Many systems have been developed in the past few years to assist researchers in the discovery
of knowledge published as English text, for example in the PubMed database. At the same time,
higher level collective knowledge is often published using a
graphical notation representing all the entities in a pathway and their interactions.
We believe that these pathway visualizations could serve as an effective user
interface for knowledge discovery if they can be linked to the text in publications.
Since the graphical elements in a Pathway are of a very different nature to their
corresponding descriptions in English text, we have developed PathText to serve as a bridge between these two systems.
PathText is being developed to connect Natural Language Processing (NLP) technology
to the graphs and diagrams that are so often used by biologists.
The current prototype uses the Payao Web 2.0 community tagging system for
biological networks as a web based user interface to let the user quickly
find related text snippets and articles related to the different parts of the Pathway.
The Text Mining is done by the MEDIE, Facta and KLEIO systems.
MEDIE, Facta and KLEIO rely on many databases and other enabling technologies like
the Systems Biology Markup Language (SBML) (Hucka and et al., 2003), Graphical Notation (SBGN)
(Kitano et al., 2007) and the CellDesigner program (Funahashi et al., 2007)
which is used to show graphical models.
The PathText project is planned for release in the near future, but a public demonstration
is not yet on line. A video demonstration is available below which highlights the key
functionality and benefits of the project.
EKOSS
EKOSS (Engineering/Environmental Knowledge Ontology-based Semantic Search) has been developed for sharing expert knowledge using semantic web technologies. The website provides a collaborative knowledge sharing environment where knowledge experts can submit advertisements of the knowledge resources that they have developed, such as research papers, databases and computer simulation models. It then allows users to make requests for knowledge resources related to some condition or system problem that they are studying. The semantic search system matches user requests to knowledge resource advertisements using logical inference based on any domain ontology that is registered to the system.
Publications
Community Platform for Pathway Model Building.
Yukiko Matsuoka, Samik Ghosh, Norihiko Kikuchi, Rune Saetre, Brian Kemper, Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii, and Hiroaki Kitano. In Proceedings of the 10th International Conference on Systems Biology (ICSB 2009), pages 139-140, Stanford University, USA, September 2009. HTML
PathText/payao development: Text/pathway annotations
Rune Sætre, Brian Kemper, Kanae Oda, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Sophia Ananiadou, Jun'ichi Tsujii 9th International Conference on Systems Biology (ICSB), Abstract book
Gothenburg, Sweden, pp. 191-192, 22-28 August 2008. DS3-3-52
PDF (1.6mb)
Connecting Text Mining and Pathways using the PathText Resource
Rune Sætre, Brian Kemper, Kanae Oda, Naoaki Okazaki, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii Proceedings of the 2008 Language Resources and Evaluation Conference (LREC 2008) Marrakech, Morocco, May 2008
PDF (152kb)
PathText: Text Mining Tools Integrated with Biological Pathway
Rune Sætre, Brian Kemper, Kanae Oda, Naoaki Okazaki, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii Genomes to Systems Conference 2008 Handbook Manchester, UK, pp. 65, The Consortium for Post-Genome Science, 17-19 March 2008.
PDF (1.9mb)
'PAYAO': Web community tagging system to SBML models
Yukiko Matsuoka, Norihiro Kikuchi, Rune Sætre, Brian Kemper, Naoaki Okazaki, Haruka Sugimura, Akemi Hayama, Sophia Ananiadou, Jun'ichi Tsujii, Hiroaki Kitano Genomes to Systems Conference 2008 Handbook Manchester, UK, pp. 91, The Consortium for Post-Genome Science, 17-19 March 2008.
PDF (1.4mb)
EKOSS: A Knowledge-User Centered Approach to Knowledge Sharing, Discovery, and Integration on the Semantic Web
Steven Kraines, Weisen Guo, Brian Kemper, Yutaka Nakamura International Semantic Web Conference Athens, GA, USA, November 5-9, 2006, LNCS 4273
PDF (1.9mb)
A semantic web application for expert knowledge sharing, discovery, and integration.
Kraines S. B., W. Guo, B. E. Kemper, and Y. Nakamura. 2006. Proceedings of the 2006 International Semantic Web Conference.
Semantic searching based on ontologies and agent systems for knowledge discovery.
Kraines S.B., R. Batres, B. Kemper, M. Koyama, V. Wolowski. 2006. Journal of Industrial Ecology 10(4): 37-60.
Related Work
Systems Biology Graphical Notation (SBGN) Super-Hackathon "standards and ontologies for Systems Biology"
January 27, 2008 Conference Website