Cell Biology in Ontology workshop (CELLS-2017 @ ICBO) - Call for participation

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Cell Biology in Ontology workshop (CELLS-2017 @ ICBO) - Call for participation

Sirarat Sarntivijai
Dear all,

Apologies for cross-postings. Please find below the announcement of the Cells in Experimental Life Science workshop (CELLS-2017) at the International Conference on Biolomedical Ontology (ICBO) in Newcastle, UK. This workshop aims to encourage collaboration and discussion between the technical ontologists and the field expert biologists. Topics include challenges of the new single-cell technologies and defining standard terminologies for newly-discovered cell types.

  • Individual Workshop Papers Due: June 9, 2017
  • Notification of Acceptance: June 25, 2017
  • Camera Ready: July 1, 2017
  • Workshop: Sept. 13, 2017
  • First Revision due to BMC Bioinformatics: Sept 30, 2017

Organizing Committee
Sirarat Sarntivijai, European Bioinformatics Institute (EMBL-EBI)
Yongqun ‘Oliver’ He, University of Michigan
Alexander D. Diehl, University at Buffalo, The State University of New York

Please forward this message widely to any interested parties.

Thank you very much,


Call for Papers for the Workshop on Cells in ExperimentaL Life Science (CELLS-2017)
In conjunction with the International Conference on Biomedical Ontology (ICBO)
September 13, 2017 in Newcastle upon Tyne, UK
** Selected submissions will be published with BMC Bioinformatics - Submission Deadline: June 9th, 2017  **

CELLS-2017 (https://sites.google.com/site/cellsworkshop/) is the latest addition to the workshop series at the International Conference on Biomedical Ontology (ICBO) that aims to cover topics of metadata management of experimental cells within the biological context. The rise of single-cell RNA sequencing technologies has brought the challenge of metadata handling to the field of experimental biology and biomedical ontology. More urgently than ever now, biologists and ontologists have to reach consensus on various topics such as naming conventions and standards for novel cell type nomenclature, and modeling biological reality into an ontology and semantic framework.

The rise of cell technologies has provided science with a fast lane to advance discovery in biomedical research. Experimental cell cultures and cell lines are widely used and often generated in a de novo fashion at the laboratory. Normalization of experimental cell data produced in different laboratory settings is sometimes difficult, even when the cell types studied are nominally the same. It can also be unclear where the separation between data and metadata is due to the level of granularity of the details. Furthermore, there are no real unified modeling solutions that are universal to all experimental questions and situations. Therefore, data representation and modeling is very much driven by individual experiments, and consolidation of heterogeneous metadata in large central data repositories is a real challenge.  New knowledge obtained through use of high-resolution technologies such as CyTOF and single-cell RNA sequencing introduces even more data that require robust representation, especially regarding novel cell populations that have never been seen before and do not belong to any existing classes of well-established OBO ontologies.

The CELLS-2017 Workshop aims to provide a venue for discussion in various hot topics in single-cell technology domain. This will include input from both the biology and ontology metadata sides of life sciences. The organizers will provide the background on the development, maintenance, and application of the Cell Ontology (CL) and the Cell Line Ontology (CLO) before expanding the presentations and discussions from the submissions which will:
  1. Bring together the participants from all tiers in experimental cell research and data analysis to facilitate communication and collaboration towards a consensus data representation in experimental cell research.
  2. Identify research problems and challenges in the ontological representation and applications of experimental cells and related topics via the real use cases.
  3. Identify and discuss possible solutions for the problems and challenges presented in the workshop.
  4. Initiate a sustainable venue for future collaborations and discussions among the participants.

Key Dates
  • Submission Deadline: June 9, 2017
  • Acceptance Notification: June 25, 2017
  • Early Bird Registration: June 15, 2017
  • Meeting: September 13-15, 2017

Call for Submissions
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 a variety of areas, such as the availability and interoperability of existing resources for cell and cell line terminologies and catalogues, applications and challenges of cell modeling, and improvements to 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 to paying the open-access  publishing fee.

Deadlines and Presentation Length
We welcome research papers (6-8 pages), works in progress/late-breaking results (2-4 page) and statements of interest (1 page) in PDF format using the Bio-ontologies template (http://conferences.ncl.ac.uk/icbo17/callforpapers.html). Submissions can be made on the easychair site (https://easychair.org/conferences/?conf=cells2017). Please note that accepted submissions require that one author present the work. The research presentations will be allocated 15-20 minutes while works in progress/late-breaking results and statements of interest will be allocated 10-15 minutes and 5-10 minutes, respectively. The presenter must register and pay to attend the ICBO 2017 conference, and the presenter should identify themselves as the corresponding author during the submission process.

Review Criteria
  1. Relevance to the attendees including both computational semantic and biology-centric participants.
  2. Significance of the problem and impact
  3. Novelty of the approach, and relevance to existing work.
  4. Quality of writing, including readability and clearly stated contribution(s)

Organizing Committee
Sirarat Sarntivijai, European Bioinformatics Institute (EMBL-EBI)
Yongqun ‘Oliver’ He, University of Michigan
Alexander D. Diehl, University at Buffalo, The State University of New York

Contact: [hidden email]

Sirarat Sarntivijai, PhD
Bioinformatics, Class of 2012
Department of Computational Medicine and Bioinformatics
University of Michigan, Ann Arbor, MI 48109

IG: @siiraa
Twitter: @SSirarat

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