=Paper=
{{Paper
|id=Vol-1327/26
|storemode=property
|title=Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis
|pdfUrl=https://ceur-ws.org/Vol-1327/icbo2014_paper_58.pdf
|volume=Vol-1327
|dblpUrl=https://dblp.org/rec/conf/icbo/XiangLH14
}}
==Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis==
https://ceur-ws.org/Vol-1327/icbo2014_paper_58.pdf
ICBO 2014 Proceedings
Ontobat: An Ontology-based Semantic Web
Approach for Linked Data Processing and Analysis
Zuoshuang Xiang, Yu Lin, Yongqun He*
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and
Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Abstract — The Linked (Open) Data (LD/LOD) strategy extends (i.e., "dereferenced") by people and user agents [4]. Ontobee
the Web by publishing various open datasets as RDF links on the uniquely dereferences and presents ontology term URIs with a
Web. To support linked data query and analysis, we developed
user-friendly HTML web display while providing RDF source
Ontobat, a Semantic Web strategy for automatic generation of linked
data RDFs using ontology formats, data uploading to a RDF triple code for remote Semantic Web query by software applications
store, SPARQL query, browsing, and statistical data analysis. This [3]. To support LOD data dereferencing and query, Lodbee
report introduces the rationale, design, and preliminary adopts the Ontobee technology for representing instance data
implementation of the Ontobat system (http://ontobat.hegroup.org). stored in LOD RDF triple stores.
Keywords — Ontobat; ontology; Semantic Web; LOD Ontostat provides statistical analysis of RDF-based LOD
data, using open source software programs such as R-Sparql
I. INTRODUCTION (http://code.google.com/p/r-sparql/) which runs SPARQL
Ontologies are one of the major components of the queries inside R and stores the results as an R data frame.
Semantic Web and Linked Data movements. The Semantic
Ontovert: convert
Web enables machines to understand the meaning of Ontoload: upload data
instance data to RDF/
to RDF triple store
information on the Web. The Linked Open Data (LOD) XML format
community aims to extend the Web by publishing various
open datasets as Resource Description Framework (RDF) Lodquery: LOD data
links on the Web. These RDF links between data items can RDF triple stores SPARQL query
come from different data sources and be accessed anywhere run R Sparql
online [1]. Existing LOD data are primarily instance data.
Lodbee: LOD data Ontostat: LOD data
Ontologies provide classifications and relations among these display and RDF statistical analysis
instance data. source generation (e.g., meta-analysis)
To support LOD data query and analysis, we have started to
develop Ontobat (http://ontobat.hegroup.org), a web-based Fig. 1. Ontobat components and workflow design. The Ontobat will store
instance RDF data formatted based on OWL ontologies. The RDF data comes
biodata analysis tool that utilizes ontology-based Semantics from automatic data conversion and loading. The data can be visualized by
Web methods. Ontobat is developed to support LOD data Lodbee and queried by Lodquery. Statistical tools will be developed under
generation, upload, query, browsing, and statistical analysis. Ontostat. Statistical results can also be uploaded to a RDF triple store.
In Ontobat, all RDF/OWL-based LOD data are generated
based on reliable existing ontologies such as the OBO III. CURRENT ONTOBAT DEVELOPMENT
Foundry ontologies [2]. This report provides the first time Since the Ontobat system contains many components, we
introduction of the Ontobat system design and development. do not expect to develop all the programs simultaneously. Our
development strategy is to implement one program at a time
II. ONTOBAT SYSTEM DESIGN and later integrate all programs together.
Ontobat is designed to be an integrative system including Currently, a prototype Ontobat program called Ontovert
several components (Fig. 1): (http://ontobat.hegroup.org/ontovert/) has been developed
Ontovert supports efficient conversion of instance data (Fig. 2). The basic idea of Ontovert is to use the first row (or
from tab-delimited text or MS Excel format to an ontology header) to list ontology class term URIs, and use other rows to
format using the Web Ontology Language (OWL). represent data as instances of the class terms listed in the first
Ontoload loads instance data to RDF triple store. row. The Ontovert web page provides an example tab-limited
The RDF triple stores can be developed using different data extracted from a vaccine protection meta-analysis study
systems, such as the Open-Source Virtuoso platform as [5]. The first row of the tab-limited input data lists term IDs
implemented in our Hegroup RDF triple store [3]. from the Vaccine Ontology (VO) [6]. After the VO is selected
Lodquery provides RDF data query functions based on the and the data is provided, the Ontovert program generates an
SPARQL Protocol and RDF Query Language. A user-friendly OWL output file that specifies the instance data as named
web interface is usually required. individuals of the VO terms. The relations of the VO terms are
Lodbee supports the browsing and dereferencing of LOD specified in VO and can be retrieved using the tool OntoFox
data. The LOD movement requires the usage of URIs to [7]. The OntoFox feature is not yet implemented in Ontovert.
