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!)
Arguments
- 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.- onlyValid
logical(1)to import only valid or all elements (defaults toonlyValid = TRUE)- nonStop
logical(1)whether file content specific errors should only reported as warnings and not break the full import process. The value of this parameter is passed to parameterskipErrorsof theChemmineR::read.SDFset()function.
Value
A tibble::tibble with general compound information (one row per compound):
compound_id: the ID of the compound.name: the compound's name.inchi: the InChI of the compound.inchikey: the InChI key.formula: the chemical formula.exactmass: the compound's (monoisotopic exact) mass.synonyms: the compound's synonyms (aliases). This type of this column is by default alistto support multiple aliases per compound, unless argumentcollapseis provided, in which case multiple synonyms are pasted into a single element separated by the value ofcollapse.smiles: the compound's SMILES (if provided).
Details
Column "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".
Note
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 compound table. Feedback on how to reduce this redundancy would be highly welcome!
LIPID MAPS was tested August 2020. Older SDF files might not work as the field names were changed.
See also
createCompDb() for a function to create a SQLite-based compound
database.
Other compound table creation functions:
compound_tbl_lipidblast()
Examples
## Read compound information from a subset of HMDB
fl <- system.file("sdf/HMDB_sub.sdf.gz", package = "CompoundDb")
cmps <- compound_tbl_sdf(fl)
cmps
#> # A tibble: 9 × 8
#> compound_id name inchi inchikey formula exactmass synonyms smiles
#> <chr> <chr> <chr> <chr> <chr> <dbl> <named > <chr>
#> 1 HMDB0000001 1-Methylhistidine InCh… BRMWTNU… C7H11N… 169. <chr> "CN1C…
#> 2 HMDB0000002 1,3-Diaminopropa… InCh… XFNJVJP… C3H10N2 74.1 <chr> "NCCC…
#> 3 HMDB0000005 2-Ketobutyric ac… InCh… TYEYBOS… C4H6O3 102. <chr> "CCC(…
#> 4 HMDB0000008 2-Hydroxybutyric… InCh… AFENDNX… C4H8O3 104. <chr> "CCC(…
#> 5 HMDB0000010 2-Methoxyestrone InCh… WHEUWNK… C19H24… 300. <chr> "[H][…
#> 6 HMDB0000011 (R)-3-Hydroxybut… InCh… WHBMMWS… C4H8O3 104. <chr> "C[C@…
#> 7 HMDB0000012 Deoxyuridine InCh… MXHRCPN… C9H12N… 228. <chr> "OC[C…
#> 8 HMDB0004370 N-Methyltryptami… InCh… NCIKQJB… C11H14… 174. <chr> "CNCC…
#> 9 HMDB0006719 5,6-trans-Vitami… InCh… QYSXJUF… C27H44O 384. <chr> "CC(C…
## Column synonyms contains a list
cmps$synonyms
#> $CMP1
#> [1] "1 Methylhistidine" "1-Methyl histidine" "1-Methyl-Histidine"
#> [4] "1-Methyl-L-histidine" "1-MHis" "1-N-Methyl-L-histidine"
#> [7] "L-1-Methylhistidine" "N1-Methyl-L-histidine" "Pi-methylhistidine"
#>
#> $CMP2
#> [1] "1,3-Diamino-N-propane" "1,3-Propanediamine"
#> [3] "1,3-Propylenediamine" "1,3-Trimethylenediamine"
