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Is There An R Library Similar To Libraries Like Bioperl, Biopython Or Bioruby (Main Goal Is To For Retrieve Data From Pubmed'S Eutils)

I invested some time into learning R and would prefer not to learn Python or Ruby just for convenience of parsing XML.

I am not a pro R programmer so I need a higher level library then XML package of R. getNodeSet and XPath is very hard to use.

r pubmed
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updated by hnakhoul • hnakhoul • written by User56 • User56

You could find at least dome resources here.

rseek.org is also a good resource

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updated by Ram Ram • written by Manu Prestat Manu Prestat

@jeremy: nice. I never got nice info on NodeSet class. pasting your code here:

nihUrl<-concat("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",term,"+",year,"[pdat]")
  #cleanurl<-gsub('\]','%5D',gsub('\[','%5B',x=url))
  #http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=microarray%5btitle%5d+2003%5bpdat%5d
  xml<-xmlTreeParse(URLencode(nihUrl),isURL=TRUE)
  #Data Mashups in R, pg17
  as.numeric(xmlValue(xml$doc$children$eSearchResult$children$Count$children$text))
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updated by Ram Ram • written by User56 • User56

Hi User56 - I'd be interested to know exactly what you'd like to do with the EUtils api. I have some R code for this stuff, and we are discussing possible developments to it here

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written by David W David W

4 answers

raygozak answered the first part of your question: Bioconductor is the nearest equivalent for R of the Bio* libraries. Unfortunately, it does not include a package to handle EUtils queries.

I appreciate your difficulties when using R to parse XML; compared with other languages it is not very intuitive and the documentation is poor (lots of it but rather technical). However, I think you may just have to bite the bullet and get to grips with the R XML library. There are a few good tutorials and blog posts around on the Web (see comments under your question).

There are also some good examples in Chapter 8 of the book Bioinformatics and computational biology solutions using R and Bioconductor, some of which you can read at Google Books.

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written by Neilfws Neilfws

Please note that this answer is now very out of date. Rentrez is great for EUtils and XML handling/documentation are now much improved.

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written by Neilfws Neilfws

There are at least four packages (I haven't tried any of them) I found on crantastic.org:

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updated by Ram Ram • written by Recology_ • Recology_

per link#2 - EUtilslibs has no user accessible libraries

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written by User56 • User56

As for biophyton and bioperl counterpart in R you can use Bioconductor, however it may not have all the functionality you find in those libraries, and bioconductor is the project, you would need to search in biconductor's website for specific packages.

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written by Raygozak Raygozak

It's true that Bioconductor is, in a sense, the "Bio*" project for R. Unfortunately (and perplexingly) it lacks a good library for EUtils.

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written by Neilfws Neilfws

This comment now out of date; see answer by hnakhoul.

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written by Neilfws Neilfws

One option is rentrez, from the rOpenSci family of packages.

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updated by Ram Ram • written by hnakhoul • hnakhoul

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