number
(default 1 )
|
-Typo Tolerance following the Levenshtein algorithm |
options.pubmeds.boostFields object
(default {title:2,abstract:1,meshHeadings:1} )
|
Fields weights, higher weight means higher importance |
options.pubmeds.queryFields Array<string>
(default ['title','abstract','meshHeadings'] )
|
Fields to query |
Summarize the active or natural details with the given terms
(string)
The terms to search
Promise<Object>
:
The summarized active or natural details
sort taxonomies by superkingdom, kingdom, phylum, class, order, family, genus, species
(any)
(any)
number
:
Creates a tree structure from an array of taxonomies.
(any)
(any
= {}
)
Array<Object>
:
The tree structure.