[BioC] Fetching documents from PubMed

[Morten Mattingsdal]

Kaustubh Patil wrote:

>Hi,
> 
> I want to fetch documents from PubMed. So first I get all the PMIDs and then use the "pubmed" function from the "annotate package". But does this function take care of the NCBI rule for waiting 3 seconds between queries? 
>  
>
Dont know about the "pubmed" function from annotate, but Ive seen a 
function which does excaly this in the MedlineR package (im just pasting 
the code below)

pauseBetweenQueries<- function (
   sleep.peak=15,                # pause (in seconds) during peak hours
   sleep.offpeak=3               # pause (in seconds) during off-peak
  ) {
 # sleep.peak<-15; sleep.offpeak<-3
 # Date example:
 # "Thu"      "Jan"      "15"       "16:46:11" "2004"
 result.date<- unlist (strsplit(
   date(), split=" "))
 hour<- as.numeric(unlist (strsplit (result.date[4], split=':'))[1])
 # off peak hours are Sat, Sun or anytime between 9 pm and 5 am
 if (
   (result.date[1]=="Sat") | (result.date[1]=="Sun") |
   (hour > 21) | (hour<5)
  ) {off.peak<-T} else {off.peak<-F}

 # perform the sleep
 if (off.peak) {
  Sys.sleep (sleep.offpeak)
 } else {
  Sys.sleep (sleep.peak)
 }
}

you may want to try more code from MedlineR. you can find the complete 
code here:
http://www.dbsr.duke.edu/pub/MedlineR/MedlineR_v30.txt

hope this can be usefull :)
morten


> 
> Also I have a list of 718 PMIDs but the function retrieves only 377 of them? I don't understand why. Suggestions appreciated.
> 
> Thank you and regards,
> Kaustubh
> 
>		
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