Analyzing Publications from Pubmed via XML

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("
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.

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("
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.

Has anyone ever done this and could you share your script? Are there any
published examples where the end result is a dataframe.

I guess what I am looking for is an easy and simple way to parse the feed
and extract the data. Alternatively how does one turn an RSS feed into a CSV
file?

I am afraid not! The only thing I know about Python (or Perl, Ruby  
etc) is that they exist and that I have been able to download some  
amazing freeware or open source software thanks to their existence.
The XML package and specifically the xmlTreeParse function looks as  
if it is begging to do the task for me. Is that not true?

On Dec 13, 2007 9:03 PM, Farrel Buchinsky <fjbuch at gmail.com> wrote:

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("
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.

Has anyone ever done this and could you share your script? Are there any
published examples where the end result is a dataframe.

I guess what I am looking for is an easy and simple way to parse the feed
and extract the data. Alternatively how does one turn an RSS feed into a CSV
file?

Try this:

library(XML)
doc <-
xmlTreeParse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-",
isURL = TRUE, useInternalNodes = TRUE)
sapply(c("//author", "//category"), xpathApply, doc = doc, fun = xmlValue)

The problem is that the RSS feed you linked to, does not contain the
year of the article in an easily accessible XML element. Rather you
have to process the HTML content of the description element - which,
is something R could do, but you'd be using the wrong tool for the job.

or just try looking in the annotate package from Bioconductor

The problem is that the RSS feed you linked to, does not contain the
year of the article in an easily accessible XML element. Rather you
have to process the HTML content of the description element - which,
is something R could do, but you'd be using the wrong tool for the job.

Yes. I have noticed that there two sorts of xml that pubmed will
provide. The kind I had hooked into was an rss feed which provides a
lot of the information simply as a formatted table for viewing in a
rss reader. There is another way to get the xml to come out with more
tags. However, I found the best way to do this is probably through the
bioconductor annotate package

x <- pubmed("18046565", "17978930", "17975511")
a <- xmlRoot(x)
numAbst <- length(xmlChildren(a))
absts <- list()
for (i in 1:numAbst) {
absts[[i]] <- buildPubMedAbst(a[[i]])
  }

I am now trying to work through that approach to see what I can come up with.

The problem is that the RSS feed you linked to, does not contain the
year of the article in an easily accessible XML element. Rather you
have to process the HTML content of the description element - which,
is something R could do, but you'd be using the wrong tool for the job.

Yes. I have noticed that there two sorts of xml that pubmed will
provide. The kind I had hooked into was an rss feed which provides a
lot of the information simply as a formatted table for viewing in a
rss reader. There is another way to get the xml to come out with more
tags. However, I found the best way to do this is probably through the
bioconductor annotate package

x <- pubmed("18046565", "17978930", "17975511")
a <- xmlRoot(x)
numAbst <- length(xmlChildren(a))
absts <- list()
for (i in 1:numAbst) {
absts[[i]] <- buildPubMedAbst(a[[i]])
   }

I am now trying to work through that approach to see what I can come up with.

On Dec 13, 2007 11:35 PM, Robert Gentleman <rgentlem at fhcrc.org> wrote:

or just try looking in the annotate package from Bioconductor

Yip. annotate seems to be the most streamlined way to do this.
1) How does one turn the list that is created into a dataframe whose
column names are along the lines of date, title, journal, authors etc

2) I have already created a standing search in pubmed using MyNCBI.
There are many ways I can feed those results to the pubmed() function.
The most brute force way of doing it is by running the search and
outputing the data as a UI List and getting that into the pubmed
brackets. A way that involved more finesse would allow me to create a
rss feed based on my search and then give the rss feed url to the
pubmed function. Or perhaps once could just plop the query inside the
pubmed functions
pubmed(somefunction("Laryngeal Neoplasms"[MeSH] AND "Papilloma"[MeSH])
OR ((("recurrence"[TIAB] NOT Medline[SB]) OR "recurrence"[MeSH Terms]
OR recurrent[Text Word]) AND respiratory[All Fields] AND
(("papilloma"[TIAB] NOT Medline[SB]) OR "papilloma"[MeSH Terms] OR
papillomatosis[Text Word])))

Does "somefunction" exist?

pm.srch<- function (){

pm.srch()

"Farrel Buchinsky" <fjbuch at gmail.com> wrote in
news:bd93cdad0712141216s23071d27n17d87a487ad06950 at mail.gmail.com: 

