Ontoden

Biomedical ontology development and applications form a major research focus in Dr. Oliver He's group. OntoDen is the web page that summarizes and integrates our ontology research activities.

News: 07/07/2013: The 2013 International workshop on Vaccine and Drug Ontology Studies (VDOS 2013) will be held on Montreal, Qc, Canada, on July 7, 2013. The deadline for submitting papers to the workshop is on April 22, 2013.

Table of contents:

1. Development of ontology-related software
2. Development of biomedical ontologies
3. Group members working on ontology research (with photos)
4. Ontology publications
5. Recent actvitites
6. Tutorial: check out ontology code using SVN: Go to: the section on this page, or directly to the Tutorial page.

A. Ontology software development:

We have several software programs that supports ontology development and applications. These tools are summarized in the following figure:

It is noted that most of our ontology tools use our Hegroup Resource Description Framework (RDF) triple store. The SPARQL endpoint of our triple store is:

http://sparql.hegroup.org/sparql/

Tools for development of new ontologies or ontology community views:

	OntoFox: An Ontology tool that Fetches ontology terms and axioms. OntoFox is a web-based system to support ontology reuse. OntoFox facilitates ontology development by automatically fetching ontology terms and their annotations from existing ontologies and saving the results in an importable RDF/OWL format.
	Ontodog: A web-based ontology community view generator.
	Ontorat: An ontology tool that supports Ontology representation of axioms using templates and design patterns. Ontorat is a web server that automatically generates new ontology terms and axioms based on user-provided input file.

Tools for applying ontologies to different purposes:

	Ontobee: A Linked Data Server that publishes RDF and HTML data simultaneously. The Ontobee web server aimed to facilitate ontology visualization, query, and development. OntoBee provides a user-friendly web interface for displaying the details and its hierarchy of a specific ontology term. Meanwhile, OntoBee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web.
	Ontobat: An Ontology-based biodata analysis tool. Ontobat is a web-based Semantic Web tool to support ontology-based biological data query and analysis.
	OntoCOG: An Ontology-based statistical tool for supporting analysis of Clusters of Orthologous Groups of proteins (COG).

B. Ontology development:

1. Development of community-based ontologies under Dr. Oliver He's leadership:

We are currently leading the development of many communited-based ontologies. These ontology development all follows the OBO Foundry principles and uses BFO as the upper level ontology:

	Ontology of Adverse Events (OAE): A community-based ontology targeting to represent adverse events for drugs, vaccines, and other biomedical reagents. Note: OAE was previously named AEO.
	Brucellosis Ontololgy (IDOBRU): Brucellosis Ontology is an extension of the Infectious Disease Ontology (IDO). It focuses on representation of brucellosis caused by facultative, Gram-negative bacterium Brucella.
	Cell Line Ontology (CLO): A community-based cell line ontology. The CLO development originated from the research done by Sirarat (Sira) Sarntivijai before she joined He Lab for PhD thesis research. Sira is actively working on CLO update with international collaborations.
	Interaction Network Ontology (INO): an ontology in the domain of interaction networks. INO develoment follows the OBO Foundry principles. INO can be used for automated reasoning such as literature mining and Bayesian network reasoning.
	Role Ontology (RoleO): A ontology of different roles (Note: this ontology has not been actively maintained and developed).
	Vaccine Ontology (VO): The VO project is a community-based project with an aim to develop the VO to ensure vaccine data standardization, exchange, and automated reasoning.

2. Active participation of other biomedical ontology development projects:

Oliver is an active member of the Ontology for Biomedical Investigations (OBI) consoritum. OBI is a community-based ontology targeting for biomedical investigations. Oliver represents the vaccine community in the OBI consortium.

Oliver and his lab members Asiyah Yu Lin and Allen Xiang are also active participants of the Infectious Disease Ontology (IDO) development. IDO is a community-based ontology targeting for different aspects of infectious diseases. We are developing the Brucellosis Ontology (BO), an extension of the IDO core.

C. He Group ontology team members:

From left to right: Joseph (Joe) Ostrow, Sirarat (Sira) Sarntivijai (now at FDA), Rebecca (Becca) Racz, Shelley Zhang, Oiver He, Abra Guo, Erica Marcos, Asiyah Yu Lin, and Desikan Jagannathan (DJ). Note: Taken on April 12, 2013 in Ann Arbor.

Asiyah (right), Allen (middle), and Oliver (left). Taken on Feb, 2013. .

The members in our group ontology team includes:

• Asiyah Yu Lin, Research Fellow
• Sirarat (Sira) Sarntivijai, PhD Candidate in Bioinformatics (graduated in spring 2012 and then became a postdoc research fellow in Dr. Darrell R. Abernethy's laboratory at US FDA)
• Becca Racz, Research Assistant
• Joseph Ostrow, UROP undergraduate student
• Desikan Jagannathan (DJ), UROP undergraduate student
• Abra Guo, undergraduate student
• Erica Marcos, undergraduate student
• Shelley Zhang, undergraduate student
• Zuoshuang "Allen" Xiang, Bioinformatician
• Yongqun "Oliver" He (PI), Assistant Professor of Laboratory Animal Medicine, Microbiology & Immunology, and Bioinformatics, University of Michigan Medical School

We also collaborate with many ontology experts and researchers in the world.

