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https://ceur-ws.org/Vol-2969/preface_jowo2021.pdf
JOWO 2021
The Joint Ontology Workshops
Proceedings of the Joint Ontology Workshops 2021
Episode VII: The Bolzano Summer of Knowledge 2.0
co-located with FOIS 2021 and ICBO 2021
Virtual & Bozen-Bolzano, Italy, September 10–18, 2021
Edited by
Emilio M. Sanfilippo | Oliver Kutz | Nicolas Troquard
Torsten Hahmann | Claudio Masolo
Robert Hoehndorf | Randi Vita
and for
CAOS | FOMI | FOUST IV
OntoCom | ROBONTICS | SoLEE
S4BioDiv | IFOW
FOIS ECS | FOIS Demo | FOIS Ontology Showcase
FOIS 2021 Workshops
M. M. Hedblom, O. Kutz, G. Righetti (CAOS V)
D. Šormaz, W. Terkaj (FOMI)
T. P. Sales, E. M. Sanfilippo (FOUST V)
S. de Cesare, F. Gailly, G. Guizzardi, M. Lycett,
C. Partridge, O. Pastor (OntoCom)
D. Beßler, S. Borgo, M. Diab, A. Gangemi,
A. Olivares-Alarcos, M. Pomarlan, R. Porzel (RobOntics)
L. Jansen, M. Brochhausen, G. Guizzardi, D. Porello (SoLEE)
ICBO 2021 Workshops
A. Algergawy, N. Karam, F. Klan, F. Michel, I. Rosati (S4BioDiv)
D. Dooley, R. Warren, H. K. McGinty, M. Lange (IFOW)
Other FOIS Satellite Events
P. Garbacz, S. Seppälä (Early-Career Symposium)
M. Grüninger (Ontology Showcase)
R. Hoehndorf, A. Vizedom (Demonstrations)
https://www.iaoa.org/jowo/2021/
PREFACE
JOWO – The Joint Ontology Workshops
These proceedings include the papers presented at JOWO 2021, the seventh edi-
tion of the Joint Ontology WOrkshops (JOWO). JOWO is a venue of workshops
that, together, address a wide spectrum of topics related to ontology research,
ranging from cognitive science to knowledge representation, natural language pro-
cessing, artificial intelligence, logic, philosophy, and linguistics.
JOWO’s mission is to provide a platform for the diverse communities interested
in building, reasoning with, and applying formalised ontologies both in theory
and applications.
The previous editions of the JOWO series were the following:
• The first JOWO edition was ‘Episode I: The Argentine Winter of Ontology’,
held in Buenos Aires, Argentina, in co-location with the 24th International
Joint Conference on Artificial Intelligence (IJCAI 2015). The proceedings of
JOWO 2015 appeared as volume 1517 of CEUR.1
• The second JOWO edition was ‘Episode II: The French Summer of Ontology’,
held in Annecy, France, in co-location with the 9th International Conference
on Formal Ontology in Information Systems (FOIS 2016). The proceedings of
JOWO 2016 appeared as volume 1660 of CEUR.2
• The third JOWO edition was ‘Episode III: The Tyrolean Autumn’, hosted by
the Free University of Bozen-Bolzano in Bolzano, Italy, in September 21–23,
2017. The proceedings of JOWO 2017 appeared as volume 2050 of CEUR.3
• The fourth JOWO edition was ‘Episode IV: The South African Spring (JOWO
2018 @ FOIS 2018)’, held in Cape Town, South Africa, in co-location with
the 10th International Conference on Formal Ontology in Information Systems
(FOIS 2018). The proceedings of JOWO 2018 appeared as volume 2205 of
CEUR.4
• The fifth JOWO edition was ‘Episode V: The Styrian Autumn of Ontology
(JOWO 2019)’, held in Graz, Austria, on September 23–25, 2019. The proceed-
ings of JOWO 2019 appeared as volume 2518 of CEUR.5
• The sixth JOWO edition was ‘Episode VI: The Bolzano Summer of Knowledge
(JOWO 2020)’, (virtually) held in Bolzano, Italy, between August 31st and
October 7th, 2020. The proceedings of JOWO 2020 appeared as volume 2708
of CEUR.6
1 See http://ceur-ws.org/Vol-1517/.
2 See http://ceur-ws.org/Vol-1660/.
3 See http://ceur-ws.org/Vol-2050/.
4 See http://ceur-ws.org/Vol-2205/.
5 See http://ceur-ws.org/Vol-2518/.
6 See http://ceur-ws.org/Vol-2708/.
1
JOWO 2021 comprised a confederation of 11 ontology workshops that were asso-
ciated with the 12th International Conference on Formal Ontology in Information
Systems (FOIS 2021) or the 12th International Conference on Biomedical Ontolo-
gies (ICBO 2021). The workshops were, just like the main conferences themselves,
held in a hybrid format with the physical component taking place at the Free
University of Bozen-Bolzano, Italy.
