ROBONTICS j SKALE j WOMoCoE http://www.iaoa.org/jowo/2020/
(DeepOntoNLP) (FOUST IV) (RobOntics)
(SKALE) (WOMoCoE)
These proceedings include the papers presented at JOWO 2020, the sixth edition 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 processing, arti cial 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 rst 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 Arti cial 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 fth JOWO edition was `Episode V: The Styrian Autumn of Ontology (JOWO 2019)', held in Graz, Austria, on September 23{25, 2019. The proceedings of JOWO 2019 appeared as volume 2518 of CEUR.5 JOWO 2020 comprised a confederation of nine ontology workshops, covering a broad spectrum of contemporary applied ontology research, including its foundational aspects (FOUST IV), its methodology, evaluation and collaboration (WOMoCoE, COB) and scalable ontology tooling supporting industrial uptake (SKALE). The JOWO workshops also discussed and contributed to the appli1See http://ceur-ws.org/Vol-1517/. 2See http://ceur-ws.org/Vol-1660/. 3See http://ceur-ws.org/Vol-2050/. 4See http://ceur-ws.org/Vol-2205/. 5See http://ceur-ws.org/Vol-2518/. cation of and intersection between ontology and other technologies, including deep learning (DeepOntoNLP), robotics (RobOntics), agriculture and nutrition (IFOW), the life sciences (CELLS, VDOS).
The proceedings of ve of those workshops are presented in this volume, while the remaining four will publish proceedings through, e.g., journal special issues. A total of 43 papers were submitted for this volume, of which 32 were accepted. JOWO workshops published in this volume: • DeepOntoNLP: Deep Learning meets Ontologies and Natural Language Processing { 1st International Workshop6 • FOUST IV: 4th Workshop on Foundational Ontologies7 • RobOntics: International Workshop on Ontologies for Autonomous Robotics8 • SKALE: Workshop on Scalable Knowledge Graph Engineering9 • WOMoCoE: 5th International Workshop on Ontology Modularity, Contextuality, and Evolution10
• CELLS: 4th International Cells in Experimental Life Science Workshop11 • COB: A Core set of Open Biological and Biomedical Ontology (OBO) Foundry
Terms • IFOW: Integrated Food Ontology Workshop12 • VDOS: 9th International Workshop on Vaccine and Drug Ontology Studies 13 6See https://www.dl-onto-nlp-fois2020.ml. 7See https://foust.inf.unibz.it/foust4. 8See https://robontics2020.github.io. 9See https://skale-workshop.gitlab.io. 10See https://womocoe20.fbk.eu. 11See https://sites.google.com/view/cells-2020-workshop/home. 12See https://foodon.org/icbo-2020-food-workshop/. 13See https://sites.google.com/site/vdosworkshop/VDOS-2020. 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 International Association for Ontology and its Applications (IAOA)14 for providing support and facilities.