On Dec 13, 2007 11:35 PM, Robert Gentleman <rgentlem at fhcrc.org>
wrote: 

or just try looking in the annotate package from Bioconductor

Yip. annotate seems to be the most streamlined way to do this.
1) How does one turn the list that is created into a dataframe whose
column names are along the lines of date, title, journal, authors etc

Gabor's example already did that task.

substring(out, 1, 25) # display it

David Winsemius <dwinsemius at comcast.net> wrote in
news:Xns9A077F740B4A0dNOTwinscomcast at 80.91.229.13:

"Farrel Buchinsky" <fjbuch at gmail.com> wrote in
news:bd93cdad0712141216s23071d27n17d87a487ad06950 at mail.gmail.com:

On Dec 13, 2007 11:35 PM, Robert Gentleman <rgentlem at fhcrc.org>
wrote:

or just try looking in the annotate package from Bioconductor

Yip. annotate seems to be the most streamlined way to do this.
1) How does one turn the list that is created into a dataframe whose
column names are along the lines of date, title, journal, authors etc

Gabor's example already did that task.

Actually the object returned by Gabor's method was a list of lists. Here
is one way (probably very inefficient) of getting "doc" into a
data.frame:

colvals <-sapply(c("//title", "//author", "//category"), xpathApply,
          doc = doc, fun = xmlValue)

titles=as.vector(unlist(colvals[1])[3:17])

# needed to drop extraneous titles for search name and an NCBI header
#>str(colvals)
#List of 3
# $ //title   :List of 17
#  ..$ : chr "PubMed: (\"Laryngeal Neoplasm..."
#  ..$ : chr "NCBI PubMed"

authors=colvals[[2]]
jrnls=colvals[[3]]

# not sure why, but trying to do it in one step failed:
#  cites<-data.frame(titles=as.vector(unlist(colvals[1])[3:17]),
#                     authors=colvals[[2]],jnrls=colvals[[3]])
# Error in data.frame(titles = as.vector(unlist(colvals[1])[3:17]),
# authors = colvals[[2]],  :
#  arguments imply differing number of rows: 15, 1
# but the following worked

 cites<-data.frame(titles=as.vector(titles))
 cites$author<-authors
 cites$jrnls<-jrnls
 cites

I am still wondering how to extract material that does not have an XML
tag.  Each item looks like:

 <item>
  <title>Gastroesophageal reflux in patients with recurrent laryngeal
papillomatosis.</title>
  <link>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
tmpl=NoSidebarfile&amp;db=PubMed&amp;cmd=Retrieve&amp;list_uids=17589729
&amp;dopt=Abstract</link>
  <description>
   <![CDATA[
   <table border="0" width="100%"><tr><td align="left"><a
href="http://www.scielo.br/scielo.php?script=sci_arttext&amp;pid=S0034-
72992007000200011&amp;lng=en&amp;nrm=iso&amp;tlng=en"><img
src="http://www.ncbi.nlm.nih.gov/entrez/query/egifs/http:--www.scielo.br-
img-scielo_en.gif" border="0"/></a> </td><td align="right"><a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
db=PubMed&amp;cmd=Display&amp;dopt=PubMed_PubMed&amp;from_uid=17589729">
Related Articles</a></td></tr></table>
       <p><b>Gastroesophageal reflux in patients with recurrent
laryngeal papillomatosis.</b></p>
       <p>Rev Bras Otorrinolaringol (Engl Ed). 2007 Mar-Apr;73(2):210-4
</p>
       <p>Authors:  Pignatari SS, Liriano RY, Avelino MA, Testa JR,
Fujita R, De Marco EK</p>
       <p>Evidence of a relation between gastroesophaeal reflux and
pediatric respiratory disorders increases every year. Many respiratory
symptoms and clinical conditions such as stridor, chronic cough, and
recurrent pneumonia and bronchitis appear to be related to
gastroesophageal reflux. Some studies have also suggested that
gastroesophageal reflux may be associated with recurrent laryngeal
papillomatosis, contributing to its recurrence and severity. AIM: the aim
of this study was to verify the frequency and intensity of
gastroesophageal reflux in children with recurrent laryngeal
papillomatosis. MATERIAL AND METHODS: ten children of both genders, aged
between 3 and 12 years, presenting laryngeal papillomatosis, were
included in this study. The children underwent 24-hour double-probe pH-
metry. RESULTS: fifty percent of the patients had evidence of
gastroesophageal reflux at the distal sphincter; 90% presented reflux at
the proximal sphincter. CONCLUSION: the frequency of proximal
gastroesophageal reflux is significantly increased in patients with
recurrent laryngeal papillomatosis.</p>
       <p>PMID: 17589729 [PubMed - in process]</p>    ]]>
  </description>
  <author>Pignatari SS, Liriano RY, Avelino MA, Testa JR, Fujita R, De
Marco EK</author>
  <category>Rev Bras Otorrinolaringol (Engl Ed)</category>
  <guid isPermaLink="false">PubMed:17589729</guid>
 </item>

