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Generates an Excel workbook which lists all records in the database that contain a given set of DTXSIDs.

Source: R/chemi_amos_batch.R
chemi_amos_batch.Rd

[Experimental]

Usage

chemi_amos_batch(
  additional_record_info = NULL,
  always_download_file = NULL,
  base_url = NULL,
  ids = NULL,
  include_classyfire = NULL,
  include_external_links = NULL,
  include_functional_uses = NULL,
  include_source_counts = NULL,
  methodologies = NULL,
  record_types = NULL
)

Arguments

additional_record_info

Optional parameter

always_download_file

If false, a search that does not find any matching records in the database will just return a message instead of a file.

base_url

URL for the AMOS frontend. Used to construct the internal links in the output file.

ids

List of DTXSIDs or other identifiers to search for.

include_classyfire

Flag for whether to include the top four levels of a ClassyFire classification for each of the searched substances, if it exists.

Flag for whether to include database records that are purely external links (e.g., spectra that we can link to but cannot store directly in the database).

include_functional_uses

Flag for whether to include functional use classifications based on the ChemFuncT ontology. Only exists for around 21,000 substances in the database.

include_source_counts

Flag for whether to include counts of a substance's appearances in patents, PubMed articles, and other external sources.

methodologies

Filters the returned results by analytical methodologies. This argument should be a dictionary with four keys with boolean values – "all", "GC/MS", "LC/MS", and "NMR". There are some methodologies with small numbers of records (e.g., IR spectra) which will only appear in the data if "all" is set to true.

record_types

Filters returned results by record type. This argument should be a dictionary with three keys with boolean values – "Fact Sheet", "Method", and "Spectrum". Note that the "Spectrum" flag will return spectra of all types – mass, NMR, etc.

Value

Returns a tibble with results

API stage

This wrapper was generated from the public API schema.

Examples

if (FALSE) { # \dontrun{
chemi_amos_batch(additional_record_info = "DTXSID1024122")
} # }