=Paper=
{{Paper
|id=Vol-1747/D201_ICBO2016
|storemode=property
|title=Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion
|pdfUrl=https://ceur-ws.org/Vol-1747/D201_ICBO2016.pdf
|volume=Vol-1747
|authors=Edison Ong,Zuoshuang Xiang,Jie Zheng,Barry Smith,Yongqun He
|dblpUrl=https://dblp.org/rec/conf/icbo/OngXZSH16
}}
==Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion ==
https://ceur-ws.org/Vol-1747/D201_ICBO2016.pdf
Ontobull and BFOConvert: Web-based programs to support
automatic ontology conversion
Edison Ong1, Zuoshuang Xiang1, Jie Zheng2, Barry Smith3, Yongqun He1*
1
University of Michigan, Ann Arbor, Michigan, USA; 2 University of Pennsylvania, Philadelphia, PA, USA; 3 University at
Buffalo, Buffalo, NY, USA.
ABSTRACT previously developed the BFOConvert software. In light of
When a widely reused ontology appears in a new version which is not the fact that the IRI conversion issue exists also in other
compatible with older versions, the ontologies reusing it need to be updated
accordingly. Ontobull (http://ontobull.hegroup.org) has been developed to
cases, we have now expanded the BFOConvert program to
automatically update ontologies with new term IRI(s) and associated create Ontobull, a program with greater flexibility and a
metadata to take account of such version changes. To use the Ontobull web more user-friendly web interface.
interface a user is required to (i) upload one or more ontology OWL source
files; (ii) input an ontology term IRI mapping; and (where needed) (iii) In addition to ontology version updating, Ontobull can
provide update settings for ontology headers and XML namespace IDs. be used for other purposes, including term IRI updating and
Using this information, the backend Ontobull Java program automatically updating of ontology metadata such as ontology header
updates the OWL ontology files with desired term IRIs and ontology (e.g., owl:imports) and XML namespaces (xmlns) informa-
metadata. The Ontobull subprogram BFOConvert supports the conversion
of an ontology that imports a previous version of BFO. A use case is pro- tion (https://www.w3.org/TR/owl-guide/). The owl:imports
vided to demonstrate the features of Ontobull and BFOConvert. attribute in ontology header specifies an OWL file to import
into current ontology. The xmlns attribute qualifies element
1 INTRODUCTION and attribute names of the ontology.
Biological ontologies are sets of computer- and human- In this software demonstration, we will introduce the
interpretable terms and relations that represent entities in the tool design and use cases of Ontobull and BFOConvert.
biological world and how they relate to each other.
Hundreds of ontologies have been developed. Over 150 2 ONTOBULL SOFTWARE DESIGN
biomedical ontologies have been developed following the
The Ontobull web program provides a user-friendly
Open Biological and Biomedical Ontologies (OBO)
interface for input of an ontology file and conversion
Foundry principles [1]. NCBO BioPortal [2] currently
settings. The Ontobull Java program, developed using the
comprises more than 400 ontologies including both OBO
Spring Model-view-controller (MVC) framework and
and non-OBO ontologies.
Thymeleaf template engine, processes the user’s requests
The Basic Formal Ontology (BFO) [1, 3] has been used and generates an Ontobull OWL output file. The
as the top ontology by some 175 other ontologies BFOConvert program is a subprogram of Ontobull
(http://ifomis.uni-saarland.de/bfo/users), with the goal of specifically targeting conversions involving a move from
facilitating interoperability among these ontologies. In addi- use of BFO 1.1 to BFO 2.0.
tion to BFO, other OBO Foundry ontologies use relations \
defined in the OBO Relation Ontology (RO)
(https://github.com/oborel/obo-relations). For example, the
information Artifact Ontology (IAO) and the Ontology for
Biomedical Investigations (OBI) [4] both import BFO and
RO.
One challenge in reusing external ontologies is that
once the reused source ontology is updated with modified
IRIs, it is difficult to update the target ontologies. Although
these reference ontologies are designed to be maximally
stable, they do sometimes still undergo major changes. For
example, BFO 1.0 and 1.1 do not follow OBO Foundry ID
policy (http://obofoundry.org/id-policy.html). As a result,
BFO has been updated from BFO 1.0/1.1 to 2.0. To support
automatic conversion of ontologies aligned with BFO, we
Fig. 1. Ontobull web interface. The circled settings are used in
the use case demonstration described next.
* To whom correspondence should be addressed: yongqunh@umich.edu
1
Ong et al.
3 ONTOBULL WEB INTERFACE Ontobull can also be used to integrate multiple OWL
The use of the Ontobull web interface (Fig. 1) involves three files. The OWL ontology files may have different IRIs re-
steps: ferring to the same entities. For integration, we need to re-
Upload an ontology source file: An OWL file or a zip place these different IRIs with common ones across all sali-
file including an OWL file(s) can be selected and uploaded. ent files. For example, the OWL representation of Beta cell
The zip file format is typically used when an ontology in- genomics data (http://www.betacell.org/gbco/) integrates
cludes many unmerged OWL files. In this case, Ontobull information from two resources that include terms assigned
can automatically process all the OWL files in succession. with different IRIs. Ontobull was used to update IRIs to
Define ontology term IRI mapping: The user is required enable this integration.
to provide at least one pair consisting of an original ontolo-
gy term IRI and a new IRI that will be used to replace it. 5 BFOCONVERT SUBPROGRAM
Multiple mapping pairs can be specified using the dynamic The BFOConvert subprogram is now available at:
web user-interface. Alternatively, a user can choose a file http://ontobull.hegroup.org/bfoconvert. It provides a pre-
that includes all the IRI mapping pairs organized in a simple designed mapping file according to the current stage of
tab-delimited format. BFO/RO development.
Provide an ontology header and XML namespace
updating setting (optional): This setting is used to remove, 6 SOURCE CODE AND LICENSE
add, or replace xmlns or owl:imports contents in the OWL The Ontobull source code is openly available at:
output file. https://github.com/OntoZoo/Ontobull. The Ontobull source
Use cases are shown in what follows. code license is Apache License 2.0.
4 ONTOBULL USE CASE DEMONSTRATION 7 SUMMARY
Fig. 2 illustrates how Ontobull is used to convert the With ever increasing needs for ontology updating, the web-
Parasite Life Cycle ontology (OPL) which uses terms from based Ontobull and BFOConvert programs provide a timely
the Relation Ontology from an old version to a new version. platform for automatic ontology conversion.
OPL is an ontology designed to provide a consistent
representation of lifecycle stages in parasitic organisms [5]. ACKNOWLEDGEMENTS
The “OPL.owl” highlighted in the first circle in Fig. 1,
This research is supported by an NIH R01 grant
above, represents the OWL file of the original version of
(1R01AI081062). We acknowledge the assistance of James
this ontology. The second highlighted circle in Fig. 1
A. Overton and Alan Ruttenberg in the development of
represents the setting for an IRI mapping. Fig. 2A represents
BFOConvert.
the results of the conversion of the IRI for the RO
expression ‘part of ’. The third highlighted circle in Fig. 1
represents one header cleanup option, illustrated in Fig. 2B. REFERENCES
[1] B. Smith, M. Ashburner, C. Rosse, J. Bard, W. Bug, et al.,
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