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ORCIDJournal of Biomedical Semantics, Volume 7
Volume 7, 2016
- Randi Vita
, James A. Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L. Tallmadge, Shirley Ellis, John Hammond, Geoff W. Butcher, Alessandro Sette, Bjoern Peters:
An ontology for major histocompatibility restriction. 1 - Anika Oellrich, Terrence F. Meehan, Helen E. Parkinson, Sirarat Sarntivijai, Jacqueline K. White, Natasha A. Karp:
Reporting phenotypes in mouse models when considering body size as a potential confounder. 2 - Ferdinand Dhombres, Olivier Bodenreider:
Interoperability between phenotypes in research and healthcare terminologies - Investigating partial mappings between HPO and SNOMED CT. 3 - Giorgos Bamparopoulos, Evdokimos I. Konstantinidis, Charalampos Bratsas, Panagiotis D. Bamidis:
Towards exergaming commons: composing the exergame ontology for publishing open game data. 4 - Mike Conway, Artem Khojoyan, Fariba Fana, William Scuba, Melissa Castine, Danielle L. Mowery, Wendy W. Chapman, Simon Jupp:
Developing a web-based SKOS editor. 5 - Cui Tao, Yongqun He, Sivaram Arabandi:
Vaccine and Drug Ontology Studies (VDOS 2014). 6 - Josh Hanna, Jiang Bian, William R. Hogan:
An accurate and precise representation of drug ingredients. 7 - Sirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen E. Parkinson, James Malone:
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. 8 - Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig, Christopher G. Chute:
Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards. 10 - Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Extracting drug-enzyme relation from literature as evidence for drug drug interaction. 11 - Patrick L. Ray, Alexander P. Cox, Mark Jensen, Travis Allen, William D. Duncan, Alexander D. Diehl:
Representing vision and blindness. 15 - Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen E. Parkinson, James Malone:
Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates. 17 - Carrine E. Blank, Hong Cui, Lisa R. Moore, Ramona L. Walls:
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. 18 - Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel:
Extending gene ontology in the context of extracellular RNA and vesicle communication. 19 - Yu Lin, Jie Zheng, Yongqun He:
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. 20 - Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction. 21 - Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker:
miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. 9 - Aleksandra Sojic, Walter Terkaj, Giorgia Contini, Marco Sacco:
Modularising ontology and designing inference patterns to personalise health condition assessment: the case of obesity. 12 - Jingcheng Du, Yi Cai, Yong Chen, Cui Tao:
Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011. 13 - Susan M. Bello, Janan T. Eppig:
Inferring gene-to-phenotype and gene-to-disease relationships at Mouse Genome Informatics: challenges and solutions. 14 - Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara:
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. 16 - Xu Han, Jung-Jae Kim, Chee Keong Kwoh:
Active learning for ontological event extraction incorporating named entity recognition and unknown word handling. 22 - Mathias Brochhausen, Jie Zheng, David L. Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis, Christian J. Stoeckert Jr.:
OBIB-a novel ontology for biobanking. 23 - Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan:
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. 24 - Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan, Alan Ruttenberg:
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. 25 - Danielle L. Mowery, Brian E. Chapman, Mike Conway, Brett R. South, Erin Madden, Salomeh Keyhani, Wendy W. Chapman:
Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis. 26 - Farrokh Mehryary, Suwisa Kaewphan, Kai Hakala, Filip Ginter:
Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification. 27 - Simon Jupp, James Malone, Tony Burdett, Jean-Karim Hériché, Eleanor Williams, Jan Ellenberg, Helen E. Parkinson, Gabriella Rustici:
The cellular microscopy phenotype ontology. 28 - Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He:
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. 29 - Warren J. Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens, Jerry Winter:
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. 30 - Giorgos Bamparopoulos, Evdokimos I. Konstantinidis, Charalampos Bratsas, Panagiotis D. Bamidis:
Erratum to: Towards exergaming commons: composing the exergame ontology for publishing open game data. 31 - María Del Carmen Legaz-García, José Antonio Miñarro-Giménez, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis:
Generation of open biomedical datasets through ontology-driven transformation and integration processes. 32 - Mercedes Argüello Casteleiro, Julie Klein, Robert Stevens:
The Proteasix Ontology. 33 - Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, María Del Carmen Legaz-García, Ikuo Uchiyama:
The Orthology Ontology: development and applications. 34 - Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard A. Baldock, Albert Burger, Helen E. Parkinson:
PhenoImageShare: an image annotation and query infrastructure. 35 - Abdulaziz Alamri, Mark Stevenson:
A corpus of potentially contradictory research claims from cardiovascular research abstracts. 36 - Tiffany I. Leung, Michel Dumontier:
Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications. 37 - Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King, Georgios V. Gkoutos, John P. Sundberg, Paul N. Schofield:
DermO; an ontology for the description of dermatologic disease. 38 - Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock:
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. 39 - Khadim Dramé, Fleur Mougin, Gayo Diallo:
Large scale biomedical texts classification: a kNN and an ESA-based approaches. 40 - Hugo P. Bastos, Lisete Sousa, Luka A. Clarke, Francisco M. Couto:
Functional coherence metrics in protein families. 41 - William Scuba, Melissa Tharp, Danielle L. Mowery, Eugene Tseytlin, Yang Liu, Frank A. Drews, Wendy W. Chapman:
Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction. 42 - Danielle L. Mowery, Brett R. South, Lee M. Christensen, Jianwei Leng, Laura-Maria Peltonen, Sanna Salanterä, Hanna Suominen, David Martínez, Sumithra Velupillai, Noémie Elhadad, Guergana Savova, Sameer Pradhan, Wendy W. Chapman:
Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2. 43 - Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall:
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. 44 - Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius, Philipp Senger:
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. 45 - Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer:
COMODI: an ontology to characterise differences in versions of computational models in biology. 46 - Amanda Hicks, Josh Hanna, Daniel Welch, Mathias Brochhausen, William R. Hogan:
The ontology of medically related social entities: recent developments. 47 - Asma Ben Abacha, Júlio Cesar dos Reis, Yassine Mrabet, Cédric Pruski, Marcos Da Silveira:
Towards natural language question generation for the validation of ontologies and mappings. 48 - Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. 49 - William R. Hogan, Michael M. Wagner, Mathias Brochhausen, John D. Levander, Shawn T. Brown, Nicholas Millett, Jay DePasse, Josh Hanna:
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. 50 - Giandomenico Pozza, Stefano Borgo, Alessandro Oltramari, Laura Contalbrigo, Stefano Marangon:
Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases. 51 - Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter, Karin M. Verspoor:
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. 52 - Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He:
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. 53 - William R. Hogan, Werner Ceusters:
Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis. 54 - Seung-Cheol Baek, Jong-Chan Park:
Making adjustments to event annotations for improved biological event extraction. 55 - Pablo López-García, Stefan Schulz:
Can SNOMED CT be squeezed without losing its shape? 56 - Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls, Christopher J. Mungall:
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. 57 - Magnus Ahltorp, Maria Skeppstedt, Shiho Kitajima, Aron Henriksson, Rafal Rzepka, Kenji Araki:
Expansion of medical vocabularies using distributional semantics on Japanese patient blogs. 58 - Prudence Mutowo-Meullenet, A. Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax, John P. Overington:
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. 59 - Idoia Berges, David Antón, Jesús Bermúdez, Alfredo Goñi, Arantza Illarramendi:
TrhOnt: building an ontology to assist rehabilitation processes. 60 - Nicholas A. Thapen, Donal Stephen Simmie, Chris Hankin:
The early bird catches the term: combining twitter and news data for event detection and situational awareness. 61 - María del Mar Roldán García, María Jesús García-Godoy, José Francisco Aldana Montes:
Dione: An OWL representation of ICD-10-CM for classifying patients' diseases. 62 - Astrid Duque-Ramos, Manuel Quesada-Martínez, Miguela Iniesta-Moreno, Jesualdo Tomás Fernández-Breis, Robert Stevens:
Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE. 63 - Martin Boeker, Fábio França, Peter Bronsert, Stefan Schulz:
TNM-O: ontology support for staging of malignant tumours. 64:1-64:11 - Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos, Claus Weiland:
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. 65:1-65:11 - Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa N. Soldatova, Michel Dumontier, Nigam Shah:
Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. 66:1-66:4 - Maciej Rybinski, José Francisco Aldana Montes:
tESA: a distributional measure for calculating semantic relatedness. 67:1-67:14
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