CELLS 2020 Workshop

4th International Cells in Experimental Life Science Workshop, CELLS 2020

A virtual workshop associated with ICBO 2020 and JOWO 2020

Friday, September 25, 2020, 11 am to 1:30 pm, US Eastern Time Zone

CELLS 2020 Program

11:00 am – 11:10 am Introduction

11:10 am – 11:40 am Depositing single cell sequencing data to shared data portals abstract

Shrikant Pawar, Anthony Melillo , Hailong Meng , Darwin D'Souza , Bjoern Peters , Randi Vita , Steven H. Kleinstein , Kei-Hoi Cheung

11:40 am – 12:10 pm Building semantics driven resources for neurobiology

David Osumi-Sutherland

12:10 pm – 12:40 pm The Cell Line Ontology 2020: expanded content and ontology interoperability abstract

Yongqun He, Edison Ong, Stefanie Seltmann, Xiaolin Yang, Daniel J. Cooper, Stephan Schurer, William D. Duncan, Alexander D. Diehl, Sirarat Sarntivijai

12:40 pm – 1:10 pm Innate lymphoid cells and a new paradigm for the implementation of taxon restrictions in the Cell Ontology abstract

Alexander D. Diehl, James A. Overton, Lewis L. Lanier, HIPC Cell Ontology Expert Group, Cell Ontology Editorial Working Group, Steven H. Kleinstein, Randi Vita, Nico Matentzoglu, Bjoern Peters

1:10 pm – 1:30 pm General discussion period

CELLS 2020 Registration

Registration for the CELLS 2020 Workshop is free, but required, in order to receive the Zoom link for the meeting. Please register for the CELLS 2020 workshop via the Bolzano Summer of Knowledge website. Choose "Participant Registration (free)" and follow the instructions.

CELLS 2020 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 4th International Cells in Experimental Life Science Workshop, CELLS 2020, 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 2020

(i) full research papers (6-10 pages)

(ii) work in progress reports (4 pages)

(iii) extended abstracts (one page) for short presentations

(iv) abstracts for virtual poster session

The paper template for CELLS 2020 will be the same used in ICBO 2020, from IOS Press, and will be submitted via EasyChair. All full-length and short-length submissions will go through peer reviews by at least two reviewers, and abstracts will be reviewed by the organizers. We will provide a late abstract deadline for short reports of late-breaking results as well.

Selected submissions will be featured in a BMC Bioinformatics thematic CELLS 2020 issue, as those from previous CELLS workshops have been. With a virtual presentation format, we hope that we may attract presenters and attendees who have not previously had the opportunity to participate in the CELLS workshop series.

The workshop is planned as a half-day 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. Panel discussions will be arranged at the end of each section. We will also host a virtual poster session with the opportunity to speak with poster authors.

Participation in the CELLS 2020 workshop does not require ICBO 2020 registration, though we encourage it.

Important Dates

August 25, 2020 – Paper and abstract deadline for CELLS 2020

September 4, 2020 – Notification of paper and abstract acceptance

September 25, 2020, 11 am to 1:30 pm, US Eastern Time Zone – CELLS 2020 Virtual Workshop will be held in conjunction with ICBO 2020


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

2019, 2018, 2017

Image: M Uhlen, P Oksvold, L Fagerberg, E Lundberg, K Jonasson, M Forsberg, M Zwahlen, C Kampf, K Wester, S Hober, H Wernerus, L Björling, F Ponten (2012) CIL:41685, Homo sapiens, epidermoid carcinoma. CIL. Dataset. https://doi.org/doi:10.7295/W9CIL41685