The workshops cover a broad spectrum of contemporary applied ontology re-
search, including its foundational aspects (FOUST V, OntoCom) as well as the ap-
plication of ontologies in specific domains, in particular, cognitive science (CAOS
V), industry (FOMI), robotics (RobOntics), social, legal and economic domains
(SoLEE), life sciences (S4BioDiv, IFOW).
A total of 95 workshop papers were submitted for this volume, of which 79 were
accepted.
FOIS workshop proceedings published in this volume:
• CAOS V: 5th International Workshop on Cognition And Ontologies7
• FOMI: 11th International Workshop on Formal Ontology meets Industry8
• FOUST V: 5th Workshop on Foundational Ontologies9
• OntoCom: 8th International Workshop on Ontologies and Conceptual Mod-
elling10
• RobOntics: 2nd International Workshop on Ontologies for Autonomous
Robotics11
• SoLEE: 2nd International Workshop on Ontology of Social, Legal and Eco-
nomic Entities12
ICBO workshop proceedings published in this volume:
• IFOW: 2nd Integrated Food Ontology Workshop13
• S4BioDiv: 3rd International Workshop on Semantics for Biodiversity14
In addition, this volume publishes the short papers from three satellite events
associated with FOIS 2021:
• Early Career Symposium: A venue for current graduate students to present
and discuss their research programme with the ontology community
• Ontology Showcase: Short papers that describe existing ontologies in order
to facilitate the sharing and reuse of ontologies
• Demonstrations: Short papers that accompany demonstrations of software,
methodologies, patterns, dynamics, and challenges arising in use of ontologies
at FOIS 2021
7 See http://caos.inf.unibz.it/.
8 See https://www.ohio.edu/fomi2021/.
9 See https://foust.inf.unibz.it/.
10 See https://www.mis.ugent.be/ontocom2021/.
11 See https://robontics2021.github.io/.
12 See https://soleeworkshop.wordpress.com/.
13 See https://foodon.org/ifow-2021-workshop/.
14 See https://fusion.cs.uni-jena.de/s4biodiv2021/.
2
Acknowledgements
We would like to thank all authors and speakers for their contributions, and
the programme committee members and additional reviewers for their timely
reviewing. Moreover, we would like to thank the Free University of Bozen-Bolzano
for their generous event support and sponsoring and the International Association
for Ontology and its Applications (IAOA)15 for providing support and facilities.
FOIS Workshops and Tutorials Chairs
Torsten Hahmann University of Maine, USA
Claudio Masolo Laboratory for Applied Ontology (ISTC-CNR), Italy
ICBO Workshops and Tutorials Chairs
Randi Vita La Jolla Institute for Immunology, USA / OBO Foundry
Robert Hoehndorf King Abdullah University of Science and Technology (KAUST),
Saudi Arabia
Local Chairs
Oliver Kutz Free University of Bozen-Bolzano, Italy
Nicolas Troquard Free University of Bozen-Bolzano, Italy
Proceedings Chair
Emilio M. Sanfilippo Laboratory for Applied Ontology (ISTC-CNR), Italy
Web Chair
Selja Seppälä University College Cork, Ireland
JOWO Steering Committee
Stefano Borgo Laboratory for Applied Ontology (ISTC-CNR), Italy
Oliver Kutz Free University of Bozen-Bolzano, Italy
Frank Loebe University of Leipzig, Germany
Fabian Neuhaus Otto-von-Guericke-University of Magdeburg, Germany
15 See http://iaoa.org.
3
JOWO 2021:
FOIS 2021 Workshops
CAOS V
5th International Workshop on Cognition And Ontologies
Programme Chairs
Maria M. Hedblom University of Bremen, Germany
Guendalina Righetti Free University of Bozen-Bolzano, Italy
Oliver Kutz Free University of Bozen-Bolzano, Italy
Programme Committee
Ana Tanevska Italian Institute of Technology, Italy
Ana-Maria Olteteanu Free University Berlin, Germany
Antonio Lieto University of Turin, Italy
Brandon Bennett University of Leeds, UK
Daniel Beßler University of Bremen, Germany
Daniele Porello University of Genova, Italy
Gabriele Kern-Isberner University of Dortmund, Germany
João Miguel Cunha University of Coimbra, Portugal
Karl Hammar Jönköping University, Sweden
Lucas Bechberger Osnabrück University, Germany
Marco Schorlemmer Artificial Intelligence Research Institute, IIIA-CSIC, Spain
Michaël Verdonck Universitair Ziekenhuis Brussel, Belgium
Roberta Ferrario Laboratory for Applied Ontology (ISTC-CNR), Italy
Sanju Tiwari Universidad Autonoma de Tamaulipas, Mexico
Taisuke Akimoto Kyushu Institute of Technology, Japan
Tony Veale University College Dublin, Irland
Ever since its first edition was held in Annecy, France, in July 2016, ‘CAOS: Cog-
nition And OntologieS’ is devoted to the formal modelling, the ontology, and the
simulation and representation of the relationships between cognition, behaviour
and thought. With the primary focus on how key cognitive phenomena and be-
haviours can be formally represented to aid the advancement of artificial intelli-
gence, knowledge representation and cognitive robotics towards more cognitively
plausible, explainable, and human-friendly directions, CAOS has become a venue
for researchers on all career levels to discuss their work.
