Helen Parkinson

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.

Egon Willighagen

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 27Tuesday, July 28 Wednesday, July 29Thursday, July 30
Room 8.2.06Room 8.2.10Room 8.2.06Room 8.2.10 Room 8.2.30Room 8.2.30
08:30RegistrationRegistration 08:30Registration08:30Registration
9:00 - 10:30IWOODTawny-OWLGenomics HackathonBFO 9:00 - 9:10Opening Session9:00 - 10:00Keynote: Egon Willighagen.
'The role of ontologies in chem-
and bioinformatics'
9:10 - 10:10Keynote: Helen Parkinson.
'Using Ontologies in the Wild'
10:30 - 11:00Coffee Break 10:10 - 10:30Coffee Break10:00 - 10:30Coffee Break
11:00-12:30IWOODTawny-OWLGenomics HackathonBFO 10:30 - 11:45Paper session
"Foundations of ontology"
10:30 - 12:15Paper Session
"Ontology resources"
11:45 - 12:30Flash talks
12:30 - 14:00Lunch 12:30 - 14:00Lunch12:15 - 13:45Lunch
14:00-15:30VDOSBioPaxOBO 14:00 - 14:45Workshop Summaries13:45 - 14:30Early Career Session
14:45 - 16:00Paper session
"Ontology Evaluation"
14:30 - 15:45Paper session
15:30 - 16:00Coffee Break16:00 - 16:30Coffee Break15:45 - 16:15Coffee Break
16:00-17:30VDOSBioPaxOBO 16:30 - 18:00Poster & demo session16:15 - 17:30Paper session
"Ontology Use and Alignment"
20:00Social Dinner17:30 - 18:00Closing session

Accepted Papers

Paper session "Foundations of ontology". Chair: Janna Hastings

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

Paper session "Ontology Evaluation". Chair: Barry Smith

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

Paper Session "Ontology resources". Chair: Matthew Horridge

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

Paper session "SNOMED CT". Chair: Mélanie Courtot

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

Paper session "Ontology Use and Alignment". Chair: Stefan Schulz

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
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

Early Career Session Papers

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

Accepted Posters and Demos

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.

Presentation and poster instructions

Full paper

  • Presentation: 17 minutes
  • Q&A time: 8 minutes
  • Total: 25 minutes

Early Career papers

  • Presentation: 7 minutes
  • Q&A time: 2 minutes
  • Total: 9 minutes

Flash talks

  • Flash presentation: 90 seconds
  • WHAT: Prepare one or two teaser slides for your work. You will talk over these slides for a maximum of 90 seconds (1.5 minutes) at the Flash talks session. You must not talk longer than 90 seconds! If you do, we will stop you!
  • FORMAT: The slides must be PDF format. They should be in a standard 4:3 format that is suitable for presenting on at projector set to a resolution of 1024x768. Please ensure that your slides work and look good in this format.
  • WE WILL PROVIDE: A title slide. Your slides will be preceded by a title slide that we will generate (to ensure a uniform appearance). You should introduce yourself on the title slide and then advance your slides as necessary.
  • DEADLINE: Wednesday 22nd July. Please upload your slides in PDF format via EasyChair ( Please make sure that you upload your slides as Flash Talk proceedings.

Workshop summaries

  • Presentation: 5 minutes
  • Presented by the workshop/tutorial organizer
  • Prepare two or three slides detailing your workshop/tutorial/hackathon experience.


  • Size: up to A0 in portrait
  • If possible bring adhesive tape
  • Put up your poster BEFORE the session


  • We will provide one table and one chair.
  • Electrical output will be available - bring adapter if needed

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