ODLS 2019: Final CfP, by June 15 (Ontologies and Data in Life Sciences; part of JOWO 2019, Sep 23-25, Graz, Austria)

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ODLS 2019: Final CfP, by June 15 (Ontologies and Data in Life Sciences; part of JOWO 2019, Sep 23-25, Graz, Austria)

Frank Loebe
        (apologies for cross-posting   ...   please distribute)
        -------------------------------------------------------

               Final Call for Papers    >> ODLS 2019 <<

        Submission deadline:  June 15, 2019 (UTC-12)   !STRICT!

  https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2019-ODLS 
 
  UPDATES in this CfP compared to the previous one:
  * registration remains open for new submissions until June 15
  * time zone UTC-12 / "Anywhere on Earth" applies to all deadlines

                          ------------------

     Workshop on Ontologies and Data in Life Sciences (ODLS 2019)

       held as part of the Joint Ontology Workshops (JOWO 2019)

              September 23-25, 2019        Graz, Austria


Scope and Goals of the Workshop
-------------------------------

Medicine, biology and life sciences produce hardly manageable and
often incomprehensible amounts of data, information, and knowledge.
Their computer-based retrieval, processing, integration, as well as
their conceptual foundation, application, and reuse present ever new
challenges to existing methods of knowledge representation, data
bases, and data analysis and retrieval. In the life sciences, enormous
data sets are being produced in connection with biological and medical
experiments, e.g. by high-throughput methods, aiming to unravel
biological interconnections for a better understanding in order to
offer patients the best possible therapies. Data management and data
processing in the life sciences and in health care demand
sophisticated methods and solutions for the integration and usage of
distributed, heterogeneous data.

This workshop covers the overall spectrum of biomedical information
management, from experimental data acquisition and preprocessing
across analysis, structuring and interpretation of data, up to
developing structured representations of knowledge, in particular in
the form of ontologies, with their various applications. The aims of
this workshop are to exchange ideas, to discuss new results and
applications as well as to inspire cooperation. The workshop has an
interdisciplinary character. It fosters the collaboration between
ontologists, computer scientists, bio-informaticians, medical
information scientists, philosophers, and applied logicians, as well
as the cooperation with physicians, bio-chemists, and biometricians.
Scientists, professionals as well as students in academia and industry
are welcome to share their knowledge and experience at ODLS.

As in 2017, ODLS is part of the Joint Ontology Workshops (JOWO) [2].
This yields a stimulating environment of several thematically close
workshops and tutorials, including shared keynote talks and possibly
further joint sessions, thereby raising interdisciplinary exchange to
a new level.


Topics
------

The following topics are all of equal relevance to the workshop, while
the list is not exhaustive. Submissions regarding other related or
similar topics are likewise welcome.

* Ontologies and ontological analysis in biology, medicine and
  clinical research, e.g.
  * Ontologies for biological or medical phenotypes
  * Ontologies for biochemistry, neuro-biology, ecology
  * Process ontologies in systems biology and medicine
  * Ontologies for the specification of clinical trial data
* Foundational ontologies (with indicated applications in life
  sciences), e.g. of time and space, properties, roles, functions,
  material objects
* Medical terminologies and their applications
* Linking ontologies to terminologies, models and data standards
* Methods and tools for the development, management and application
  of ontologies, e.g.
  * Ontology crossreferencing, mapping, integration and evolution
  * Quality assurance, best practices and evaluation of ontologies
  * Provenance, audit and evidence ontologies in life sciences
  * Ontology learning and refinement, e.g. by text mining
  * Ontology portals and libraries
* Integrative data semantics
* Semantic or ontology-based data annotation, enrichment, analysis
  and interpretation
* Data management methods and systems in biology, medicine and
  health care, e.g. for
  * Heterogeneity and integration of data, including of Linked Data
    and Big Data
  * Management, retrieval and sharing of big data and/or complex
    data sets
  * Curation, analysis and visualization of data in life sciences
  * Omics-data for diagnosis and therapy
  * Biomedical metadata and metadata management
  * Generic transformation of clinical data into Semantic Web standards
  * Data protection of clinical data
* Text mining and transformation of unstructured into structured data
* Use of biomedical ontologies in text mining
* Applications of biomedical ontologies in the Semantic Web, for
  Linked Open Data or Big Data
* Life sciences applications enabled by the Semantic Web or
  Linked Open Data


Important Dates
---------------
                                              [all dates in 2019]
Submission of contributions
  1. register title and abstract paragraph(s)  June 15  (Sat) extended
  2. submission of contribution(s)             June 15  (Sat) !STRICT!
Author notification                            July 19  (Fri)
Submission of camera-ready version           August 13  (Tue)
Registration for ODLS/JOWO                (TBA by JOWO)
ODLS Workshop during                   September 23-25  (Mon-Wed)

All deadlines assume as time zone UTC-12 / "Anywhere on Earth".

Please NOTE:
The submission deadline includes no further room for extensions and
adheres to (updated) constraints imposed by JOWO.

Registering planned contributions was a new requirement for all JOWO
workshops as of May 08, 2019. It suffices to specify a title and
abstract paragraph(s), both of which can be tentative, but should be
indicative of the coming submission. EasyChair remains open for new
registrations until the actual submission deadline, but it will be
helpful if planned submissions are registered as early as possible.