CAOS thus aims to engage a diverse and interdisciplinary audience coming from
research areas in philosophy and linguistics, psychology, cognitive science and
computer science, and related fields. The purpose of the workshop is to promote
the development of excellent research, strengthen research collaborations, and to
offer a venue where unconventional topics can be discussed in an open, yet chal-
lenging and ambitious environment. Therefore, we are happy that the fifth edition
of CAOS has accepted papers from a broad spectrum of topics.
4
Contributions to the workshop range from logical treatments of areas such as
formal concept combinations and narrative structure, to ontological issues of cog-
nitive bias and rhetorical figures. In addition, it includes works that investigate
more applied areas within cognitive ontologies, such as the use of image schemas
in cognitive robotics, hybrid AI systems combining neural networks with seman-
tics, and the lexicalisation of visual properties of concepts. Perhaps due to the
hybrid format of the workshop, we are proud to announce that the eight accepted
submissions are authored by people from four different countries and seven dif-
ferent institutions. The interdisciplinary CAOS community also shows an excel-
lent gender balance, with half of the accepted papers first-authored by women
(and a total of around 25 percent female authors). Likewise, our program com-
mittee consists of a wide variety of scholars with expertise from different scientific
backgrounds and 16 different institutions.
FOMI
11th International Workshop on Formal Ontology meets Industry
Programme Chairs
Dušan Šormaz Department of Industrial and Systems Engineering, Ohio Univer-
sity, USA
Walter Terkaj Institute for Intelligent Industrial Systems and Technologies for
Advanced Manufacturing (STIIMA-CNR) Italy
Programme Committee
Arkopaul Sarkar ENIT, France
Bahar Aameri University of Toronto, Canada
Bob Young Loughborough University, UK
Boonserm Kulvatunyou National Institute of Standards and Technology, USA
Daniele Spoladore STIIMA-CNR, Italy
David Koonce Ohio University, USA
Dimitris Kiritsis École Polytechnique Fédérale de Lausanne, Switzerland
Dimitris Mourtzis University of Patras, Greece
Eeva Järvenpää Tampere University of Technology, Finland
Elisa Negri Politecnico di Milano, Italy
Emilio M. Sanfilippo Laboratory for Applied Ontology (ISTC-CNR), Italy
Farhad Ameri Texas State University, USA
Georg Schneider Schaeffler, Germany
Hedi Karray ENIT, France
Hervé Panetto University of Lorraine, France
Hyunmin Cheong Autodesk Research, Canada
José Parente De Oliveira Technological Institute of Aeronautics, Brazil
Lorenzo Solano Polytechnic University of Valencia, Spain
Marı́a Poveda-Villalon Universidad Politécnica de Madrid, Spain
Michael Grüninger University of Toronto, Canada
Pedro Rosado Castellano Universitat Jaume I de Castelló, Spain
Pieter Pauwels Eindhoven University of Technology, Netherlands
5
Rebeca Arista Rangel Airbus, Spain
Riichiro Mizoguchi Japan Advanced Institute of Science and Technology, Japan
Stefano Borgo Laboratory for Applied Ontology, (ISTC-CNR), Italy
Tiago Prince Sales Free University of Bozen-Bolzano, Italy
FOMI is an international forum where academic researchers and industrial practi-
tioners meet to analyse and discuss application issues related to methods, theories,
tools and applications based on formal ontologies. There is today wide agreement
that knowledge modelling and the semantic dimension of information play an in-
creasingly central role in networked economy: semantic-based applications aim to
provide a framework for information and knowledge sharing, reliable information
exchange, meaning negotiation and coordination between distinct organizations
or among members of the same organization. Theoretical ideas seem often very
promising but their actual implementation brings up unexpected problems and
issues. The FOMI 2021 Workshop deals with:
1. Experience with problems in ontology application;
2. New insights on known problematic issues;
3. New results;
4. Successes and observations in ontology implementation;
5. Lessons learned on the best way to apply ontological methodologies to real-
world situations
FOMI 2021 will facilitate open discussion and experience sharing. Very similar
problems arise in disparate ontology applications and an open discussion helps
to highlight commonalities and to spread ideas for possible solutions. For this
reason, FOMI welcomes researchers and practitioners that embrace this perspec-
tive without restrictions on the domains they deal with: business, medicine, en-
gineering, finance, law, biology, geography, electronics, etc. Indeed, the accepted
contributions at FOMI 2021, nine in total, tackle heterogeneous topics.
