bperry / pubmedportable

PubMedPortable automatically builds a PostgreSQL relational database schema and a Xapian full text index on PubMed XML files as well as it provides an interface to BioC.

PubMedPortable

PubMedPortable automatically builds a PostgreSQL relational database schema and a Xapian full text index on PubMed XML files as well as it provides an interface to BioC.

Please, have a look at our Wiki for more information.

• Introduction
• Installation instructions
• Setting up a database
• Creating a full-text index
• Querying a database
• Examples for using BioC and PubTator
• Indexing of PMC Articles
• Named Entity Recognition Tools
• Lucene as an Alternative to Xapian

To cite PubMedPortable, please reference:

Döring K, Grüning BA, Telukunta KK, Thomas P, Günther S (2016) PubMedPortable: A Framework for Supporting the Development of Text Mining Applications. PLoS ONE 11(10): e0163794. doi:10.1371/journal.pone.0163794