I would like to access, for instance, the PMID or the abstract within the
<description> element, but I do not think that they have names in the the
same way that <author> or <category> have xml named nodes. I suspect that
getting the output in a different format, say as MEDLINE, might produce
output that was tagged more completely.


--
David Winsemius

If we can assume that the abstract is always the 4th paragraph then we
can try something like this:

library(XML)
doc <-
xmlTreeParse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss
_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-", isURL = TRUE,
useInternalNodes = TRUE, trim = TRUE) 

out <- cbind(
     Author = unlist(xpathApply(doc, "//author", xmlValue)),
     PMID = gsub(".*:", "", unlist(xpathApply(doc, "//guid",
     xmlValue))), 
     Abstract = unlist(xpathApply(doc, "//description",
          function(x) {
               on.exit(free(doc2))
               doc2 <- htmlTreeParse(xmlValue(x)[[1]], asText = TRUE,
                    useInternalNodes = TRUE, trim = TRUE)
               xpathApply(doc2, "//p[4]", xmlValue)
          }
     )))
free(doc)
substring(out, 1, 25) # display first 25 chars of each field


The last line produces (it may look messed up in this email):

substring(out, 1, 25) # display it

      Author                      PMID       Abstract

substring(get.info(doc), 1, 25)

# in the debugging phase I needed to set useInternalNodes = TRUE to see the
tags. Never did find a way to "print" them when internal.

On Dec 16, 2007 2:53 PM, David Winsemius <dwinsemius at comcast.net>
wrote: 

# in the debugging phase I needed to set useInternalNodes = TRUE to
see the tags. Never did find a way to "print" them when internal.

I assume you mean FALSE.  See:
?saveXML

On Dec 16, 2007 2:53 PM, David Winsemius <dwinsemius at comcast.net>
wrote: 

# Never did find a way to "print" them when internal.

?saveXML

On 15 Dec 2007, you wrote in gmane.comp.lang.r.general:

If we can assume that the abstract is always the 4th paragraph then we
can try something like this:

library(XML)
doc <-
xmlTreeParse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss
_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-", isURL = TRUE,
useInternalNodes = TRUE, trim = TRUE) 

out <- cbind(
     Author = unlist(xpathApply(doc, "//author", xmlValue)),
     PMID = gsub(".*:", "", unlist(xpathApply(doc, "//guid",
     xmlValue))), 
     Abstract = unlist(xpathApply(doc, "//description",
          function(x) {
               on.exit(free(doc2))
               doc2 <- htmlTreeParse(xmlValue(x)[[1]], asText = TRUE,
                    useInternalNodes = TRUE, trim = TRUE)
               xpathApply(doc2, "//p[4]", xmlValue)
          }
     )))
free(doc)
substring(out, 1, 25) # display first 25 chars of each field


The last line produces (it may look messed up in this email):

substring(out, 1, 25) # display it

      Author                      PMID       Abstract

 [1,] " Goon P, Sonnex C, Jani P" "18046565" "Human papillomaviruses (H"
 [2,] " Rad MH, Alizadeh E, Ilkh" "17978930" "Recurrent laryngeal papil"
 [3,] " Lee LA, Cheng AJ, Fang T" "17975511" "OBJECTIVES:: Papillomas o"
 [4,] " Gerein V, Schmandt S, Ba" "17935912" "BACKGROUND: Human papillo"
snip

It looked beautifully regular in my newsreader. It is helpful to see an 
example showing the indexed access to nodes. It was also helpful to see the 
example of substring for column display. Thank you (for this and all of 
your other contributions.)

