Call for Papers: ICBO-2017 workshop on Cells in ExperimentaL Life Science (CELLS-2017)

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Call for Papers: ICBO-2017 workshop on Cells in ExperimentaL Life Science (CELLS-2017)

Alexander Diehl-3

Dear Colleagues,

 

Call for Papers for the Workshop on Cells in ExperimentaL Life Science (CELLS-2017)

In conjunction with the 2017 International Conference on Biomedical Ontology (ICBO-2017)

September 13, 2017 in Newcastle upon Tyne, UK

** Selected submissions will be published with BMC Bioinformatics - Submission Deadline: June 9th, 2017  **

 

Workshop Website: 

https://sites.google.com/site/cellsworkshop/

 

Paper submission deadline: July 1, 2017

 

Workshop Theme and Topics

 

CELLS is the latest addition to the workshop series at the International Conference on Biomedical Ontology (ICBO) that aims to cover topics of data and metadata representation, standardization, management, and analysis of experimental cells in the biological and biomedical 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 urgent than ever now, biologists and ontologists have to reach the consensus on the agreement on various topics such as naming convention and standard for novel cell type nomenclature, and modeling the 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 has also become 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 experiment. Consolidation of heterogeneous metadata in a large central data repository is a real challenge. New knowledge obtained by 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.

 

CELLS-2017 workshop aims to provide a venue for discussion in various hot topics in the single-cell and multi-cell technology domains. This will include the input from both biology and ontology metadata sides of life sciences. The organizers will lay 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 communications 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 challenged presented in the workshop.

    4.    Initiate a sustainable venue for future collaborations and discussions among the participants.

 

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 on the website: https://sites.google.com/site/cellsworkshop/.

 

All the papers will be submitted and handled through Easy Chair.  https://easychair.org/conferences/?conf=cells2017

 

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: July 1, 2017

Notification of Acceptance: July 22, 2017

Camera Ready: July 30, 2017

Workshop: Sept. 13, 2017

First Revision due to BMC Bioinformatics: Sept 30, 2017

 

Workshop Organizers

 

Sirarat Sarntivijai, PhD Samples, Phenotypes, and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, 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: [hidden email]

 

 


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