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

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ncbitaxonomy has dependencies on other libraries; Maven is by far the easiest way to deal with this. To use ncbitaxonomy in your Maven project, just add these to your pom.xml: 

<repositories>
	<repository>
		<id>dev.davidsoergel.com releases</id>
		<url>http://dev.davidsoergel.com/artifactory/repo</url>
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
	</repository>
	<repository>
		<id>dev.davidsoergel.com snapshots</id>
		<url>http://dev.davidsoergel.com/artifactory/repo</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 it here: ncbitaxonomy-0.9.jar (x KB) date

Or get the latest stable build from the continuous integration server.

You can also browse the source, or get the source with svn: 

svn co http://svn.davidsoergel.com/repos/ncbitaxonomy/trunk ncbitaxonomy

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