Using Ontologies in the Wild
Helen Parkinson leads the Samples, Phenotypes and Ontologies Team at the European BioInformatics Institute. She has been involved in ontology development since DAML+OIL was the state of the art, and develops ontologies to apply them to data in resources such as the NHGRI/EBI GWAS Catalog, EBI's Gene Expression Atlas and recently in the Centre for Therapeutic Target Validation, a collaboration between EMBL-EBI, the Wellcome Trust Sanger Institute and GSK.
The role of ontologies in chem- and bioinformatics
Ontologies is the last minimal component needed for upscaling data analysis in chem- and bioinformatics. While computer representation of chemical entities and phenomena is quite well established, and while computation on such representations has scaled enormously too, the semantic meaning of many solution has not caught up. That is disappointing, because while they make representations larger is size, the added value opens up a great wide open field of research. This overview will show how semantics and ontologies have been adopted by the fields, and what applications these have made possible. Examples from the fields of drug discovery, metabolomics, and predictive toxicology, originating from various projects and various research lines will show how ontologies scale up data integration, pattern recognition and machine learning. The presentation will conclude with various open issues.
Monday, July 27 | Tuesday, July 28 | Wednesday, July 29 | Thursday, July 30 | |||||
Room 8.2.06 | Room 8.2.10 | Room 8.2.06 | Room 8.2.10 | Room 8.2.30 | Room 8.2.30 | |||
08:30 | Registration | Registration | 08:30 | Registration | 08:30 | Registration | ||
9:00 - 10:30 | IWOOD | Tawny-OWL | Genomics Hackathon | BFO | 9:00 - 9:10 | Opening Session | 9:00 - 10:00 | Keynote: Egon Willighagen. 'The role of ontologies in chem- and bioinformatics' |
9:10 - 10:10 | Keynote: Helen Parkinson. 'Using Ontologies in the Wild' | |||||||
10:30 - 11:00 | Coffee Break | 10:10 - 10:30 | Coffee Break | 10:00 - 10:30 | Coffee Break | |||
11:00-12:30 | IWOOD | Tawny-OWL | Genomics Hackathon | BFO | 10:30 - 11:45 | Paper session "Foundations of ontology" | 10:30 - 12:15 | Paper Session "Ontology resources" |
11:45 - 12:30 | Flash talks | |||||||
12:30 - 14:00 | Lunch | 12:30 - 14:00 | Lunch | 12:15 - 13:45 | Lunch | |||
14:00-15:30 | VDOS | BioPax | OBO | 14:00 - 14:45 | Workshop Summaries | 13:45 - 14:30 | Early Career Session | 14:45 - 16:00 | Paper session "Ontology Evaluation" | 14:30 - 15:45 | Paper session "SNOMED CT" |
15:30 - 16:00 | Coffee Break | 16:00 - 16:30 | Coffee Break | 15:45 - 16:15 | Coffee Break |
16:00-17:30 | VDOS | BioPax | OBO | 16:30 - 18:00 | Poster & demo session | 16:15 - 17:30 | Paper session "Ontology Use and Alignment" | |
20:00 | Social Dinner | 17:30 - 18:00 | Closing session |
Aboutness: Towards Foundations for the Information Artifact Ontology
Barry Smith and Werner Ceusters
An ontological analysis of diagnostic assertions in electronic healthcare records
Werner Ceusters and William Hogan
Formalization of indicators of diagnostic performance in a realist ontology
Adrien Barton, Régis Duvauferrier and Anita Burgun
Analysis of the evolution of ontologies using OQuaRE: Application to EDAM
Manuel Quesada-Martínez, Astrid Duque-Ramos and Jesualdo Tomás Fernández-Breis
Investigating Term Reuse and Overlap in Biomedical Ontologies
Maulik R. Kamdar, Tania Tudorache and Mark Musen
Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
Luke Slater, Georgios Gkoutos, Paul N. Schofield and Robert Hoehndorf
Scaffolding the Mitochondrial Disease Ontology from extant knowledge sources
Jennifer Warrender and Phillip Lord
BIM: An Open Ontology for the Annotation of Biomedical Image
Ahmad C. Bukhari, Michael Krauthammer, Paolo Ciccarese, Mate Nagy and Christopher J.O Baker
TNM-O an Ontology for the Tumor-Node-Metastasis Classification of Malignant Tumors: a Study on Colorectal Cancer
Martin Boeker, Fabio Franca, Peter Bronsert and Stefan Schulz
A UML Profile for Functional Modeling Applied to the Molecular Function Ontology
Patryk Burek, Frank Loebe and Heinrich Herre
Can SNOMED CT be Squeezed Without Losing its Shape?
