Biomedical Knowledge Engineering Group

Publications

Cycles of Scientific Investigation in DiscourseBurns, G. A., de Waard, A, Dasigi, P, Hovy, E. H.
In Biocreative
2016, pagesRSSBibTex
‘Its All Made Up’ - Why we should stop building representations based on interpretive models and focus on experimental evidence insteadGully A. P. C. Burns, Chalupsky, H
In Discovery Informatics: Scientific Discoveries Enabled by {AI}
2014, pagesRSSBibTex
DISCOVERY INFORMATICS: AI TAKES A SCIENCE-CENTERED VIEW ON BIG DATA: PAPERS FROM THE AAAI SYMPOSIUMGully A. P. C. Burns, Yolanda Gil, Yan Liu, Natalia Vilanueva Rosales
In DISCOVERY INFORMATICS: AI TAKES A SCIENCE-CENTERED VIEW ON BIG DATA: PAPERS FROM THE AAAI SYMPOSIUM
2013, pagesRSSBibTex
Virk: An Active Learning-based System for Bootstrapping Knowledge Base Development in the NeurosciencesAmbert, Kyle H, Cohen, Aaron M, Gully A. P. C. Burns, Boudreau, Eilis, Sonmez, Kemal
In Frontiers in Neuroinformatics
2013, 38 pagesRSSBibTex
Finna: A Paragraph Prioritization System for Biocuration in the NeurosciencesK Ambert, A Cohen, Burns, G., E Boudreau, K Sonmez
In Discovery Informatics 2013
2013, pagesRSSBibTex
Modelling Functional Magnetic Resonance Imaging (fMRI) Experimental Variables in the Ontology of Experimental Variables and Values (OoEVV)Gully A. P. C. Burns, Jessica A. Turner
In Neuroimage
2013, - pagesRSSBibTex
Preliminary meta-analyses of experimental design with examples from HIV vaccine protection studiesMarcelo Tallis, Dave, Drashti, Gully Burns
In Discovery Informatics
2012, pagesRSSBibTex
Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV)Gully A. P. C. Burns, Jessica A. Turner
In Bio-Ontologies SIG, ISMB
2012, pagesRSSBibTex
A lightweight Ontology Design Pattern to curate and represent experimental variables from vaccine protection studies.Gully A. P. C. Burns, Dave, Drashti
In Vaccine and Drug Ontology in the Study of Mechanism and Effect, ICBO 2012
2012, pagesRSSBibTex
Layout-Aware Text Extraction from Full-text PDF of Scientific ArticlesRamakrishnan, Cartic, Patnia, Abhishek, Hovy, Eduard, Gully Burns
In Source Code for Biology and Medicine
2012, 7 pagesRSSBibTex
Toward interoperable bioscience dataSansone, Susanna-Assunta, Rocca-Serra, Philippe, Field, Dawn, Maguire, Eamonn, Taylor, Chris, Hofmann, Oliver, Fang, Hong, Neumann, Steffen, Tong, Weida, Amaral-Zettler, Linda, Begley, Kimberly, Booth, Tim, Bougueleret, Lydie, Gully Burns, Chapman, Brad, Clark, Tim, Coleman, Lee-Ann, Copeland, Jay, Das, Sudeshna, de Daruvar, Antoine, de Matos, Paula, Dix, Ian, Edmunds, Scott, Evelo, Chris T, Forster, Mark J, Gaudet, Pascale, Gilbert, Jack, Goble, Carole, Griffin, Julian L, Jacob, Daniel, Kleinjans, Jos, Harland, Lee, Haug, Kenneth, Hermjakob, Henning, Sui, Shannan J Ho, Laederach, Alain, Liang, Shaoguang, Marshall, Stephen, McGrath, Annette, Merrill, Emily, Reilly, Dorothy, Roux, Magali, Shamu, Caroline E, Shang, Catherine a, Steinbeck, Christoph, Trefethen, Anne, Williams-Jones, Bryn, Wolstencroft, Katherine, Xenarios, Ioannis, Hide, Winston
In Nature Genetics
2012, 121–126 pagesRSSBibTex
Text mining for the biocuration workflowHirschman, L., Burns, G. a. P. C., Krallinger, M., Arighi, C., Cohen, K. B., Valencia, a., Wu, C. H., Chatr-Aryamontri, a., Dowell, K. G., Huala, E., Lourenco, a., Nash, R., a.-L. Veuthey, Wiegers, T., Winter, a. G.