denote things and these URIs to be referred to and looked up
93
ICBO 2014 Proceedings
However, the Ontovert and OntoFox OWL output files can the ANOVA analysis feature can be implemented in the
then be merged to show the output results seen in Fig. 2. Ontostat program in Ontobat. The Ontology of Biological and
Clinical Statistics (OBCS) is a newly reported ontology that
aligns with OBI and supports semantic biostatistics analysis
[10]. Ontostat may use OBCS at the backend ontology for
enhanced statistical analysis.
While Ontobat is still under its early development stage, we
would like to demonstrate the Ontobat design strategy and
discuss the program design and implementation issues with
researchers at the ICBO-2014 conference.
ACKNOWLEDGMENT
As OntoFox input
This research was supported by NIH grant R01AI081062.
REFERENCES
OntoFox output
Merge two OWL files
[1] T. Berners-Lee. (2009). Design Issues: Linked Data.
Available: http://www.w3.org/DesignIssues/LinkedData
[2] B. Smith, M. Ashburner, C. Rosse, J. Bard, W. Bug, W.
Ceusters, et al., "The OBO Foundry: coordinated evolution of
ontologies to support biomedical data integration," Nat Biotechnol,
vol. 25, pp. 1251-5, Nov 2007.
[3] Z. Xiang, C. Mungall, A. Ruttenberg, and Y. He, "Ontobee:
A linked data server and browser for ontology terms," in The 2nd
VO_0001203
International Conference on Biomedical Ontologies (ICBO), Buffalo,
NY, USA, 2011, pp. Pages 279-281 [http://ceur-ws.org/Vol-
833/paper48.pdf].
Fig. 2. Ontovert example. The output shows “42” days, an instance data of [4] R. Lewis. (2007, Nov 13). Dereferencing HTTP URIs.
the VO class ‘vaccination-challenge interval in days’ (VO_0001203). See the
text for more explanation. Available: http://www.w3.org/2001/tag/doc/httpRange-14/2007-05-
31/HttpRange-14
A prototype Lodquery has also been established [5] T. E. Todd, O. Tibi, Y. Lin, S. Sayers, D. N. Bronner, Z.
(http://ontobat.hegroup.org/lodquery). The Lodquery uses the Xiang, et al., "Meta-analysis of variables affecting mouse protection
Hegroup RDF triple store [3] as the default triple store. The efficacy of whole organism Brucella vaccines and vaccine
other programs listed in Fig. 1 (e.g., Ontoquery and Ontostat) candidates," BMC Bioinformatics, vol. 14 Suppl 6, p. S3, 2013.
are still under development. [6] Y. He, L. Cowell, A. D. Diehl, H. L. Mobley, B. Peters, A.
To show the usage of Semantic Web in solving scientific Ruttenberg, et al., "VO: Vaccine Ontology," in The 1st International
questions in a specific domain, we have developed an Ontobat Conference on Biomedical Ontology (ICBO-2009), Buffalo, NY,,
program OntoCOG (http://ontobat.hegroup.org/ontocog) [8]. 2009, URL: http://precedings.nature.com/documents/3552/version/1.
OntoCOG demonstrates how we uses the Semantic Web [7] Z. Xiang, M. Courtot, R. R. Brinkman, A. Ruttenberg, and
approach to support statistical enrichment analysis of the Y. He, "OntoFox: web-based support for ontology reuse," BMC Res
Clusters of Orthologous Groups of proteins (COGs) [8]. Notes, vol. 3, p. 175, 2010.
[8] Y. Lin, Z. Xiang, and Y. He, "Towards a Semantic Web
IV. DISCUSSION application: Ontology-driven ortholog clustering analysis,"
Ontobat is an ontology-based Semantic Web system Proceedings of the second International Conference on Biomedical
primarily targeting for ontology-based instance data processing Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011, pp.
and analysis. The reliance on ontology for instance RDF data Pages 33 - 40. , 2011.
generation can be reflected in our Ontovert example (Fig. 2). [9] Y. He, Z. Xiang, T. Todd, M. Courtot, R. R. Brinkman, J.
