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| Overview
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CRAB is a collaborative project between
It has been funded by
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Project Description
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The amount of scientific evidence showing a strong link between environmental chemicals and cancer calls for
urgent efforts to issue exposure limits on the use of harmful chemicals. The critical tool used in making
decisions on exposure limits is Cancer Risk Assessment (CRA). CRA involves examining existing published
evidence to determine the relationship between exposure to a substance and the likelihood of developing cancer
from that exposure. Performed manually, it is a costly and challenging task which requires combining scientific
expertise with elaborate literature search and review. Given the exponentially growing volume of articles under
inspection, it is gradually getting too challenging to manage via manual means.
CRAB investigates a novel approach to cancer RA which could greatly assist risk assessors with the management
of large textual data, increase their productivity, and aid knowledge discovery. This approach is based on
Text Mining (TM) - a growing field of computer science which discovers new knowledge by automatically
extracting information from written texts. We develop TM technology for the needs of CRA with the
aim to integrate this technology in a practical tool which can risk assessors in their work and contribute
to effective management of health risks in the future.
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Publications
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Yufan Guo, Anna Korhonen, Ilona Silins and Ulla Stenius. 2011. Weakly-supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine? Bioinformatics 2011; doi: 10.1093/bioinformatics/btr536.
LINK
Yufan Guo, Anna Korhonen, Maria Liakata, Ilona Silins, Johan Hogberg and Ulla Stenius. 2011. A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment. BMC Bioinformatics 2011, 12:69.
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Yufan Guo, Anna Korhonen, Maria Liakata, Ilona Silins, Lin Sun and Ulla Stenius. 2010. Identifying the Information Structure of Scientific Abstracts: An Investigation of Three Different Schemes. In
Proceedings of the BioNLP 2010. Uppsala, Sweden.
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Anna Korhonen, Lin Sun, Ilona Silins, and Ulla Stenius. 2009.
The First Step in the Development of Text
Mining Technology for Cancer Risk Assessment: Identifying and Organizing
Scientific Evidence in Risk Assessment Literature.
In BMC Bioinformatics 10:303.
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Lin Sun, Anna Korhonen, Ilona Silins, and Ulla Stenius. 2009.
User-Driven Development of Text Mining Resources for
Cancer Risk Assessment. In Proceedings of the BioNLP 2009. Boulder, Colorado.
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Ian Lewin, Ilona Silins, Anna Korhonen, Johan Hogberg, and Ulla Stenius. 2008. A New Challenge for Text Mining: Cancer Risk Assessment.
In
Proceedings of the ISMB BioLINK Special Interest Group on Text Data Mining. Toronto, Canada.
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Conference Presentations and Posters
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Sandeep Kadekar, Ilona Silins, Anna Korhonen, Johan Hogberg, Kristian Dreij, and Ulla Stenius. 2010.
Carcinogen-induced inflammation and pancreatic cancer.
101th Annual Meeting of the American Association for Cancer Research. Washington D.C.
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Ilona Silins, Anna Korhonen, Johan Hogberg, Lin Sun, and Ulla Stenius. 2009.
Improved Cancer Risk Assessment Using Text Mining.
Proceedings of the 100th Annual Meeting of the American Association for Cancer Research. Denver, Colorado.
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Emma Westerholm, Jordi Boix, Hanna Miettinen, Robert Roos, Elsa
Antunes-Fernandes, Remco Westerink, Majorie van Duursen, Mia Stenberg,
Sara Carreira, Miroslav Machala, Ilona Silins, Ulla Stenius, Krister
Halldin, Annika Hanberg, and Helen Hakansson. 2009.
ATHON NDL-PCB effect database - a tool to facilitate the cumulative risk assessment of NDL-PCBs.
In Toxicology Letters, Volume 189, Supplement 1, 13 September 2009.
Abstracts of the 46th Congress of the European Societies of Toxicology.
Anna Korhonen, Ian Lewin, Ilona Silins, Johan Hogberg, and Ulla Stenius. 2008.
CRAB - Cancer Risk Assessment and Biomedical Text Mining .
European Conference on Computational Biology. Sardinia, Italy.
See the ECCB08 website
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| Contact
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Cambridge CB3 OFD
United Kingdom
Anna Korhonen: alk23 at cl.cam.ac.uk
Lin Sun: lin.sun at cl.cam.ac.uk
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Ulla Stenius: ulla.stenius at ki.se
Johan Hogberg: johan.hogberg at ki.se
Ilona Silins: Ilona.Silins at ki.se
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