CELLS 2022 Workshop
6th International Cells in Experimental Life Science Workshop, CELLS 2022
A free virtual workshop associated with ICBO 2022
September 21, 2022, 11 am - 2 pm EDT, 8 - 11 am PDT, 4 - 7 pm BST, 5 -8 pm CEST
CELLS 2022 Program (all times US Eastern Time, UTC -4)
11:00 – 11:10 Introduction (slides)
Alexander Diehl, University at Buffalo, Buffalo, NY, USA
11:10 – 11:55 Cell Ontologies, Atlases, and Knowledge Graphs (slides)
David Osumi-Sutherland, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
11:55 –12:20 Summarising scRNAseq Expression Data in FlyBase (slides)
Damien Goutte-Gattat, University of Cambridge, Cambridge, UK
12:20 – 12:45 CellCards: An Ontology-based Knowledgebase for Categorization and Analysis of Individual Cells and Cell Connectomes (slides)
Yougqun He, University of Michigan, Ann Arbor, MI, USA
12:45 –1:05 Rapid Prototype for Cell Type Data Catalog Collection Interface
Joshua Fortriede, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
1:05 –1:25 Cellular Electrophysiology Ontology Modelling (slides)
Patrick L. Ray, Allen Institute for Brain Science, Seattle, WA, USA
1:25 – 2:00 Open Discussion
CELLS 2022 Recording
CELLS 2022 Workshop Themes
(i) knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data and other high-throughput data types
(ii) understanding the relationships of cell types to their anatomical contexts
(iii) the use of machine learning approaches for automatically assigning cell type data to ontology classes
(iv) knowledge representation of cell types in disease states
Background
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 and cell line 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 6th International Cells in Experimental Life Science Workshop, CELLS 2022, 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 for ontological representation of cell types 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 2022
(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 2022 is the same used in ICBO 2022, and will be submitted via EasyChair using the CEURART one column template. All submissions will go through peer reviews by at least two reviewers. CELLS 2022 submissions will be published as part of the ICBO 2022 Proceedings in CEUR Workshop Proceedings (CEUR-WS.org).
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
July 8, 2022 – Deadline for paper submissions
July 22, 2022 – Notification of paper acceptances
August 1, 2022 – Deadline for abstracts or extended abstracts
August 15, 2022 – Notification of abstract acceptances
September 21, 2022 - CELLS 2022 Workshop held virtually via Zoom
Organizers
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.eduYongqun “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.eduImage courtesy Markus I. Diehl (Exp Cell Res 393(2):112014)