Full Text PDFs for PubMed Articles

Question

While working on a project I need to download and process full text articles for PubMed abstracts, is there any implemented code or tool that allows the user to input a set of PubMed ids and downloads the free full text articles for the same. Any kind of help or tips is greatly appreciated.

Answer 1

I don't think it's possible in general, due to the nature of PubMed. The best you are going to do is get articles from the Open Access subset of PubMedCentral. PubMedCentral have a number of online utilities for doing the job.

Answer 2

The utilities StompChicken points to are for publishers to validate their XML before submission to PMC, they are not tools for downloading.

Note that the vast majority of articles in PMC are not open access (OA) and therefore cannot be downloaded automatically (legally) by any means. NCBI warns:

• The majority of the articles in PMC are subject to traditional copyright restrictions and are not part of this subset. Read the PMC Copyright Notice for more information.
• The PMC OAI service and the PMC FTP service are the only services that may be used for automated downloading of articles from this open access subset.
• Systematic retrieval (bulk downloading) of articles through any other automated process is prohibited, even if you are only retrieving articles from this subset.
• Some journals use the label "open access" for an article that is available free at time of publication, but is still subject to traditional copyright restrictions. Such articles are not part of this subset.

For downloading PMC content, the best way is to use the PMC Open Access FTP service: http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/

You can also use eutils to query the PMC and download full-text of the OA subset as well as abstracts of the remainder: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html

Another alternative is to use the OAI service: http://www.ncbi.nlm.nih.gov/pmc/tools/oai/

The OAI service is horribly documented, but some tips to get started are here: http://www.biostars.org/p/2076/#13338

If you want to maintain and update a PMC repository, try pubtools: http://code.google.com/p/pubtools/