Anastasia Dimou Karl Hammar Torsten Hahmann Claudio Masolo Randi Vita Robert Hoehndorf
Oliver Kutz
Karl Hammar
Selja Seppala
Ghent University, Belgium Jonkoping University, Sweden University of Maine, USA Laboratory for Applied Ontology, ISTC-CNR, Italy La Jolla Institute for Immunology, USA / OBO Foundry King Abdullah University of Science and Technology (KAUST), Saudi Arabia Free University of Bozen-Bolzano, Italy Jonkoping University, Sweden
University College Cork, Ireland
Stefano Borgo Oliver Kutz Frank Loebe Fabian Neuhaus
Laboratory for Applied Ontology, ISTC-CNR, Italy Free University of Bozen-Bolzano, Italy University of Leipzig, Germany
Otto-von-Guericke-University of Magdeburg, Germany 14See http://iaoa.org. JOWO 2020 Workshops
Deep Learning meets Ontologies and Natural Language Processing { 1st International Workshop Sarra Ben Abbes Rim Hantach Philippe Calvez Lynda Temal Nada Mimouni Ra ka Boutalbi
Engie, France Engie, France Engie, France ENGIE, France CNAM, France Trinov, France
Deep Learning (DL) meets Natural Language Processing (NLP) to solve human language problems for further applications, such as information extraction, machine translation, search and summarization. Previous works has attested the positive impact of domain knowledge on data analysis and vice versa, for example pre-processing data, searching data, redundancy and inconsistency data, knowledge engineering, domain concepts and relationships extraction, etc. Ontology is a structured knowledge representation that facilitates data access (data sharing and reuse) and assists the DL process as well. DL meets recently ontologies and tries to model data representations with many layers of non-linear transformations. The combination of DL, ontologies and NLP might be bene cial for di erent tasks: • Deep Learning for Ontologies: ontology population, ontology extension, ontology learning, ontology alignment and integration, • Ontologies for Deep Learning: semantic graph embeddings, latent semantic representation, hybrid embeddings (symbolic and semantic representations), • Deep Learning for NLP: summarization, translation, named entity recognition, question answering, document classi cation, etc. • NLP for Deep Learning: parsing (part-of-speech tagging), tokenization, sentence detection, dependency parsing, semantic role labeling, semantic dependency parsing, etc.
Foundational ontology is about categories of reality or thought which are common to all or almost all subject-matters. Commonly considered examples of such categories include `object', `quality', `function', `role', `process', `event', `time', and `place'. There are several foundational ontologies that provide a systematic formal 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 entities su ciently 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., parthood) from the foundational ontology. The utilisation of foundational ontologies for the development of domain and application ontologies has two main bene ts. 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 o ers researchers in foundational ontology an opportunity to present their results. This includes work on speci c areas of foundational ontology as well as work on a particular foundational ontology. Topics covered in this edition of FOUST include, amongst others, processes, events, functions, roles, and identity criteria. International Workshop on Ontologies for Autonomous Robotics Daniel Be ler Stefano Borgo Mohammed Diab Aldo Gangemi Alberto Olivares-Alarcos Mihai Pomarlan Robert Porzel 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 autonomous robotics? how should notions such as capability or context be modelled? • Robustness: how can ontologies help robots cope with the variety and relatively uid structure of human environments? • Ontologies in the perception-action loop: how might ontologies be used to recognize 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? Workshop on Scalable Knowledge Graph Engineering Martin G. Skj veland Daniel P. Lupp Ian Horrocks Johan W. Kluwer Christian Kindermann While the use of knowledge bases is rapidly gaining industrial interest, ontologies are by and large still a fringe technology in most industries. A major impediment for industrial uptake is often attributed to the lack of scalable knowledge engineering tools and methodologies. Moreover, the development, maintenance, and use of knowledge bases and the tools and methods that are built to support these tasks usually require considerable specialist training. Enterprises that wish to explore the bene ts of using semantic technologies will likely lack the necessary competence and will nd that there are a few o -the-shelf ontologies, tools, and methodologies that t their existing system architecture and information ow. The SKALE workshop wants to attract and stimulate novel research and innovative advances of semantic technologies with the aim of making these technologies more easily accessible to and useful for modern data-driven industries. The workshop also wants to investigate where the real world problems are, and where and what are the current show-stoppers for e cient large-scale deployments of ontology-based information systems? 5th International Workshop on Ontology Modularity, Contextuality, and Evolution
Stefano Borgo Loris Bozzato Till Mossakowski Luciano Sera ni Laboratory for Applied Ontology, ISTC-CNR, Italy Fondazione Bruno Kessler, Italy Otto-von-Guericke University Magdeburg, Germany Fondazione Bruno Kessler, Italy
Valeria De Paiva Samsung Research America and University of Birmingham, UK Jose M. Gimenez-Garc a Universite Jean Monnet Saint-Etienne, France Adila A. Krisnadhi University of Indonesia, Indonesia Raphael Pen~aloza University of Milano-Bicocca, Italy Patrick Rodler Alpen-Adria Universitat Klagenfurt, Austria Vojtech Svatek Univ. Economics Prague, Czech Republic George Vouros University of Piraeus, Greece In the area of ontologies for Knowledge representation and reasoning, knowledge is rarely considered as a monolithic and static structure: partitioning knowledge into distinct modular structures is central to organize knowledge bases, from their design to their management, from their maintenance to their use in knowledge sharing. Moreover, keeping knowledge in separate modules is essential for representing and for reliable and e ective reasoning in changing situations. Finally, evolution of knowledge resources, in terms of updates by newly acquired knowledge, is an important factor in uencing the meaningfulness of stored knowledge over time.
