=Paper=
{{Paper
|id=Vol-1747/D205_ICBO2016
|storemode=property
|title=Easy Extraction of Terms and Definitions with OWL2TL
|pdfUrl=https://ceur-ws.org/Vol-1747/D205_ICBO2016.pdf
|volume=Vol-1747
|authors=John Judkins,Joseph Utecht,Mathias Brochhausen
|dblpUrl=https://dblp.org/rec/conf/icbo/JudkinsUB16
}}
==Easy Extraction of Terms and Definitions with OWL2TL ==
https://ceur-ws.org/Vol-1747/D205_ICBO2016.pdf
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.