Yuan-Fang Li's Homepage



I’m a senior lecturer at Clayton School of Information Technology, Faculty of IT, Monash University. I'm a member of the Monash Adaptive Visualisation Lab (MArVL). You can find me in Room 121, Building 63 on the Clayton Campus.

Contact info:


Feel free to explore

Phone: +61 3 9905 9688
Fax: +61 3 9905 5400
Email: yuanfang.li AT monash.edu
RDF: foaf.rdf

Research interests

  1. The Semantic Web, ontology languages (DAML+OIL, OWL, RDF/RDFS, SWRL), SPARQL query answering and reasoning

  2. Information visualisation

  3. Data management for bioinformatics research

  4. Software requirements analysis, software complexity

  5. Formal design methods (Alloy, Z, PVS)

  6. Real-time concurrent systems (TCOZ)

  7. XML environment for formal languages (CZT)

Education & Awards


  1. Ph.D. in Computer Science

          School of Computing (SoC), National University of Singapore (NUS), Dec 2006.

          Advisor: A/P Jin Song Dong.

  1. Bachelor of Computing (honours)

          SoC, NUS, Jun 2002.

  1. Bachelor of Engineering (honours)

          Tsinghua University, China, 1997.


  1. The inaugural University of Queensland Confucius Institute Visiting Fellowship

          Tianjin University, China Sep - Nov 2010.

  1. President’s Graduate Fellowship Scholarship

          NUS, 2005 - 2006.

  1. Singapore Millennium Foundation Scholarship (SMF)

          Singapore, 2004 - 2006.

  1. Ministry of Education of Singapore Scholarship

          Singapore, 1997 - 2002.


  1. 25th Marktoberdorf Summer School on Engineering Theories of Software Intensive Systems

          NATO Science Committee, Marktoberdorf, Germany, Aug 2004.


  1. Faculty Honours, Minor Thesis Coordinator, 2015-2016.

  2. FIT3013 - Formal specification for software engineering, Semester 2, 2011-2016.

  3. FIT4002 - Software engineering studio projects, 2013.

  4. FIT4004/FIT5171 - System validation and verification, quality and standards, Semester 1, 2011, 2012, 2013.

  5. FIT2001 - Systems development, Semester 1, 2012.


  1. Skeletome - A Curated Online Knowledge Base for Integrating Clinical and Biological Information - Co-CI, ARC Linkage, 2010 - 2012.

  2. Skeletome is a Semantic Web-enabled knowledge base for skeletal dysplasias; it aims at utilising novel Semantic Web and Web 2.0 technologies to create a community-driven, expert-curated semantic knowledge base that supports semantic content annotation, aggregation and visualisation.

  3. PODD - Phenomics Ontology Driven Data repository - Lead Developer, NeAT, 2009 - 2011.

  4. Co-funded by Australian National Data Service (ANDS) and Australian Research Collaboration Service (ARCS) under the National e-Research Architecture Taskforce (NeAT), the PODD (Phenomics Ontology Driven Database) project. PODD is a multi-disciplinary, collaborative, open-source project aimed at developing a state-of-the-art online data repository to meet the data management needs of the Australian phenomics research community. Being world’s first ontology-driven data repository, PODD is designed to be more extensible, flexible and open, enabling effective data storage, contextualisation, sharing, management and publishing of raw data. Responsibilities include (1) overall ontology-driven system architecture modelling and design; (2) developing the PODD ontology in the OWL ontology language; and (3) leading all aspects of the software development activities, including the development of the entire backend system.

  1. BioMANTA - Modelling and Analysis of Biological Network Activity, Researcher/developer, Pfizer, 2007 - 2009.

  2. The BioMANTA project focusses on the computational modelling and analysis, primarily using Semantic Web technologies, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, sub-cellular localisation and disease state attributes is included in the resulting data model. Semantic Web technologies allow for flexible data integration, inherent inferencing capabilities and advanced machine learning methods. The BioMANTA project aims to bring together these areas through the modelling of PPI data in a semantic web framework, using technologies such as RDF and OWL, and then to apply in silico and experimental analysis methods to analyse aspects of the BioMANTA data model.

