The 3rd International Workshop on

Cells in ExperimentaL Life Science

CELLS-2019

Buffalo, NY, USA  

1-4 pm, July 31st, 2019

in conjunction with the

International Conference on Biomedical Ontology (2019)

Contact: icbo.cells@gmail.com


The rapid advancement of cell technologies has led to major challenges in keeping up with the volume of the data as well as the dynamic evolution of data formats and requirements for knowledge representation. Experimental cell cultures and cell lines are widely used and often generated de novo as a part of research in a variety of biomedical domains, and  normalization of experimental cell data produced in different laboratory settings is difficult due to the offline non-synchronous nature of multiple laboratories working on similar questions on the same timeline. Similarly, it can be difficult to distinguish data from metadata due to the level of granularity of the details obtained from high-content technologies. Knowledge representation and modeling is often driven by individual experiments, and consolidation of heterogeneous metadata is an ongoing challenge. New knowledge obtained by high-resolution technologies (e.g., single-cell RNA sequencing) adds more data volume that requires robust analysis and representation, especially regarding novel cell populations that do not correspond to existing classes of the Cell Ontology or Cell Line Ontology. A community-driven consensus on the minimal set of information to represent new discoveries within the evolving knowledge needs to be found. In the CELLS-2019 workshop, we will discuss how ontologies support the modeling, representation, and analysis of cell-related data, metadata, and knowledge learned from experimental cell studies. The organizers will ensure that the workshop is relevant to international audiences from both industry and academia. This workshop will be extremely useful to designers and implementers of experimental cell metadata framework in large and complex enterprises, nationwide clinical data repositories, electronic health systems for healthcare, and biomedical science analysis.


Program


CELLS-2019 Workshop (July 31, 2019 (Wed) 1:00 - 4:00 PM)
1:00 - 1:10 pm Welcome
1:10 - 1:40 pm An ontology for standardizing RNA-Seq analysis: ORSA (Lucas M. Serra, Rudiyanto Gunawan, Nan Papili Gao, Saber Meamardoost, Alexander D. Diehl) - full length paper
1:40 - 2:10 pm hPSCreg-CLO: CLO ontology representation and analysis of human pluripotent stem cell line cells stored in the hPSCreg repository (Stefanie Seltmann, Edison Ong, Yongqun He) - full length paper
2:10 - 2:30 pm Improving the ability to reason over cell type definitions and experimental gating strategies using the Cell Ontology, Protein Ontology, Gene Ontology and Ontology of Biomedical Investigations (James A. Overton, Randi Vita, Alexander D. Diehl, Bjoern Peters) - podium length paper
2:30 - 2:45 pm Break 
2:45 - 3:05 pm Improved representation of cell types of the prostate and salivary glands incorporating scRNAseq results (Aaron Chen, Khusbu Patel, Alexander D. Diehl) - podium presentation
  3:05 - 3:25 pm CLO updates (Yongqun He, Edison Ong, Xiaolin Yang, Stefanie Seltmann, Stephan Schurer, William D. Duncan, Alexander D. Diehl, Sirarat Sarntivijai) - podium presentation
3:25 - 4:00 pm General discussion (coordinated by workshop organizers)
Theme: Design pattern representation of normal vs diseased conditions in cells 
* What are the common design patterns for normal and diseased cells? 
* Difference between normal and diseased cells, and how to ontologically represent the transformation from a normal cell to diseased cell?
* How to represent additional information (e.g., gene markers) in ontology? 



Workshop Theme and Topics

CELLS-2019 Topics:

This workshop covers all kinds of topics related to cells and ontology. The topics to be presented include but are not limited to the following: 

  1. Ontological representation of stem cells in vivo and in vitro.

  2. Ontological representation of cell types that are newly discovered using different experimental technologies.

  3. Ontological representation of cells in disease states such as cancers, autoimmunity, and infectious diseases.

  4. Challenges and opportunities in ontological knowledge representation and their applications.

  5. Future collaboration opportunities.  

Cells and cell cultures are a crucial component in life science experiments and come in the form of primary cells direct from biopsies, primary cell cultures and maintainable immortal cell lineages. High-content genotyping and phenotyping methods are leading to many newly discovered cell types. New molecular cell markers and pathways are also being found as differential indicators between normal and diseased cells. Stem cells and stem cell line cells are widely used for therapeutic discovery and treatment. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO Foundry framework.   

This workshop provides 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.

This is the third CELLS workshop. We have successfully held our first CELLS workshop (CELLS-2017) in Newcastle, UK, on September 2017, and the second CELLS workshop (CELLS-2018) in Oregon, US, on August 7th, 2018. The CELLS-2017 and CELLS-2018 proceedings papers were revised and accepted for publication in the journal BMC Bioinformatics. The CELLS-2017 introductory paper in BMC Bioinformatics summarizes the papers from the CELLS-2017 workshop. The CELLS-2018 papers will be published soon in BMC Bioinformatics as well. 


Submission

For the paper submission, we will allow three submission formats:

  • full research papers (6-10 pages) format
  • work in progress / late breaking results (2-4 pages), and
  • a statement of interest (one page) for podium presentation.

The paper format will be the same as the format used in ICBO 2019. Templates can be found here.

All the papers will be submitted and handled through Easy Chair: https://easychair.org/conferences/?conf=cells2019 

After the full papers are accepted, we will work with BMC Bioinformatics editors and reviewers to decide which papers will be formally invited for revision and inclusion in a thematic series in the  journal. All full-length (6-10 pages) and work in progress reports (2-4 pages maximum) submissions will go through peer reviews by at least two reviewers. The one-page statement-of-interest submissions will be reviewed by the workshop organizers. 

We invite the submission of research papers, work in progress/late-breaking results and statement of interest for presentation at CELLS-2019. Papers are invited in areas, such as availability and interoperability of existing resources for cell and cell line terminologies and catalogues, applications and challenges of cell modeling, and improvement and best practices of the current experimental cell ontology landscape. Example topics include (but not limited to):
    •    Collaborative ontology development for experimental cell modeling.
    •    Ontologies in cell type and cell culture metadata and standards.
    •    Knowledge representation and knowledge discovery for novel discovery.
    •    Biocuration of experimental cell data
    •    The usage of standard cell and cell line nomenclatures in literature.
    •    Updates on work in progress and statement of interest of cell modeling questions.
Selected submissions will also be published in the CELLS thematic issue of BMC Bioinformatics. Should the authors accept the offer to publish BMC Bioinformatics, they will agree to a secondary review-for-publication process and the publishing fee.


Workshop Schedule/Important Dates

  • Individual Workshop Papers due date: May 15, 2019
  • Notification of Acceptance: June 25, 2019
  • Camera Ready: July 15, 2019.  
  • Workshop: 1-4 pm, July 31st, 2019 
  • First Revision due to BMC Bioinformatics: to be determined. 


    Workshop Organizers

    • Sirarat Sarntivijai, PhD, ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK. 
    • Yongqun “Oliver” He, DVM, PhD, Department of Microbiology and Immunology Unit for Laboratory Animal Medicine Center for Computational Medicine and Bioinformatics University of Michigan Medical School, Ann Arbor, MI, USA. 
    • Alexander D. Diehl, PhD, Department of Biomedical Informatics, University at Buffalo, The State University of New York, Buffalo, NY, USA.
    • Contact: icbo.cells@gmail.com

    Program Committee (PC) Members

    • To be added ...