how to get articles from pubmed

Question

[dreamzz.4you]

Hi,

Please if anyone could help me, I want to download few thousands pubmed articles and organize in some format so that later on I could read it through python to identify the MeSH terms and kind of publications these are. I am new in health informatics and have never done such kinda work before.

[Pierre Lindenbaum]

search this site for "NCBI EFETCH pubmed xml" https://www.google.fr/search?q=NCBI+EFETCH+pubmed+xml+site%3Abiostars.org

[dreamzz.4you]

Dear Pierre. well, I am confused :(. Being novice i am getting difficulty. How to use EFETCH for it. I want to download articles for this search http://www.ncbi.nlm.nih.gov/pubmed/?term=clinicaltrials.gov+%5Bsi%5D . There are 35,919 paper for this search and I want to download all. So that later on I could read them in python

Sadia

Answer 1

[Sean Davis]

Since it seems you want to use python, consider looking into biopython. Here is an example (one of many) showing how to use biopython to search and then retrieve records.

Note that pubmed does not store papers and many papers indexed in pubmed are not available for public consumption.