The usage of reliable ontologies for RDF/OWL data generation Zheng, et al., "Ontology representation and ANOVA analysis of
provides a feasible way for data integration and sharing, and it vaccine protection investigation," in Bio-Ontologies 2010: Semantic
supports consistent and integrative data analysis. Applications in Life Sciences, Boston, MA, USA, 2010, pp. Pages 1-8
The Fig. 2 example was originated from a previous study [http://ceur-ws.org/Vol-754/he_krmed2010.pdf].
that modeled an Analysis of Variance (ANOVA) statistical [10] J. Zheng, M. R. Harris, A. M. Masci, Y. Lin, A. Hero, B.
analysis using the framework of the Ontology for Biomedical Smith, et al., "OBCS: The Ontology of Biological and Clinical
Investigations (OBI) [9]. To make Ontovert function more Statistics," in The 2014 International Conference on Biomedical
efficiently, the OntoFox feature as shown in the Fig. 2 use case Ontologies (ICBO 2014), Houston, TX, USA, 2014, pp. 1-6.
can be incorporated into the Ontovert program. Furthermore,
94
ICBO 2014 Proceedings
Ontobat: An Ontology-based Semantic Web Approach
Tel: (734) 615 8231
for Linked Data Processing and Analysis yongqunh@umich.edu
Zuoshuang “Allen” Xiang, Yu “Asiyah” Lin, and Yongqun “Oliver” He http://www.hegroup.org
University of Michigan Medical School, Ann Arbor, MI 48109, USA
Abstract Current Ontobat Development
The Linked (Open) Data (LD/LOD) strategy extends the Web by publishing Since the Ontobat system contains many components, we do not expect to
various open datasets as RDF links on the Web. To support linked data query develop all the programs simultaneously. Our development strategy is to
and analysis, we developed Ontobat, a Semantic Web strategy for automatic implement one program at a time and later integrate all programs together.
generation of linked data RDFs using ontology formats, data uploading to a RDF Currently, a prototype Ontobat program called Ontovert
triple store, SPARQL query, browsing, and statistical data analysis. This report (http://ontobat.hegroup.org/ontovert/) has been developed (Fig. 2). The basic idea
introduces the rationale, design, and preliminary implementation of the Ontobat of Ontovert is to use the first row (or header) to list ontology class term URIs, and
system (http://ontobat.hegroup.org). use other rows to represent data as instances of the class terms listed in the first
row. The Ontovert web page provides an example tab-limited data extracted from
a vaccine protection meta-analysis study [3].
Introduction A prototype Lodquery has also been established
(http://ontobat.hegroup.org/lodquery). The Lodquery uses the Hegroup RDF triple
Ontologies are one of the major components of the Semantic Web and Linked store [2] as the default triple store. The other programs listed in Fig. 1 (e.g.,
Data movements. The Semantic Web enables machines to understand the Ontoquery and Ontostat) are still under development.
meaning of information on the Web. The Linked Open Data (LOD) community To show the usage of Semantic Web in solving scientific questions in a specific
aims to extend the Web by publishing various open datasets as Resource domain, we have developed an Ontobat program OntoCOG
Description Framework (RDF) links on the Web. These RDF links between data (http://ontobat.hegroup.org/ontocog) [4]. OntoCOG demonstrates how we uses
items can come from different data sources and be accessed anywhere online the Semantic Web approach to support statistical enrichment analysis of the
[1]. Existing LOD data are primarily instance data. Ontologies provide Clusters of Orthologous Groups of proteins (COGs) [4].
classifications and relations among these instance data.
Fig. 2. An Ontovert example.
To support LOD data query and analysis, we have started to develop Ontobat The Ontovert output shows
(http://ontobat.hegroup.org), a web-based biodata analysis tool that utilizes “42” days, an instance data of
ontology-based Semantics Web methods. Ontobat is developed to support LOD the Vaccine Ontology (VO)
class ‘vaccination-challenge
data generation, upload, query, browsing, and statistical analysis. In Ontobat, all interval in days’ (VO_0001203).
