UniProtJAPI

UniProt Knowledgebase Release [2013_09]

Introduction

This library provides a remote API for accessing the UniProt data. Using the API you can blast or search against UniProt, UniParc, UniRef or UniMes to retrieve detailed entry information.

Justification

The Universal Protein Resource (UniProt) provides a comprehensive and freely accessible central resource of protein sequences and functional annotation. We know from experience that programmatically a number of problems exist in integrating this data within bioinformatics applications. Firstly the sheer amount of data across the entire UniProt - over 46 million entries and rising, requires large amounts of computational resources. Further frequent and necessary format changes, of all UniProt databases, causes many parsing and ultimately maintenance issues for internal and external users. Additionally integrating supplemental data sources for example GO and InterPro can be problematic due to the update cycles of these sources being different from the UniProt update cycle. These problems and many other Java based application integration issues are mitigated with the use of this java library UniProtJAPI.

Licenses & Disclaimer

Please read our licenses and disclaimers before using this tool.

Requirements

• Java 6 SDK. A distribution can be downloaded from Oracle.
• Java 7 SDK is required from the 2013_09 release on 18.9.2013
• Hypertext Transfer Protocol (HTTP), connection be available.

Where to start?

Download the UniProtJAPI. It is recomended that you download the below zip file as it contains all the supporting libraries needed to get UniProtJAPI running. Simply download the file and extract to a directory. Navigate to the uniprotjapi directory where you will find a README providing details on the distribution and on how to run the examples included. To start building your own applications simply include all the jar files in the lib directory in your Java CLASSPATH.

Documentation can be found in the distributions doc directory or here Using the UniProJAPI the object model java doc is available in the distribution and here.

Alert Me!

UniProtJAPI provides a mail service that will alert users to new developments, including new database releases that will require upgrades in Jar files. Please provide the information requested below so that we may add you to the list. UniProtJAPI does not disclose mail list members.

Access The UniProtJAPI via Maven

EBI's maven repository contains all the necessary dependencies and files to integrate UniProtJAPI into your Java application.

Firstly you need to specify the EBI Maven repository as the location to find the UniProtJAPI. To do this you need to add the below repository either to you pom xml or you add this globally through your settings.xml file. For more, on using repositories, please refer to the Maven documentation available here.

    <repository>
        <id>ebi-repo</id>
        <name>ebi-repo</name>
        <url>http://www.ebi.ac.uk/~maven/m2repo</url>
    </repository>

The last part of your configuration is specify the dependency on the UniProtJAPI you do this by adding the below dependency section to you pom file. For more details, on dependency mechanism, please refer to the Maven documentation available here.

    <dependency>
        <groupId>uk.ac.ebi.uniprot.kraken</groupId>
        <artifactId>uniprotjapi</artifactId>
        <version></version>
    </dependency>

Additional downloads

Further we provide options to download slimmed down versions and examples.