Mercurial > repos > prog > lcmsmatching
diff biodb-common.R @ 0:e66bb061af06 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty
| author | prog |
|---|---|
| date | Tue, 12 Jul 2016 12:02:37 -0400 |
| parents | |
| children | 253d531a0193 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biodb-common.R Tue Jul 12 12:02:37 2016 -0400 @@ -0,0 +1,181 @@ +if ( ! exists('RBIODB.COMPOUND')) { # Do not load again if already loaded + + ############# + # CONSTANTS # + ############# + + # Entry types + RBIODB.COMPOUND <- 'compound' + RBIODB.SPECTRUM <- 'spectrum' + + # Entry content types + RBIODB.HTML <- 'html' + RBIODB.TXT <- 'txt' + RBIODB.XML <- 'xml' + RBIODB.CSV <- 'csv' + RBIODB.ANY <- 'any' + + # Class names + RBIODB.CHEBI <- 'chebi' + RBIODB.KEGG <- 'kegg' + RBIODB.PUBCHEM <- 'pubchem' + RBIODB.HMDB <- 'hmdb' + RBIODB.CHEMSPIDER <- 'chemspider' + RBIODB.ENZYME <- 'enzyme' + RBIODB.LIPIDMAPS <- 'lipidmaps' + RBIODB.MIRBASE <- 'mirbase' + RBIODB.NCBIGENE <- 'ncbigene' + RBIODB.NCBICCDS <- 'ncbiccds' + RBIODB.UNIPROT <- 'uniprot' + RBIODB.MASSBANK <- 'massbank' + + # Fields + RBIODB.COMPOUND <- 'compound' + RBIODB.ACCESSION <- 'accession' + RBIODB.DESCRIPTION <- 'description' + RBIODB.PROTEIN.DESCRIPTION <- 'protdesc' + RBIODB.NAME <- 'name' + RBIODB.FULLNAMES <- 'fullnames' + RBIODB.SYNONYMS <- 'synonyms' + RBIODB.SYMBOL <- 'symbol' + RBIODB.GENE.SYMBOLS <- 'genesymbols' + RBIODB.CHEBI.ID <- 'chebiid' + RBIODB.LIPIDMAPS.ID <- 'lipidmapsid' + RBIODB.KEGG.ID <- 'keggid' + RBIODB.HMDB.ID <- 'hmdbid' + RBIODB.ENZYME.ID <- 'enzymeid' + RBIODB.NCBI.CCDS.ID <- 'ncbiccdsid' + RBIODB.NCBI.GENE.ID <- 'ncbigeneid' + RBIODB.PUBCHEM.ID <- 'pubchemid' + RBIODB.UNIPROT.ID <- 'uniprotid' + RBIODB.INCHI <- 'inchi' + RBIODB.INCHIKEY <- 'inchikey' + RBIODB.MSDEV <- 'msdev' + RBIODB.MSDEVTYPE <- 'msdevtype' + RBIODB.MSTYPE <- 'mstype' + RBIODB.MSMODE <- 'msmode' + RBIODB.MSPRECMZ <- 'msprecmz' # numeric + RBIODB.MSPRECANNOT <- 'msprecannot' + RBIODB.FORMULA <- 'formula' + RBIODB.SUPER.CLASS <- 'superclass' + RBIODB.MASS <- 'mass' + RBIODB.AVERAGE.MASS <- 'averagemass' + RBIODB.MONOISOTOPIC.MASS <- 'monoisotopicmass' + RBIODB.SEQUENCE <- 'sequence' + RBIODB.LOCATION <- 'location' + RBIODB.LENGTH <- 'length' + RBIODB.NB.PEAKS <- 'nbpeaks' + RBIODB.NB.PEAKS <- 'nbpeaks' + RBIODB.PEAKS <- 'peaks' + + # Mode values + RBIODB.MSMODE.NEG <- 'neg' + RBIODB.MSMODE.POS <- 'pos' + + # Cardinalities + RBIODB.CARD.ONE <- '1' + RBIODB.CARD.MANY <- '*' + + # Field attributes + RBIODB.FIELDS <- data.frame(matrix(c( + # FIELD NAME CLASS CARDINALITY + RBIODB.COMPOUND, 'BiodEntry', RBIODB.CARD.ONE, + RBIODB.ACCESSION, 