I find upon further browsing that the pmfetch access point is obsolete. 
Experimentation with the PubMed eFetch server access point results in fully 
xml-tagged results:

e.fetch.doc<- function (){
   fetch.stem <-
        "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
   src.mode <- "db=pubmed&retmode=xml&"
   request <- "id=11045395"
   doc<-xmlTreeParse(paste(fetch.stem,src.mode,request,sep=""),
                          isURL = TRUE, useInternalNodes = TRUE)
     }
# in the debugging phase I needed to set useInternalNodes = TRUE to see the  
tags. Never did find a way to "print" them when internal.

doc<-e.fetch.doc()
get.info<- function(doc){
         df<-cbind(
 	Abstract = unlist(xpathApply(doc, "//AbstractText", xmlValue)),
 	Journal =  unlist(xpathApply(doc, "//Title", xmlValue)),
 	Pmid =  unlist(xpathApply(doc, "//PMID", xmlValue))
                   )
   return(df)
   } 

# this works

substring(get.info(doc), 1, 25)

     Abstract                    Journal                     Pmid      
[1,] "We studied the prevalence" "Pediatric nephrology (Ber" "11045395"

After quite a bit of hacking (in the sense of ineffective chopping with
a dull ax), I finally came up with:

pm.srch<- function (){
  srch.stem<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="
  query<-readLines(con=file.choose())
  query<-gsub("\\\"","",x=query)
  doc<-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE,
                     useInternalNodes = TRUE)
  return(sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue) )
     }

pm.srch()  #choosing the search-file
      //Id
 [1,] "18046565"
 [2,] "17978930"
 [3,] "17975511"
 [4,] "17935912"
 [5,] "17851940"
 [6,] "17765779"
 [7,] "17688640"
 [8,] "17638782"
 [9,] "17627059"
[10,] "17599582"
[11,] "17589729"
[12,] "17585283"
[13,] "17568846"
[14,] "17560665"
[15,] "17547971"
[16,] "17428551"
[17,] "17419899"
[18,] "17419519"
[19,] "17385606"
[20,] "17366752"

get.info<- function(doc){
         df<-cbind(
 	Abstract = unlist(xpathApply(doc, "//AbstractText", xmlValue)),
 	Journal =  unlist(xpathApply(doc, "//Title", xmlValue)),
 	Pmid =  unlist(xpathApply(doc, "//PMID", xmlValue))
                   )
   return(df)
   } 

On Dec 15, 2007 6:31 PM, David Winsemius <dwinsemius at comcast.net> wrote:

After quite a bit of hacking (in the sense of ineffective chopping with
a dull ax), I finally came up with:

pm.srch<- function (){
  srch.stem<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="
  query<-readLines(con=file.choose())
  query<-gsub("\\\"","",x=query)
  doc<-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE,
                     useInternalNodes = TRUE)
  return(sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue) )
     }

pm.srch()  #choosing the search-file
      //Id
 [1,] "18046565"
 [2,] "17978930"
 [3,] "17975511"
 [4,] "17935912"
 [5,] "17851940"
 [6,] "17765779"
 [7,] "17688640"
 [8,] "17638782"
 [9,] "17627059"
[10,] "17599582"
[11,] "17589729"
[12,] "17585283"
[13,] "17568846"
[14,] "17560665"
[15,] "17547971"
[16,] "17428551"
[17,] "17419899"
[18,] "17419519"
[19,] "17385606"
[20,] "17366752"

I tried the example above, but only the first 20 PMIDs will be
returned. How can I circumvent this (I guesss its a restraint from
pubmed)?
-- 
Armin Goralczyk, M.D.
--
Universit?tsmedizin G?ttingen
Abteilung Allgemein- und Viszeralchirurgie
Rudolf-Koch-Str. 40
39099 G?ttingen
--
Dept. of General Surgery
University of G?ttingen
G?ttingen, Germany
--
http://www.chirurgie-goettingen.de

pm.srch<- function (){

   srch.stem <-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="
   query <-as.character(scan(file="",what="character"))
   doc <-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE,
         useInternalNodes = TRUE)
   sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue)
     }

pm.srch()

1: "laryngeal neoplasms[mh]"
2:
Read 1 item
      //Id
 [1,] "18042931"
 [2,] "18038886"
 [3,] "17978930"
 [4,] "17974987"
 [5,] "17972507"
 [6,] "17970149"
 [7,] "17967299"
 [8,] "17962724"
 [9,] "17954109"
[10,] "17942038"
[11,] "17940076"
[12,] "17848290"
[13,] "17848288"
[14,] "17848287"
[15,] "17848278"
[16,] "17938330"
[17,] "17938329"
[18,] "17918311"
[19,] "17910347"
[20,] "17908862"

pm.srch()