RDF/OWL-based LOD data are generated based on reliable existing ontologies The first row of the tab-limited
such as the OBO Foundry ontologies. This report provides the first time input data lists term IDs from
introduction of the Ontobat system design and development. the VO [5]. After the VO is
As OntoFox input selected and the data is
provided, Ontovert generates
Ontobat System Design an OWL output file that
OntoFox output specifies the instance data as
Merge two OWL files named individuals of the VO
Ontobat is designed to be an integrative system with many components (Fig. 1): terms. The relations of the VO
• Ontovert supports efficient conversion of instance data from tab-delimited text terms are specified in VO and
or MS Excel format to an ontology format using the Web Ontology Language can be retrieved using the tool
OntoFox [6]. The OntoFox
(OWL). feature is not yet implemented
• Ontoload loads instance data to RDF triple store. in Ontovert. However, the
• The RDF triple stores can be developed using different systems, e.g., Open- Ontovert and OntoFox OWL
Source Virtuoso platform as implemented in our Hegroup RDF triple store [2]. VO_0001203
output files can then be merged
• Lodquery provides RDF data query functions based on the SPARQL Protocol to show the output results.
and RDF Query Language. A user-friendly web interface is usually required.
• Lodbee supports the browsing and dereferencing of LOD data. The LOD Discussion
movement requires the usage of URIs to denote things and these URIs to be
referred to and looked up (i.e., "dereferenced") by people and user agents. Ontobat is an ontology-based Semantic Web system primarily targeting for
Ontobee uniquely dereferences and presents ontology term URIs with a user- ontology-based instance data processing and analysis. The usage of reliable
friendly HTML web display while providing RDF source code for remote ontologies for RDF/OWL data generation provides a feasible way for data
Semantic Web query by software applications. To support LOD data integration and sharing, and it supports consistent and integrative data analysis.
dereferencing and query, Lodbee adopts the Ontobee technology for
The ANOVA analysis feature can be implemented in the Ontostat program in
representing instance data stored in LOD RDF triple stores.
Ontobat. The Ontology of Biological and Clinical Statistics (OBCS) is a newly
• Ontostat provides statistical analysis of RDF-based LOD data, using open
reported ontology that aligns with OBI and supports semantic biostatistics
source software programs such as R-Sparql (http://code.google.com/p/r-
analysis [7]. Ontostat may use OBCS at the backend ontology for enhanced
sparql/) which runs SPARQL queries inside R and stores the results as an R
statistical analysis.
data frame.
Acknowledgements
Ontovert: convert This work is supported by NIH-NIAID Grant 1R01AI081062 to YH.
Ontoload: upload data Fig. 1. Ontobat components and
instance data to RDF/
to RDF triple store workflow design. The Ontobat will References
XML format
store instance RDF data formatted
1. T. Berners-Lee. (2009). Design Issues: Linked Data. Available: http://www.w3.org/DesignIssues/LinkedData
based on OWL ontologies. The RDF 2. Z. Xiang, C. Mungall, A. Ruttenberg, and Y. He, "Ontobee: A linked data server and browser for ontology terms," in The 2nd International
Lodquery: LOD data data comes from automatic data Conference on Biomedical Ontologies (ICBO), Buffalo, NY, USA, 2011, pp. Pages 279-281 [http://ceur-ws.org/Vol-833/paper48.pdf].
3. He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN,
RDF triple stores SPARQL query conversion and loading. The data can Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies
be visualized by Lodbee and queried 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA.
run R Sparql 4. Y. Lin, Z. Xiang, and Y. He, "Towards a Semantic Web application: Ontology-driven ortholog clustering analysis," Proceedings of the
by Lodquery. Statistical tools will be second International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011, pp. Pages 33 - 40. , 2011.
Lodbee: LOD data Ontostat: LOD data developed under Ontostat. Statistical 5. Y. He, L. Cowell, A. D. Diehl, H. L. Mobley, B. Peters, A. Ruttenberg, et al., "VO: Vaccine Ontology," in The 1st International Conference on
Biomedical Ontology (ICBO-2009), Buffalo, NY,, 2009, URL: http://precedings.nature.com/documents/3552/version/1.
display and RDF statistical analysis results can also be uploaded to a RDF 6. Z. Xiang, M. Courtot, R. R. Brinkman, A. Ruttenberg, and Y. He, "OntoFox: web-based support for ontology reuse," BMC Res Notes, vol. 3,
source generation (e.g., meta-analysis)
triple store. 7.
p. 175, 2010.
J. Zheng, M. R. Harris, A. M. Masci, Y. Lin, A. Hero, B. Smith, et al., "OBCS: The Ontology of Biological and Clinical Statistics," in The
2014 International Conference on Biomedical Ontologies (ICBO 2014), Houston, TX, USA, 2014, pp. 1-6.
95