The 2nd International Workshop on

Cells in ExperimentaL Life Science

CELLS-2018

CH2M HILL Alumni Conference Center, Oregon State University, Corvallis, OR, USA  

August 7th, 2018

in conjunction with the

International Conference on Biomedical Ontology (2018)

Contact: icbo.cells@gmail.com


The rapid advancement of cell technologies has inevitably come up with the challenges in keeping up with the volume of the data as well as the dynamic evolution of the data format and knowledge representation. Experimental cell cultures and cell lines are widely used and often generated de novo and de facto at the laboratory of origin, while 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. It is also difficult to separate out 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. Consolidation of heterogeneous metadata is an eminent 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 belong to existing classes of CL or CLO. A community-driven consensus on the minimal set of information to represent new discoveries within the evolving knowledge needs to be found. We will need to discuss how ontologies support the modeling, representation, and analysis of cell-related data, metadata, and knowledge learned from experimental cell studies. We will benefit from a shared consensus experimental cell metadata model which can only be derived by community participation, discussion, and collaboration wherever possible. The proposers 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-2018 Workshop (August 7, 2018 (Tuesday) 4:00 - 6:00 PM)
4:00 - 4:05 pmWelcome
4:05 - 4:25 pmThe Cell Line Ontology-based Representation, Integration and Analysis of Cell Lines Used in China (Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Yuqin Liu, and Xiaolin Yang) - full length paper
4:25 - 4:45 pmOSCI: Standardized stem cell ontology representation and use cases for stem cell investigation (Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas Serra, Jie Zheng, Sirarat Sarntivijai, Stephan Schurer, K. Sue O’shea, and Alexander D. Diehl) - full length paper
4:45 - 5:05 pmThe Cancer Cell Ontology (Lucas Serra, William Duncan and Alexander Diehl) - full length paper
5:05 - 5:15 pmConnecting cell population descriptions and gating definitions through ontologies (Randi Vita, James A. Overton, Alexander Diehl, Kei-Hoi Cheung, Patrick Dunn, Steven Kleinstein, and Bjoern Peters) - podium presentation
5:15 - 5:25 pmSemantic Interoperability: Challenges and Opportunities in Cell Type Knowledge Representation (Richard Scheuermann, Brian Aevermann, and Mohamed Keshk) - podium presentation
5:25 - 6:00 pmGeneral 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-2018 Topics:

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

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

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

  4. Future collaboration opportunities.  

Cell cultures are a crucial component in life science experiments. Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortal cell lineages. These cells are versatile and widely used in different domains. High-content genotyping and phenotyping lead to many newly discovered cell types. New molecular cell markers and pathways are also being found to be differential indicators between normal and diseased cells in this process. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework. This year’s CELLS workshop will focus on two themes: (i) challenges in the knowledge representation of newly-discovered cell types, and (ii) challenges in the knowledge representation of cells in disease states. This workshop will provide 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 second CELLS workshop. We have successfully held our first CELLS workshop (CELLS-2017) in Newcastle, UK, on September 2017 on the theme of identifying challenges from the ontology semantic perspective, and the experimental laboratory perspective. There were 6 oral presentations in CELLS-2017. The corresponding six proceeding papers were extended, submitted, and eventually accepted for publication in the journal BMC Bioinformatics. The CELLS-2017 introductory paper in BMC Bioinformatics introduces this event and summarizes the papers. 


Submission

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

  • full research papers (6-8 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.

Templates can be found here.

All the papers will be submitted and handled through Easy Chair: https://easychair.org/conferences/?conf=cells2018 

After the full papers are accepted, we will work with BMC Bioinformatics editors and reviewers to decide which papers will be formally invited for extension to be included in a thematic series in the  journal. All full-length (10 pages maximum) and short-length (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-2017. 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: June 15, 2018. (note: this is extended from previous May 31)
  • Notification of Acceptance: July 1, 2018. (note: this is extended from previous June 15)
  • Camera Ready: July 15, 2018. (note: this is extended from previous June 22
  • Workshop: August 7, 2018
  • First Revision due to BMC Bioinformatics: August 30, 2018


    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 Diehl, PhD University at Buffalo, The State University of New York, Buffalo, NY, USA.
    • Contact: icbo.cells@gmail.com

    Program Committee (PC) Members

    • Liwei Wang, Jilin University
    • Jie Zheng, Department of Genetics and Institute of Biomedical Informatics, Parelman School of Medicine University of Pennsylvania
    • Matthew Brush, Oregon Health and Science University
    • Terrence Meehan, Samples, Phenotypes, and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory
    • Nicole Vasilevsky, Oregon Health and Science University
    • Chris Mungall, Lawrence Berkeley National Laboratory
    • David Osumi-Sutherland, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory
    • Lindsay Cowell, University of Texas Southwestern Medical Center at Dallas
    • Sebastian Köhler, Charité Berlin