Selected publications (see this page for full list of publications)

  1. I. Guclu, Y.-F. Li, J. Z. Pan, and M. J. Kollingbaum, Predicting Energy Consumption of Ontology Reasoning over Mobile Devices, In Proceedings of 15th International Semantic Web Conference (ISWC-16), 2016 (accepted). [pdf]

  2. C. Gavankar, Y.-F. Li, and G. Ramakrishnan, Explicit Query Interpretation and Diversification for Context-driven Concept Search across Ontologies, In Proceedings of 15th International Semantic Web Conference (ISWC-16), 2016 (accepted). [dataset+pdf]

  3. N. Chmait, D. Dowe, Y.-F. Li, D. Green, and J. Insa-Cabrera, Factors of Collective Intelligence: How Smart Are Agent Collectives?, In Proceedings of 22nd European Conference on Artificial Intelligence (ECAI-16), 2016 (accepted). [pdf]

  4. A. Sadiq, Y.-F. Li, S. Ling, and I. Ahmad, Extracting Permission-based Specifications from a Sequential Java Program, In Proceedings of 21st International Conference on Engineering of Complex Computer Systems (ICECCS 2016), 2016 (accepted). [pdf]

  5. Y.-B. Kang, S. Krishnaswamy and Y.-F. Li, R2O2: an Efficient Ranking-based Reasoner for OWL Ontologies, In Proceedings of 14th International Semantic Web Conference (ISWC-15), 2015. [html+pdf]

  6. Y.-B. Kang, Y.-F. Li and R. L. Coppel, Capturing Researcher Expertise through MeSH Classification, In Proceedings of 8th International Conference on Knowledge Capture (K-CAP-15), 2015. [pdf]

  7. J. S. Dong, Y. Feng, Y.-F. Li, C. K.-Y. Tan, B. Wadhwa, and H. H Wang, BOWL: augmenting the Semantic Web with beliefs, In Innovations in Systems and Software Engineering, a NASA Journal, 2015. [html]

  8. J. Z. Pan, S. Krishnaswamy, Y.-F. Li, and M. Hauswirth (editors), Special Issue on the Ubiquitous Semantic Web, In International Journal on Semantic Web and Information Systems (IJSWIS), 10(4), 2014. [html+pdf]

  9. Y.-F. Li, J. Z. Pan, S. Krishnaswamy, M. Hauswirth, and H. H. Nguyen, The Ubiquitous Semantic Web: Promises, Progress and Challenges, In International Journal on Semantic Web and Information Systems (IJSWIS), 10(4), 2014. [html]

  10. N. Chmait, D. Dowe, D. Green, and Y.-F. Li, Observation, Communication and Intelligence in Agent-Based Systems, In Proceedings of the eighth annual conference on Artificial General Intelligence AGI-15, 2015. [pdf]

  11. Y.-B. Kang, J. Z. Pan, S. Krishnaswamy, W. Sawangphol and Y.-F. Li, How Long Will It Take? Accurate Prediction of Ontology Reasoning Performance, In Proceedings of AAAI-14, 2014. [pdf+html]

  12. Y.-F. Li, P. Das and D. L. Dowe, Two Decades of Web Application Testing—A Survey of Recent Advances, In Information Systems, 2014.

  13. C. Gavankar, V. Kumar, Y.-F. Li, and G. Ramakrishnan, Enriching Concept Search across Semantic Web Ontologies , In Proceedings of 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, October 21-25, 2013.

  14. S. Krishnaswamy and Y.-F. Li, The Mobile Semantic Web (tutorial) , In Proceedings of 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, October 21-25, 2013.

