compound_tbl_sdf: Extract compound data from a file in SDF format
In michaelwitting/CompoundDb: Creating and using (Chemical) Compound Annotation Databases

Description Usage Arguments Details Value Note Author(s) See Also Examples

compound_tbl_sdf extracts basic compound annotations from a file in SDF format (structure-data file). The function currently supports SDF files from:

HMDB (Human Metabolome Database): http://www.hmdb.ca
ChEBI (Chemical Entities of Biological Interest): http://ebi.ac.uk/chebi
LMSD (LIPID MAPS Structure Database): http://www.lipidmaps.org
PubChem: https://pubchem.ncbi.nlm.nih.gov/
MoNa: http://mona.fiehnlab.ucdavis.edu/ (see notes below!)

1	compound_tbl_sdf(file, collapse)

`file`	`character(1)` with the name of the SDF file.
`collapse`	optional `character(1)` to be used to collapse multiple values in the columns `"synonyms"`. See examples for details.

Column "compound_name" reports for HMDB files the "GENERIC_NAME", for ChEBI the "ChEBI Name", for PubChem the "PUBCHEM_IUPAC_TRADITIONAL_NAME", and for Lipid Maps the "COMMON_NAME", if that is not available, the first of the compounds synonyms and, if that is also not provided, the "SYSTEMATIC_NAME".

A tibble::tibble with general compound information (one row per compound):

compound_id: the ID of the compound.
compound_name: the compound's name.
inchi: the InChI of the compound.
inchikey: the InChI key.
formula: the chemical formula.
mass: the compound's mass.
synonyms: the compound's synonyms (aliases). This type of this column is by default a list to support multiple aliases per compound, unless argument collapse is provided, in which case multiple synonyms are pasted into a single element separated by the value of collapse.
smiles: the compound's SMILES (if provided).

compound_tbl_sdf supports also to read/process gzipped files.

MoNa SDF files organize the data by individual spectra (i.e. each element is one spectrum) and individual compounds can not easily and consistently defined (i.e. not all entries have an InChI ID or other means to uniquely identify compounds). Thus, the function returns a highly redundant compount table. Feedback on how to reduce this redundancy would be highly welcome!

Johannes Rainer and Jan Stanstrup

createCompDb() for a function to create a SQLite-based compound database.

Other compound table creation functions: compound_tbl_lipidblast()

## Read compound information from a subset of HMDB
fl <- system.file("sdf/HMDB_sub.sdf.gz", package = "CompoundDb")
cmps <- compound_tbl_sdf(fl)
cmps

## Column synonyms contains a list
cmps$synonyms

## If we provide the optional argument collapse, multiple entries will be
## collapsed.
cmps <- compound_tbl_sdf(fl, collapse = "|")
cmps
cmps$synonyms