Easy Extraction of Terms and Definitions with OWL2TL John Judkins, Joseph Utecht, and Mathias Brochhausen Department of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock, USA mbrochhausen@uams.edu Abstract—Facilitating good communication between semantic properties of terms (e.g. rdfs:label, etc.) and definitions web specialists and domain experts is necessary to efficient (rdfs:comment, iao:definition, etc.). When the form is ontology development. This development may be hindered by the submitted, a list of terms and annotation properties is produced. fact that domain experts tend to be unfamiliar with tools used to create and edit OWL files. This is true in particular when changes to definitions need to be reviewed as often as multiple II. METHODS times a day. We developed "OWL to Term List" (OWL2TL) Accessing [cafe-trauma.com/owl2tl/] loads a form (Figure with the goal of allowing domain experts to view the terms and 1) for the user to input URIs for: the OWL ontology (required) definitions of an OWL file organized in a list that is updated each and five additional annotation properties (e.g. time the OWL file is updated. The tool is available online and http://purl.obolibrary.org/obo/IAO_0000115 for definitions). currently generates a list of terms, along with additional Terms are extracted using a SPARQL query that extracts each annotation properties that are chosen by the user, in a format class by its RDFS label. The query also retrieves the values for that allows easy copying into a spreadsheet. annotation properties specified by the user on the form, if any. The array containing the results of the query is posted to a web Keywords—ontology development; semantic web; software; web application; controlled vocabulary form – Figure 2 shows as an example term list from the Non- Coding RNA Ontology [3] with definitions (iao:definition) and alternative terms (iao:alternativeTerm). I. INTRODUCTION Ontology development requires ongoing collaboration III. RESULTS between domain experts from various fields, programmers and ontology developers. After the initial phase of domain analysis OWL2TL currently generates a list of terms and additional quite often an iterative process during which definitions are annotation properties for any ontology in which owl:Class vetted by ontology developers to fit certain requirements [1] introduces a class description, as Figure 2 shows. The list loads and then reviewed and agreed upon by the domain experts is in a format that allows easy copying into a spreadsheet while necessary. We encounter this situation in the NIH funded preserving the structure of the table, and even works for project “Comparative Assessment Framework for ontologies with hundreds of thousands of terms. Environments of Trauma Care” (CAFÉ, 5R01GM111324) Fig. 1. Screenshot of results after form submission. [www.cafe-trauma.com]. It is frequently the case that domain experts are not familiar with ontology development tools, such as e.g. Protégé [2], if they are not themselves creating OWL files. Hence, the process of optimizing definitions can become tedious as changes implemented in OWL need to be fed back to the domain experts, especially during a project phase where multiple – often minimal – edits per day occur. To allow domain experts to review all terms and definition in an OWL file as soon as updates get available in a format that is familiar to them, we provide a tool called "OWL to Term List" (OWL2TL). OWL2TL is a web application that is part of the CAFE project, hosted at [cafe-trauma.com/owl2tl/], and has source available at [github.com/johnwjudkins/OWL2TL]. While an initial release has been made, we will continue to tweak, optimize, and expand the tool. The goal of OWL2TL is the quick generation of a list of terms and definition from an OWL file. OWL2TL provides a web form to enter the URI for the ontology itself and URIs for additional annotation Fig. 2. Screenshot of [cafe-trauma.com/owl2tl/]. ACKNOWLEDGMENT The research presented in this demonstration is funded by the National Institute of General Medical Sciences of the National Institutes of Health under award number 1R01GM111324. REFERENCES [1] J. Köhler, K. Munn, A. Rüegg, A. Skusa, and B. Smith, “Quality control for terms and definitions in ontologies and taxonomies”, BMC Bioinformatics, 2006, 7: 212, PMC1482721 [2] N. F. Noy, M. Crubézy, R. W. Fergerson, H. Knublauch, S. W. Tu, J. Vendetti, M. A. Musen, “Protégé-2000: An open-source ontology- development and knowledge-acquisition environment”, AMIA Annu. Symp. Proc., 2003, 2003: 953, PMC1480139 [3] J. Huang, K. Eilbeck, B. Smith, J. A. Blake, D. Dou, W. Huang, D. A. IV. DISCUSSION AND CONCLUSION Natale, A. Ruttenberg, J. Huan, M. T. Zimmermann, G. Jiang, Y. Lin, B. Wu, H. J. Strachan, Y. He, S. Zhang, X. Wang, Z. Liu, G. M. Borchert, The main goal of OWL2TL has been achieved – the “The non-coding RNA ontology (NCRO): A comprehensive resource application generates a list of terms and definitions from any for the unification of non-coding RNA biology.” J. Biomed. Semantics, ontology that has up to one thousand terms and uses owl:Class 2016, 7:24, PMC4857245 for class descriptions. The next step in development is editing the code to redirect the generated term list to a unique URL that can be shared, while maintaining the same functionality and quick response. Efforts to make the code more versatile – for instance, extracting only terms belonging to a particular superclass in an ontology – are underway.