UniProtJAPI

UniProt Knowledgebase Release [2015_06]

News

A completely new version of the UniProtJAPI is under development. The new JAPI is currently in Beta

The new JAPI aims to tackle several issues encountered by the current version:

• Frequent library updates
• Retrieval speeds
• Server availability

Frequent library updates

The current version of the JAPI requires its users to update the jar file whenever a UniProt data release occurs. The new version will greatly reduce this, by introducing new jars only when newer features are added, bugs are fixed or a major domain model redesign is introduced

Retrieval speeds

The newest version of the JAPI is much more responsive. Users will be able to retrieve data in a fraction of the time.

Server availability

During peek usage times users may have experienced server timeouts with the current JAPI. We have taken active measures to mitigate these timeouts, by introducing improvements in server responsiveness, and have added reasonable user retrieval caps.

If you would like to try out the new JAPI client please go to the site: http://wwwdev.ebi.ac.uk/uniprot/remotingAPI/index.html

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 7 SDK. A distribution can be downloaded from Oracle.
• 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.