2.13.1(any
= {})
Search for a specific natural or active compound using its ID
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 |
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 |
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.
Names that differ only by case or by surrounding whitespace are the same
taxon: sources disagree on the binomial (CMAUP writes Stevia Mercedensis
where LOTUS, NPASS and COCONUT write Stevia mercedensis). They are merged
into one node, displayed with the spelling closest to the convention — an
initial capital and nothing capitalized after it.
(any)
(any
= {})
Array<Object>:
The tree structure.
How far a spelling is from the convention; the lowest score wins.
(any)