#> [5] "3-Aminopropylamine" "a,w-Propanediamine"
#> [7] "Propane-1,3-diamine" "Trimethylenediamine"
#>
#> $CMP3
#> [1] "2-Ketobutanoate" "2-Ketobutanoic acid"
#> [3] "2-Ketobutyrate" "2-Oxo-Butanoate"
#> [5] "2-Oxo-Butanoic acid" "2-Oxo-Butyrate"
#> [7] "2-Oxo-Butyric acid" "2-Oxo-N-butyrate"
#> [9] "2-Oxo-N-butyric acid" "2-Oxobutanoate"
#> [11] "2-Oxobutanoic acid" "2-Oxobutyrate"
#> [13] "2-Oxobutyric acid" "3-Methylpyruvate"
#> [15] "3-Methylpyruvic acid" "a-Keto-N-Butyrate"
#> [17] "a-Keto-N-Butyric acid" "a-Ketobutyrate"
#> [19] "a-Ketobutyric acid" "a-Oxo-N-butyrate"
#> [21] "a-Oxo-N-butyric acid" "a-Oxobutyrate"
#> [23] "a-Oxobutyric acid" "alpha-Keto-N-butyrate"
#> [25] "alpha-Keto-N-butyric acid" "alpha-Ketobutric acid"
#> [27] "alpha-Ketobutyrate" "alpha-Ketobutyric acid"
#> [29] "alpha-Oxo-N-butyrate" "alpha-Oxo-N-butyric acid"
#> [31] "alpha-Oxobutyrate" "alpha-Oxobutyric acid"
#> [33] "Methyl-Pyruvate" "Methyl-Pyruvic acid"
#> [35] "Propionyl-formate" "Propionyl-formic acid"
#>
#> $CMP4
#> [1] "(RS)-2-Hydroxybutyrate" "(RS)-2-Hydroxybutyric acid"
#> [3] "2-Hydroxy-Butanoate" "2-Hydroxy-Butanoic acid"
#> [5] "2-Hydroxy-DL-Butyrate" "2-Hydroxy-DL-Butyric acid"
#> [7] "2-Hydroxy-N-butyrate" "2-Hydroxy-N-butyric acid"
#> [9] "2-Hydroxybutanoate" "2-Hydroxybutanoic acid"
#> [11] "2-Hydroxybutyrate" "a-Hydroxy-N-butyrate"
#> [13] "a-Hydroxy-N-butyric acid" "a-Hydroxybutanoate"
#> [15] "a-Hydroxybutanoic acid" "a-Hydroxybutyrate"
#> [17] "a-Hydroxybutyric acid" "alpha-Hydroxy-N-butyrate"
#> [19] "alpha-Hydroxy-N-butyric acid" "alpha-Hydroxybutanoate"
#> [21] "alpha-Hydroxybutanoic acid" "alpha-Hydroxybutyrate"
#> [23] "alpha-Hydroxybutyric acid" "DL-2-Hydroxybutanoate"
#> [25] "DL-2-Hydroxybutanoic acid" "DL-a-Hydroxybutyrate"
#> [27] "DL-a-Hydroxybutyric acid" "DL-alpha-Hydroxybutyrate"
#> [29] "DL-alpha-Hydroxybutyric acid"
#>
#> $CMP5
#> [1] "2-(8S,9S,13S,14S)-3-Hydroxy-2-methoxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one"
#> [2] "2-Hydroxyestrone 2-methyl ether"
#> [3] "2-Methoxy-17-oxoestra-1,3,5(10)-trien-3-ol"
#> [4] "2-Methoxy-3-hydroxyestra-1,3,5(10)-trien-17-one"
#> [5] "3-Hydroxy-2-methoxy-Estra-1,3,5(10)-trien-17-one"
#> [6] "3-Hydroxy-2-methoxyestra-1,3,5(10)-trien-17-one"
#> [7] "Methoxy-Estrone"
#>
#> $CMP6
#> [1] "(R)-(-)-b-Hydroxybutyrate" "(R)-(-)-b-Hydroxybutyric acid"
#> [3] "(R)-(-)-beta-Hydroxybutyrate" "(R)-(-)-beta-Hydroxybutyric acid"
#> [5] "(R)-3-Hydroxybutanoate" "(R)-3-Hydroxybutanoic acid"
#> [7] "(R)-3-Hydroxybutyrate" "3-D-Hydroxybutyrate"
#> [9] "3-D-Hydroxybutyric acid" "3-delta-Hydroxybutyrate"
#> [11] "3-delta-Hydroxybutyric acid" "BHIB"
#> [13] "D-(-)-3-Hydroxybutyrate" "D-3-Hydroxybutyrate"
#> [15] "D-3-Hydroxybutyric acid" "D-beta-Hydroxybutyrate"
#> [17] "delta-(-)-3-Hydroxybutyrate" "delta-3-Hydroxybutyrate"
