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ICBO/BioCreative 2016: Corvallis, Oregon, USA
- Pankaj Jaiswal, Robert Hoehndorf, Cecilia N. Arighi, Austin Meier:
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016. CEUR Workshop Proceedings 1747, CEUR-WS.org 2016
BioCreative Plenary Session #1 : Text Mining-facilitated Models of Curation
- Gully A. P. C. Burns, Anita de Waard, Pradeep Dasigi, Eduard H. Hovy:
Cycles of Scientific Investigation in Discourse - Machine Reading Methods for the Primary Research Contributions of a Paper. - Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir:
Collaborative Workspaces for Pathway Curation. - Matt Jeffryes, Maria Liakata, Alex Bateman:
Crowdsourcing Protein Family Database Curation. - Benjamin M. Good, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka, Timothy Putman, Andrew I. Su, Andra Waagmeester:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration.
Plenary Session #2 : Text Mining in Precision Medicine
- Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad, Hongfang Liu:
MutD - A PubMed Scale Resource for Protein Mutation-Disease Relations through Bio-Medical Literature Mining. - Jake Lever, Martin Jones, Steven J. Jones:
CancerMine: Knowledge Base Construction for Personalised Cancer Treatment. - Sherri Matis-Mitchell:
Text Mining for Drug Development: Gathering Insights to Support Decision Making.
BioCreative Plenary Session #3 : Domain Portability or Generalizability Across Medical Literature
- Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu:
BioCconvert: A Conversion Tool Between BioC and PubAnnotation.
ICBO and BioCreative Joint Posters and Demo Session #1
- Justin Preece, Justin Elser, Pankaj Jaiswal, Kristian Kvilekval, Dmitry V. Fedorov, B. S. Manjunath, Ryan Kitchen, Xu Xu, Dmitrios Trigkakis, Sinisa Todorovic, Seth Carbon:
Plant Image Segmentation and Annotation with Ontologies in BisQue. - Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf:
SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL. - James P. Balhoff:
The Phenoscape Knowledgebase: Tools and APIs for Computing Across Phenotypes from Evolutionary Diversity and Model Organisms. - Miguel Ángel Rodríguez-García, Luke T. Slater, Imane Boudellioua, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Updates to the AberOWL Ontology Repository. - Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart:
Enhancing Information Accessibility of Publications with Text Mining and Ontology.
Joint ICBO and BioCreative Plenary Session #1 : Natural Language Processing & Data Mining with Ontologies
- Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Large-scale Semantic Indexing with Biomedical Ontologies. - Lars Juhl Jensen:
One Tagger, Many Uses: Illustrating the Power of Ontologies in Dictionary-based Named Entity Recognition. - Karen E. Ross, Darren A. Natale, Cecilia N. Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K. Vijay-Shanker, Cathy H. Wu:
Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. - Vimala Ponna, Aaron Baer, Matthew Lange:
Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies. - Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart:
A Web Application for Extracting Key Domain Information for Scientific Publications Using Ontology. - Senay Kafkas, Ian Dunham, Helen E. Parkinson, Johanna R. McEntyre:
Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation.
ICBO Plenary Session #2 : SDGIO: Sustainable Development Goals Interface Ontology--Semantics for Sustainability
- Pier Luigi Buttigieg, Mark Jensen, Ramona L. Walls, Christopher J. Mungall:
Environmental Semantics for Sustainable Development in an Interconnected Biosphere. - Mark Jensen:
Sustainable Development Goals Interface Ontology. - Ramona L. Walls:
Defining and Sustaining Populations and Communities. - Medha Devare, Céline Aubert, Marie-Angélique Laporte, Léo Valette, Elizabeth Arnaud, Pier Luigi Buttigieg:
Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics. - Barry Smith, Mark Jensen:
The UNEP Ontologies and the OBO Foundry.
ICBO and BioCreative Joint Posters and Demo : Session #2
- Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He:
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. - Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo Kaboré, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier, Pierre Larmande:
Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal. - James A. Overton:
Humane OWL: RDF and OWL for Humans. - John Judkins, Joseph Utecht, Mathias Brochhausen:
Easy Extraction of Terms and Definitions with OWL2TL.
ICBO Plenary Session #4 : Ontology Development and Application
- Lucy Lu Wang, John H. Gennari, Neil F. Abernethy:
An Analysis of Differences in Biological Pathway Resources. - Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Chris Mungall, Peter N. Robinson, Sebastian Köhler, Melissa A. Haendel:
Enhancing the Human Phenotype Ontology for Use by the Layperson. - Fernanda Farinelli, Maurício Barcellos de Almeida, Peter L. Elkin, Barry Smith:
Dealing with Social and Legal Entities in the Obstetric and Neonatal Domain. - Mélanie Courtot, James Malone, Chris Mungall:
Ten Simple Rules for Biomedical Ontology Development. - Hande Küçük-McGinty, Saurabh Mehta, Yu Lin, Nooshin Nabizadeh, Vasileios Stathias, Dusica Vidovic, Amar Koleti, Christopher Mader, Jianbin Duan, Ubbo Visser, Stephan C. Schürer:
Building Concordant Ontologies for Drug Discovery. - Laurel Cooper, Austin Meier, Justin Elser, Justin Preece, Xu Xu, Ryan Kitchen, Botong Qu, Eugene Zhang, Sinisa Todorovic, Pankaj Jaiswal, Marie-Angélique Laporte, Elizabeth Arnaud, Seth Carbon, Chris Mungall, Barry Smith, Georgios V. Gkoutos, John H. Doonan:
The Planteome Project. - Austin Meier, Laurel Cooper, Justin Elser, Pankaj Jaiswal, Marie-Angélique Laporte:
Annotating Germplasm to Planteome Reference Ontologies.
