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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.

Table of contents:

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

A. Onto-animal ontology software programs (see more: Ontozoo:http://www.hegroup.org/ontozoo):

We have several software programs that supports ontology development and applications. Many of these tools have the names of "Onto" followed by an animal name, resulting in a collection of "Onto-animal" tools. See more about the Onto-animal tools and other ontology tools, please visit the newly developed Ontozoo web page: http://www.hegroup.org/ontozoo.

Below is a quick summary of these Onto-animal tools.

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. (Reference: PMID: 20569493).
Ontodog: A web-based ontology community view generator. (Reference: PMID: 24413522).
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. (Reference: Xiang et al, 2012).

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. (Reference: Xiang et al., 2011).
Ontobat: An Ontology-based biodata analysis tool. Ontobat is a web-based Semantic Web tool to support ontology-based biological data query and analysis. As a use case, Ontobat includes a program called OntoCOG:, which is an ontology-based statistical tool for analysing the Clusters of Orthologous Groups of proteins (COG).

 

B. Ontology development:

1. Development of community-based ontologies primarily developed under the He Group:

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:

AEO 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. (Reference: PMID: 25093068).
BO 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. (Reference: PMID: 22041276).
CLO 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 got her PhD with ontology-focused research in 2012. Sira is still actively working on CLO update with international collaborations. (Reference: http://www.jbiomedsem.com/content/5/1/37/).
OGG Ontology of Genes and Genomes (OGG): A community-driven ontology of genes and genomes. (Reference: ICBO 2014 full length proceeding paper).
OGSF Ontology of Genetic Susceptibility Factors OGSF): A community-driven ontology of genetic susceptibility and genetic susceptibility factors. OGSF is primarily developed by Dr. "Asiyah" Yu Lin in the He Group. (Reference: PMID: 24963371).
INO 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. (References: JBMS INO paper; arXiv:1311.3355).
RoleO 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. (Reference: Nature Procedings 2009; PMID: 23256535; PMID: 21624163; PMID: 24209834) .

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. Selected papers in our ontology research:

Note: The ontology publication list here may not be most updated or complete, For the most updated and complete list, please check PubMed:

https://www.ncbi.nlm.nih.gov/pubmed/?term=yongqun+he%2C+ontology

~ Ontology Reuse (OntoFox and Ontodog), Display (Ontobee), or New Term Generation (Ontorat) Software ~

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]

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.

Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu008. [PDF] PMID: 24413522.

Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term 
dereferencing, linkage, query, and integration. Nucleic Acid Research. 2016 Oct 12. pii: gkw918. PMID: 27733503.

Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), July 28-30, 2011, Buffalo, NY, USA. Pages 279-281. URL: http://ceur-ws.org/Vol-833/paper48.pdf.

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]

~ Ontology-based Literature Mining ~

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.

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.

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. [Note: this paper also introduces our VO-SciMiner software]

Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Systems Biology. 2013, 7(Suppl 3):S9. doi:10.1186/1752-0509-7-S3-S9. (note: this paper was also presented in InCoB2013 and collected in F1000Posters; see the presentation slides) [Note: MeSH is considered as an ontology here]

~ 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. [Note: this paper is introduced above already]

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. [Note: this paper is introduced above already]

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. [Note: this paper is introduced above already]

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) [Note: this paper is introduced above already]

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 of Adverse Events (OAE) ~

Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29  doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.

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.

~ Ontology of Vaccine Adverse Events (OVAE) ~

Marcos E , Zhao B, He Y. The ontology of vaccine adverse events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. Journal of Biomedical Semantics. 2013 Nov 26;4(1):40. PMID: 24279920.

~ Interaction Network Ontology (INO) and Human INO (HINO) ~

Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. doi:10.1186/2041-1480-6-2.

He Y, Xiang Z. HINO: a BFO-aligned ontology representing human molecular interactions and pathways. arXiv. 2013. arXiv:1311.3355.

~ Ontology of Genes and Genomes (OGG) ~

He Y, Liu Y, Zhao B. OGG: a biological ontology for representing genes and genomes in specific organisms. Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Pages 13-20. [http://ceur-ws.org/Vol-1327/icbo2014_paper_23.pdf, or: https://ogg.googlecode.com/svn/trunk/docs/papers/ogg-icbo2014.pdf]

~ Ontology of Genetic Susceptibility Factors (OGSF) ~

Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19. PMID: 24963371. PMCID: PMC4068904.