On Dec 15, 2007 6:31 PM, David Winsemius <dwinsemius at comcast.net>
wrote: 

pm.srch<- function (){

   srch.stem
   <-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pub
   med&term=" query <-as.character(scan(file="",what="character"))
   doc <-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE,
         useInternalNodes = TRUE)
   sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue)
     }

pm.srch()

1: "laryngeal neoplasms[mh]"
2:
Read 1 item
      //Id
 [1,] "18042931"

I tried the above function with simple search terms and it worked fine
for me (also more output thanks to Martin's post) but when I use
search terms attributed to certain fields, i.e. with [au] or [ta], I
get the following error message:

pm.srch()

1: "laryngeal neoplasms[mh]"
2:
Read 1 item
Fehler in .Call("RS_XML_ParseTree", as.character(file), handlers,
as.logical(ignoreBlanks),  :
  error in creating parser for
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&ter
m=laryngeal neoplasms[mh]
I/O warning : failed to load external entity
"http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubme
d&term=laryngeal%20neoplasms%5Bmh%5D" 

What's wrong?

pm.srch<- function (){

doc.xml<-pm.srch()

doc.xml

"Armin Goralczyk" <agoralczyk at gmail.com> wrote in
news:a695fbee0712171238g4995040x579e58f52f83376e at mail.gmail.com: 

I tried the above function with simple search terms and it worked
fine for me (also more output thanks to Martin's post) but when I use
search terms attributed to certain fields, i.e. with [au] or [ta], I
get the following error message:

pm.srch()

1: "laryngeal neoplasms[mh]"
2:

I am wondering if you used spaces, rather than "+"'s? If so then you
may want your function to do more gsub-processing of the input string.

David Winsemius <dwinsemius at comcast.net> wrote in
news:Xns9A09CA51DB1E4dNOTwinscomcast at 80.91.229.13:

"Armin Goralczyk" <agoralczyk at gmail.com> wrote in
news:a695fbee0712171238g4995040x579e58f52f83376e at mail.gmail.com:

I tried the above function with simple search terms and it worked
fine for me (also more output thanks to Martin's post) but when I use
search terms attributed to certain fields, i.e. with [au] or [ta], I
get the following error message:

pm.srch()

1: "laryngeal neoplasms[mh]"
2:

I am wondering if you used spaces, rather than "+"'s? If so then you
may want your function to do more gsub-processing of the input string.

I tried my theory that one would need "+"'s instead of spaces, but
disproved it. Spaces in the input string seems to produce acceptable
results on my WinXP/R.2.6.1/RGui system even with more complex search
strings.

--

On 12/18/07, David Winsemius <dwinsemius at comcast.net> wrote:

David Winsemius <dwinsemius at comcast.net> wrote in
news:Xns9A09CA51DB1E4dNOTwinscomcast at 80.91.229.13:

"Armin Goralczyk" <agoralczyk at gmail.com> wrote in
news:a695fbee0712171238g4995040x579e58f52f83376e at mail.gmail.com:

I tried the above function with simple search terms and it worked
fine for me (also more output thanks to Martin's post) but when I
use search terms attributed to certain fields, i.e. with [au] or
[ta], I get the following error message:

pm.srch()

1: "laryngeal neoplasms[mh]"
2:

I am wondering if you used spaces, rather than "+"'s? If so then
you may want your function to do more gsub-processing of the input
string. 

I tried my theory that one would need "+"'s instead of spaces, but
disproved it. Spaces in the input string seems to produce acceptable
results on my WinXP/R.2.6.1/RGui system even with more complex search
strings.

--

It's not the spaces, the problem is the tag (sorry that I didn't
specify this), or maybe the string []. I am working on a Mac OS X 10.4
with R version 2.6. Is it maybe a string conversion problem? In the
following warning strings in the html adress seem to be different:
Fehler in .Call("RS_XML_ParseTree", as.character(file), handlers,
as.logical(ignoreBlanks),  :
 error in creating parser for
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&ter
m=laryngeal neoplasms[mh]
I/O warning : failed to load external entity
"http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubme
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