Three works are related to the aerospace industry, addressing the reconfiguration
of production systems (Arista et al.), the modelling of aircraft assembly processes
(Zheng et al.), and the modelling of flight procedures (Tarbouriech et al.). Two
more papers deal with the manufacturing domain, in particular maintenance of
manufacturing assets (Woods et al.) and modelling of manufacturing resource ca-
pabilities (Borgo et al.). Other specific domains are addressed like the construc-
tion industry (Cao et al.), the corrosion protection of metallic surfaces (Klein
et al.), the modelling of assembled systems (Compagno et al.), and web services
to support ontology-driven conceptual modelling (Fonseca et al.). In addition,
different foundational ontologies are exploited in the industrial applications, like
PSL (Tarbouriech et al.), DOLCE (Borgo et al.), UFO (Fonseca et al.), and BFO
(Zheng et al., Woods et al.).
6
FOUST V
5th Workshop on Foundational Ontology
Programme Chairs
Tiago Prince Sales Free University of Bozen-Bolzano, Italy
Emilio M. Sanfilippo Laboratory for Applied Ontology (ISTC-CNR), Italy
Programme Committee
Adrien Barton Institut de Recherche en Informatique de Toulouse, CNRS, France
Andrew Spear Grand Valley State University, USA
Antony Galton University of Exeter, UK
Bahar Aameri University of Toronto, Canada
Barry Smith University of Buffalo, USA
Boyan Brodarich Geological Survey of Canada, Canada
Claudenir M. Fonseca Free University of Bozen-Bolzano, Italy
Claudio Masolo Laboratory for Applied Ontology, (ISTC-CNR), Italy
Daniele Porello University of Genova, Italy
Frank Loebe University of Leipzig, Germany
Fumiaki Toyoshima Université de Sherbrooke, Canada
Giancarlo Guizzardi Free University of Bozen-Bolzano, Italy; University of Twente, The
Netherlands
Jim Logan NoMagic Inc, USA
João Paulo Almeida Federal University of Espı́rito Santo, Brazil
John Bateman University of Bremen, Germany
Laure Vieu Institut de Recherche en Informatique de Toulouse, CNRS, France
Ludger Jansen University of Rostock, Germany
Markus Stumptner University of South Australia, Australia
Massimiliano Carrara University of Padova, Italy
Mattia Fumagalli Free University of Bozen-Bolzano, Italy
Michael Grüninger University of Toronto, Canada
Nicola Guarino Laboratory for Applied Ontology (ISTC-CNR), Italy
Nicolas Troquard Free University of Bozen-Bolzano, Italy
Pawel Garbacz John Paul II Catholic University of Lublin, Poland
Pierre Grenon National Center for Ontological Research, Buffalo, USA
Riichiro Mizoguchi Japan Advanced Institute of Science and Technology, Japan
Roberta Ferrario Laboratory for Applied Ontology (ISTC-CNR), Italy
Stefano Borgo Laboratory for Applied Ontology (ISTC-CNR), Italy
Foundational ontology is about categories of reality or thought which are common
to all or almost all subject-matters. Commonly considered examples of such cat-
egories include ‘object’, ‘quality’, ‘function’, ‘role’, ‘process’, ‘event’, ‘time’, and
‘place’. There are several foundational ontologies that provide a systematic for-
mal representation of these categories, their relationships, and interdependencies.
Amongst existing foundational ontologies, there is both a substantial measure
of agreement and some dramatic disagreements. There is currently no uniform
consensus concerning how a foundational ontology should be organised, how far
its ‘reach’ should be (e.g., is the distinction between physical and non-physical
7
entities sufficiently fundamental to be included here?), and even what role it
should play in relation to more specialised domain ontologies.
The main use of foundational ontologies is as a starting point for the development
of domain ontologies and application ontologies. A foundational ontology provides
an ontology engineer with a conceptual framework that enables her to analyse a
given domain, identify the entities in the domain as specialisations of the generic
categories in the foundational ontology, and often reuse relationships (e.g., part-
hood) from the foundational ontology. The utilisation of foundational ontologies
for the development of domain and application ontologies has two main benefits.
Firstly, the ontology engineer can reuse an existing set of well-studied ontological
distinctions and design principles instead of having to develop an ad-hoc solution.
Secondly, if two domain ontologies are based on the same foundational ontology,
it is easier to integrate them.
FOUST is an ontology workshop series that offers researchers in foundational
ontology an opportunity to present their results. This includes work on specific
areas of foundational ontology as well as work on a particular foundational ontol-
ogy. Topics covered in this edition of FOUST include, amongst others, processes,
events, functions, roles, and identity criteria.
