Increasing data accessibility and reuse in phylogenetics by employing externally defined ontologies

Wiechers S, Müller KF, Stöver BC

Abstract

In philosophy ontology is defined as the study of the nature and relations of being. Information sciences apply this concept to create naming conventions describing types, properties and interrelationships of certain entities. Ontologies aim to limit complexity and organize information. In phylogenetics they allow scientists to provide semantic information on data in a machine-readable way. Using fixed vocabularies from external ontologies makes the data more easily accessible for other researchers and facilitate its reuse. This is becoming more and more important with a rapidly increasing amount of biological data available in online sources. Here we present three software projects developed in our group that foster the use of external ontologies to enable users to handle according metadata. JPhyloIO is a software library that allows developers to support reading and writing different phylogenetic file formats (modeling alignments and trees), including full support for the format's metadata models and the use of externally defined ontologies. LibrAlign and TreeGraph 2 on the other hand allow to process and visualize such metadata in bioinformatical software applications. LibrAlign is a library providing GUI components to display and edit multiple sequence alignments allowing externally implemented data areas for metadata described using externally defined ontologies. Different types of branch labels available in TreeGraph 2 offer a similar functionality for phylogenetic trees. In combination our software components simplify the use of metadata from externally defined ontologies both in data storage and in data processing for the main phylogenetic data types to foster accessibility and reuse.