D. Selected papers in our ontology research:

~ Ontology Software Development ~

Xiang Z, Lin Y, He Y. Ontorat web server for automatic ontology term generation and annotations. International Conference on Biomedical Ontologies (ICBO 2012), University of Graz, Austria, July 2012. [One page abstract][Poster][Flash Talk]

Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Extended abstract.

Xiang Z, Lin Y, He Y. OntoFox and its Application in Development of Brucellosis Ontology. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Software Demonstration.

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. [PMID: 20569493]

~ Vaccine Ontology (VO) ~

Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of Biomedical Semantics. 2012, 3:17.

Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics. 2012, 3:18.

Tao C, He Y, Yang H, Gregory PA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. Journal of Biomedical Semantics. 2012, 3:13.

Racz R, Chung M, Xiang Z, and He Y. Systematic annotation and analysis of “virmugens” - virulence factors whose mutants can be used as live attenuated vaccines. Vaccine. Available online December 6, 2012. DOI: 10.1016/j.vaccine.2012.11.066. (NOTE: all virmugens are recorded in VO)

Sayers S, Ulysse G, Xiang Z, and He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. Journal of Biomedicine and Biotechnology. 2012;2012:831486. Epub 2012 Mar 13. PMID: 22505817. (NOTE: All vaccine adjuvants are recorded in VO)

Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 12(1):49 2011 Aug 26. PMID: 21871085.

Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163.

Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2010. In press [PMID: 20959289]. (NOTE: all protective antigens are recorded in VO)

He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Research. 2010 Sep 27;6 Suppl 1:S5. [PMID: 20875156]. (NOTE: All Brucella vaccines are recorded in VO)

Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. (Note: this proceeding paper is expanded and becomes a journal article, see above)

He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, Xiang Z, Chen F, Todd T, Colby L, Rush H, Whetzel T, Musen MA, Athey BD, Omenn GS, Smith B. VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO 2009), July 24-26, 2009. Buffalo, NY, USA; 2009. Nature Precedings: http://precedings.nature.com/documents/3553/version/1. (NOTE: This reference can be used for formal VO citation)

Link: Search "Vaccine Ontology" in Google Scholar.

~ Ontology for Biomedical Investigations (OBI) ~

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, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper, accepted. (NOTE: This paper also uses VO)

Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Turner J, Zheng J, the OBI consortium. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. [PMID: 20626927]

In alphabetic order: Brinkman RR, Courtot M, Derom D, Foste JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Jessica Turner J, Zheng J, and the OBI consortium. 2009. The modeling of biomedical experimental processes with OBI. Bio-Ontolgies Workshop (at ISMB 2009). Full length paper. (Note: this proceeding paper is expanded and becomes a journal article, see above).

~ Brucellosis Ontology (IDOBRU) ~

Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. [Epub ahead of print] PMID: 22041276.

~ Ontology of Adverse Events (OAE) ~

Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, and He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS ONE. 2012, 7(11): e49941. doi:10.1371/journal.pone.0049941.

He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Pages 309 - 315. (Note: AEO has been renamed OAE)

Tao C, He Y, Yang H, Gregory PA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. Journal of Biomedical Semantics. 2012, 3:13.

~ Cell Line Ontology (CLO) ~

Sarntivijai S, Xiang Z, Meehan TF, Diehl AD,Vempati U, Schurer S, Pang C, Malone J, Parkinson H, Athey BD, He Y. Cell Line Ontology: Redesigning Cell Line Knowledgebase to Aid Integrative Translational Informatics. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Pages 25 - 32.

~ Semanitc Web Applications ~

Lin Y, Xiang Z, He Y. Towards a Semantic Web application: Ontology-driven ortholog clustering analysis. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Page 33 - 40.

~ Editorials ~

He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). Journal of Biomedical Semantics 2012, 3:12.

Lin Y, He Y. New era of developing and using ontologies for microbiology research and diagnosis. Journal of Microbiology and Diagnosis. 2012. 1:e107. doi:10.4172/2161-0703.1000e107.

E. Recent activities (since May 2012):

• 7/21-25/2012: Oliver attended the ICBO2012 meeting. Oliver co-chaired the VDOSME 2012 workshop. Oliver chaired two sessions of the workshop and presented two talks in the workshop. Oliver also presented a flash talk about the workshop in the general meeting. Oliver also presented an Ontorat poster and a flash talk about the Ontorat poster in the general meeting. Besides these presentations, Oliver is also a co-author of two other papers/talks in the workshop and a co-author of an Ontodog poster presentation in the general meeting.
• 7/13-14: Junguk Hur attended the Bio-ontologies 2012 meeting in California and presented an ontology-based literature mining flash talk and a poster: http://www.bio-ontologies.org.uk/programme/day-2.
• 6/10-13/2012: Oliver and Asiyah from He Group will attend a workshop in Buffalo: Immunology Ontologies and Their Applications in Processing Clinical Data.
• 5/30-6/1/2012: Oliver and He lab ontology team hosted a Face-2-Face workshop of the Ontology of Biomedical Investigations (OBI) at Ann Arbor, MI.

F. How to check out a project from SVN repository:

Please visit our detailed tutorial.