OntoCom
8th International Workshop on Ontologies and Conceptual Modelling
Programme Chairs and Committee
Sergio de Cesare University of Westminster, UK
Frederik Gailly Ghent University, Belgium
Giancarlo Guizzardi Free University of Bozen-Bolzano, Italy; University of Twente, The
Netherlands
Mark Lycett Royal Holloway, University of London, UK
Chris Partridge BORO Solutions Ltd., UK; University of Westminster, UK
Oscar Pastor Universitat Politécnica de Valencia,, Spain
The International Workshop on Ontologies and Conceptual Modelling (OntoCom)
is an academic workshop that concerns the practical and formal application of
ontologies to conceptual modelling. While models pervade the information sys-
tems lifecycle from requirements to implementation, there appears to be a lack
of theoretical foundation in the way that models are developed. As a result it
is quite common for practitioners, even working together, to produce different
representations of the same real world domain or system. Conversely, a preferred
approach would be one in which IS practitioners have the necessary conceptual
tools to enable them to accurately represent the things that exist in the real
world. Foundational or upper ontologies have the potential to resolve the difficult
problems that derive from a lack of a consistent and sound ontological theory. The
8
benefits that can derive from the application of a foundational ontology include
improved mapping to the real world domain, increased level of communication
and understanding among stakeholders, model reuse, semantic integration and
interoperability and increased overall efficiency and effectiveness of information
systems development and evolution. The theme of OntoCom continues to be foun-
dational ontologies and their meta-ontological choices. The workshop will be both
theoretically and practically oriented with discussions and worked examples.
RobOntics
2nd International Workshop on Ontologies for Autonomous Robotics
Programme Chairs
Daniel Beßler University of Bremen, Germany
Stefano Borgo Laboratory for Applied Ontology (ISTC-CNR), Italy
Mohammed Diab Imperial College London, UK
Aldo Gangemi University of Bologna, Italy; ISTC-CNR, Italy
Alberto Olivares-Alarcos Institut de Robòtica i Informàtica Industrial (CSIC-
UPC), Spain
Mihai Pomarlan University of Bremen, Germany
Robert Porzel University of Bremen, Germany
Programme Committee
Julita Bermejo Universidad Isabel I, Spain
Maria M. Hedblom University of Bremen, Germany
Sebastian Höffner University of Bremen, Germany
Oliver Kutz Free University of Bozen-Bolzano, Italy
Daniele Porello University of Genova, Italy
Ricardo Sanz Bravo Universidad Politécnica de Madrid, Spain
Paulo Jorge Sequeira Gonçalves Polytechnic Institute of Castelo Branco, Portugal
Elisa Tosello University of Padova, Italy
Abhijit Vyas University of Bremen, Germany
RobOntics focuses on the area of robot autonomy enabled by knowledge-driven
approaches, and in particular formal ontologies. It aims to foster interaction across
robotics, ontology, and knowledge representation and reasoning, to match open
problems to promising approaches, and to review progress in knowledge-driven
robotics.
A partial list of topics of interest includes:
• Foundational issues: which ontological approaches are better suited for au-
tonomous robotics? how should notions such as capability or context be mod-
elled?
• Robustness: how can ontologies help robots cope with the variety and relatively
fluid structure of human environments?
9
• Ontologies in the perception-action loop: how might ontologies be used to rec-
ognize action possibilities?
• Interactivity: how should conversations be formalized, in particular the giving
of instructions?
• Normed behavior: how can we represent, and then have a robot act according
to, norms on behavior?
• Explainability: what is an explanation, and how can one be generated from a
collection of knowledge items?
SoLEE
2nd International Workshop on Ontology of Social, Legal and Economic
Entities
Programme Chairs
Ludger Jansen University of Rostock, Germany
Mathias Brochhausen University of Arkansas for Medical Sciences, Little Rock
Giancarlo Guizzardi Free University of Bozen-Bolzano, Italy; University of Twente, The
Netherlands
Daniele Porello University of Genova, Italy
Programme Committee
Mauricio Almeida Universidade Federal de Minas Gerais, Brasil
Mike Bennett Hypercube Ltd., UK
Roberta Ferrario Laboratory for Applied Ontology (ISTC-CNR), Italy
Mattia Fumagalli Free University of Bozen-Bolzano, Italy
Cristine Griffo Free University of Bozen-Bolzano, Italy
Paul Johannesson Royal Institute of Technology, Sweden
Riichiro Mizoguchi JAIST, Japan
J. Neil Otte Johns Hopkins University, USA
Tiago Prince Sales Free University of Bozen-Bolzano, Italy
Barry Smith University at Buffalo, USA
Understanding the ontological nature of social, legal and economic concepts and
institutions is crucial for providing principled modelling in many important do-
mains, such as enterprise modelling, business processes, and social ontology. A
significant number of fundamental concepts that are ubiquitous in economics, so-
cial, and legal sciences (such as value, risk, capability, good, service, exchange,
transaction, competition, social norm, group, institution) have only recently been
approached from a specifically ontological perspective. It is therefore important
to offer a venue to gather the recent contributions to this topic. The workshop
encouraged submissions on both theoretical and methodological issues in the use
of ontologies for modelling social, legal and economic concepts and institutions, as
well as submissions on concrete use of ontologies in application for these domains.