#> [19] "delta-3-Hydroxybutyric acid" "delta-beta-Hydroxybutyrate"
#>
#> $CMP7
#> [1] "1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione"
#> [2] "1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione"
#> [3] "1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione"
#> [4] "1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione"
#> [5] "1-(2-Deoxy-D-erythro-pentofuranosyl)uracil"
#> [6] "1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil"
#> [7] "2'-Deoxyuridine"
#> [8] "2'-Desoxyuridine"
#> [9] "Deoxyribose uracil"
#> [10] "Desoxyuridine"
#> [11] "Uracil deoxyriboside"
#> [12] "Uracil desoxyuridine"
#>
#> $CMP8
#> [1] "1-Methyl-2-(3-indolyl)ethylamine"
#> [2] "2-(1H-Indol-3-yl)-N-methylethanamine"
#> [3] "3-(2-(Methylamino)ethyl)indole"
#> [4] "Dipterine"
#> [5] "Dl-Methyltryptamine"
#> [6] "Methyltryptamine"
#> [7] "N-Methylindoleethylamine"
#> [8] "N-Monomethyltryptamine"
#> [9] "N-Omega-methyltryptamine"
#>
#> $CMP9
#> [1] "3-[(2E)-2-[(1R,3aS,7aR)-1-[(1R)-1,5-dimethylhexyl]octahydro-7a-methyl-4H-inden-4-ylidene]ethylidene]-4-methylene-Cyclohexanol"
#> [2] "5,6-trans-Cholecalciferol"
#> [3] "5,6-trans-Vitamin D3"
#> [4] "trans-Vitamin D3"
#>
## If we provide the optional argument collapse, multiple entries will be
## collapsed.
cmps <- compound_tbl_sdf(fl, collapse = "|")
cmps
#> # A tibble: 9 × 8
#> compound_id name inchi inchikey formula exactmass synonyms smiles
#> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 HMDB0000001 1-Methylhistidine InCh… BRMWTNU… C7H11N… 169. 1 Methy… "CN1C…
#> 2 HMDB0000002 1,3-Diaminopropa… InCh… XFNJVJP… C3H10N2 74.1 1,3-Dia… "NCCC…
#> 3 HMDB0000005 2-Ketobutyric ac… InCh… TYEYBOS… C4H6O3 102. 2-Ketob… "CCC(…
#> 4 HMDB0000008 2-Hydroxybutyric… InCh… AFENDNX… C4H8O3 104. (RS)-2-… "CCC(…
#> 5 HMDB0000010 2-Methoxyestrone InCh… WHEUWNK… C19H24… 300. 2-(8S,9… "[H][…
#> 6 HMDB0000011 (R)-3-Hydroxybut… InCh… WHBMMWS… C4H8O3 104. (R)-(-)… "C[C@…
#> 7 HMDB0000012 Deoxyuridine InCh… MXHRCPN… C9H12N… 228. 1-(2-De… "OC[C…
#> 8 HMDB0004370 N-Methyltryptami… InCh… NCIKQJB… C11H14… 174. 1-Methy… "CNCC…
#> 9 HMDB0006719 5,6-trans-Vitami… InCh… QYSXJUF… C27H44O 384. 3-[(2E)… "CC(C…
cmps$synonyms
#> CMP1
#> "1 Methylhistidine|1-Methyl histidine|1-Methyl-Histidine|1-Methyl-L-histidine|1-MHis|1-N-Methyl-L-histidine|L-1-Methylhistidine|N1-Methyl-L-histidine|Pi-methylhistidine"
#> CMP2
#> "1,3-Diamino-N-propane|1,3-Propanediamine|1,3-Propylenediamine|1,3-Trimethylenediamine|3-Aminopropylamine|a,w-Propanediamine|Propane-1,3-diamine|Trimethylenediamine"
#> CMP3
