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.
- 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