10
The first SoLEE workshop took place in 2019 at JOWO in Graz, Austria, con-
tinuing strands of discusssions from two previous events, SoLE-BD and Ontology
of Economics 2018. The SoLEE workshop intends to broaden the focus in order
to explore the emerging question of how to deal with social entities in general,
and to connect well established domains like biomedicine and business ontologies
in this respect. As its precursors, SoLEE 2021 collects approaches to deal with
social, legal and economic entities in foundational and applied ontologies and dis-
cusses applications of these approaches to social, legal and economic entities in
ontologies for biomedicine and business informatics.
11
ICBO 2021 Workshops
IFOW
2nd Integrated Food Ontology Workshop
Programme Chairs
Damion Dooley Simon Fraser University, Canada
Robert Warren Myra Analytics, Toronto
Hande Küçük McGinty Ohio State University
Matthew Lange Int. Center for Food Ontology Operability Data and Semantics
Programme Committee
Chen Yang Ghent University, Belgium
Gurinder Pal Simon Fraser University, Canada
Larisa Soldatova University of London, UK
Leigh Carmody Robinson Lab / Jackson Laboratory, USA
Melissa Haendel Oregon State University, USA
Lauren Chan Oregon State University, USA
Lynn Schriml University of Maryland, USA
Duccio Cavalieri University of Florence, Italy
Tarini Naravane University of California, Davis, USA
Damion Dooley University of British Columbia, Canada
Jessica Singer Myra Analytics, Canada
Ontologies are new entrants into the food controlled vocabulary domain, bring-
ing a wave of Semantic Web technology and philosophy to bear on the issue
of data sharing and modeling of food-related activity and research which are
becoming critical in the face of rapid change to our environment and anthro-
posphere. Examples range from BBC’s Food Ontology, driving its culinary me-
dia universe, to recent research laboratory initiated ontologies like OBOFoundry
members FoodOn, the Food Biomarker Ontology (FOBI), the Ontology for Nu-
tritional Studies (ONS), the Ontology for Nutritional Epidemiology (ONE), the
Food Interactions with Drugs Evidence Ontology (FIDEO), and the Crop Di-
etary Nutrition Ontology (CDNO). Underpinning these mid-level, model-focused
ontologies are environmental, chemical, biological, anatomical, disease and phe-
notype ontologies.
Academic, agricultural and public health agencies are considering the benefits and
complexities of adopting ontology in their research and data management and re-
porting infrastructure. How can ontologies interface to legacy datasets and online
databases described by existing vocabularies? What vocabulary, tool ecosystem
and data models are needed to correlate agricultural treatments, nutritional data,
eating patterns, biomarkers, pathogens, and phytochemical levels with disease
and health phenotypes? Encouraged by the success of the inaugural 2020 IFOW
workshop, this second round in 2021 will explore the evolution of food-related
12
ontologies as they integrate ecological, agricultural, nutritional, dietary, public
health, one health surveillance, food security, and trade domain vocabulary, and
the use of curation, validation, mapping and visualization tools for food ontology
maintenance.
