39106 Magdeburg, Germany
International Conference on Biomedical Ontologies (ICBO), part of the Bolzano Summer of
Janna Hastings, Frank Loebe (eds.): ICBO 2020 – International Conference on Biomedical Ontologies. Proceedings of the 11th International Conference on Biomedical Ontologies held jointly with the 10th Ontologies and Data in the Life Sciences (ODLS), Bolzano, Italy, September 17th, 2020. CEUR-WS.org.
It is recommended to include further the CEUR-WS.org volume number and the URL to that volume.
Copyright © 2020 for the individual papers by the papers' authors. Copyright © 2021 for the volume as a collection by its editors. This volume and its papers are published under the
Against the background of a globally unfolding pandemic, 2020 was a radically different year for researchers and academic conferences around the world. Like many conferences forced to adapt under the novel circumstances of restrictions on travel and congregation, ICBO|ODLS 2020 took place as a slimmed-down virtual event. Nevertheless, the virtual event was lively and well attended. The virtual program, hosted by the Bolzano team of local organizers using the platform Zoom, consisted of short pre-recorded presentations followed by virtual question and answer sessions. In parallel, a virtual poster session was offered across the platforms WordPress and Discord.
Each submission to ICBO|ODLS 2020 was assessed by three reviewers. Contributions were accepted to four tracks: main research papers, tools and applications papers, early career abstracts, and poster abstracts. Across these tracks, 35 submissions were received, of which 26 were accepted. Among the topics of contributions to this were topics that were on everyone’s minds in these challenging times – ontologies for coronavirus description and data integration in support of health research were prominent themes. Aside from this, other themes included electronic healthcare graphs, clinical documents, cross-references within and between bioontologies, molecular structures, and the ontology authoring process.
This year was also the first year that ICBO and ODLS were held together. The ICBO series of conferences began in Buffalo, USA in 2009, and is held annually in locations that alternate between the US and Europe. The ODLS workshop started with a workshop on Ontologies in Biomedicine and Life Sciences (OBML) in 2009. In 2013, integration with the formerly independent workshop on Data in Life Sciences led to the renaming to Ontologies and Data in Life Sciences (ODLS). Since then, ODLS workshops were held annually, except for in 2015 and 2018, and mostly as independent events. Three times they were organized as a part of other events, namely of INFORMATIK 2013 in Koblenz, Germany, as well as of the Joint Ontology Workshops (JOWO) in Bolzano, Italy, in 2017 and in Graz, Austria, in 2019. The website https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/ provides further information on the workshop series.
The organizers thank everyone involved in making ICBO|ODLS 2020 happen: the team of local organizers in Bolzano, the keynote speakers, the authors of contributions, the Program Committee members, those who contributed to the organization behind the scenes, as well as those participating in the sessions, with or without their own presentation. Moreover, we appreciate the acknowledgement of the conference by the International Association for Ontology and its Applications (IAOA) as an IAOA Supported Event and we are grateful for the services provided by EasyChair and the free services provided by CEUR-WS.org.
