CELLS 2021 Workshop

5th International Cells in Experimental Life Science Workshop, CELLS 2021

A virtual workshop associated with ICBO 2021 and JOWO 2021

September 15th, 2021, 10 am - 1 pm EDT (USA), 3 - 6 pm BST, 4 - 7 pm CEST

CELLS 2021 Program (all times US Eastern Time, UTC -4)

10:00 – 10:10 Introduction

10:10 – 10:30 Recent Development of the Cell Ontology: Breadth and Depth

Alexander D. Diehl

10:30 –11:00 Towards a Minimum Information About a New Cell Type Standard

Tiago Lubiana, Paola Roncaglia, Christopher J. Mungall, Ellen M. Quardokus, and Alexander D. Diehl

11:00 – 11:30 CellTypist: Towards Automated Cell Type Annotation

Chuan Xu, Tomás Gomes, Cecilia Dominguez-Conde, and Sarah Teichmann

11:30 –12:00 Brain Data Standards ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex

Shawn Zheng Kai Tan, Huseyin Kir, Brian D. Aevermann, Tom Gillespie, Jeremy A. Miller, Christopher J. Mungall, Patrick L. Ray, Richard H. Scheuermann, and David Osumi-Sutherland

12:00 – 12:30 Open Discussion

CELLS 2021 Workshop Themes

(i) addressing the challenges of knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data

(ii) addressing the challenges of knowledge representation of cell types in disease states

(iii) addressing the challenges of the representation of homologous cell types across species

(iv) addressing the challenges of identification and representation of cell types of importance as targets of SARS-CoV2 infection and in the immune response during COVID-19


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 flow 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, and 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 5th International Cells in Experimental Life Science Workshop, CELLS 2021, will provide a venue for discussions of the application of biomedical ontologies to represent and analyze in vivo and in vitro cell- and cell line-related knowledge and data, including single cell RNA sequencing data and stem cell technologies. The workshop will also cover the extension of CL and CLO for ontological representation of cell types and cell lines based on new methodologies and experiments. In addition it will cover real-world use cases which may require other ontological adaptations beyond CL and CLO.

Submission Formats for CELLS 2021

(i) full research papers (10 pages)

(ii) short papers (5 pages)

(iii) abstracts or extended abstracts (1-3 pages) for presentations

Abstracts are one page, references optional. Extended abstracts are formatted as mini-papers, and should include references.

The paper template for CELLS 2021 is the same used in ICBO 2021, and will be submitted via EasyChair using the CEURART one column template. All submissions will go through peer reviews by at least two reviewers.

The workshop is planned as a three hour event and will be organized into different sections based on the topics of presentations. Presentation time allocation will be determined after the number of each submission type is finalized. A panel discussion will be arranged at the end of the workshop.

Important Dates

September 15, 2021– CELLS 2021 Virtual Workshop will be held in conjunction with ICBO 2021

CELLS 2021 Registration

Registration for the CELLS 2021 Workshop is free, and occurs via the ICBO 2021 registration process (free for virtual attendees) which is part of the the Bolzano Summer of Knowledge 2021 (BOSK) registration.


Alexander D. Diehl, PhD

Associate Professor of Biomedical InformaticsJacobs School of Medicine and Biomedical Sciences, University at Buffalo77 Goodell St, Suite 540Buffalo, New York, 14203, USAaddiehl@buffalo.edu

Sirarat Sarntivijai, PhD

ELIXIR Interoperability Platform CoordinatorELIXIR Hub, South BuildingWellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKsirarat.sarntivijai@elixir-europe.org

Yongqun “Oliver” He, DVM, PhD

Associate ProfessorUnit for Laboratory Animal Medicine, Department of Microbiology and ImmunologyCenter for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center University of Michigan Medical SchoolOffice: 2511F ARF, 1150 W. Medical Center Dr.Ann Arbor, MI 48109-0168, USAyongqunh@med.umich.edu

Previous CELLS Workshops

2020, 2019, 2018, 2017