  15. Z. Jiao, Q, Liu, Y.-F. Li, K. Marriott, M. Wybrow, Visualization of Large Ontologies with Landmarks , In Proceedings of 4th International Conference on Information Visualization Theory and Applications (IVAPP 2013), Barcelona, Spain, February 21-24, 2013. [pdf]

  16. Y.-B. Kang, Y.-F. Li, S. Krishnashiwamy, Predicting Reasoning Performance Using Ontology Metrics , In Proceedings of 11th International Semantic Web Conference (ISWC2012), Boston, USA, November 11-15, 2012. [html]

  17. Y.-B. Kang, Y.-F. Li, S. Krishnashiwamy, A Rigorous Characterization of Classification Performance - A Tale of Four Reasoners , In OWL Reasoner Evaluation Workshop (ORE 2012), Collocated with 6th International Joint Conference on Automated Reasoning (IJCAR 2012), Manchester, UK, June 26 - July 1, 2012. [pdf]

  18. S. Krishnashiwamy, Y.-F. Li, Semantic Mobile Web (Tutorial), In Proceedings of the Joint Semantic Technology Conference, (JIST 2011) , Springer, Hangzhou, China, December 4-7, 2011. [html]

  19. T. Groza, A. Zankl, Y.-F. Li, J. Hunter, Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain, In Proceedings of the 10th International Semantic Web Conference (ISWC 2011), Semantic Web In-Use track, Springer, Bonn, Germany, Octorer 23-27 , 2011. [pdf]

  20. Y.-F. Li, G. Kennedy, F. Ngoran, P. Wu, J. Hunter, An Ontology-centric Architecture for Extensible Scientific Data Management Systems, In Future Generation Computer Systems, 29(2):641–653, Elsevier, 2013. [pdf+html]

  21. Y.-F. Li, H. Zhang, Integrating Software Engineering Data Using Semantic Web Technologies, In Proceedings of 8th Working Conference on Mining Software Repositories (MSR 2011), ACM Press, Honululu, Hawaii, May 21-22, 2011.

  22. Y.-F. Li, G. Kennedy, F. Davies, J. Hunter, PODD - Towards An Extensible, Domain-agnostic Scientific Data Management System, In Proceedings of 6th IEEE e–Science conference (eScience 2010), Brisbane, Australia, December 8 - 10, 2010. [pdf]

  23. H. Zhang, Y.-F. Li and H. B. K. Tan, Measuring Design Complexity of Semantic Web Ontologies, In Journal of Systems and Software, 83(5):803-814. [pdf+html]

  24. A. Newman, Y.-F. Li, and J. Hunter, Scalable Semantics - the Silver Lining of Cloud Computing, In 4th IEEE International Conference on e-Science (e-Science) 2008. Indianapolis, USA, December 7-12, 2008. [pdf]

  25. S. Ferndriger, A. Bernstein, J. S. Dong, Y. Z. Feng, Y.-F. Li and J. Hunter. Enhancing Semantic Web Services with Inheritance, In Proceedings of the 7th International Semantic Web conference (ISWC'08), Karlsruhe, Germany, 2008. [bib+pdf+abstract]

  26. H. H. Wang, J. S. Dong, J. Sun, T. Payne, N. Gibbins, Y.-F. Li, and J. Pan. An Integrated Formal Approach to Semantic Work Environments Design, chapter of Emerging Technologies for Semantic Work Environments: Techniques, Methods,and Applications, IGI Publishing, 2007.

  27. H. H. Wang, Y.-F. Li, J. Sun, H. Zhang and J. Pan. Verifying Feature Models Using OWL. In Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 5(2):117-129, June 2007. [pdf+abstract]

  28. Y. Feng, Y.-F. Li, C. K-Y. Tan and B. Wadhwa. Belief-augmented OWL (BOWL) - Engineering the Semantic Web with Beliefs. In 12th IEEE International Conference on Engineering of Complex Systems (ICECCS'07), Auckland, New Zealand, July 11-14, 2007. [bib+abstract]

  29. D. Lucanu, Y.-F. Li, J. S. Dong. Semantic Web Languages - Towards an Institutional Perspective. In Algebra, Meaning, and Computation: A Festschrift in Honor of Prof. Joseph Goguen, Eds. Futatsugi, Jouannaud, and Meseguer, pages 99-123, 2006. LNCS 4060, Springer-Verlag. [bib+pdf+abstract]

