[BioC] Fetching documents from PubMed

[Robert Gentleman]

Hi,
  pubmed makes precisely one request, so there is no issue with timing. 
In many cases you can make a single request for lots of things, rather 
than lots of requests for one thing. If you stick it in a for loop then 
there could be problems, but so far not a single person has reported 
hitting this particular wall.

As for why only 377 came back, did you check to see what happens if you 
request one of the missing ones by itself? Or go to the website at NLM 
and see if you Pubmed id is valid?

Also, please do read the posting guide and tell us something about your 
system.

thanks
  Robert


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? 
>  
>  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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org