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

Question

[User56]

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.

[Michael Kuhn]

Try searching for "ncbi eutils" on RSeek: http://www.rseek.org – there seem to be a few useful hits.

[Jeremy Leipzig]

If you just want to use the "XML" library and shake the tree by hand, check out my most recent blog post.

[Manu Prestat]

You could find at least dome resources here.

rseek.org is also a good resource

[User56]

@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))

[David W]

Hi User - I'd be interested to know exactly what you'd like to do with the EUtils api. I have (some R code)['https://github.com/dwinter/rentrez'] for this stuff, and we are discussing possible developments to it ('http://groups.google.com/forum/#!topic/ropensci-discuss/bETWlEcrS4s')

[David W]

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

Answer 1

[Neilfws]

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.

[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.

Answer 2

[Recology_]

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

• RNCBIAxis2Libs
• RNCBIEUtilsLibs
• NCBI2R
• RNCBI

[User56]

per link#2 - EUtilslibs has no user accessible libraries

Answer 3

[Raygozak]

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.

[Neilfws]

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

[Neilfws]

This comment now out of date; see answer by hnakhoul.

Answer 4

[hnakhoul]

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