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3 results on '"protein-interaction database"'

1. Finding melanoma drugs through a probabilistic knowledge graph

Author

Michel Dumontier, Deborah L. McGuinness, Rui Yan, James P. McCusker, Jonathan S. Dordick, and Sylvia He

Subjects
0301 basic medicine, General Computer Science, Systems biology, Computational biology, Bioinformatics, Uncertainty reasoning, lcsh:QA75.5-76.95, MALIGNANT-MELANOMA, 03 medical and health sciences, LUNG-CANCER, 0302 clinical medicine, Knowledge graphs, Medicine, Probabilistic analysis of algorithms, COMPREHENSIVE RESOURCE, CANCER-CELLS, Melanoma, GENE-EXPRESSION, PROTEIN-INTERACTION DATABASE, business.industry, Drug repositioning, Probabilistic logic, medicine.disease, APOPTOSIS, Clinical trial, METASTASES, 030104 developmental biology, DISCOVERY, 030220 oncology & carcinogenesis, Personalized medicine, lcsh:Electronic computers. Computer science, Skin cancer, User interface, business, PHASE-II TRIAL
Abstract

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates, however filtering criteria remain challenging, and systems biology approaches have become fragmented with many disconnected databases. Using drug, protein, and disease interactions, we built an evidence-weighted knowledge graph of integrated interactions. Our knowledge graph-based system, ReDrugS, can be used via an API or web interface, and has generated 25 high quality melanoma drug candidates. We show that probabilistic analysis of systems biology graphs increases drug candidate quality compared to non-probabilistic methods. Four of the 25 candidates are novel therapies, three of which have been tested with other cancers. All other candidates have current or completed clinical trials, or have been studied in in vivo or in vitro. This approach can be used to identify candidate therapies for use in research or personalized medicine.

Published
2016
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2. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Author

Pjotr Prins, Hammad Afzal, Kyung Hoon Kwon, Bruno Aranda, Toshihisa Takagi, Luke McCarthy, Fumikazu Konishi, Young Joo Kim, Toshiaki Katayama, James Taylor, Taro L. Saito, Shuichi Kawashima, Peter J. A. Cock, Kazuhiro Hayashi, Kozo Nishida, Keiichiro Ono, Venkata P. Satagopam, Richard Smith, Gos Micklem, Kazuki Oshita, Hideya Kawaji, Nobuhiro Kido, David Withers, Shinobu Okamoto, Pierre Lindenbaum, Keun Joon Park, Alberto Labarga, Tatsuya Nishizawa, Mark Wilkinson, Eli Kaminuma, Ryosuke Ishiwata, Andrea Splendiani, Hong-Woo Chun, Arek Kasprzyk, Soichi Ogishima, Kenta Oouchida, Kiyoshi Asai, Katsuhiko Murakami, Jerven Bolleman, Christian M. Zmasek, Jan Aerts, Raoul J. P. Bonnal, Erick Antezana, Mitsuteru Nakao, Naohisa Goto, Shoko Kawamoto, Yasunori Yamamoto, Chisato Yamasaki, Hideaki Sugawara, Atsuko Yamaguchi, Koji Nagao, Kosaku Okubo, Brad Chapman, Francois Belleau, Rutger A. Vos, Tore Eriksson, Paul M. K. Gordon, Yu Lin, Anna-Lena Lamprecht, Akira R. Kinjo, Heiko Horn, Yasumasa Shigemoto, Kunihiro Nishimura, Hideyuki Morita, Matthias Samwald, Kazuharu Arakawa, Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository

Subjects
services, representation, Computer Networks and Communications, Computer science, Interoperability, Interfaces, Health Informatics, Review, Ontology (information science), computer.software_genre, Semantic data model, World Wide Web, Databases, Data visualization, framework, ontology, Laboratorium voor Nematologie, Semantic Web, Web services, language, EPS-2, business.industry, systems biology, tool, bioinformatics, Open source, Data science, Computer Science Applications, networks, Middleware (distributed applications), BioHackathon, protein-interaction database, Data integration, Laboratory of Nematology, Web service, business, computer, Software, Information Systems
Abstract

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Published
2012
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3. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Author

Katayama, T., Wilkinson, D.W., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, T., Okamoto, S., Oouchida, K., Chung, H., Aerts, J., Afzal, H., Antezana, E., Arakawa, K., Aranda, B., Belleau, F., Bolleman, J., Bonnal, R.J.P., Chapman, B., Cock, P.J.A., Eriksson, T., Gordon, P.M.K., Goto, N., Hayashida, K., Horn, H., Ishiwata, R., Kaminuma, E., Kasprzyk, A., Kawaji, H., Kido, N., Kim, Y., Kinjo, A.R., Konishi, F., Kwon, K.H., Labarga, A., Lamprecht, A., Lin, Y., Lindenbaum, P., McCarthy, L., Morita, H., Murakami, K., Nagao, K., Nishida, K., Nishimura, K., Nishizawa, T., Ogishima, S., Ono, K., Oshita, K., Park, K., Prins, J.C.P., Saito, T., Samwald, M., Satagopam, V.P., Shigemoto, Y., Smith, R., Splendiani, A., Sugawara, H., Taylor, J., Vos, R.A., Withers, D., Yamasaki, C., Zmasek, C.M., Kawamoto, S., Okubo, K., Asai, K., Takagi, T., Katayama, T., Wilkinson, D.W., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, T., Okamoto, S., Oouchida, K., Chung, H., Aerts, J., Afzal, H., Antezana, E., Arakawa, K., Aranda, B., Belleau, F., Bolleman, J., Bonnal, R.J.P., Chapman, B., Cock, P.J.A., Eriksson, T., Gordon, P.M.K., Goto, N., Hayashida, K., Horn, H., Ishiwata, R., Kaminuma, E., Kasprzyk, A., Kawaji, H., Kido, N., Kim, Y., Kinjo, A.R., Konishi, F., Kwon, K.H., Labarga, A., Lamprecht, A., Lin, Y., Lindenbaum, P., McCarthy, L., Morita, H., Murakami, K., Nagao, K., Nishida, K., Nishimura, K., Nishizawa, T., Ogishima, S., Ono, K., Oshita, K., Park, K., Prins, J.C.P., Saito, T., Samwald, M., Satagopam, V.P., Shigemoto, Y., Smith, R., Splendiani, A., Sugawara, H., Taylor, J., Vos, R.A., Withers, D., Yamasaki, C., Zmasek, C.M., Kawamoto, S., Okubo, K., Asai, K., and Takagi, T.

Abstract

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. source provider, through middleware, to the end-consumer.

Published
2013

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