In Database
2012, bas020–bas020 pagesRSSBibTex
Knowledge synthesis with maps of neural connectivityTallis, M., Thompson, R., Russ, T., Burns, GAPC
In Frontiers in Neuroinformatics
2011, 5:24 pagesRSSBibTex
Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use CaseRuss, T., Ramakrishnan, C., Hovy, E. H., Bota, M., Burns, GAPC
In BMC Bioinformatics
2011, 12: 351 pagesRSSBibTex
The Role of Information Extraction in the Design of a Document Triage Application for BiocurationPokkunuri, Sandeep, Ramakrishnan, Cartic, Riloff, Ellen, Eduard H. Hovy, Gully A. P. C. Burns
In Workshop on Biomedical Natural Language Processing (BioNLP 2011) at ACL/HLT 2011
2011, pagesRSSBibTex
Database of NIH grants using machine-learned categories and graphical clusteringEdmund M. Talley, David Newman, Mimno, David, Herr, Bruce W, Wallach, Hanna M, Gully A. P. C. Burns, Leenders, A G Miriam, McCallum, Andrew
In Nature Methods
2011, 8(6):443-444 pagesRSSBibTex
Building the Scientific Knowledge Mine (SciKnowMine1): a community-driven framework for text mining tools in direct service to biocurationRamakrishnan, Cartic, Jr., William A. Baumgartner, Blake, Judith, Gully A. P. C. Burns, Cohen, K. Bretonnel, Drabkin, Harold, Eppig, Janan, Hovy, Eduard, Hsu, Chun-Nan, Hunter, Lawrence E., Tommy Ingulfsen, Livingston, Kevin, Onda, Hiroaki 'Rocky', Pokkunuri, Sandeep, Riloff, Ellen, Roeder, Christophe, Verspoor, Karin
In Language Resources and Evaluation (LREC)
2010, pagesRSSBibTex
Biocuration Workflow Catalogue - Text Mining for the Biocuration WorkflowBurns, GAPC, Krallinger, M., Cohen, K. B., Wu, C. H., Hirschman, L.
In 3rd International Biocurators Meeting
2009, pagesRSSBibTex
The NIH Visual Browser: An Interactive Visualization of Biomedical ResearchHerr, B. W., Talley, E. M., Burns, GAPC, Newman, D., LaRowe, G.
In 13th International Conference on Information Visualization (IV09)
2009, pagesRSSBibTex
Biomedical knowledge engineering tools based on experimental design: a case study based on neuroanatomical tract-tracing experimentsGully A. P. C. Burns, Thomas A. Russ
In K-CAP
2009, 173-174 pagesRSSBibTex
Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and ExamplesGully Burns, Donghui Feng, Eduard H. Hovy
In Computational Intelligence in Medical Informatics
2008, 17-50 pagesRSSBibTex
Towards Automated Semantic Analysis on Large Scale Biomedical TextFeng, D., Burns, GAPC, Hovy, E. H.
In Proceedings of the International Joint Conference on NLP (IJCNLP).
2008, pagesRSSBibTex
Analyses over multiple scientific text corpora: combining MEDLINE, CRISP and the proceedings of the annual meetings of the Society for NeuroscienceBurns, G. A., Newman, D., Herr, B, Holloway, A., Smyth, P., Borner, K.
In
2008, pagesRSSBibTex
Using large-scale semi-automated information extraction for the biocuration of experimental observations: the million-paper challenge.Burns, GAPC, Ingulfsen, T., Feng, D., Hovy, E. H.
In 2nd International Biocurators meeting
2007, pagesRSSBibTex
Extracting Data Records from Unstructured Biomedical Full TextFeng, D., Burns, G., Hovy, E.
In The Joint Meeting of Conference on Empirical Methods in Natural Language Processing and Conference on Computational Natural Language Learning (EMNLP-CoNLL 2007)
2007, pagesRSSBibTex
Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and PracticeGully Burns, Donghui Feng, Tommy Ingulfsen, Eduard H. Hovy
In 2007 IEEE International Conference on Services Computing - Workshops (SCW 2007), 9-13 July 2007, Salt Lake City, Utah, USA
2007, 122-129 pagesRSSBibTex
A snapshot of neuroscience: unsupervised natural language processing of abstracts from the Society for Neuroscience 2006 annual meetingBurns, GAPC, Herr, B, Newman, D., Ingulfsen, T., Pantel, P, Smyth, P.
