search for: eutils

Displaying 16 results from an estimated 16 matches for "eutils".

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2005 May 02
2
"Special" characters in URI
Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document but I have a problem to use URI to retrieve that file, since URI can also contain characters, which should not be there according to http://www.faqs.org/rfcs/rfc2396.html I encountered problems...
2007 Dec 14
6
Analyzing Publications from Pubmed via XML
...ch journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse(" http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ",isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities...
2017 Jun 09
1
efetch result not in character format
Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate, because I get the error: Error in file.exists(destfile) : object 'destfile' not found This is wha...
2005 Jun 14
0
question about SSOAP
Dear R folks: I am trying to use SSOAP (version 0.2-2) package in R (version 2.1.0,linux) to access SOAP service on NCBI (http://www.ncbi.nlm.nih.gov) its WSDL file is at http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <- genSOAPClientInterface(ncbi at operations[[1]], def = ncbi, ncbi at name, verbose=FALSE) > ff at functions$run_eInfo("db=pubmed&quo...
2012 Dec 11
1
query multiple terms in PubMed abstract
Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")), useInternalNodes=TRUE) I want to get the reply where BOTH the...
2012 Dec 27
1
Conjunction and disjunction in pubmed query
Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <- xmlTre...
2005 May 08
2
Extract just some fields from XML
Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only node 'pubdate' and its children, but I don'...
2005 Jun 14
1
protection stack overflow??
Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards
2005 Aug 08
2
[LLVMdev] cfrontend building
...nstructions *to the letter* > with zero deviations. > > If you didn't do "make bootstrap", then I don't have a clue what this > problem is :) > > Reid. > Hallo, do you know if bootstrap is the default target? This is what I'm doing: <code> inherit eutils DESCRIPTION="C, C++ Frontend for Low Level Virtual _Machine" HOMEPAGE="http://llvm.org/" SRC_URI="http://llvm.cs.uiuc.edu/releases/${PV}/cfrontend-${PV}.source.tar.gz" LICENSE="llvm" SLOT="0" KEYWORDS="~ppc ~sparc ~x86" IUSE=""...
2005 May 10
0
Fwd: Extract just some fields from XML]
...xmlName(node) == "PubDate") > print(node) > ) Gorjanc Gregor wrote: > Hello! > > I am trying to get specific fields from an XML document and I am totally > puzzled. I hope someone can help me. > > # URL > URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" > # download a XML file > tmp <- xmlTreeParse(URL, isURL = TRUE) > tmp <- xmlRoot(tmp) > > Now I want to extract only node 'pubdate' and its...
2011 Jan 19
6
rake aborted! can't convert Hash into String
...e aborted! can''t convert Hash into String Here is the trace result: ** Invoke db:migrate (first_time) ** Invoke environment (first_time) ** Execute environment rake aborted! can''t convert Hash into String /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/fileutils.rb:1408:in `directory?'' /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/fileutils.rb:1408:in `fu_each_src_dest0'' /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/fileutils.rb:1393:in `fu_each_src_dest'' /System/Library/Framewo...
2005 Aug 08
0
[LLVMdev] cfrontend building
Stephan, I've seen this before. It happens when you do "make bootstrap" in llvm-gcc. While "make bootstrap" is the correct way to build GCC, its not the correct way to build llvm-gcc. Based on my experience with this, I suggest you completely erase your build tree and then follow the CFEBuildInstr.html instructions *to the letter* with zero deviations. If you
2005 Aug 08
0
[LLVMdev] cfrontend building
Answers inline .. Stephan Wienczny wrote: > > Hallo, > > do you know if bootstrap is the default target? No, "all" is the default. > > This is what I'm doing: > <code> > inherit eutils > > DESCRIPTION="C, C++ Frontend for Low Level Virtual _Machine" > HOMEPAGE="http://llvm.org/" > SRC_URI="http://llvm.cs.uiuc.edu/releases/${PV}/cfrontend-${PV}.source.tar.gz" > > LICENSE="llvm" > SLOT="0" > KEYWORDS="...
2005 Aug 08
2
[LLVMdev] cfrontend building
Am Montag, 8. August 2005 04:15 schrieb Chris Lattner: > > I have never seen this, and don't really have any ideas. What configure > options did you use? Did you follow the directions here? > > http://llvm.cs.uiuc.edu/docs/CFEBuildInstrs.html > Yes I followed those instructions - almost. This is my configure line: ../src/configure --prefix=/usr --disable-threads
2009 Nov 03
1
help with SSOAP (can't find working examples)
...after updating XMLSchema (which happened to be the same version as what I have). I tried a couple of WSDL's that I have for creating python webservices, as well as a "hello world" example, and they all have the same error as well. While KEGG.wsdl, and others gave the above error, the eutils.wsdl gave me the below error: Error: Cannot resolve SOAP type in empty context Interop.wsdl got me the below error: Error: Cannot resolve string in SchemaCollection nwis.wsdl failes in processWSDL() itself, with the below error: Error in parse(text = paste(txt, collapse = "\n")) :...
2010 Jul 18
6
CRAN (and crantastic) updates this week
...n alpha release. Retrieve information from the ncbi web service. * RNCBIAxis2Libs (0.9) Martin Schumann http://crantastic.org/packages/RNCBIAxis2Libs Provides selected Apache Axis2 libraries for the use with the RNCBI package. For license information see the inst/java directory. * RNCBIEUtilsLibs (0.9) Martin Schumann http://crantastic.org/packages/RNCBIEUtilsLibs Provides the libraries of the EUtils operations for the RNCBI package. * rocc (1.0) Martin Lauss http://crantastic.org/packages/rocc Functions for a classification method based on receiver operating characteri...