The 4th International Workshop
on Conceptual Modeling for Life Sciences


6th November, 2023 in Lisbon, Portugal

In conjunction with the 42nd International Conference on Conceptual Modeling (ER 2023)

6-9th November, 2023


The workshop will run on Monday November 6th, 2023.
Please refer to the ER conference website for information on the full conference program (ER 2023 program).

Welcome and introduction to the CMLS workshop

Sipan Arevshatyan, José Fabián Reyes Román, Elisa Caballero Calabuig, Mari Carmen Plancha, Alejandra Abella, Pedro Abreu and Óscar Pastor. Integrating Nuclear Medicine and Radiopharmacy Data: A Conceptual Model for Precision Medicine and Enhanced Patient Care.

Mireia Costa, Alberto García, Ana León and Oscar Pastor. Comprehensive Representation of Variation Interpretation Data via Conceptual Modeling.

Lidia Contreras-Ochando, Pere Marco Garcia, Ana León, Lluís F. Hurtado, Ferran Pla and Encarna Segarra. Enhancing Precision Medicine: An Automatic Pipeline Approach for Exploring Genetic Variant-Disease Literature.

Coffee Break 11.00-11.30

Yasmine Anchén, Edelweis Rohrer and Regina Motz. An Ontology for Breast Cancer Screening.

Invited keynote talk by Prof. Stefano Ceri, Politecnico di Milano. Data Modeling in life sciences, from theory to applications.

Invited Talk


Stefano Ceri (Politecnico di Milano)
(see Google Scholar, Personal Webpage)

Stefano Ceri is professor of Data Managenent at Politecnico di Milano, he was visiting professor at Stanford University between 1983 and 1992. He designed and then directed the Alta Scuola Politecnica. His main research interests were concerned with extending data management - by giving foundational contributions in distributed, deductive, active, object-oriented and bio-informatic data technologies - and then acting as data scientists in numerous domains - including social analytics, fake news detection, genomics for biology and for precision medicine, and recently the study of the SARS-CoV-2 viral genome.
With an H-Index 83 and about 35K citations on Google Scholar, he authored over 450 articles on international venues, receiving Best Paper and 10-Years awards at VLDB; he co-authored many books, including “Distributed Databases: Principles and Systems”, “Logic Programming and Databases”, “Conceptual Database Design: an Entity-Relationship Approach”, “Active Database Systems”.
In 1988 he was Endowment founder and first General Chair of the “Extending Database Technology” Conference. He is co-founder and shareholder of WebRatio, a development platform for Web applications based on patented technology, currently employing about 50 people. He is the recipient of two ERC AdG, “Search Computing” (2008-2013) and “data-driven Genomic Computing” (2016-2021). He received the ACM-SIGMOD "Edward T. Codd Innovation Award" (June 2013). He is an ACM Fellow, member of Academia Europeae and of Istituto Lombardo di Scienze e Lettere.

Topic:Data Modeling in life sciences, from theory to applications

Talk abstract: Progress in life sciences is often the result of collecting huge, well-organized, high quality datasets and then applying data science methods to understand their hidden messages. In this talk, Prof. Ceri will report some of the results of his last ten years of research, when he discovered a strong interest in life sciences. He will argue that data must be initially mastered at a conceptual level, i.e. abstracted and simplified so as to become more manageable – and he will explain three data models, first one for patient care targeted upon COVID-19, then two models respectively addressing the human and viral genome. Prof. Ceri will then describe the process of integrating human and viral genomic data sources so as to build huge data repositories, thereby facilitating and improving research projects. Finally, he will discuss some new approaches, purely based upon big data and statistical methods of data science, recently developed for the finding variants and recombinations in the SARS-CoV-2 genome; he will also report some interesting results in other scientific domains. Most of reported work is the outcome of the ERC-AdG grant “data-driven Genomic Computing” (GeCo, 2016-2021), and some follow-up projects.


