 Dear all,
 My area of research is on metabolomics and  my aim is to know if 2
metabolites are associated in the literature. Since, I can retrieve article
where these molecules are cited given a set of identified molecules, adding
further constraints such as disease or organism of interest. MedlineR seemed
to be doing exactly what I was looking for.

My code snippet to get the list of PMID:

library(XML)
query='coombes kr[au] OR kimpel mw[au]'
query=gsub('\\s+','+',query)
url = "
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=50000" ##
maybe necessary in the present example ;-)
url = paste(url, "&db=pubmed&term=", query,sep = "")
datafile = tempfile(pattern = "pub")
try(download.file(url, destfile = datafile, method = "internal", mode =
"wb", quiet = TRUE), silent = TRUE)
xml <- xmlTreeParse(datafile, asTree = TRUE)
nid = xmlValue(xmlElementsByTagName(xmlRoot(xml), "Count")[[1]])
lid = xmlElementsByTagName(xmlRoot(xml), "IdList", recursive = TRUE)[[1]]
unlist(lapply(xmlElementsByTagName(lid, "Id"), xmlValue))

I have not had time to quantify and measure the degree of association...
There are several problems associated with querying for molecules and it is
probably a clever idea to first generate a small database of abstract for
each of my metabolite and starts the data mining from this.

 Cheers!

 David


2008/10/11 Mark Kimpel <mwkimpel@gmail.com>

> I have been using a hacked copy of the script for a couple of years. It is
> not a formal packaged, more a script that does what I need. I use it to
> collect abstracts on genes of interest and used an online database to
> construct an alias for all rat genes on the Affy chipset I have been using.
> Let me know exactly what inputs you want and I'll post something that might
> suit your needs.
>
> Mark
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
> ******************************************************************
>
>
>
> On Fri, Oct 10, 2008 at 5:25 PM, Kevin R. Coombes <krcoombes@mdacc.tmc.edu
> > wrote:
>
>> I suspect that the email address in your message will not work, since
>> Simon Lin has since moved from Duke to Northwestern. With the help of
>> google, you can get his current email address:
>>        s-lin2  AT  northwestern.edu
>> I have no idea if he is still supporting this R package.
>>
>> Best,
>>        Kevin
>>
>>
>> Herve Pages wrote:
>>
>>> Hi David,
>>>
>>> David Enot wrote:
>>>
>>>>  Dear all,
>>>>
>>>>  I came across a paper mentionning package called MedlineR. However the
>>>> original link mentionned in the paper (
>>>> http://dbsr.duke.edu/pub/MedlineR)
>>>> does not seem to be working anymore.  Because it must been have used by
>>>> few
>>>> members of this list, I wonder if someone could point me to an
>>>> alternative
>>>> address where I could access this package.
>>>>
>>>>
>>> Doesn't seem that this package has ever be part of Bioconductor or CRAN.
>>> I would suggest that you contact the first author of the paper:
>>>
>>>  Lin SM <Lin00025@mc.duke.edu>
>>>
>>> Cheers,
>>> H.
>>>
>>>
>>>   Thanks in advance.
>>>>
>>>>  David
>>>>
>>>> ##########
>>>> David Enot
>>>> http://sites.google.com/site/enotdavid/
>>>>
>>>>    [[alternative HTML version deleted]]
>>>>
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>>>
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>>
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