README.md

Another Java implementation of BioC

Data structures and code to read/write BioC XML.

BioC

BioC XML format can be used to share text documents and annotations. The development of Java BioC IO API is independent of the particular XML parser used.

Getting started

<dependency>
  <groupId>com.pengyifan.bioc</groupId>
  <artifactId>pengyifan-bioc</artifactId>
  <version>1.0.2</version>
</dependency>

or

<repositories>
    <repository>
        <id>oss-sonatype</id>
        <name>oss-sonatype</name>
        <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
        <snapshots>
            <enabled>true</enabled>
        </snapshots>
    </repository>
</repositories>
...
<dependency>
  <groupId>com.pengyifan.bioc</groupId>
  <artifactId>pengyifan-bioc</artifactId>
  <version>1.0.3-SNAPSHOT</version>
</dependency>

Developers

• Yifan Peng (yip4002@med.cornell.edu)

Acknowledgment

• Don Comeau
• Rezarta Islamaj Dogan
• Haibin Liu
• Thomas C. Wiegers
• John Wilbur

Webpage

The official BioC webpage is available with all up-to-date instructions, code, and corpora in the BioC format, and other research on, based on and related to BioC.

• http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/
• http://bioc.sourceforge.net/

Reference

• Comeau,D.C., Doğan,R.I., Ciccarese,P., Cohen,K.B., Krallinger,M., Leitner,F., Lu,Z., Peng,Y., Rinaldi,F., Torii,M., Valencia,V., Verspoor,K., Wiegers,T.C., Wu,C.H., Wilbur,W.J. (2013) BioC: A minimalist approach to interoperability for biomedical text processing. Database: The Journal of Biological Databases and Curation.
• Peng,Y., Tudor,C., Torii,M., Wu,C.H., Vijay-Shanker,K. (2014) iSimp in BioC standard format: Enhancing the interoperability of a sentence simplification system. Database: The Journal of Biological Databases and Curation.