OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Abstract

Background: Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment.Results: We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedical ontologies. Conclusions: Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Translational research combining orthologous genes and human diseases with the OGOLOD dataset

“…However, in a LOD setting this is not possible so any entity that exploits punning must 6 http://www.w3.org/TR/owl2-new-features/ #F12:_Punning 7 http://www.geneontology.org/GO.format. obo-1_2.shtml 8 The general process of translating OBO ontologies to OWL using punning is described in detail in [2]. be divided in the dataset into different entities (with different URIs) to represent every role.…”

NCBI BLAST + integrated into Galaxy

“…bx.psu.edu), which is a public repository of tools and workflows [9], from where they can then be installed on individual Galaxy servers. A few examples were recently published [10,11,12,13].…”

Technical Perspectives on Knowledge Management in Bioinformatics Workflow Systems

“…Biomedical ontologies are playing an important role in life sciences semantic web since they help in capturing the semantics of entities and their interrelationships within biology domain, thereby reducing conceptual ambiguity, increasing reusability and computational automation that aids in knowledge gathering and discovery [15]. Ontologies can be classified according to the degree of conceptualization which includes [12]:…”

“…Executor then run the completed workflow and updates the knowledge base with the results of workflow execution that can be used to make new inference. Galaxy in [15] is a workflow web-based platform for analysing genomic sequences. In Galaxy several tools can be merged, ranging from simply manipulating data to complex analysis tasks.…”