Considering these emerging needs, the International Workshop on Ontology Modularity, Contextuality, and Evolution (WOMoCoE) o ers the ground to practitioners and researchers to discuss current work on practical and theoretical aspects of modularity, contextuality and evolution of ontology based knowledge resources.
WOMoCoE 2020, the 5th edition of the Workshop on Ontology Modularity, Contextuality, and Evolution, takes place (as a virtual workshop) in Bolzano on Sept. 16, 2020 within the framework of the 6th Joint Ontology WOrkshops (JOWO 2020) and the 22nd International Conference on Knowledge Engineering and Knowledge Management (EKAW 2020).
The workshop schedule included the oral presentation of the accepted contributions included in this volume. As in the past, in order to foster active, broad and cross-disciplinary interactions, much time is dedicated to the discussion of the papers. Each submitted paper was reviewed by at least three members of the program committee. The 4th International Cells in Experimental Life Science Workshop
Alexander D. Diehl Sirarat Sarntivijai Yongqun \Oliver" He
University at Bu alo, USA ELIXIR, UK
University of Michigan, USA The rapid advancement of experimental technologies for understanding cellular biology has led to challenges in keeping up with the volume and format of the data being produced and its distillation into new biological knowledge. Current high throughput methods such as single cell RNA sequencing and ow and mass cytometry are producing a large amount of data related to existing and novel cell types in health and disease. At the same time, experimental approaches such as microscopy, genomics, and metabolomics are expanding understanding of cellular functioning in relation to neighboring cells and the whole organism. Ontologies are being increasingly used as a tool for integrating and analyzing these diverse data types. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework for representing cell type information, but additional ontologies such as the Gene Ontology, Protein Ontology, and the Ontology for Biomedical Investigation are also important for representing not only experimental data about cell types but also the methods used to produce that data. There is a continuing need for improve automated analysis techniques to link data about cells with appropriate ontologies. The CELLS 2020 workshop will focus on two themes: (i) challenges in the knowledge representation of newly-discovered and known cell types, and (ii) challenges in the knowledge representation of cells in disease states. This workshop will provide a venue for panel discussions of innovative solutions as well as the challenges in the development and application of biomedical ontologies to represent and analyze in vivo and in vitro cell- and cell line-related knowledge and data, including stem cell technologies. The workshop will cover the extension of CL and CLO for ontological representation of cell types and cell lines in new methodologies and experiments. It will also cover the applications and challenges in real-world use cases which may require other ontological adaptations beyond CL and CLO. Selected submissions will be featured in a BMC Bioinformatics thematic CELLS issue, as those from previous CELLS workshops have been. A Core set of Open Biological and Biomedical Ontology (OBO) Foundry Terms
Randi Vita
La Jolla Institute for Immunology, USA The Open Biological and Biomedical Ontology (OBO) project is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The OBO Foundry mission is to develop a family of interoperable ontologies that are both logically well-formed and scienti cally accurate. Participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations. The OBO Foundry provides services to the community such as hosting persistent URLs and ontology les, recording metadata for all ontologies in the OBO registry, as well as supporting discussion forums and regular calls between participants. We have developed a set of key top-level ontology terms that unify the many OBO Foundry ontologies, termed COB. COB simpli es the identi cation of terms, organizes terms, and helps users navigate across OBO projects. It includes logic that links OBO ontologies together, allowing interoperability problems to be detected and corrected. It also allows users to see related ontology terms from multiple ontologies at the same time. This helps users understand how OBO ontologies and their terms are related, as well as aiding developers to ensure interoperability. The purpose of this workshop is to continue active development of COB, taking advantage of the ICBO meeting to gather together, in person, representatives from the diverse OBO Foundry ontologies. As COB is still in development, we are eager to obtain feedback from the ontology community. We want to collect actionable suggestions on how OBO ontologies work or do not work for users, and what users most want to see included in COB.
