OBO-Edit—an ontology editor for biologists

John Day-Richter 2 4 Midori A. Harris 1 4 Melissa Haendel 0 4 The Gene Ontology OBO-Edit Working Group 3 4 Suzanna Lewis 2 4 Associate Editor: Alex Bateman 0 Zebrafish Information Network, University of Oregon , Eugene, OR 97403 , USA 1 GO Editorial Office, EMBL Outstation-European Bioinformatics Institute , Hinxton, Cambridge CB10 1SD , UK 2 Berkeley Bioinformatics and Ontology Project, Lawrence Berkeley National Laboratory , Berkeley, CA, 94720 USA 3 Gene Ontology Consortium 4 The OBO-Edit Working Group is composed of Midori A. Harris , Jennifer I. Clark, Amelia Ireland, Jane Lomax (GO-EBI, Hinxton , UK) ; Karen Eilbeck , Suzanna Lewis, Chris Mungall, John Day-Richter (BBOP, LBNL, Berkeley, CA, USA); Alexander D. Diehl, Harold Drabkin (MGI , The Jackson Laboratory , Bar Harbor, ME , USA) ; Karen R. Christie (SGD, Department of Genetics, Stanford University , Stanford, CA , USA) ; Tanya Berardini (TAIR, Carnegie Institution, Department of Plant Biology , Stanford, CA, USA); Petra Fey (DictyBase , Northwestern University , Chicago, IL , USA) ; Carol A. Bastiani, Ranjana Kishore (WormBase, California Institute of Technology , Pasadena, CA, USA); Victoria Petri (RGD , Medical College of Wisconsin , Milwaukee, WI , USA) ; Shuly Avraham (Cold Spring Harbor Laboratory , Cold Spring Harbor, NY); Pankaj Jaiswal (Gramene , Department of Plant Breeding, Cornell University , Ithaca, NY, USA); Melissa Haendel (ZFIN, University of Oregon, Eugene, OR , USA) ; and John Osborne (Robert H. Lurie Cancer Center, Northwestern University , Chicago, IL , USA) Summary: OBO-Edit is an open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses a graph-oriented approach to display and edit ontologies. OBO-Edit is particularly valuable for viewing and editing biomedical ontologies. Availability: https://sourceforge.net/project/showfiles.php?group_id 36855 Contact: The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: - INTRODUCTION In response to the ever-increasing amount and variety of data in biomedical research, ontologies are becoming widely used to make biomedical information more computable. An ontology is a shared representation of a subject area, or domain, in which terms and hierarchical relationships among them are defined (Bard and Rhee, 2004; Blake, 2004; Gruber, 1993; Jones and Paton, 1999; Smith et al., 2005; Wroe and Stevens, 2006). The Gene Ontology Consortium developed OBO-Edit, a general editor for ontologies, to meet the needs of biology domain experts to browse, search and edit ontologies. OBO-Edit is now being used to develop many of the Open Biomedical Ontologies (OBO; http://obo.sourceforge.net/), such as the cell ontology (Bard et al., 2005) and a growing number of species-specific anatomy ontologies (for example, see Bard, 2005). A diverse group of biologists have contributed to the development and documentation of OBO-Edit, ensuring that it is versatile, configurable and user friendly. The included users guide provides detailed information on both basic and complex applications of the program. VIEWING ONTOLOGIES IN OBO-Edit OBO-Edit uses a graph-based approach to ontology editing, in which an ontology is presented as a labeled hierarchical graph, with ontology terms as the graph nodes and relationships between terms as labeled links between graph nodes. *To whom correspondence should be addressed. This graphical approach makes OBO-Edit intuitive for biologist users, and is well suited to the rapid generation of large ontologies focusing on relationships between relatively simple classes. By default, and as a means of managing complex graphs, OBO-Edit displays an ontology in a normalized tree view. Each line in the tree view represents a relationship between terms, with an arrow indicating the direction of the relationship. A term in the tree view may be expanded to show its child relationships (i.e. relationships pointing from another term to the term of interest). Since a term may have any number of relationships to other terms, a term may appear several times in the tree view (Fig. 1A). In many contexts, a non-redundant picture of some part of the ontology graph can be useful. OBO-Edits Graph Viewer plugin (which requires the additional installation of AT&Ts open-source GraphViz software; Gansner and North, 1999) displays a more traditional and intuitive graphical view of a selected part of the graph (Fig. 1A). OBO-Edit includes additional plugins to provide alternate views of the ontology structure. The DAG Viewer plugin displays every path from a selected term to the ontology root (Fig. 1A). The Parent plugin displays a list of all the relationships between the selected term and other ontology terms. OBO-Edit presents structural ontology editing operations, such as adding new terms or new relationships, to the user as graph editing operations. There are several different ways to perform most edits, including drop-down menus, right-click menus, hot keys and drag-and-drop gestures. Textual meta-data, such as the term name, definition, synonyms, etc., can be edited via the Term Editor component (Fig. 1B). The text editor also allows cross-products to be specified, whereby a term can refer explicitly to other terms, including terms from different ontologies. All edits in OBO-Edit are tracked, allowing users to undo any change they make during an editing session. OBO-Edit provides a number of tools for managing edit lists, including a viewer plugin, command-line tools and a data adapter for saving edit lists (the history of changes to individual terms over time) to disk in XML format. SEARCHING AND FILTERING The search facility in OBO-Edit is built around filters. Basic filters specify a term attribute (such as name, definition, number of relationships to other terms, etc.), a comparison (equals, starts with, is less than, etc.) and a value. Compound filters combine a number of filters together using the Boolean operators AND and OR. Filters can be used for a wide variety of tasks. A simple search returns a list of all the terms in the ontology that match a given filter. Filters can then be used to alter the display, either to show only matching terms, or to highlight matching terms by changing fonts, colors or other style attributes (Fig. 1C). Filters can also be used, either within OBO-Edit at save time or using command-line tools distributed with OBO-Edit, to control which terms and relationships are saved to a file. FILE FORMATS OBO-Edit uses pluggable data adapters to load and save ontologies and other data. OBO-Edit currently includes adapters for the OBO file format, the GO Flat File Format and Java serial files, and supports the addition of third-party adapters for other file formats. For example, writing and limited reading in OWL format are supported via a downloadable plugin (http://xrl.us/oboinowl). OBO- (...truncated)