ncbitaxonomy

A Java library for easy access to an NCBI taxonomy database

• Provides a Hibernate-based object-relational interface to the NCBI taxonomy database, and convenience classes for navigating it.
• In particular, makes the NCBI taxonomy available as objects conforming to phyloutils APIs.

Documentation

• API docs

Download

Maven is by far the easiest way to make use of ncbitaxonomy. Just add these to your pom.xml:

<repositories>
	<repository>
		<id>dev.davidsoergel.com releases</id>
		<url>http://dev.davidsoergel.com/nexus/content/repositories/releases</url>
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
	</repository>
	<repository>
		<id>dev.davidsoergel.com snapshots</id>
		<url>http://dev.davidsoergel.com/nexus/content/repositories/snapshots</url>
		<releases>
			<enabled>false</enabled>
		</releases>
	</repository>
</repositories>

<dependencies>
	<dependency>
		<groupId>edu.berkeley.compbio</groupId>
		<artifactId>ncbitaxonomy</artifactId>
		<version>0.9</version>
	</dependency>
</dependencies>

If you really want just the jar, you can get the latest release from the Maven repo; or get the latest stable build from the build server.