#> "2-Ketobutanoate|2-Ketobutanoic acid|2-Ketobutyrate|2-Oxo-Butanoate|2-Oxo-Butanoic acid|2-Oxo-Butyrate|2-Oxo-Butyric acid|2-Oxo-N-butyrate|2-Oxo-N-butyric acid|2-Oxobutanoate|2-Oxobutanoic acid|2-Oxobutyrate|2-Oxobutyric acid|3-Methylpyruvate|3-Methylpyruvic acid|a-Keto-N-Butyrate|a-Keto-N-Butyric acid|a-Ketobutyrate|a-Ketobutyric acid|a-Oxo-N-butyrate|a-Oxo-N-butyric acid|a-Oxobutyrate|a-Oxobutyric acid|alpha-Keto-N-butyrate|alpha-Keto-N-butyric acid|alpha-Ketobutric acid|alpha-Ketobutyrate|alpha-Ketobutyric acid|alpha-Oxo-N-butyrate|alpha-Oxo-N-butyric acid|alpha-Oxobutyrate|alpha-Oxobutyric acid|Methyl-Pyruvate|Methyl-Pyruvic acid|Propionyl-formate|Propionyl-formic acid"
#> CMP4
#> "(RS)-2-Hydroxybutyrate|(RS)-2-Hydroxybutyric acid|2-Hydroxy-Butanoate|2-Hydroxy-Butanoic acid|2-Hydroxy-DL-Butyrate|2-Hydroxy-DL-Butyric acid|2-Hydroxy-N-butyrate|2-Hydroxy-N-butyric acid|2-Hydroxybutanoate|2-Hydroxybutanoic acid|2-Hydroxybutyrate|a-Hydroxy-N-butyrate|a-Hydroxy-N-butyric acid|a-Hydroxybutanoate|a-Hydroxybutanoic acid|a-Hydroxybutyrate|a-Hydroxybutyric acid|alpha-Hydroxy-N-butyrate|alpha-Hydroxy-N-butyric acid|alpha-Hydroxybutanoate|alpha-Hydroxybutanoic acid|alpha-Hydroxybutyrate|alpha-Hydroxybutyric acid|DL-2-Hydroxybutanoate|DL-2-Hydroxybutanoic acid|DL-a-Hydroxybutyrate|DL-a-Hydroxybutyric acid|DL-alpha-Hydroxybutyrate|DL-alpha-Hydroxybutyric acid"
#> CMP5
#> "2-(8S,9S,13S,14S)-3-Hydroxy-2-methoxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one|2-Hydroxyestrone 2-methyl ether|2-Methoxy-17-oxoestra-1,3,5(10)-trien-3-ol|2-Methoxy-3-hydroxyestra-1,3,5(10)-trien-17-one|3-Hydroxy-2-methoxy-Estra-1,3,5(10)-trien-17-one|3-Hydroxy-2-methoxyestra-1,3,5(10)-trien-17-one|Methoxy-Estrone"
#> CMP6
#> "(R)-(-)-b-Hydroxybutyrate|(R)-(-)-b-Hydroxybutyric acid|(R)-(-)-beta-Hydroxybutyrate|(R)-(-)-beta-Hydroxybutyric acid|(R)-3-Hydroxybutanoate|(R)-3-Hydroxybutanoic acid|(R)-3-Hydroxybutyrate|3-D-Hydroxybutyrate|3-D-Hydroxybutyric acid|3-delta-Hydroxybutyrate|3-delta-Hydroxybutyric acid|BHIB|D-(-)-3-Hydroxybutyrate|D-3-Hydroxybutyrate|D-3-Hydroxybutyric acid|D-beta-Hydroxybutyrate|delta-(-)-3-Hydroxybutyrate|delta-3-Hydroxybutyrate|delta-3-Hydroxybutyric acid|delta-beta-Hydroxybutyrate"
#> CMP7
#> "1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione|1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione|1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione|1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione|1-(2-Deoxy-D-erythro-pentofuranosyl)uracil|1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil|2'-Deoxyuridine|2'-Desoxyuridine|Deoxyribose uracil|Desoxyuridine|Uracil deoxyriboside|Uracil desoxyuridine"
#> CMP8
#> "1-Methyl-2-(3-indolyl)ethylamine|2-(1H-Indol-3-yl)-N-methylethanamine|3-(2-(Methylamino)ethyl)indole|Dipterine|Dl-Methyltryptamine|Methyltryptamine|N-Methylindoleethylamine|N-Monomethyltryptamine|N-Omega-methyltryptamine"
#> CMP9
#> "3-[(2E)-2-[(1R,3aS,7aR)-1-[(1R)-1,5-dimethylhexyl]octahydro-7a-methyl-4H-inden-4-ylidene]ethylidene]-4-methylene-Cyclohexanol|5,6-trans-Cholecalciferol|5,6-trans-Vitamin D3|trans-Vitamin D3"