Last but not least, we acknowledge the generous hosting of the virtual event by the Free University of Bozen-Bolzano, Italy. Frank Loebe Adrien Barton Robert Hoehndorf Phillip Lord James Overton Randi Vita Jennifer Warrender
Oliver Kutz Guendalina Righetti Nicolas Troquard
Susan Michie
Sivaram Arabandi Christopher Baker Jonathan Bona Melanie Courtot Alexander D. Diehl William Duncan Jesualdo Tomás FernándezBreis Yongqun He Heinrich Herre William Hogan Rebecca C. Jackson Ludger Jansen Mark Jensen James Malone Bjoern Peters Paul Schofield Lynn Schriml Robert Stevens Chris Stoeckert Dagmar Waltemath Yue Zhang Jie Zheng Otto-von-Guericke University Magdeburg, Germany & University College London, UK University of Leipzig, Germany CNRS-IRIT, France & Sherbrooke University, Canada King Abdullah University of Science and Technology, Saudi Arabia Newcastle University, UK Knocean, inc., Canada La Jolla Institute for Immunology, USA Newcastle University, UK Free University of Bozen-Bolzano, Italy Free University of Bozen-Bolzano, Italy Free University of Bozen-Bolzano, Italy University College London, UK Intelligent Medical Objects, USA University of New Brunswick, Canada University of Arkansas, USA EMBL-EBI, UK University at Buffalo, USA Lawrence Berkeley National Laboratory, USA University of Murcia, Spain University of Michigan, USA University of Leipzig, Germany University of Florida, USA Knocean, inc., Canada Ruhr University Bochum & University of Rostock, Germany University at Buffalo, USA SciBite, UK La Jolla Institute for Immunology, USA University of Cambridge, UK University of Maryland, USA University of Manchester, UK University of Pennsylvania, USA University of Greifswald, Germany Oregon State University, USA University of Pennsylvania, USA
Ontologies for Behavioural Science: The Human Behaviour-Change Project Behaviour change interventions (BCI), their contexts and evaluation methods are heterogeneous, making it difficult to synthesise evidence and make recommendations for realworld policy and practice. The Human Behaviour-Change Project (HBCP) is creating an online ‘Knowledge System’ that uses Artificial Intelligence, in particular Natural Language Processing and Machine Learning, to extract information from intervention evaluation reports to answer key questions about the evidence. The Knowledge System will continually search publication databases to find behaviour change intervention evaluation reports, extract and synthesise the findings, provide up-to-date answers to questions, and draw inferences about behaviour change. Practitioners, policy makers and researchers will be able to query the system to obtain answers to variants of the key question: ‘What intervention(s) work, compared with what, how well, with what exposure, with what behaviours, for how long, for whom, in what settings and why?’ Ontologies are one of the means for addressing this challenge. They represent knowledge formally as entities and relationships using a common language able to cross disciplinary boundaries and topic domains. The HBCP are developing the Behaviour Change Intervention Ontology (BCIO) to provide a systematic way to characterise BCIs, their contexts and their evaluations. The upper level of the BCIO includes the BCI scenario and the BCI evaluation study. BCI scenario entities include the behaviour change intervention (content and delivery), outcome behaviour, mechanism of action, and its context, which includes population and setting. These entities have corresponding entities relating to the planning and reporting of interventions and their evaluations. The BCIO provides a comprehensive and systematic framework for representing BCIs, their contexts and their evaluations. Session 1: 16:00 – 16:55 • Elizabeth Hobbs, Stephen Goralski, Ashley Mitchell, Andrew Simpson, Dorjan Leka, Emmanuel Kotey, Matt Sekira, James Munro, Suvarna Nadendla, Rebecca C. Jackson, Aitor Gonzalez-Agirre, Martin Krallinger, Michelle Giglio and Ivan Erill. Corpora as evolving entities: embedding corpora in biomedical ontologies. • Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Jiangan Xie, Jung Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Barry Smith, Brian Athey and Sivaram Arabandi. CIDO: The Community-Based Coronavirus Infectious Disease Ontology. • Amir Laadhar, Elcio Abrahão and Clement Jonquet. Investigating One Million XRefs in
Thirty Ontologies from the OBO World. • Jana Vataščinová, Viet Bach Nguyen, Vojtěch Svátek and Ondřej Zamazal. Best-Practice
Patterns for Biomedical Ontologies: Moving Under the Meta-Modeling Hood. Session 2: 17:00 – 17:55 • • • •
Asiyah Lin, Stephan Gebel, Qingliang Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun He and Alpha Kodamullil. CTO: A Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView Adrien Barton, Fumiaki Toyoshima and Jean-Francois Ethier. Clinical documents and their parts.
Paul Fabry, Adrien Barton and Jean-François Ethier. QUESTO – An ontology for questionnaire.
