W156 Nucleic Acids Research, 2010, Vol. 38, Web Server issue Figure 1. Growth chart of the OLS data content. The amount of data loaded into the OLS, based on unique terms, has shown a 7-fold increase since the service went online. The ﬁrst large increase is due to the incorporation of the NEWT taxonomy and the second large increase is due to the addition of a large number of ontologies at once. Table 1. A list of ontologies that have been added to the OLS in the last 2 years Ontology Preﬁx Ontology name AAO APO ATO CCO EFO ENA FBsp FMA HAO HOM HP IDO LSM MIAA MIRO MPATH MS PAR PRO TADS TTO WBbt WBls WBPhenotype ZFA Amphibian Gross Anatomy Ontology Yeast Phenotype Ontology Amphibian Taxonomy Cell Cycle Ontology ArrayExpress Experimental Factor Ontology European Nucleotide Archive Submission Ontology Flybase Taxonomy Foundational Model of Anatomy Ontology Hymenoptera Anatomy Ontology Homology Ontology Human Phenotype Ontology Infectious Disease Ontology Leukocyte Surface Marker Ontology Minimal Information about Anatomy Ontology Mosquito Insecticide Resistance Ontology Mouse Pathology Ontology Mass Spectrometry Ontology Protein Aﬃnity Reagents Ontology Protein Ontology Tick Gross Anatomy Ontology Teleost Taxonomy C. elegans Gross Anatomy Ontology C. elegans Development Ontology C. elegans Phenotype Ontology Zebraﬁsh Anatomy and Development Ontology diﬀerent Concurrent Versioning System (CVS) repositories, complemented with three Subversion (SVN) Version Control repositories thanks to the recently added SVN support. A mechanism to download individual ﬁles available by HTTP or FTP has also been implemented, which allows the loaders to track changes in ﬁles that are not in CVS or SVN The OLS codebase is made available under the permis- sive Apache 2.0 Open Source License and is freely avail- able from the Google Code project repository (http://code.google.com/p/ols-ebi/). A weekly updated MySQL database dump is also made available from the EBI FTP server (ftp://ftp.ebi.ac.uk/pub/databases/ols). DATA MODEL IMPROVEMENTS The OLS data loaders have been upgraded to be able to parse ontologies produced according to the Open Biomedical Ontology (OBO) 1.2 speciﬁcation (http://www.geneontology.org/GO.format.obo-1_2.shtml) and can now capture previously unavailable information, such as custom name–value pairs and new synonym types (Figure 2). Another important feature of the OBO 1.2 speciﬁcation is the ability to ‘import’ other ontologies and create relationships between local and imported terms. In order to avoid loading multiple copies of imported ontologies, the loaders and database back end has been refactored such that each ontology is only loaded once. The OLS loaders are conﬁgured so that ontologies and CVs deﬁne one or more term preﬁxes that are local to itself (e.g. GO for the Gene Ontology). If the loaders en- counter term identiﬁers that begin with a non-local preﬁx, they will query the OLS database and retrieve the latest version of the term in question and then proceed as normal. In this way, relationships across linked ontologies always refer to the most up-to-date data. These cross-ontology links can now also be queried and browsed, as shown in Figure 3.