In Annual Meeting of the Society for Neuroscience
2007, 100.6 / XX26 pagesRSSBibTex
Tools for Knowledge Acquisition within the NeuroScholar system and their application to anatomical tract-tracing dataBurns, G. A., Cheng, W. C.
In J Biomed Discov Collab
2006, 10 pagesRSSBibTex
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlasesGully A. P. C. Burns, Wei-Cheng Cheng, Richard H. Thompson, Larry W. Swanson
In BMC Bioinformatics
2006, 531 pagesRSSBibTex
NeuroScholar WebService Developer's ManualCheng, W-C, Burns, GAPC
In
2006, pagesRSSBibTex
NeuARt II Developers ManualCheng, W-C, Burns, GAPC
In
2006, pagesRSSBibTex
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases.Burns, G., Cheng, W-C, Thompson, R. F., Swanson, L.
In BMC Bioinformatics
2006, 531 pagesRSSBibTex
NeuroScholar's Electronic Laboratory Notebook and its Application to NeuroendocrinologyKhan, A. M., Hahn, JD, Cheng, W-C, Watts, A. G., Burns, GAPC
In Neuroinformatics
2006, 139-160 pagesRSSBibTex
Extracting and managing model parameters from the literature.Burns, G.
In World Assocation of Modellers, Biologically Accurate Modeling
2005, pagesRSSBibTex
Projections from the Subfornical Region of the Lateral Hypothalamic AreaGoto, M, Canteras, NS, Burns, GAPC, Swanson, L. W.
In J Comp Neurol
2005, 412-38 pagesRSSBibTex
An Overview of Sangam: A System for Integrating Data to Investigate Stress-Circuitry-Gene CouplingSaxena, M, Kim, S, Burns, GAPC, Khan, AM., Su, J, Hamadi, Y, Ghandeharizadeh, S.
In IVNET, submitted
2005, pagesRSSBibTex
Tools for knowledge representation, acquisition and retrieval of neuroanatomical data mapped onto a standard atlas.Cheng, W-C, Burns, GAPC, Thompson, R. H., Swanson, L. W.
In Annual Meeting of the Society for Neuroscience
2005, 571.4 pagesRSSBibTex
A computational knowledge representation for physiological experiments with direct links to the primary literature and raw dataBurns, GAPC, Khan, A. M., Cheng, W-C, Watts, A. G.
In Annual Meeting of the Society for Neuroscience
2005, pagesRSSBibTex
A 'Stress Management' System: Computational knowledge representation of experiments that delineate neural circuits and histochemical expression patterns based on the primary literature and raw dataBurns, GAPC, Khan, A. M., Cheng, W. C., Watts, A. G.
In 2005 Workshop on the Neuroendocrinology of Stress
2005, pagesRSSBibTex
Histochemical studies of stress-activated paraventricular hypothalamic neuroendocrine neurons: a neuroinformatics-based digital lab notebook to relate the primary literature to raw, unpublished dataKhan, A. M., Cheng, W. C., Watts, A. G., Burns, GAPC
In Society for Neuroscience Annual Meeting
2004, pagesRSSBibTex
Two-phase Decision Fusion Based on User PreferenceChen, Y-S, Shahabi, C, Burns, GAPC
In Hawaii International Conference on Computer Sciences
2004, pagesRSSBibTex
Web services as tools within a scientific knowledge engineering environmentBurns, GAPC, Cheng, W-C, Zhang, N, Ghandeharizadeh, S.
In SCI
2003, pagesRSSBibTex
Tools for knowledge management of the neuroscientific literature, plugins for the NeuroScholar systemSong, S, Chan, K, Golypayegani, A, Ghandeharizadeh, S., Shahabi, C, Burns, GAPC
In Computational Neuroscience
2003, pagesRSSBibTex
Tools and approaches for the construction of knowledge models from the neuroscientific literatureBurns, G. A., Khan, A. M., Ghandeharizadeh, S., O'Neill, M. A., Chen, Y. S.