Controlled vocabulary standardization e orts covering agricultural and food domains are evolving since their inception decades ago thanks to the mandates and continued support of institutional caretakers. Popular examples are FoodEx2, the European Food Safety Authority (EFSA) food classi cation and description system, the Global Language of Business GS1 product categorization scheme, the EUROFIR promoted LanguaL food composition thesaurus, the UN Food and Agriculture Organization's AGROVOC SKOS-based vocabulary, and its support of the International Network of Food Data Systems (INFOODS) vocabulary for food nutrition testing. These vocabularies are used in a growing interconnected food database landscape but su er from format issues like textual or spreadsheet formats, unresolvable identi ers, and inconsistent category semantics. Ontologies are new entrants into the food domain, bringing a wave of Semantic Web technology and philosophy to bear on the issue of data sharing and modeling of foodrelated activity and research which are becoming critical in the face of rapid change to our environment and anthroposphere. Examples range from BBC's Food Ontology, driving its culinary media universe, to recently published research laboratory initiated ontologies like OBOFoundry members FoodOn, the Food Biomarker Ontology (FOBI), and the Ontology for Nutritional Studies (ONS), and related ontologies like the Medical Action Ontology (MAxO) and the Environmental Conditions, Treatments and Exposures ontology (ECTO) that are under development. Underpinning these mid-level, model-focused ontologies are environmental, chemical, biological, anatomical, disease and phenotype ontologies. Academic, agricultural and public health agencies are considering the bene ts and complexities of adopting ontology in their research and data management and reporting 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? This workshop seeks to de ne the coverage of the di erent ecological, agricultural, nutritional, dietary, public health, one health surveillance, food security, and trade domains that food-related ontologies are modeling, and the use of data translation tools for bringing legacy data into the ontology fold. 9th International Workshop on Vaccine and Drug Ontology Studies Drugs and vaccines have contributed to dramatic improvements in public health worldwide. Over the last decades, there have been e orts in the biomedical ontology community that represent various areas associated with drugs including vaccines that extend existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF- RT, and MedDRA), vernacular medical terminologies, and their applications to research and clinical data. This workshop will provide a platform for discussing innovative solutions as well as the challenges in the development and application of biomedical ontologies to representing and analyzing drugs and vaccines, their administration, immune responses induced, adverse events, and similar topics. The workshop will cover two main areas: (i) ontology representation of vaccines, drugs, and vaccine/drug-related domains (e.g., adverse events), and (ii) applications of the ontologies in real world situations { administration, adverse events, etc. Examples of biomedical subject matter in the scope of this workshop: drug components (e.g., drug active ingredients, vaccine antigens, and adjuvants), administration details (e.g., dosage, administration route, and frequency), gene immune responses and pathways, drug-drug or drug-food interactions, and adverse events. Both research and clinical subjects will be covered. We will also focus on computational methods used to study these, for example, literature mining of vaccine/drug-gene interaction networks, pathway analysis, meta-analysis of host immune responses, and time event analysis of the pharmacological e ects. We encourage submissions related to the COVID-19 pandemic. Drugs and vaccines are critical to ght against the COVID-19. We welcome papers in the domain of drugs and vaccines against COVID-19.