Updates to the AberOWL ontology repository Miguel Ángel Rodrı́guez-Garcı́a 1∗, Luke T Slater 2 , Imene Boudellioua 1 , Paul N Schofield 2 , Georgios V Gkoutos 3 , Robert Hoehndorf 1 1 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, KSA 2 College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, B15 2TT, United Kingdom 3 University of Cambridge, Downing Street, CB2 3EG, England, UK ABSTRACT and query these ontologies (i.e., AberOWL is used as a “Reasoning A large number of ontologies have been developed in the as a Service” provider). biological and biomedical domains, which are mostly expressed in the Web Ontology Language (OWL). These ontologies form a 1.2 Manual curation of ontologies: logical foundation for our knowledge in these domains, and they are We have also manually curated the ontologies in AberOWL, in widespread use to annotate biomedical and biological datasets. assigning a set of ‘topics’ to them and allowing users to The use of the semantics provided by ontologies requires the use browse the ontologies through these means. The set of topics of automated reasoning – inferring new knowledge by evaluating were extracted from the ontology EMBRACE Data and Methods the asserted axioms. AberOWL is an ontology repository which (EDAM) [4] which is essentially a taxonomy of well established utilises an OWL 2 EL reasoner to provide semantic access to terms with synonyms and definitions related primarily within classified ontologies. Since our original presentation of the AberOWL bioinformatics. The annotations covered 177 different EDAM topics framework, we have developed several additional tools and features spanning all EDAM top-level topics such as: Medicine, Biology, which enrich its ability to integrate and explore data, make use of Data management, Laboratory techniques, Computer science, the semantic and inferred content of ontologies. Here we present Chemistry, Mathematics, Physics, Ontology and terminology an overview of AberOWL and the enhancements and new features and Literature and reference. For instance, the Amphibian which have been developed since its conception. AberOWL is freely Gross Anatomy Ontology (AAO) was classified with the topics available at http://aber-owl.net. eukaryotes, anatomy, and amphibians, and the Ascomycete Phenotype Ontology (APO) was annotated with fungi, phenomics and ascomycetes. The figure 1 shows a list of annotated ontologies 1 INTRODUCTION in AberOWL. In recent years, several biological and biomedical ontology repositories have been developed, such as BioPortal [5], Ontobee [7] 1.3 Ontology Browsing and Visualisation: and the Ontology Lookup Service [2]. These provide web services We have improved the tools available for browsing and exploring and front-end interfaces for users to query and explore the content ontologies. The class view in the ontology browser now shows the of ontologies. AberOWL [3] is an ontology repository which utilises definition of the class in Manchester OWL Syntax. Additionally, automated reasoning to allow users to access the semantic content the visualization module has been completely redesigned and we of the ontologies. AberOWL provides both a web-based interface plan to further integrate a new library called Dagre [6], which for the exploration and browsing of ontologies and a set of REST provides another way of representing ontologies by graphs instead services which make the core functionality of AberOWL available of trees. Thus, while the current visualization module represents using the JSON standard [1]. cycles as a repeated subtree, the new module can easily include cycles without any repeated structure. Moreover, we plan to improve 1.1 Updates to AberOWL the performance of this module by transforming the ontologies into Ontology Acquisition, Curation and Statistics: When AberOWL RDF graphs which will contain the inferred model of each ontology. was originally presented in 2013, it contained 328 loadable Thus, we will be able to significantly reduce the delay involved in ontologies. Since then, our repository has grown to a total of 522 subclass computation. ontologies. The amount of ontologies in AberOWL has increased due to the growing number of ontologies in the biological and REFERENCES biomedical domains, improved coverage of synchronization with other ontology portals, and manual uploads of ontologies by [1]Tim Bray. The javascript object notation (json) data interchange users. Manually uploaded ontologies in AberOWL primarily serve format. 2014. the purpose of making fully axiomatised versions of ontologies [2]Richard G Côté, Philip Jones, Rolf Apweiler, and Henning available so that the AberOWL webservices can be used to classify Hermjakob. The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries. BMC bioinformatics, 7(1):97, 2006. ∗ To whom correspondence should be addressed: [3]Robert Hoehndorf, Luke Slater, Paul N Schofield, and miguel.rodriguezgarcia@kaust.edu.sa Georgios V Gkoutos. Aber-owl: a framework for ontology-based 1 Rodrı́guez-Garcı́a et al Fig. 1. Screenshot of AberOWL that shows the list of annotated ontologies by using the EDAM topics. data access in biology. BMC bioinformatics, 16(1):1, 2015. Rubin, Margaret-Anne Storey, Christopher G Chute, et al. [4]Jon Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Bioportal: ontologies and integrated data resources at the click Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, of a mouse. Nucleic acids research, page gkp440, 2009. Steve Pettifer, and Peter Rice. Edam: an ontology of [6]Chris Pettitt. dagre - graph layout for javascript, 2015. bioinformatics operations, types of data and identifiers, topics [7]Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, and and formats. Bioinformatics, 29(10):1325–1332, 2013. Yongqun He. Ontobee: A linked data server and browser for [5]Natalya F Noy, Nigam H Shah, Patricia L Whetzel, Benjamin ontology terms. In ICBO, 2011. Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Daniel L 2