Paul Fabry, Adrien Barton and Jean-Francois Ethier. An ontological representation of sex and gender information.
Session 3: 18:00 – 18:55 Session 4: 19:05 – 20:00 • •
KEYNOTE: Susan Michie. Ontologies for Behavioural Science: The Human Behaviour-Change Project.
Rolf Grütter and C. Maria Keet. Towards a Framework for Meaning Negotiation and Conflict Resolution in Ontology Authoring. • Jona Thai and Michael Gruninger. A BioSequence Ontology from Molecular
Structure. • Georgeta Bordea, Jean Noel Nikiema, Romain Griffier, Thierry Hamon and Fleur
Mougin. FIDEO: Food Interactions with Drugs Evidence Ontology. • Pierre Lemordant, Bernard Gibaud, Cyril Garde, Sébastien Delarche, Didier Goudet and Marc Cuggia. Ontology-based classification of radiological procedures for consistent sharing in Clinical Data Warehouses. Tools & Applications Track • • •
FIDEO: Food Interactions with Drugs Evidence Ontology L.1-10 Georgeta Bordea, Jean Nöel Nikiema, Romain Griffier, Thierry Hamon, Fleur Mougin The ARK Platform: Enabling Risk Management Through M.1-10 Semantic Web Technologies Ademar Crotti Jr., Maryam Basereh, Yalemisew Abgaz, Junli Liang, Natalia Duda, Nick McDonald, Rob Brennan Ontology-Based Classification of Radiological Procedures for Consistent Sharing in Clinical Data Warehouses N.1-11 Pierre Lemordant, Bernard Gibaud, Cyril Garde, Sébastien Delarche, Didier Goudet, Marc Cuggia Posters • • • • • • • • • • • •
An Ontological Representation of Sex and Gender Information Paul Fabry, Adrien Barton, Jean-François Ethier OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses Anthony Huffman, Yongqun He Best-Practice Patterns for Biomedical Ontologies: Moving Under the Meta-Modeling Hood Jana Vataščinová, Viet Bach Nguyen, Vojtěch Svátek, Ondřej Zamazal O.1-5 P.1-5 Q.1-5 A Python Utility for Working with OBO Foundry Terms R.1-2 Jonathan P. Bona A New Alignment Method Based on FoodOn as Pivot Ontology to S.1-2 Manage Incompleteness in Nutritional Legacy Data Sources Patrice Buche, Cufi Julien, Stéphane Dervaux, Juliette Dibie, Liliana Ibanescu, Alrick Oudot, Magalie Weber The Plant Trait Ontology Links Wheat Traits for Crop Improvement and T.1-2 Genomics Laurel Cooper, Marie-Angélique Laporte, Justin Elser, Victoria Carollo Blake, Taner Z. Sen, Chris Mungall, Elizabeth Arnaud, Pankaj Jaiswal Wikidata WikiProject COVID-19: Modelling the Pandemic in Real Time U.1-2 Tiago Lubiana Current OBO Ontologies Are Not Sufficient to Annotate COVID-19- V.1-2 Related Cell Types Tiago Lubiana An Insight into Food Semantics: Review, Analysis, and Lessons Learnt W.1-2 over Food-Related Studies Gorjan Popovski, Gordana Ispirova, Eva Valenčič, Riste Stojanov, Tome Eftimov, Barbara Koroušić Seljak An Ontological Model for the (Digital) Patient X.1-2 Louis P. Ter Meer, Jan Hazelzet, Marleen de Mul Mondo Disease Ontology: Harmonizing Disease Concepts Across the World Y.1-2 Nicole Vasilevsky, Shahim Essaid, Nico Matentzoglu, Nomi L. Harris, Melissa Haendel, Peter Robinson, Christopher J. Mungall Expanding the eNanoMapper Ontology Z.1-2 Laurent A. Winckers, Egon L. Willighagen