similar to: query multiple terms in PubMed abstract

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 <-

I would like to track in which 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("

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

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

I am looking for the syntax to capture XML tags marked with /DescriptorName MajorTopicYN="Y"/ , but the combination of the internal space (between "Name" and "Major" and the embedded quote marks are defeating me. I can get all the "DescriptorName" tags, but these include both MajroTopicYN = "Y" and "N" variants. Any suggestions?

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 <-

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

Hi, Anybody know what are the common Standard statistical methods used for the analysis of a dataset,and anybody know which of these methods give similar results Ram [[alternative HTML version deleted]]

Hi, This is a question regarding technique rather than an R specific issue. I have been asked to evaluate a 30+ year long term continuous survey of bird presence/absence data that has an associated ocular estimate of the vegetation community percent coverage. The data are organized by subpopulations (5), and by year ( 1991 - present). We are interested in gaining understanding on whether bird

Am Montag, 8. August 2005 18:12 schrieb Reid Spencer: > 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

Hi, I actually need to download pdfs through R code. The thing which I want to do is that, search for a paper in pubmed, which is possible by using GetPubMed function in the package "NCBI2R?". GetPubMed(searchterm, file = "", download = TRUE , showurl = FALSE, xldiv = ";", hyper = "HYPERLINK", MaxRet = 30000, sme = FALSE, smt = FALSE, quiet = TRUE,

I''d like to extend bleucloth or redcloth to support custom tags, e.g. I want to use markup like this: [pubmed:18332676] which shall be extended to: <a href="http://www.ncbi.nlm.nih.gov/pubmed/18332676">Behav Pharmacol. 2008 Mar;19(2):121-128.</a> Does anyone know, if this is possible and has some hints how to do this?! I have not decided, wether I want to use

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 what I tried: UIDs<-esearch( "Methylation" ) accession_numbers

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

I am trying to do a power analysis to get the number of replicas per treatment. If I try to get the power it works just fine: setn=c(2,3) sdx=c(1.19,4.35) power.t.test(n = setn, delta = 13.5, sd = sdx, sig.level = 0.05,power = NULL) If I go the other way to obtain the "n" I have problems. sdx=c(1.19,4.35) pow=c(.8,.8) power.t.test(n = NULL, delta = 13.5, sd = sdx, sig.level = 0.05,

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't generate more clumsy website addresses .... Sorry for that. Thank you in advance, Maura tutti i

I want to analyze binary, multinomial, and count outcomes (as well as the occasional continuous one) for clustered data. The more I search the less I know, and so I'm hoping the list can provide me some guidance about which of the many alternatives to choose. The nlme package seemed the obvious place to start. However, it seems to be using specifications from nls, which does non-linear

Hello everyone, I need to do a sample size calculation. The study two arms and two endpoints. The two arms are two different cancer drugs and the two endpoints reflect efficacy (based on progression free survival) and toxicity. Until now, I have been trying to understand this in terms of a one-arm design, where the acceptable rate of efficacy might be 0.40, the unacceptable rate of efficacy

Hello, I encouter a problem when i try to do "rake db:migrate": rake 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