Submission Instructions
-----------------------

The primary type of submissions called for the workshop are
(i) papers of 5-12 pages. Any such length is equally welcome,
including all references and a required abstract of at most 300 words.
In addition, (ii) extended abstracts of 2-4 pages are another type of
acceptable submissions in order to ease participation and presentation
at the workshop, but extended abstracts may not be included in the
proceedings eventually.

Papers are expected to present previously unpublished work, whereas
extended abstracts may also cover recent work that has been accepted
or presented elsewhere.

Authors submit their contributions via EasyChair to JOWO 2019 [3],
selecting the relevant track for ODLS.

[3] https://easychair.org/conferences/?conf=jowo2019
   
Contributions must be delivered in English, non-anonymously and as a
single PDF file. The formatting for all workshops of JOWO 2019 shall
comply with the IOS Press formatting guidelines for book authors.
Templates [4] are available for LaTeX as well as for Microsoft Word.

Accepted papers will be made freely available in a joint JOWO volume
of CEUR Workshop Proceedings, published in the IAOA Series [5].
After the workshop authors of selected contributions will be invited
to submit extended versions to the Journal of Biomedical Semantics
(JBMS) [6]. These manuscripts must also be written in English and
will be re-reviewed.


Scientific Organization
-----------------------

ODLS 2019 is associated with the workgroup Ontologies in Medicine and
Life Sciences (OBML) [7] within the German Informatics Society (GI),
and it relates to the International Association for Ontology and its
Applications (IAOA) [8] by being part of JOWO 2019 [2].


Scientific Organizers:

* Martin Boeker,  University of Freiburg, Germany
* Ludger Jansen,  University of Rostock, Germany
* Frank Loebe,    University of Leipzig, Germany      <-- main contact
* Stefan Schulz,  Medical University of Graz, Austria


Program Committee
-----------------

* Adrien Barton,    Toulouse Institute of Computer Science Research
                    (IRIT), France
* Martin Boeker,    University of Freiburg, Germany
* Jesualdo Tomas Fernandez-Breis, University of Murcia, Spain
* Fred Freitas, Federal University of Pernambuco (UFPE), Recife, Brazil
* Heinrich Herre,   University of Leipzig, Germany
* Robert Hoehndorf, King Abdullah University of Science and Technology
                    (KAUST), Thuwal, Saudi Arabia
* Ralf Hofestaedt,  Bielefeld University, Germany
* Ludger Jansen,    University of Rostock, Germany
* Toralf Kirsten,   Mittweida University of Applied Sciences, Germany
* Frank Loebe,      University of Leipzig, Germany
* Phillipp Lord,    Newcastle University, UK
* Mariana Neves,    Federal Institute for Risk Assessment,
                    Berlin, Germany
* Axel-Cyrille Ngonga Ngomo, Paderborn University, Germany
* Daniel Schober,   Matter Wave Semantics, Suedharz, Germany
* Stefan Schulz,    Medical University Graz, Austria
* Aleksandra Sojic, Institute of Biomedical Technologies,
                    National Research Council (ITB-CNR), Milano, Italy
* Holger Stenzhorn, University Hospital Tuebingen, Germany
* Robert Stevens,   University of Manchester, UK
* Dagmar Waltemath, University of Greifswald, Germany

< 5 further inquiries still pending >


Location and Local Organization
-------------------------------

The workshop is part of JOWO 2019 [2], which is hosted by the

  Medical University of Graz, Austria [9].

Local Organizers:
* Pablo Lopez-Garcia
* Catalina Martinez Costa          <-- main local contact
* Jose Antonio Minarro Gimenez
* Stefan Schulz


Thematically Related Tutorials at JOWO 2019
-------------------------------------------

At least two of the five tutorials offered at JOWO 2019 [10] are
highly related to some topics of ODLS:

* Semantic similarity and machine learning with ontologies [11]
  Organizer: Robert Hoehndorf, KAUST, Thuwal, Saudi-Arabia

* SNOMED CT Tutorial
  Organizer: Stefan Schulz, Medical University of Graz, Austria

The remaining three tutorials at JOWO [10] may also be interest.


Links
-----
[1] ODLS 2019 Workshop

    https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2019-ODLS

[2] JOWO 2019 website

    https://iaoa.org/jowo/2019/

[3] JOWO 2019 conference in EasyChair

    https://easychair.org/conferences/?conf=jowo2019

[4] IOS Press templates for book authors

    https://www.iospress.nl/service/authors/latex-and-word-tools-for-book-authors/

[5] CEUR Workshop Proceedings: IAOA Series

    http://ceur-ws.org/iaoa.html

[6] Journal of Biomedical Semantics

    https://jbiomedsem.biomedcentral.com/

[7] OBML workgroup

    https://wiki.imise.uni-leipzig.de/Gruppen/OBML

[8] IAOA

    https://iaoa.org/

[9] Local organization: Medical University of Graz

    https://www.medunigraz.at/en/

[10] JOWO 2019 Tutorials

     https://iaoa.org/jowo/jowo2019tutorials.html

[11] Semantic similarity and machine learning with ontologies

     https://github.com/bio-ontology-research-group/ontology-tutorial 

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