Using BioMed Central's open access full-text corpus for text mining research

As of 02 Sep 2014 BioMed Central (with Chemistry Central and SpringerOpen) has published 212604 articles of peer-reviewed research, all of which are covered by our open access license agreement which allows free distribution and re-use of the full-text article, including the highly structured XML version.

As a result, BioMed Central's open access corpus is ideally suited for use by text mining researchers.

An XSLT preview stylesheet, which will render any BioMed Central article XML file into HTML, is available:

preview.xsl (37K)

Sample code for developers, demonstrating the use of the stylesheet, is also available:

How to download BioMed Central's corpus

1. By FTP

Server: ftp.biomedcentral.com
Username: datamining
Password: $8Xguppy

File/directory Description
/articles/ A subdirectory containing the full-text XML file for each article, each named based on its unique identifier - i.e. [ui].xml
/articles.zip A single ZIP-compressed file containing all the full-text XML files
Remember to set FTP transfer mode to BINARY

2. Via the Open Archive Initiative Metadata Harvesting Protocol (OAI protocol)

The OAI protocol is an HTTP/XML web service standard for the exchange of data between archives and repositories. Full-text XML is one of the metadata formats that the BioMed Central OAI protocol interface supports. See BioMed Central's OAI page for more details.

Use the following OAI 'set' to download all open access articles via BioMed Central's OAI interface.
articletype:research


3. From PubMed Central (standard NLM DTD format)

BioMed Central's open access articles are part of the open access subset of PubMed Central. This means that they are available for bulk xml download from PubMed Central in the standard NLM Archiving and Interchange DTD format, via FTP or OAI.

Publish your text mining research with BioMed Central

BioMed Central is keen to publish high quality research in the area of text mining and biomedical literature analysis.

See this list of recent publications on this topic that have appeared in BioMed Central's journals.

All research articles published by BioMed Central are covered by our open access policy, and so are freely available without subscription.

For more information about submitting an article, visit the home pages of BMC Bioinformatics or BioData Mining.

More information

For more information on using BioMed Central's articles for text mining purposes info@biomedcentral.com.

Useful links

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