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

To be announced

Accepted Papers

Formalization of indicators of diagnostic performance in a realist ontology
Adrien Barton, Régis Duvauferrier and Anita Burgun

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

BIM: An Open Ontology for the Annotation of Biomedical Image
Ahmad C. Bukhari, Michael Krauthammer, Paolo Ciccarese, Mate Nagy and Christopher J.O Baker

A UML Profile for Functional Modeling Applied to the Molecular Function Ontology
Patryk Burek, Frank Loebe and Heinrich Herre

An ontological analysis of diagnostic assertions in electronic healthcare records
Werner Ceusters and William Hogan

Formal representation of disorder associations in SNOMED CT
Edward Cheetham, Yongsheng Gao, Bruce Goldberg, Robert Hausam and Stefan Schulz

Structured Data Acquisition with Ontology-Based Web Forms
Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney and Mark A. Musen

Investigating Term Reuse and Overlap in Biomedical Ontologies
Maulik R. Kamdar, Tania Tudorache and Mark Musen

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

Can SNOMED CT be Squeezed Without Losing its Shape?
Pablo López-García and Stefan Schulz

Analysis of the evolution of ontologies using OQuaRE: Application to EDAM
Manuel Quesada-Martínez, Astrid Duque-Ramos and Jesualdo Tomás Fernández-Breis

An ontology-based approach for SNOMED-CT translation
Mário J. Silva, Tiago Chaves and Bárbara Simões

Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
Luke Slater, Georgios Gkoutos, Paul N. Schofield and Robert Hoehndorf

Aboutness: Towards Foundations for the Information Artifact Ontology
Barry Smith and Werner Ceusters

Medical and Transmission Vector Vocabulary Alignment with
William Smith, Alan Chappell and Courtney Corley

Scaffolding the Mitochondrial Disease Ontology from extant knowledge sources
Jennifer Warrender and Phillip Lord

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