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News
June 2007: Maintenance Release

Implementation documentation has been updated to include more recent dependencies. Please note that unless stated otherwise in specific instances, newer versions of given depencies should work without issue.

April 2007: Maintenance Release

There is a new release of the OLS available, which includes mostly maintenance fixes and loader code improvements (such as failover database support). The source code and clients are available in the downloads section.

January 2007: Data and inferface upgrades

The OLS got a facelift in order to better integrate with the new look&feel deployed sitewide at the EBI. In other news, the Medical Subject Heading vocabulary (MeSH) has been removed from the OLS in order to comply with requests from the National Library of Medicine (NLM). The full list of loaded ontologies can be seen here.

November 2006: Data and inferface upgrades

The unit ontology (UO) has been added to the OLS. The full list of loaded ontologies can be seen here. Furthermore, a quick term ID lookup has been added to the search interface to look up terms by their unique identifiers.

October 2006: OLS presented at HUPO 2006

The OLS was featured in an oral presentation at the 6th annual HUPO Congress.

August 2006: Filtering of obsolete terms

It is now possible to exclude obsoleted terms from the auto-completion list when searching for terms. Simply uncheck the Include obselete terms box and any terms that have been marked as obsolete will no longer be returned in the search results.

August 2006: SOAPAction added to WSDL

The SOAPAction element has been added to the WSDL service declaration to improve interoperability with PHP and other languages that require it.

July 2006: New webservice deployed

As announced in the previous news item, the OLS webservice has been redeployed to make it compliant with the latest WSDL specifications and also improve its interoperability. If you are experiencing problems with the new webservice code, please do not hesitate to contact us for support.

June 2006: Notification of WSDL change

The OLS webservice will be undergoing change that will not be backwards-compatible and might break existing code at the end of June. The current WSDL defines multiple operations with the same name but with different parameters. While such method overloading was allowed under previous WSDL specifications, it will no longer be supported. Furthermore, to maximize interoperability, the WSDL will change from a RPC-style service to a document/wrapped style service. As such, users of the OLS webservice are encouraged to update their code to use the new WSDL, which will be published on June 30th.

February 2006: OLS published in BMC Bioinformatics

A paper describing the OLS has been published in BMC Bioinformatics: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

December 2005: More data, more methods!

4 new ontologies have been added: GRO, MOD, PSI and SO. See the full list here. Also, two new methods have been added to the SOAP interface. View the WSDL here

December 2005: Release of the ontology browser

An AJAX-based ontology browser has now been deployed. Select the ontology you wish to browse from the list and click on the "browse" button.

November 2005: Major increase in ontology availability

The OLS now serves 37 ontologies. See the full list here. Significant improvements have also been made to the layout of the web interface, with more in the pipeline.

August 2005: Ontology Lookup 1.0 Release

The Ontology Lookup webservice has been made publicly available for general use by the scientific community.

Ontologies currently available include:

  • Gene Ontology (GO)
  • Medical SubHeadings (MeSH)
  • PSI Molecular Interactions (PSI-MI)
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OLS - Ontology Lookup Service


Enter Ontology Term

(Include obsolete terms )
definitionA protein modification that effectively cross-links an L-cysteine residue and an L-tryptophan residue by a thioether bond to form 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide.
nullCross-link 2.
DiffAvg29.98
DiffFormulaC 0 H -2 N 0 O 2 S 0
DiffMono29.974179
FormulaC 14 H 13 N 3 O 4 S 1
MassAvg319.34
MassMono319.062677
OriginC, W
Sourcenatural
TermSpecnone
preferred name2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide
Protein feature description from UniProtKB synonym2'-cysteinyl-6'-hydroxytryptophan sulfoxide (Trp-Cys)
Systematic name from RESID synonym2-((2R)-2-amino-2carboxyethyl)sulfinyl-3-((2S)-2-amino-2-carboxyethyl)-1H-indole
xref_definitionPubMed:14354
xref_definitionRESID:14358
xref_definitionPubMed:14357
xref_definitionPubMed:14355
xref_definitionPubMed:14356
Enter a partial search term. As you are typing, you will see suggested terms that match what are you have typed so far. If you select a term from the pull-down list, its corresponding ID will be displayed in the form. If you see "... and more" in the list of suggested values, you can select this value to be redirected to a page where all possible values are listed. As an example, enter mitoc in the Term Name box while the Gene Ontology is selected.

For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp.

You can browse an ontology by clicking on the "browse" button next to the ontology selector. To view the complete ontology, do not select a term name. If a term name has been selected, it will be the root from which the ontology will be browsed.
Simple Term ID Search:

Enter a complete term ID (example: GO:0008150) and click on the 'Search' button to quickly obtain all pertinent information for this term. Searches are case-sensitive, so ensure that the proper ontology prefix is used (GO:, rather than go: or Go:).

Statistics

Version:
1.17
Ontologies Loaded:
74
Terms Loaded:
923850
Last updated:
Mon Dec 14 09:54:30 GMT 2009

See the full breakdown of loaded ontologies here and load statistics here.



Project description

  • The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format.

  • The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.

  • The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format.

Documentation: Downloads:
  • OLS is an open source project hosted on Google Code. You can access the OLS project page, the OLS documentation, or browse the SVN repository.
  • All OLS software is freely available to all users, academic or commercial, under the terms of the Apache License, Version 2.0.
  • The OLS software and the SOAP webservice are both freely available for use. If you find them useful for your own applications, we would be grateful for a mention similar to the following:

    "Uses the EBI OLS <http://www.ebi.ac.uk/ontology-lookup>."

    where both the image and URL are hyperlinked to the OLS homepage.


  • To simplify the integration of the OLS in your existing Java applications, we make available a sample code project that will use the SOAP service deployed at the EBI. You can obtain it by clicking on the following link: ols-client.tar.gz. To use this demo project, you will also need to hava java 1.5 and Apacha Ant installed

  • Source code release 1.17 on 2009-08-27 09:28:39

  • A weekly MySQL database export file can be downloaded from the EBI public FTP directory. Instructions on how obtain, install and use the export file can be found on the MySQL database export documentation page.

Mailing lists, bug reports
Acknowledgements:

  • OLS is supported through BBSRC iSPIDER.
  • Hosted by Google Code
iSPIDER BBSRC Google Code
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