ICBO Plenary Session #5 : Ontology-based Applications
- Christopher Ochs, Yehoshua Perl, Gai Elhanan, James T. Case:
A Descriptive Delta for Identifying Changes in SNOMED CT. - Yehoshua Perl, Christopher Ochs, Sherri de Coronado, Nicole Thomas:
Visualizing the "Big Picture" of Change in NCIt's Biological Processes. - Jie Zheng, Jashon Cade, Brian P. Brunk, David S. Roos, Christian J. Stoeckert Jr., San James, Emmanuel Arinaitwe, Bryan Greenhouse, Grant Dorsey, Steven Sullivan, Jane M. Carlton, Gabriel Carrasco-Escobar, Dionicia Gamboa, Paula Maguina-Mercedes, Joseph Vinetz:
Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies. - Joseph Utecht, John Judkins, Mathias Brochhausen, Terra Colvin Jr., J. Neil Otte, Nicholas Rogers, Robert Rose, Maria Alvi, Amanda Hicks, Jane Ball, Stephen M. Bowman, Robert T. Maxson, Rosemary Nabaweesi, Rohit Pradhan, Nels D. Sanddal, M. Eduard Tudoreanu, Robert J. Winchell:
OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems. - Hua Min, Stuart Turner, Sherri de Coronado, Brian Davis, Trish Whetzel, Robert R. Freimuth, Harold R. Solbrig, Richard C. Kiefer, Michael Riben, Grace A. Stafford, Lawrence W. Wright, Riki Ohira:
Towards a Standard Ontology Metadata Model. - Takeshi Imai, Emiko Yamada Shinohara, Masayuki Kajino, Ryota Sakurai, Kazuhiko Ohe, Kouji Kozaki, Riichiro Mizoguchi:
An Ontological Framework for Representing Topological Information in Human Anatomy. - Amanda Damasceno de Souza, Mauricio Barcellos Almeida:
Natural Language Definitions for the Leukemia Knowledge Domain.
ICBO Plenary Session #6 : Semantics and Interoperability
- Olivier Bodenreider:
Identifying Missing Hierarchical Relations in SNOMED CT from Logical Definitions Based on the Lexical Features of Concept Names. - Daniel Welch, Amanda Hicks, Josh Hanna, William R. Hogan:
A Semantic Web Representation of Entire Populations. - Jean-François Ethier, Ryeyan Taseen, Luc Lavoie, Adrien Barton:
Improving the Semantics of Drug Prescriptions with a Realist Ontology. - Maxwell Lewis Neal, John H. Gennari, Daniel L. Cook:
Qualitative Causal Analyses of Biosimulation Models. - Matthew H. Brush, Kent A. Shefchek, Melissa A. Haendel:
SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence. - Prashanti Manda, James P. Balhoff, Todd J. Vision:
Measuring the Importance of Annotation Granularity to the Detection of Semantic Similarity Between Phenotype Profiles.
ICBO Plenary Session #7 : Data Annotation, Standards and Computational Reasoning
- Hasan Yumak, Ling Chen, Michael Halper, Ling Zheng, Yehoshua Perl, Gai Elhanan:
A Quality-Assurance Study of ChEBI. - Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO). - Saurabh Raghuvanshi:
Semantic Digitization of Experimental Data in Biological Sciences. - Melissa D. Clarkson:
Representation of Parts within the Foundational Model of Anatomy Ontology. - Amanda Hicks:
A Realist Representation of Social Identity Data.