In Neuroinformatics
2003, 81-109 pagesRSSBibTex
An example of a neuroinformatics knowledge model derived from the primary literature: Catecholaminergic regulation of hypothalamic paraventricular neuroendocrine neuronsBurns, G., Khan, A. M.
In Annual Meeting for the Society for Neuroscience
2003, 758.2 pagesRSSBibTex
Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework (VPDMf)Gully A. P. C. Burns, Fang Bian, Wei-Cheng Cheng, Shyam Kapadia, Cyrus Shahabi, Shahram Ghandeharizadeh
In Neurocomputing
2002, 1049-1056 pagesRSSBibTex
Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework (VPDMf)Burns, GAPC, Bian, F, Cheng, W-C, Kapadia, S, Shahabi, C, Ghandeharizadeh, S.
In Neurocomputing
2002, 1049-1056 pagesRSSBibTex
Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac)Stephan, KE, Kamper, L., Bozkurt, A., Burns, G. A., Young, M. P., Kotter, R.
In Philos Trans R Soc Lond B Biol Sci
2001, 1159-86 pagesRSSBibTex
The Neuroanatomical Rat Brain Viewer (NeuARt)Dashti, A. E., Burns, GAPC, Simmons, D. M., Swanson, L., Ghandeharizadeh, S., Shahabi, C, Stone, J., Jia, S.
In Computing the Brain: A Guide to Neuroinformatics
2001, 189-202 pagesRSSBibTex
Towards a federated neuroscientific knowledge management system using brain atlasesBurns, GAPC, Stephan, KE, Ludäscher, B, Gupta, A, Kötter, R
In Neurocomputing
2001, 1633-1641 pagesRSSBibTex
Knowledge Mechanics and the NeuroScholar Project: A New Approach to Neuroscientific TheoryBurns, GAPC
In Computing the Brain, A guide to Neuroinformatics
2001, 319-335 pagesRSSBibTex
Analysis of the connectional organization of neural systems associated with the hippocampus in ratsBurns, G. A., Young, M. P.
In Philos Trans R Soc Lond B Biol Sci
2001, 55-70 pagesRSSBibTex
Knowledge management of the neuroscientific literature: the data model and underlying strategy of the NeuroScholar systemBurns, G. A.
In Philos Trans R Soc Lond B Biol Sci
2001, 1187-208 pagesRSSBibTex
Projections from the Subfornical Region of the Lateral Hypothalamic AreaGoto, M, Canteras, NS, Burns, GAPC, Swanson, L. W.
In J Comp Neurol
2005, 412-38 pagesRSSBibTex
Computational analysis of functional connectivity between areas of primate cerebral cortexStephan, KE, Hilgetag, C. C., Burns, G. A., O'Neill, M. A., Young, M. P., Kotter, R.
In Philos Trans R Soc Lond B Biol Sci
2000, 111-26 pagesRSSBibTex
Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the catHilgetag, C. C., Burns, G. A., O'Neill, M. A., Scannell, J. W., Young, M. P.
In Philos Trans R Soc Lond B Biol Sci
2000, 91-110 pagesRSSBibTex
The connectional organization of the cortico-thalamic system of the catScannell, J. W., Burns, G. A., Hilgetag, C. C., O'Neil, M. A., Young, M. P.
In Cereb Cortex
1999, 277-99 pagesRSSBibTex
Neuroscholar 1.00, a neuroinformatics databasing websiteGully Burns
In Neurocomputing
1999, 963-970 pagesRSSBibTex
Visual Information and Information Systems, Third International Conference, VISUAL '99, Amsterdam, The Netherlands, June 2-4, 1999, Proceedings
In VISUAL
1999, pagesRSSBibTex
Neuroscholar 1.00, a neuroinformatics databasing websiteBurns, GAPC
In Neurocomputing
1999, 963-970 pagesRSSBibTex
Neural connectivity in the rat: theory, methods and applicationsBurns, GAPC
In
1997, pagesRSSBibTex
Analysis of connectivity: neural systems in the cerebral cortexYoung, M. P., Scannell, J. W., Burns, G. A., Blakemore, C.
In Rev Neurosci
1994, 227-50 pagesRSSBibTex
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