The recent advances in unraveling the secrets of human conditions and diseases have encouraged new paradigms for their prevention, diagnosis, and treatment. As information is increasing at an unprecedented rate, it directly impacts the design and future development of information and data management pipelines; thus, new ways of processing data, information, and knowledge in healthcare environments are strongly needed.
The fourth edition of the workshop aims to continue being a meeting point for Information Systems (IS), Conceptual Modeling (CM), and Data Management (DM) researchers working on health care and life science problems. It is also an opportunity to share, discuss and find new approaches to improve promising fields, with a special focus on Genomic Data Management – how to use the information from the genome to better understand biological and clinical features – and Precision Medicine – giving to each patient an individualized treatment by understanding the peculiar aspects of the disease.
From the precise ontological characterization of the components involved in complex biological systems to the modeling of the operational processes and decision support methods used in the diagnosis and prevention of diseases, the joined research communities of IS, CM, and DM have an important role to play; they must help in providing feasible solutions for high-quality and efficient health care.
The COVID-19 pandemic and the recent climate disruption have attracted increasing attention to the effects of pathogens and environmental change on human health. CMLS aims to become a forum for discussing the responsibility of the conceptual modeling community in supporting the life sciences related to these new realities.

Topics of interest

The fourth edition of the workshop focuses on Conceptual Modeling as a means for facing the challenges that emerge when designing and developing systems for life sciences, focused on genomics and precision medicine. The workshop is not restricted to specific research methods; we will consider both conceptual and empirical research, as well as novel applications.

The topics of interest include, but are not limited to:

  • Conceptual modeling for genomics
  • Modeling of complex biological systems and of health ecosystems
  • Information systems for healthcare, genomics, or medicine of precision
  • Design, implementation, and evaluation of health information systems
  • Electronic/digital health information systems
  • Life science-related domain specific modeling languages
  • Data management and integration for genomics and biology
  • Ontologies and workflows for life sciences
  • Clinical and biological data interoperability
  • Interoperability of health information systems
  • Knowledge-representation for genetics
  • Business process modeling for genetic/clinical diagnosis
  • Conceptual model-driven big data analytics for genomics, clinical diagnosis or biological problems
  • Conceptual models for data-driven AI systems in life sciences
  • Models for digital transformation of healthcare systems
  • Conceptual models in life sciences: from theory to practice
  • Models to facilitate multidisciplinary exchange in healthcare contexts
  • Virology-related conceptual models and their applications
  • Conceptual models and information systems for fighting climate change and its effects

Paper submission guidelines

We invite submissions of high quality papers describing original and unpublished results regarding any of the workshop’s topics of interest.

CMLS 2023 proceedings will be part of the ER 2023 Workshop volume published by Springer in the LNCS series. The authors must submit manuscripts using the Springer-Verlag LNCS style for Lecture Notes in Computer Science. For style files and details, see the page The page limit for workshop papers is 10 pages. Papers must be submitted as PDF files using EasyChair at, choosing the track 'Workshop on Conceptual Modeling for Life Sciences'.

To ensure high quality, all papers will be thoroughly peer reviewed by the Program Committee. Manuscripts not submitted in the LNCS style or having more than 10 pages will not be reviewed and thus automatically rejected. The papers need to be original and not submitted or accepted for publication in any other workshop, conference, or journal. Submission to CMLS 2023 will be electronically only.

Important dates

  • Paper submission: August 2nd, 2023 August 9th, 2023 (extended!)
  • Notification: September 8th, 2023
  • Camera-ready version: September 15th, 2023
  • CMLS online workshop date: November 6th, 2023


Anna Bernasconi, Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
Politecnico di Milano, Italy

Anna Bernasconi is a Research Fellow in the Department of Electronics, Information, and Bioengineering also at Politecnico di Milano. Her research focuses on conceptual modeling, data integration, semantic web, and biological data analysis. Since the COVID-19 pandemic, her research has moved to viral genomics, by building models, databases, and Web search systems for viral sequences and their variants. She co-organized and chaired the first three International Workshops on Conceptual Modeling for Life Sciences (CMLS 2020 / 2021 / 2022) co-located with the ER conference and co-organized the First International Workshop on Web Applications for Life Sciences (WALS 2022) co-located with the ICWE conference.

