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

Alexander Diehl addiehl64 at gmail.com
Tue May 23 12:38:12 PDT 2017


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:icbo.cells at gmail.com <mailto:icbo.cells at gmail.com>


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