=Paper=
{{Paper
|id=Vol-1515/demo2
|storemode=property
|title=Ontorat: Automatic generation and editing of ontology terms
|pdfUrl=https://ceur-ws.org/Vol-1515/demo2.pdf
|volume=Vol-1515
|dblpUrl=https://dblp.org/rec/conf/icbo/HeZL15a
}}
==Ontorat: Automatic generation and editing of ontology terms==
https://ceur-ws.org/Vol-1515/demo2.pdf
Ontorat: Automatic generation and editing of ontology terms
Yongqun He1*, Jie Zheng2, Yu Lin1
1
University of Michigan, Ann Arbor, Michigan, USA; 2 University of Pennsylvania, Philadelphia, PA, USA
ABSTRACT Ontorat settings file or an OWL output file. The Ontorat
The web-based Ontorat (http://ontorat.hegroup.org/) program has been settings file can be stored and reused later (Fig. 1).
developed to automatically generate and edit ontology terms from a spread-
sheet format input (Excel or tab-delimited file) based on an ontology design
pattern (ODP). The Ontorat web interface is intuitive and suitable for users
with basic background in Manchester ontology format scripting, the same
language used in the Protégé OWL editor. Ontorat also collects ODPs and
provides templates and sample data for future reuse. As a demonstration,
Ontorat is applied to automatically generate assay terms with axioms and
annotations added into the Ontology for Biomedical Investigations (OBI).
1 INTRODUCTION
Manually developing a new ontology can be very time-
consuming. To reduce the time in ontology development,
we can first develop an Ontology Design Pattern (ODP) Fig. 1. Ontorat architecture and workflow.
(Noppens and Liebig, 2009), apply the ODP to generate an
Excel or text file including ODP-oriented data, and then 3 ONTORAT WEB INTERFACE
transform the structured data into an OWL format file.
Ontorat is a web-based tool to perform such a task (Xiang et Ontorat includes a user-friendly web form for adding setting
al., 2015). options, uploading a data input file, clicking for execution,
providing debugging information, and downloading the
Ontorat is developed based on the ODP strategy, and its
OWL output.
development was inspired by the Quick Term Templates
Input data file: Based on a pre-defined ODP, an Ontorat
(QTT) procedure generated by the developers of the
template file is generated to include all term and annotation
Ontology for Biomedical Investigations (OBI) (Rocca-Serra
et al., 2011). Ontorat is able to convert a QTT template in a types needed for defining a target term. The template file
spreadsheet into an OWL file. Ontorat also includes other can then be filled up with specific terms and annotations for
features as described elsewhere in this article. each type. Ontorat supports both Excel and tab-delimited
text input files.
In this software demo, we will introduce general Ontorat
Ontorat settings: Ontology axioms are represented us-
design and workflow, describe features of Ontorat, and
ing Manchester OWL Syntax (Horridge et al., 2006). The
provide use case demonstrations to show how Ontorat is
used to facilitate new ontology term addition and existing axiom settings can be added one by one via the Ontorat web
ontology term editing. form or uploaded from an Ontorat setting text file in an
Ontorat-specific setting file format. Ontorat can generate the
2 ONTORAT SOFTWARE DESIGN setting file based on the setting inputs via the Ontorat web
form.
From the Ontorat web page, a user can enter setting options Ontorat output file: The OWL output file can be
and upload the input data file via the Ontorat web input visualized using the Protégé ontology editor
form. The input data file is generated by populating a (http://protege.stanford.edu/) and imported into the target
predesigned template file guided by the ODP as mentioned ontology using the OWL import function.
above. The setting options specify the ontological meanings
of the columns in the input data file and axioms between
4 ONTORAT NEW TERM GENERATION
terms. After accepting the input data file and setting options
from the user, the web server (via a PHP script) will be able One major function of Ontorat is to generate multiple new
to execute two operations: 1) generation of new ontology ontology terms based on an ODP for a specific ontology.
classes with logical axioms and annotations, or 2) adding Fig. 2 provides a demo on how Ontorat can be used to
new axioms to existing ontology terms. The Ontorat server generate a list of assays based on a design pattern (Fig. 2A)
will process the user’s requests and generate either an out of the Ontology for Biomedical Investigations (OBI)
(Brinkman et al., 2010). Fig. 2B provides a portion of the
Ontorat setting file. Like the Protégé OWL editor, Ontorat
* To whom correspondence should be addressed: yongqunh@umich.edu
Copyright c 2015 for this paper by its authors. Copying permitted for private and academic purposes 1
He et al.
also uses the Manchester OWL Syntax (Horridge et al., The Ontorat input and output OWL files for this use case
2006) for scripting ontology axioms. For example, Ontorat are available on the Ontorat website:
uses the following Manchester syntax expression: http://ontorat.hegroup.org/designtemplates/biobank/index.p
'has participant' some hp.
6 COLLECTION OF DESIGN PATTERNS AND
to express the relation that a newly generated term has
an axiom of 'has participant' some device (which is located
TEMPLATES
in the column M of the Excel input file). Each row in the Ontology design patterns (ODPs) are reusable modeling
Excel file (Fig. 2C), starting from row 2, includes the solutions for ontology development. Ontorat has collected
information for generating a new ontology term. The output many ODPs and corresponding templates
file can be displayed using Protégé OWL editor (Fig. 2D). (http://ontorat.hegroup.org/designtemplates.). For each case,
The detailed files associated with this use case are available Ontorat provides an ODP diagram, an Excel template, a
on the Ontorat web page: setting file, and an example with populated template data
http://ontorat.hegroup.org/designtemplates/assay/obi- and output OWL file. These ODPs and templates can be
assay.php. reused to support fast and reproducible ontology
(A) Design Pattern development.
7 SOURCE CODE AND LICENSE
The Ontorat source code is openly available on GitHub:
https://github.com/ontoden/ontorat. The Ontorat source code
license is Apache License 2.0.
8 SUMMARY
With ever increasing needs of ontology development and
applications, the web-based Ontorat program provides a
(B) Ontorat setting (D) Ontorat output
shown in Protege timely platform for generating and annotating ontology
terms based on design patterns.
ACKNOWLEDGEMENTS
This research is supported by a NIH R01 grant
(C)Template and input data
(1R01AI081062).
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2 Copyright c 2015 for this paper by its authors. Copying permitted for private and academic purposes