Arif Canakoglu, Dipartimento di Anestesia, Rianimazione ed Emergenza-Urgenza,
Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy

Arif Canakoglu currently works as a data scientist at Policlinico di Milano; and he works mainly on the electronic health record of the intensive care unit's patients in the Lombardy region. He is leading the research with the support of the medical group, analyzing the life quality of the patients after the hospital discharge. Previously, he was involved in the "Data-driven Genomic Computing" ERC Awarded project (2016-2021), where he contributed to developing integration of heterogeneous genomic data and for developing computational methods for genomic applications. In 2016, he received his PhD on biomolecular knowledge data integration by using the modular schema data warehouse. His research interests include data integration and data driven genomic computing, big data analysis and processing on cloud computing, artificial intelligence applications. His main areas of expertise are heterogeneous data integration and data driven models and machine learning approaches in genomic, and big data processes, especially on cloud computing.

Alberto García S., Research Center on Software Production Methods (PROS)
Universitat Politècnica de València, Spain

Alberto García S. obtained his Ph.D. cum laude at Universitat Politecnica de Valencia under the supervision of Prof. Oscar Pastor. He is currently a researcher at the VRAIN research institute, where he focuses on conceptual modeling, data science, and User Interface design. He has participated in multiple research projects in collaboration with clinicians and geneticists to generate knowledge from genomics data effectively and efficiently.

José Fabián Reyes Román, Research Center on Software Production Methods (PROS)
Universitat Politècnica de València, Spain

José F. Reyes R. is a researcher at PROS Research Center at Universitat Politècnica de València (Spain). He holds a Ph.D. in Computer Sciences (2018) from Universitat Politècnica de València (UPV, Spain), a MSc in Software Engineering, Formal Methods and Information Systems (2013) from UPV (Spain), a Diplomate of Analysts and Systems Designers (2011) and a University Degree in System Engineering (2010) from Universidad Central del Este (Dominican Republic). Currently, his main research activities are centered on the use of Conceptual Models for the development of Genomic Information Systems (GeIS). His main research interests include Conceptual Modeling, Genomic Data Science, Engineering Requirements, SE and Information Systems.

Program Committee

  • Samuele Bovo, University of Bologna, Italy
  • Bernardo Breve, Università degli Studi di Salerno, Italy
  • Raffaele Calogero, University of Turin
  • Stefano Ceri, Politecnico di Milano
  • Pietro Cinaglia, Magna Graecia University, Italy
  • Stefano Cirillo, Università degli Studi di Salerno, Italy
  • Tommaso Dolci, Politecnico di Milano
  • Johann Eder, University of Klagenfurt, Germany
  • Jose Luis Garrido, University of Granada, Spain
  • Giovanni Giachetti, Universitat Politècnica de València, Spain
  • Giancarlo Guizzardi, University of Twente, Netherlands
  • Francesco Invernici, Politecnico di Milano
  • Khanh N.Q. Le, Taipei Medical University, Taiwan
  • Sergio Lifschitz, Pontifical Catholic University of Rio de Janeiro, Brazil
  • Roman Lukyanenko, HEC Montreal
  • Giovanni Meroni, Technical University of Denmark
  • Paolo Missier, Newcastle University, United Kingdom
  • José Palazzo, Federal University of Rio Grande do Sul, Brazil
  • Ignacio Panach, University of Valencia, Spain
  • Oscar Pastor, Universitat Politècnica de València
  • Barbara Pernici, Polytechnic University of Milan, Italy
  • Pietro Pinoli, Politecnico di Milano
  • Rosario Michael Piro, Polytechnic University of Milan, Italy
  • Tiago Prince Sales, University of Twente, The Netherlands
  • Monjoy Saha, National Cancer Institute, USA
  • Veda Storey, Georgia State University
  • Domenico Vito, Università degli Studi di Pavia, Italy
  • Emanuel Weitschek, Uninettuno University, Italy


This workshop is supported by the data-driven Genomic Computing group at Politecnico di Milano and by the VRAIN Research Center at Universitat Politecnica de Valencia (INNEST/2021/57 - Agència Valenciana de la Innovació and PDC2021-121243-I00 - Spanish State Research Agency)

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