Thank you so much. I emailed the people who are in charge of maintaining miRecords and related info. I asked them for an available data transfer protocol like ftp or similar to avoid manually downloading haindreds of sequences from their web site. I got no feedback at all.
Thanks again, Maura -----Messaggio originale----- Da: Martin Morgan [mailto:mtmor...@fhcrc.org] Inviato: mer 01/07/2009 17.51 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: [R] Is there a way to extract some fields data from HTML pages through any R function ? Hi Maura -- mau...@alice.it wrote: > I deal with a huge amount of Biology data stored in different databases. > The databases belongig to Bioconductor organization can be accessed through > Bioconductor packages. > Unluckily some useful data is stored in databases like, for instance, miRDB, > miRecords, etc ... which offer just an > interactive HTML interface. See for instance > http://mirdb.org/cgi-bin/search.cgi, > > http://mirecords.umn.edu/miRecords/interactions.php?species=Homo+sapiens&mirna_acc=Any&targetgene_type=refseq_acc&targetgene_info=&v=yes&search_int=Search > > Downloading data manually from the web pages is a painstaking time-consumung > and error-prone activity. > I came across a Python script that downloads (dumps) whole web pages into a > text file that is then parsed. > This is possible because Python has a library to access web pages. > But I have no experience with Python programming nor I like such a > programming language whose syntax is indentation-sensitive. > > I am *hoping* that there exists some sort of web pages, HTML connection from > R ... is there ?? Tools in R for this are the RCurl package and the XML package. library(RCurl) library(XML) Typically this involves manual exploration of the web form, Then you might query the web form result <- postForm("http://mirdb.org/cgi-bin/search.cgi";, searchType="miRNA", species="Human", searchBox="hsa-let-7a", submitButton="Go") and parse the results into a convenient structure html <- htmlTreeParse(result, asText=TRUE, useInternalNodes=TRUE) you can then use XPath (http://www.w3.org/TR/xpath, especially section 2.5) to explore and extract information, e.g., ## second table, first row getNodeSet(html, "//table[2]/tr[1]") ## second table, makes subsequent paths shorter tbl <- getNodeSet(html, "//table[2]")[[1]] xget <- function(xml, path) # a helper function unlist(xpathApply(xml, path, xmlValue))[-1] df <- data.frame(TargetRank=as.numeric(xget(tbl, "./tr/td[2]")), TargetScore=as.numeric(xget(tbl, "./tr/td[3]")), miRNAName=xget(tbl, "./tr/td[4]"), GeneSymbol=xget(tbl, "./tr/td[5]"), GeneDescription=xget(tbl, "./tr/td[6]")) There are many ways through this latter part, probably some much cleaner than presented above. There are fairly extensive examples on each of the relevant help pages, e.g., ?postForm. Martin > Thank you very much for any suggestion. > Maura > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. tutti i telefonini TIM! [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