ICBO Flash Talks/Posters
- Gaoussou Camara, Sylvie Desprès, Rim Djedidi, Moussa Lo:
Towards a Schistosomiasis Ontology (IDOSCHISTO) Extending the Infectious Disease Ontology. - Mathias Brochhausen, Philip E. Empey, Jodi Schneider, William R. Hogan, Richard D. Boyce:
Adding Evidence Type Representation to DIDEO. - José Leonardo Villaraza Mejino Jr., James F. Brinkley, Timothy C. Cox, Landon Detwiler:
Multi-species Ontologies of the Craniofacial Musculoskeletal System. - Yongqun He, Zhaohui S. Qin, Jie Zheng:
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. - Hua Min, Robert H. Friedman, Julie A. Wright:
An Ontological Representation for the Transtheoretical Theory. - Jean-Philippe F. Gourdine, Thomas O. Metz, David Koeller, Matthew H. Brush, Melissa A. Haendel:
Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. - Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He:
The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. - Michael Bada, Nicole A. Vasilevsky, Melissa A. Haendel, Lawrence Hunter:
Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions. - Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan:
How to Summarize Big Knowledge Subjects. - Jonathan P. Bona, Selja Seppälä, Werner Ceusters:
Analysis of SNOMED "Bleeding" Concepts & Terms. - Aaron Baer, Matthew Lange:
Uc_Sense: An Ontology for Scientifically-based Unambiguous Characterization of Sensory Experiences. - Jonathan Bisson, James McAlpine, James Graham, Guido Pauli:
NAPRALERT, from a Historical Information Silo to a Linked Resource Able to Address the New Challenges in Natural Products Chemistry and Pharmacognosy. - Kimiya Taji, Matthew Lange:
uc_Eating: Ontology for Unambiguous Characterization of Eating and Food Habits. - Ruthie Musker, Matthew Lange, Allan Hollander, Patrick Huber, Nathaniel Springer, Courtney Riggle, James Quinn, Thomas Tomich:
Towards Designing an Ontology Encompassing the Environment-agriculture-food-diet-health Knowledge Spectrum for Food System Sustainability and Resilience. - Emeline Colet, Matthew Lange:
uc_Milk: An Ontology for Scientifically-based Unambiguous Characterization of Mammalian Milk, their Composition and the Biological Processes Giving Rise to their Creation. - Daniel R. Schlegel, Selja Seppälä, Peter L. Elkin:
Definition Coverage in the OBO Foundry Ontologies: The Big Picture. - Marie-Angélique Laporte, Léo Valette, Laurel Cooper, Chris Mungall, Austin Meier, Pankaj Jaiswal, Elizabeth Arnaud:
Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies. - William D. Duncan, Travis Allen, Jonathan P. Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl:
The ImmPort Antibody Ontology. - Benjamin M. Good, Timothy Putman, Andrew I. Su, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration. - Ceri E. Van Slyke, Yvonne M. Bradford, Christian Pich:
Growth of the Zebrafish Anatomy Ontology: Expanded to Support Adult Morphology and Dynamic Changes in the Early Embryo. - Emma J. Griffiths, Damion M. Dooley, Pier Luigi Buttigieg, Robert Hoehndorf, Fiona S. L. Brinkman, William W. L. Hsiao:
FoodON: A Global Farm-to-Fork Food Ontology. - Nancy George, Sara El-Gebali, Thomas Lemberger:
SourceData: Making Data Discoverable. - Fumiaki Toyoshima:
Towards an Ontology of Schizophrenia. - Damion M. Dooley, Emma J. Griffiths, Fiona S. L. Brinkman, William W. L. Hsiao:
An OBI Ontology Datum Proof Sheet. - Yvonne M. Bradford, Ceri E. Van Slyke, Sabrina Toro, Sridhar Ramachandran:
The Zebrafish Experimental Conditions Ontology Systemizing Experimental Descriptions in ZFIN. - Jose F. Florez-Arango, Santiago Patiño-Giraldo, Jack W. Smith, M. Sriram Iyengar:
Performance Evaluation Clinical Task Ontology(PECTO). - Fernanda Farinelli, Maurício Barcellos de Almeida, Peter L. Elkin, Barry Smith:
Dealing with Elements of Medical Encounters: an Approach Based on the Ontological Realism. - Constantine Spyrou, Matthew Lange:
uc_FIDO: Unambiguous Characterization of Food Interactions with Drugs Ontology. - Caterina Caracciolo, Tom Baker, Elizabeth Arnaud:
Global Agricultural Concept Scheme: A Hub for Agricultural Vocabularies. - Marcus C. Chibucos, Suvarna Nadendla, James B. Munro, Elvira Mitraka, Dustin Olley, Nicole A. Vasilevsky, Matthew H. Brush, Michelle G. Giglio:
Supporting Database Annotations and Beyond with the Evidence & Conclusion Ontology (ECO). - Botong Qu, Jaden Diefenbaugh, Eugene Zhang, Justin Elser, Pankaj Jaiswal, Seth Carbon, Christopher J. Mungall:
Planteome Gene Annotation Enrichment Analysis. - Marijane White, Matthew H. Brush, Shahim Essaid, Robin Champieux, Adrienne Zell, Melissa A. Haendel, Colin Grove, Syeda Momina Tabish, David Eichmann:
Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology. - Arzucan Özgür, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir R. Radev, Yongqun He:
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. - Thomas Hahn, Hidayat Ur Rahman, Richard S. Segall:
Disease Named Entity Recognition Using NCBI Corpus. - Rasha Obeidat, Xiaoli Z. Fern, Prasad Tadepalli:
Label Embedding Approach for Transfer Learning.
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