~ Cell Line Ontology (CLO) ~

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. 2014, 5:37. doi:10.1186/2041-1480-5-37.

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.

~ 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 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).

~ Semanitc Web Applications ~

Y Zhang, C Tao, Y He, P Kanjamala, H Liu. Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. Accepted.

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.

 

D. Recent activities (since May 2012):

  • 10/6-9/2014: Oliver attended the ICBO 2014 conference in Houston, Texas.
  • 9/9/2014: Oliver He presented a talk on 9/9/2014 in the Computer Science Department of the Wayne State University. His talk title is: From Ontologies to an "OneNet" Theory for Representation and Analysis of Biological and Molecular Interaction Networks. In this talk, Oliver introduced ontologies and the OneNet theory. Check Here to see more information.
  • 9/27/2013: Oliver presented a talk in Soochow University. His talk title was "Development and applications of biomedical ontologies for data integration, data analysis, and literature mining". His talk was invited by Dr. Bairong Shen (沈百荣), Professor, Director, Center for Systems Biology, Soochow University, China. Dr. Shen was the local organizer of the InCoB2013 conference.
  • 7/8-9/2013: Oliver He and Asiyah Lin attended the 4th International Conference on Biomedical Ontologies (ICBO 2013), Montreal, Qc, Canada. July 7, 2013 . Oliver presented a poster presentation.
  • 7/7/2013: Oliver He and Asiyah Lin attended the Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)", International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . We presented two oral presentations.
  • 2/11-12/2013: Oliver He attended the CTSA Ontology Workshop in Orlando, FL. Oliver will present the Vaccine Ontology (VO) and the Ontology of Adverse Events (OAE) in the workshop. He will also introduce the ontology research in the Univerisity of Michigan.
  • 12/20/2012: A thematic series titled Vaccine and drug ontology in the study of mechanism and effect (VDOSME) was published in the Journal of Biomedical Semantics (JBMS). The thematic series and its associated VDOSME workshop were co-organized by Oliver. Oliver and his collaborators also presented talks and papers for the workshop and thematic series. Also, check a related BioMed Central blog.
  • 12/01/2012: Oliver He and two other professors (Alla Karnovsky and Marcelline Harris) in the University of Michigan obtained a MCubed project with a project title "Ontology Development and Applications for Clinical and Translational Science".
  • 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.

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

Please visit our detailed SVN tutorial page.

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

Please visit our detailed Git tutorial page.

 

F. He Group ontology team members:

The members in our group ontology team includes:

  • Edison Ong: M.S. bioinformatics student in UM.
  • Jiangan (Hardy) Xie: Hardy joined the He lab as a visiting PhD student on October 11, 2014. Hardy is a PhD student in the major of Computer Science from Chongqing University in China. He will stay in He lab for two full years for his PhD research.
  • Kevin Mo, UROP undergraduate student (Sept 2014 - April 2015)
  • Sydni S. Joubran, UROP undergraduate student (Sept 2014 - April 2015)
  • Natalie Dunn, LSA Undergraduate Student (starting October 2013 as aa voluteer; Credit course research Sept 2014 - April 2015)
  • Bin Zhao, Bioinformatician. Bin joined He lab as a bioinformatics research internal as a MS student in UM School of Information (May 2013 to May 2014) and then as bioinformatician from May 20014 to January 2015.
  • Asiyah Y u Lin, Research Fellow (Dec 2010 - Sept 2014)
  • Sirarat (Sira) Sarntivijai, PhD Candidate in Bioinformatics (graduated in spring 2012, then became a postdoc research fellow in Dr. Darrell R. Abernethy's laboratory at US FDA; and joined EBI since December 2014)
  • Becca Racz, Research Assistant (since Summer 2012). Becca volunteered as an undergraduate student in the lab from Feb 2011-May 2012; Becca is also a Pharmacy student since Fall 2012 in UM.
  • Joseph Ostrow, UROP undergraduate student (Sept 2012 - May 2013)
  • Desikan Jagannathan (DJ), UROP undergraduate student (Sept 2012 - May 2013)
  • Abra Guo, undergraduate student (Sept 2012 - May 2013)
  • Erica Marcos, undergraduate student (January to May 2013)
  • Shelley Zhang, undergraduate student (Sept 2012-May 2014)
  • Zuoshuang "Allen" Xiang, Bioinformatician (2005 - March 2013)
  • Yongqun "Oliver" He (PI), Associate 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.

Note: This website may not be regularly updated.

 

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