S4BioDiv
3rd International Workshop on Semantics for Biodiversity
Programme Chairs
Alsayed Algergawy Institute of Computer Science, Friedrich-Schiller-Universität Jena,
Germany
Naouel Karam Fraunhofer Institute for Open Communication Systems (FOKUS)
& Institute for Applied Informatics (InfAI e.V.), Germany
Friederike Klan Institute of Data Science, German Aerospace Center (DLR e.V.),
Germany
Franck Michel Université Cote d’Azur, CNRS, Inria, France
Ilaria Rosati Research Institute on Terrestrial Ecosystems (IRET) – Italian Na-
tional Research Council (CNR) & LifeWatch Italy
Programme Committee
Alessandro Oggioni IREA, National Research Council, Milan, Italy
Anne Toulet CIRAD Montpellier, France
Barabara Magagna Environmental Agency, Austria
Birgitta Koenig-Ries FSU Jena, Germany
Caterina Bergami ISMAR, National Research Council, Bologna, Italy
Catherine Faron Wimmics, Univ. Côte d’Azur, Inria, Sophia-Antipolis, France
Catherine Roussey IRSTEA Clermont-Ferrand, France
Claire Nédellec MaIAGE, INRA Jouy-en-Josas, France
Claus Weiland Senckenberg Biodiversity and Climate Research Centre, Germany
Clement Jonquet LIRMM, University of Montpellier, France
Dilvan Moreira Department of Computer Science, University of São Paulo
Faiez Gargouri Sfax University, Tunisia
Felicitas Löffler FSU Jena, Germany
Isabelle Mougenot ESPACE-DEV, University of Montpellier, France
Konstantin Todorov LIRMM, University of Montpellier, France
Mark Schildhauer National Center for Ecological Analysis and Synthesis, USA
Nicola Fiore LifeWatch ERIC, Italy
Olivier Corby Wimmics, Univ. Côte d’Azur, Inria Sophia-Antipolis, France
Oscar Corcho Universidad Politécnica de Madrid, Spain
Pierre Larmande DIADE, IRD, France
Salima Benbernou Université Paris 5, France
Biodiversity deals with heterogeneous data and concepts generated from a large
number of disciplines in order to build a coherent picture of the extent of life on
earth. The presence of such a myriad of data resources makes integrative biodi-
versity research increasingly important, as well as challenging given the variety
13
of ways in which data and information are produced and made available. The
Semantic Web approach enhances data discoverability, sharing, interoperability
and integration through a formalized conceptual environment providing common
formats, standards, and terminological resources. This workshop aims to bring
together computer scientists and biologists, working on Semantic Web approaches
for biodiversity, ecology and related areas such as plant sciences, agronomy, agroe-
cology or citizen science related to biodiversity. The goal is to exchange experi-
ences, build a state of the art of realizations and challenges, and reuse and adapt
solutions that have been proposed in other domains. The workshop focuses on
presenting challenging issues and novel solutions for the design of high-quality
biodiversity information systems leveraging Semantic Web techniques.
S4BioDiv 2021 welcomed topics related to the application and development of
semantic web technologies to support research in the biodiversity domain and
related areas. These include, but are not limited to the following areas:
• Applications of Semantic Web technologies for biodiversity
• Semantic representation of biodiversity data
• Ontology (or semantic resource) development for biodiversity
• Knowledge extraction and text mining
• Semantic annotation of biodiversity data
• Semantic data integration
• Development and design of domain-specific ontologies
• Ontology-based applications
• Semantic approaches for the discovery of biodiversity data and research data
services
• Semantic support for scientific workflows
• Data provenance and reproducibility
• Data lifecycle management
• Ontology learning
• Standards for biodiversity Data
• Linked Open biodiversity Data
• Interoperability of biodiversity and earth observation data
• FAIR biodiversity data with semantics
• Interoperability of biodiversity and earth observation data
• Enhancement of machine learning approaches with Semantic Web technologies
Application domains:
• Biodiversity
• Agronomy, agro-ecology, agro-biodiversity
• Plant sciences
• Citizen Science related to biodiversity and related fields
The workshop is a full-day event on September 15th co-located with the 12th In-
ternational Conference on Biomedical Ontologies (ICBO 2021), September 15-18,
Bolzano, Italy. In total, 11 paper submissions presenting new research results and
ongoing projects have been submitted. All of these were reviewed by at least three
members of the program committee. Out of the submitted contributions, four full
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papers, two short papers, and four poster papers were accepted for presentation
at the workshop and publication in these proceedings. The program included two
keynote talks highlighting two vital and challenging topics related to biodiversity
research and Open Science in general. Michael Diepenbroek, Senior consultant at
the National Research Data Infrastructure for Biodiversity (NFDI4BioDiversity)
and senior head of the World Data Center PANGAEA, talked about ”The appli-
cation of semantic resources and technologies for the discovery and integration of
geo- and biosciences data”. Mark Schildhauer, was the Director of Computing at
NCEAS from its opening in 1995 until 2017, presented his thoughts on ””.
We very much appreciate the financial support kindly provided by the Collabora-
tive Research Centre AquaDiva (CRC 1076) funded by the Deutsche Forschungs-
gemeinschaft (DFG). Finally, we thank all authors who submitted their work to
the workshop and all reviewers for their valuable support.
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Other FOIS 2021 Satellite Events
FOIS 2021 Early Career Symposium
Programme Chairs
Pawel Garbacz The John Paul II Catholic University of Lublin, Poland
Selja Seppälä University College Cork, Ireland
Programme Committee/Mentors
Mara Abel Universidade Federal do Rio Grande do Sul, Brazil
Adrien Barton Institut de Recherche en Informatique de Toulouse, France
Olivier Bodenreider US National Library of Medicine, USA
Maureen Donnelly SUNY Buffalo, USA
Pawel Garbacz The John Paul II Catholic University of Lublin, Poland
Giancarlo Guizzardi Federal University of Espirito Santo (UFES), Brazil
Emilio M. Sanfilippo Laboratory for Applied Ontology (ISTC-CNR), Italy
Selja Seppälä University College Cork, Ireland
Barry Smith SUNY Buffalo, USA
For any conference, the Early Career Symposium (ECS) represents the invest-
ment done by the current generation of researchers into the future generations
of the field. Arguably, while established researchers contribute to strengthening
the fundamentals of the research field, it is often the young generation that pro-
vides innovation and groundbreaking ideas. In order to foster the state of art in
ontology research, the ECS at FOIS welcomes early stage researchers working
on innovative and novel research topics for presentation at the conference. The
symposium encourages mentorship among established and emerging researchers
towards constructive discussions surrounding novel research. As the future re-
mains unwritten, the ECS accepts a wide variety of research topics focused on
ontologies and knowledge representation. In particular, because of its contextual-
isation within FOIS, it welcomes research addressed in an interdisciplinary way
with an open-minded aptitude towards philosophical ontology, cognitive science,
and linguistics.
