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Cytometry Development Workshop
Lab Research Topics
SLIF - Subcellular Location Image Finder
and Departments of Biological Sciences, Biomedical Engineering, and Machine Learning
Carnegie Mellon University, Pittsburgh, Pennsylvania, U.S.A.
About This Service
SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database.
An on-line summary of the architecture of SLIF can be found here.
A presentation on SLIF from the 2008 ISMB conference can be found on the Presentations page.
The initial development of SLIF was supported by grant 017396 from the Commonwealth of Pennsylvania Tobacco Settlement Fund. Further development is supported by National Institutes of Health grant R01 GM078622, and the development of the external linking capabilities (URL and XML-based) was supported by grant U54 DA021519 to the National Center for Integrative Biomedical Informatics. Papers from the Proceedings of the National Academy of Sciences (USA) used in development and testing of SLIF were obtained with the generous permission of Bruce Alberts and Ken Fulton of the National Academy of Sciences and with the kind assistance of David Lipman and his group at the
R. F. Murphy, M. Velliste, J. Yao, and G. Porreca (2001). Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. Proceedings of the 2nd IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE 2001), pp. 119-128.
William W. Cohen, Richard Wang, and Robert Murphy (2003). Understanding Captions in Biomedical Publications. Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2003), pp. 499-504.
William W. Cohen, Zhenzhen Kou, and Robert F. Murphy (2003). Extracting Information from Text and Images for Location Proteomics. Proceedings of the 3nd ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2003), pp. 2-9.
Robert F. Murphy, Zhenzhen Kou, Juchang Hua, Matthew Joffe, and William W. Cohen (2004). Extracting and Structuring Subcellular Location Information from On-line Journal Articles: The Subcellular Location Image Finder Proceedings of IASTED International Conference on Knowledge Sharing and Collaborative Engineering (KSCE-2004).
Z. Kou, W.W. Cohen, and R.F. Murphy (2005). High-recall protein entity recognition using a dictionary. Bioinformatics 21(suppl_1):i266-i273 (Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology).
Z. Kou, W.W. Cohen, and R.F. Murphy (2007). A Stacked Graphical Model for Associating Information from Text and Images in Figures. Pacific Symposium on Biocomputing 12:257-268.
J. Hua, O.N. Ayasli, W.W. Cohen, and R.F. Murphy (2007). Identifying Fluorescence Microscope Images in Online Journal Articles Using Both Image and Text Features. Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging (ISBI 2007), pp. 1224-1227.
Y. Qian and R.F. Murphy (2008). Improved Recognition of Figures containing Fluorescence Microscope Images in Online Journal Articles using Graphical Models. Bioinformatics 24:569-576.
A. Ahmed, E. Xing, W. Cohen, and R. F. Murphy (2009). Structured Correspondence Topic Models for Mining Captioned Figures in Biological Literature. Proceedings of the Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2009), pp. 39-47.
A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2009). Structured Literature Image Fider. Proceedings of the Ninth Annual Meeting of the ISMB BioLINK Special Interest Group, pp. 209-212.
L. P. Coelho, A. Ahmed, A. Arnold, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010). Structured Literature Image Finder: Extracting, Information from Text and Images in Biomedical Literature. Lecture Notes in Computer Science 6004:23-32.
A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010). Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature. Web Semantics: Science, Services and Agents on the World Wide Web 8:151-154
A.-S. Sheikh, A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, E. P. Xing, W. Cohen, and R. F. Murphy (2010). Structured literature image finder: Open source software for extracting and disseminating information from text and figures in biomedical literature. Carnegie Mellon University School of Computer Science Technical Report CMU-CB-09-101.
Images found with SLIF can be queried via the SLIF Web database.
Last Updated: 08 Nov 2012
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