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.

A. Ontology software development:

	OntoFox: 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.
	Ontobee: A 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: 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).
	Ontodog: A web-based ontology view generator.
	Ontorat: Ontorat is a web server that automatically generates new ontology terms and axioms based on user-provided input file.

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.
	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. Key members in He Group ontology team:

The key members in our group ontology team includes:

• Asiyah Yu Lin, Research Fellow
• Sirarat (Sira) Sarntivijai, PhD Candidate in Bioinformatics
• 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, 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) ~

Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. Accepted.

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) ~

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)

~ 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.

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

Please visit our detailed tutorial.