This year, the ECS committee accepted seven students that were invited to
present their work in the ECS. The topics covered diverse areas: formal approaches
to procedures, construed in terms of canonical forms, and to events, construed as
transitions among situations; goal-oriented conceptual modelling; use of upper-
level ontologies to improve metrics for semantic similarity and relatedness evalu-
ation; use of domain ontologies in explainable AI in legal classification systems;
ontological engineering for offshore petroleum production plants; and principles
of conceptual modelling based on dialectical materialism.
We wish to thank the PC members for their constructive feedback.
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FOIS 2021 Demonstrations
Programme Chairs
Amanda Vizedom Credit Suisse, USA
Robert Hoehndorf King Abdullah University of Science and Technology, Saudi Arabia
Programme Committee
Dean Allemang Working Ontologist LLC, USA
Jennifer Cooper Apple, USA
Anna Maria Masci Duke University, USA
Núria Rosinach Leiden University Medical Center, The Netherlands
Jesualdo Tomás Fernández-Breis Universidad de Murcia, Spain
Meika Ungricht Semantic Arts, Inc., USA
New to FOIS this year, the demonstrations track sought to complement the re-
search tracks by offering a series of action, interaction, and process-focused events.
The scope was drawn broadly to include software, methodologies, patterns, dy-
namics, and challenges. A goal of FOIS Demonstrations is to raise the visibility
and foster understanding of the dynamic, integrative, and use-oriented aspects of
applied ontology and its tools. The emphasis is on what happens.
This year’s demonstrations include, in various combinations, software, software
architecture, ontology design patterns, and methodologies. Huffer and Handley
present a pipeline in which ontologies and machine learning are used to create
metadata for datasets in NASA’s vast collection, then to make those datasets
discoverable and reusable. Bouter, Kruiger, and Verhoosel offer a data process-
ing and integration tool that uses a domain-independent ontology to generalize
an Ontology-Based Data Access method originally developed in the context of
horticulture. Flügel, Kleinau, Neuhaus, Glauer, and Hastings present a tool for
translating OWL ontologies to FOL, aiming at an expressivity gap that often im-
pedes integration of domain and upper ontologies. Fornara and Sterpetti present
a system architecture that uses OWL reasoning and forward chaining to moni-
tor conditions in relation to norms. Queralt-Rosinach, Wilkinson, Kaliyaperumal,
Bernabé, Long, Dumontier, Schofield, and Roos present a design pattern and a
method for applying it in modeling of heterogenous health care datasets, improv-
ing interoperability. Hunt offers a design pattern for modeling heterogenous data
while satisfying real-world requirements, via canonical entities.
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FOIS 2021 Ontology Showcase
Programme Chair and Programme Committee
Michael Grüninger University of Toronto, Canada
Roberta Ferrario Laboratory for Applied Ontology (ISTC-CNR), Italy
As the Applied Ontology community, we have reached the point where an impres-
sive variety of ontologies have been developed across a wide range of domains. For
the most part, however, there has been a lack of coordination among these efforts
and even a lack of awareness about the work that is being done by groups within
the community. How can we best support ontology repositories so that curated
ontologies are findable and accessible? What are the barriers to sharability and
reusability that still exist? The Ontology Showcase will be the venue that facili-
tates the sharing and reuse of ontologies, with the goal of achieving the vision of
seamless semantic interoperability of curated ontologies within their applications.
Submissions should follow the scope and evaluation criteria for the main track
for FOIS, giving an overview of the ontology and its application. In particular,
submissions should address the following questions:
• What is the domain of the ontology?
• How is the ontology being used? e.g. search, question answering, semantic in-
tegration
• What datasets are used in these applications?
• What other ontologies are reused?
• Are there other ontologies within the same domain?
• What are the competency questions used for the design and evaluation of the
ontology?
The Ontology Showcase will facilitate open discussion and experience sharing.
Very similar problems arise in disparate ontology applications and an open dis-
cussion helps to highlight commonalities and to spread ideas for possible solu-
tions. For this reason, FOMI welcomes researchers and practitioners that embrace
this perspective without restrictions on the domains they deal with: business,
medicine, engineering, finance, law, biology, geography, electronics, etc.
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