Pablo López-García and Stefan Schulz
Formal representation of disorder associations in SNOMED CT
Edward Cheetham, Yongsheng Gao, Bruce Goldberg, Robert Hausam and Stefan Schulz
An ontology-based approach for SNOMED-CT translation
Mário J. Silva, Tiago Chaves and Bárbara Simões
Disease Compass --Navigation System for Disease Knowledge based on Ontology and Linked Data Techniques
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe
Medical and Transmission Vector Vocabulary Alignment with Schema.org
William Smith, Alan Chappell and Courtney Corley
Structured Data Acquisition with Ontology-Based Web Forms
Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney and Mark A. Musen
Annotating biomedical ontology terms in electronic health records using crowd-sourcing
André Lamúrias, Vasco Pedro, Luka Clarke and Francisco Couto
Replacing EHR structured data with explicit representations
Jonathan Bona and Werner Ceusters
Compound Matching of Biomedical Ontologies
Daniela Oliveira and Catia Pesquita
Towards visualizing the mapping incoherences in Bioportal
Catarina Martins, Ernesto Jimenez-Ruiz, Emanuel Santos and Catia Pesquita
Ontology-driven patient history questionnaires
Jonathan Bona, Gunther Kohn and Alan Ruttenberg
Development of a discharge ontology to support postanesthesia discharge decision making
Lucy Wang and Yong Choi.
Improvements to the Drosophila anatomy ontology
Marta Costa, David Osumi-Sutherland, Steven Marygold and Nick Brown
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis
Edison Ong and Yongqun He
Onto-animal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms
Yongqun He, Jie Zheng and Yu Lin
Ontorat: Automatic generation and editing of ontology terms
Yongqun He, Jie Zheng and Yu Lin
Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis
Yongqun He and Guoqian Jiang
OnToology, a tool for collaborative development of ontologies
Ahmad Alobaid, Daniel Garijo, María Poveda-Villalón, Idafen Santana-Pérez and Oscar Corcho
2015 Disease Ontology update: DO’s expanded curation activities to connect disease-related data
Elvira Mitraka and Lynn Schriml
AberOWL: an ontology portal with OWL EL reasoning
Luke Slater, Georgios Gkoutos, Paul Schofield and Robert Hoehndorf
Using Semantics and NLP in the SMART Protocols Repository
Olga Giraldo, Alexander Garcia and Oscar Corcho
ChEBI for systems biology and metabolic modelling
Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth Owen, Pedro Mendes and Christoph Steinbeck
Mapping WordNet to the Basic Formal Ontology using the KYOTO ontology
Selja Seppälä
Representing bioinformatics datatypes using the OntoDT ontology
Pance Panov, Larisa Soldatova and Saso Dzeroski
EDN-LD: A simple linked data tool
James A. Overton
ROBOT: A command-line tool for ontology development
James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland and Christopher J. Mungall
Visualization and editing of biomedical ontology alignments in AgreementMakerLight
Catarina Martins, Catia Pesquita and Daniel Faria
Inferring logical definitions using compound ontology matching
Daniela Oliveira and Catia Pesquita
Highly Literate Ontologies
Phillip Lord and Jennifer Warrender
NCBO BioPortal Version 4
Ray W. Fergerson, Paul R. Alexander, Rafael S. Gonçalves, Manuel Salvadores, Alex Skrenchuk, Jennifer Vendetti and Mark A. Musen
OWL-based form generation and structured data acquisition
Rafael S. Gonçalves, Csongor I. Nyulas, Samson W. Tu and Mark A. Musen
Modeling and Tools for Supporting Post-Coordination in ICD-11
Csongor I Nyulas, Samson Tu, Tania Tudorache and Mark Musen
Mapping a Database Schema to the Structure of an Existing Ontology
Anahita Nafissi, Fabio Fiorani and Björn Usadel.