'character', RBIODB.CARD.ONE, + RBIODB.DESCRIPTION, 'character', RBIODB.CARD.ONE, + RBIODB.NAME, 'character', RBIODB.CARD.ONE, + RBIODB.FULLNAMES, 'character', RBIODB.CARD.MANY, + RBIODB.SYNONYMS, 'character', RBIODB.CARD.MANY, + RBIODB.PROTEIN.DESCRIPTION, 'character', RBIODB.CARD.ONE, + RBIODB.SYMBOL, 'character', RBIODB.CARD.ONE, + RBIODB.GENE.SYMBOLS, 'character', RBIODB.CARD.MANY, + RBIODB.CHEBI.ID, 'character', RBIODB.CARD.ONE, + RBIODB.LIPIDMAPS.ID, 'character', RBIODB.CARD.ONE, + RBIODB.KEGG.ID, 'character', RBIODB.CARD.ONE, + RBIODB.HMDB.ID, 'character', RBIODB.CARD.ONE, + RBIODB.ENZYME.ID, 'character', RBIODB.CARD.ONE, + RBIODB.PUBCHEM.ID, 'character', RBIODB.CARD.ONE, + RBIODB.UNIPROT.ID, 'character', RBIODB.CARD.ONE, + RBIODB.NCBI.CCDS.ID, 'character', RBIODB.CARD.ONE, + RBIODB.NCBI.GENE.ID, 'character', RBIODB.CARD.ONE, + RBIODB.INCHI, 'character', RBIODB.CARD.ONE, + RBIODB.INCHIKEY, 'character', RBIODB.CARD.ONE, + RBIODB.MSDEV, 'character', RBIODB.CARD.ONE, + RBIODB.MSDEVTYPE, 'character', RBIODB.CARD.ONE, + RBIODB.MSTYPE, 'character', RBIODB.CARD.ONE, + RBIODB.MSMODE, 'character', RBIODB.CARD.ONE, + RBIODB.MSPRECMZ, 'double', RBIODB.CARD.ONE, + RBIODB.MSPRECANNOT, 'character', RBIODB.CARD.ONE, + RBIODB.FORMULA, 'character', RBIODB.CARD.ONE, + RBIODB.SUPER.CLASS, 'character', RBIODB.CARD.ONE, + RBIODB.MASS, 'double', RBIODB.CARD.ONE, + RBIODB.AVERAGE.MASS, 'double', RBIODB.CARD.ONE, + RBIODB.MONOISOTOPIC.MASS, 'double', RBIODB.CARD.ONE, + RBIODB.SEQUENCE, 'character', RBIODB.CARD.ONE, + RBIODB.LENGTH, 'integer', RBIODB.CARD.ONE, + RBIODB.LOCATION, 'character', RBIODB.CARD.ONE, + RBIODB.NB.PEAKS, 'integer', RBIODB.CARD.ONE, + RBIODB.PEAKS, 'data.frame', RBIODB.CARD.ONE + ), byrow = TRUE, ncol = 3), stringsAsFactors = FALSE) + colnames(RBIODB.FIELDS) <- c('name', 'class', 'cardinality') + + # How to compute a missing field ? + RBIODB.FIELD.COMPUTING <- list() + RBIODB.FIELD.COMPUTING[[RBIODB.INCHI]] <- c(RBIODB.CHEBI) + RBIODB.FIELD.COMPUTING[[RBIODB.INCHIKEY]] <- c(RBIODB.CHEBI) + RBIODB.FIELD.COMPUTING[[RBIODB.SEQUENCE]] <- c(RBIODB.NCBICCDS) + + # Peaks data frame columns + RBIODB.PEAK.MZ <- 'mz' + RBIODB.PEAK.FORMULA <- 'formula' + RBIODB.PEAK.FORMULA.COUNT <- 'formula.count' + RBIODB.PEAK.MASS <- 'mass' + RBIODB.PEAK.ERROR.PPM <- 'error.ppm' + RBIODB.PEAK.INTENSITY <- 'intensity' + RBIODB.PEAK.RELATIVE.INTENSITY <- 'relative.intensity' + RBIODB.PEAK.DF.EXAMPLE <- data.frame(mz = double(), int = double(), rel.int = integer(), formula = character(), formula.count <- integer(), mass = double(), error = double(), stringsAsFactors = FALSE) + colnames(RBIODB.PEAK.DF.EXAMPLE) <- c(RBIODB.PEAK.MZ, RBIODB.PEAK.INTENSITY, RBIODB.PEAK.RELATIVE.INTENSITY, RBIODB.PEAK.FORMULA, RBIODB.PEAK.FORMULA.COUNT, RBIODB.PEAK.MASS, RBIODB.PEAK.ERROR.PPM) + + ################# + # GET ENTRY URL # + ################# + + # TODO Let the choice to use either jp or eu + RBIODB.MASSBANK.JP.WS.URL <- "http://www.massbank.jp/api/services/MassBankAPI/getRecordInfo" + RBIODB.MASSBANK.EU.WS.URL <- "http://massbank.eu/api/services/MassBankAPI/getRecordInfo" + + get.entry.url <- function(class, accession, content.type = RBIODB.ANY) { + + url <- switch(class, + chebi = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=', accession) else NULL, + chemspider = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('http://www.chemspider.com/Chemical-Structure.', accession, '.html') else NULL, + enzyme = if (content.type %in% c(RBIODB.ANY, RBIODB.TXT)) paste0('http://enzyme.expasy.org/EC/', accession, '.txt') else NULL, + hmdb = switch(content.type, + xml = paste0('http://www.hmdb.ca/metabolites/', accession, '.xml'), + html = paste0('http://www.hmdb.ca/metabolites/', accession), + any = paste0('http://www.hmdb.ca/metabolites/', accession), + NULL), + kegg = switch(content.type, + txt = paste0('http://rest.kegg.jp/get/', accession), + html = paste0('http://www.genome.jp/dbget-bin/www_bget?cpd:', accession), + any = paste0('http://www.genome.jp/dbget-bin/www_bget?cpd:', accession), + NULL), + lipidmaps = if (content.type %in% c(RBIODB.ANY, RBIODB.CSV)) paste0('http://www.lipidmaps.org/data/LMSDRecord.php?Mode=File&LMID=', accession, '&OutputType=CSV&OutputQuote=No') else NULL, + massbank = if (content.type %in% c(RBIODB.ANY, RBIODB.TXT)) paste0(RBIODB.MASSBANK.EU.WS.URL, '?ids=', paste(accession, collapse = ',')) else NULL, + mirbase = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=', accession) else NULL, + pubchem = { + accession <- gsub(' ', '', accession, perl = TRUE) + accession <- gsub('^CID', '', accession, perl = TRUE) + switch(content.type, + xml = paste0('http://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/', accession, '/XML/?response_type=save&response_basename=CID_', accession), + html = paste0('http://pubchem.ncbi.nlm.nih.gov/compound/', accession), + NULL) + }, + ncbigene = if (content.type %in% c(RBIODB.ANY, RBIODB.XML)) paste0('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=', accession, '&rettype=xml&retmode=text') else NULL, + ncbiccds = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=', accession), + uniprot = if (content.type %in% c(RBIODB.ANY, RBIODB.XML)) paste0('http://www.uniprot.org/uniprot/', accession, '.xml'), + NULL + ) + + return(url) + } +}