All the PubMed articles are available in the BioC format. This provides a large number of research articles for text mining and information retrieval research. BioC is a simple format designed for straightforward text processing. These articles are available in BioC XML or BioC JSON, in Unicode or ASCII.

If you use this resource, please cite:

• Comeau DC, Wei CH, Dogan RI, and Lu Z. PMC text mining subset in BioC: about 3 million full text articles and growing, Bioinformatics, 2019

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_[format]/[PMID]/[encoding]

The parameters are:

• format: xml or json
• PMID
• encoding: unicode or ascii

Sample URL:
https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/unicode

Same article in ASCII:
https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/ascii
Obviously, no Unicode to ASCII translation is perfect. We have found this one useful.

JSON instead of XML:
https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_json/17299597/unicode
BioC JSON follows the same structure as BioC XML.

General information about BioC XML structure:
ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/BioC.dtd

Specific information about BioC PubMed:
ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/pubmed.key

Main BioC web page:
http://bioc.sourceforge.net

If you experience any problems, please share them with us: donald.comeau@nih.gov or zhiyong.lu@nih.gov.