  30. H. Wang, Y.-F. Li, J. Sun, H. Zhang and J. Pan. A Semantic Web Approach to Feature Modeling and Verification. In Workshop on Semantic Web Enabled Software Engineering (SWESE'05), Galway, Ireland, November 2005. [bib+abstract]

  31. J. Sun, H. Zhang, Y.-F. Li and H. Wang. Formal Semantics and Verification for Feature Modeling. In 10th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS'05), IEEE Press, Shanghai, China, Jun 2005 [bib+pdf+abstract+html]

  32. J. S. Dong, C. H. Lee, H. B. Lee, Y.-F. Li and H. Wang. A Combined Approach to Checking Web Ontologies. In 13th ACM International World Wide Web Conference (WWW'04), pages 714-722, ACM Press, New York, USA, May 2004. [bib+pdf+html+abstract]

  33. J. S. Dong, C. H. Lee, Y.-F. Li and H. Wang. Verifying DAML+OIL and Beyond in Z/EVES. In 26th International Conference on Software Engineering (ICSE'04), pages 201-210, ACM/IEEE Press, Edinburgh, Scotland, UK, May 2004. [bib+pdf+abstract]

PhD Supervision

  1. Wudhichart Sawangphol: Optimising inference algorithms for expressive description logics.

  2. Nader Chmait: Anytime universal intelligence test.

  3. Steve Quenette: Software product line engineering for computational science applications on high performance computers.

  4. Chetana Gavankar (IITB-Monash Academy): Ontology population and enriching search across ontologies: methodologies and challenges.

  5. Bharath Muthukumar (IITB-Monash Academy): Process reconcilation from logs, messages and local views.

  6. Vishwajeet Kumar (IITB-Monash Academy): Speeding up complex analytics and natural language processing tasks using the inverted index.

  7. Ayesha Sadiq: Specification and verification of real time applications using formal methods.

  8. Ying Yang: Immersive visualizations of large biomedical ontologies.

Funding support

  1. K. Marriott, T. Dwyer, M. Wybrow, Y.-F. Li and F. Schreiber. Visualisation of large, complex networks through small, beautiful diagrams. ARC Disovery Projects 2014, $687,000.

  2. J. Hunter, A. Zankel and Y.-F. Li. Skeletome - A Curated Online Knowledge Base Integrating Clinical and Biological Information on Skeletal Dysplasias. ARC Linkage Projects 2010, $273,000.

Professional activities

  1. Program co-chair

  2. 20th International Conference on Engineering of Complex Computer Systems (ICECCS 2015)

  3. ACM/IEEE International Joint Conference on Digital Libraries 2010 (JCDL 2010)

  4. PC member

  5. International Conference on Asian Digital Libraries 2010 (ICADL 2010).

  6. The First International Conference on Computational Logics, Algebras, Programming, Tools, and Benchmarking (Computation Tool 2010)

  7. First International Workshop on Model Checking Secure and Reliable Systems (MoCSeRs 2010).

  8. Local organising committee member

  9. ISWC 2013.

  10. JCDL 2010  & ICADL 2010.

  11. Journal Reviewer

  12. Advances in Software Engineering (ASE)

  13. IEEE Transactions on Software Engineering (TSE)

  14. International Journal on Knowledge and Information Systems (KAIS)

  15. Journal of Software (JSW)

  16. Science of Computer Programming (SCP)

  17. Conference Reviewer



  1. The Monash Adaptive Visualisation Lab (MArVL) at Faculty of IT, Monash University

  2. Prof. Jane Hunter at School of ITEE, the University of Queensland

  3. The eResearch group, the University of Queensland

  4. My Ph.D. supervisor, A/P Dong Jin Song, SoC, NUS

  5. Jing Sun, The University of Auckland, New Zealand

  6. Hai H. Wang, Aston University, UK

  7. Jun Sun, Singapore University of Technology and Design

  8. Hongyu Zhang, Tsinghua University

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