[obml] ODLS 2016: 2nd Call for Participation (7th Workshop on Ontologies and Data in Life Sciences, Sep 29-30, Halle (Saale), Germany)
Frank Loebe
frank.loebe at informatik.uni-leipzig.de
Do Sep 15 13:11:15 CEST 2016
(apologies for cross-posting) ... (please distribute)
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2nd Call for Participation >> ODLS 2016 <<
! Register by Sep 18, 2016 - 3 days left !
[1] https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2016-ODLS
[2] http://www.onto-med.de/obml/ws2016/odls2016program.pdf
PREVIEW:
* Keynotes by ** Johannes Hübner (Halle (Saale), Germany)
** Robert Stevens (Manchester, UK)
* Program available [2], accepted submissions: 7 papers + 6 abstracts
* Contribution towards expenses: 30 / 25 / 20 EUR
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7th Workshop on Ontologies and Data in Life Sciences (ODLS 2016)
Sep 29-30, 2016 Halle (Saale), Germany
Important Dates (Upcoming) & Program
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Registration: *September 18, 2016* (Sun) !! 3 days left !!
Workshop starts: September 29 (Thu), 13:45 CEST
Workshop ends: September 30 (Fri), 15:00 CEST
The program (as of Sep 13, 2016) is available at
[2] http://www.onto-med.de/obml/ws2016/odls2016program.pdf
Keynote Talks
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Johannes Hübner, Martin-Luther-University of Halle-Wittenberg
"Dispositions, capacities, abilities. Towards a classification of
the power of living beings"
Abstract:
In my talk I want to investigate the active and passive powers of
living beings. Usually, abilities are classified as dispositions to
voluntary action. I want to argue, first, that a broader concept of
abilities is necessary both in the case of human beings and in the case
of other animals. Second, abilities are not a species of dispositions.
Robert Stevens, University of Manchester, UK
"The pragmatics and formality of authoring ontologies"
Abstract:
In this talk I will explore ideas of pragmatics and formality in our
approaches to authoring biomedical ontologies. Formality can come from
the philosophical approach to ontology development, from the area of
knowledge representation, ontological analysis used and the rigor of
the method applied in the ontology development. I will advocate a
moderately pragmatic approach for one's philosophical rigor and being
much more formal, but not always so, on the representational side. I
will illustrate both my pragmatics and formality with some recent work
on normalising the Molecular Function sub-ontology of the Gene
Ontology. This shows that the "functions" of gene products are very
few; that upper ontologies can be of practical use and avoiding
'distinctions that make no difference'. Fully normalising the GO's
molecular function ontology shows some reasonable insights in the
biology and again demonstrates how a formal KR language can help. Even
here, to make it work sensibly, pragmatics also come into play. The
formality of using a language with strict semantics can be
demonstrated, aided by some ontological rigor, but with some
representational compromises or pragmatics to make the reasoning with
the ontology sensible. At the end of the talk I will give a set of
guidelines that I use that help me decide whether or not to be
pragmatic or formal when authoring an ontology.
Accepted Submissions
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PAPERS
* Deep Learning meets the Semantic Web: A feasibility study with the
Cardiovascular Disease Ontology and PubMed citations
Mercedes Arguello Casteleiro, George Demetriou, Warren Read,
Maria Jesus Fernandez-Prieto, Diego Maseda-Fernandez,
Goran Nenadic, Julie Klein, John Keane and Robert Stevens
* A document-centric approach for developing biological ontology
Aisha Blfgeh, Jennifer Warrender, Catharien Hilkens and
Phillip Lord
* Challenges and opportunities for system biology standards and tools
in medical research
Matthias König, Anika Oellrich, Dagmar Waltemath,
Richard Jb Dobson, Tim Jp Hubbard and Olaf Wolkenhauer
* Querying standardized EHRs by a Search Ontology XML Extension (SOX)
Stefan Kropf, Alexandr Uciteli, Kerstin Denecke and Heinrich Herre
* Towards standardized evidence descriptors for metabolite annotations
Daniel Schober, Reza M. Salek and Steffen Neumann
* A Whiteheadian approach to data and knowledge
Sebastian Siemoleit and Heinrich Herre
* Risk Identification Ontology (RIO): An ontology for specification and
identification of perioperative risks
Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh,
Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding,
Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting,
Frank Portheine and Heinrich Herre
EXTENDED ABSTRACTS
* A modelling pattern for multi-track dispositions for life-science
ontologies
Adrien Barton and Ludger Jansen
* Ontological interpretation of biomedical database annotations
Filipe Santana Da Silva, Ludger Jansen, Fred Freitas and
Stefan Schulz
* FAIRDOM approach for semantic interoperability of systems biology
data and models
Olga Krebs, Katy Wolstencroft, Natalie Stanford, Norman Morrison,
Martin Golebiewski, Stuart Owen, Quyen Nguyen, Jacky Snoep,
Wolfgang Mueller and Carole Goble
* MeTMapS – Medical Terminology Mapping System
Shao Fen Liang, Talya Porat, Archana Tapuria, Brendan Delaney and
Vasa Curcin
* Qualitative assessment of annotations using SNOMED CT
Jose Antonio Miñarro-Giménez, Catalina Martínez Costa and
Stefan Schulz
* Extracting process graphs from medical text data
Andreas Niekler
Contribution towards Expenses and Registration
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Every participant is charged a contribution towards expenses, which
amounts to
* 30 EUR regular,
* 25 EUR for members of GI, GMDS or IAOA,
* 20 EUR for students.
It covers mainly catering during the breaks of both days, excluding
dinner. One lunch at the campus cafeteria might be included, depending
on the available budget.
For registration, please send an email to [3] odls2016 at ipb-halle.de and
pay the contribution towards expenses by bank transfer. Details on the
registration message as well as regarding the bank transfer are
provided at the workshop website [1].
Accommodation and Travel Information
------------------------------------
The ODLS 2016 website [1] comprises sections on accommodation options,
partially with special rate, as well as it contains some hints on maps
and directions, transport and tourism.
Scope and Goals of the Workshop
-------------------------------
Medicine, biology and life sciences produce hardly manageable and
comprehensible amounts of data, information, and knowledge. Their
computer-based retrieval, processing, integration, as well as their
conceptual foundation, interpretation and application presents ever new
challenges to existing methods of knowledge representation, data bases,
and data analysis. In the life sciences, enormous data sets are being
produced in connection with biological and medical experiments, 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 ranges from the best possible
integration and usage of distributed, heterogeneous data to the best
possible obfuscation of medical data.
This integrated 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, 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 knowledge and experience at ODLS.
Scientific Organization
-----------------------
ODLS 2016 is associated with the group Ontologies in Biomedicine and
Life Sciences (OBML) [4] within the German Informatics Society (GI),
and it is a Supported Event of the International Association for
Ontology and its Applications (IAOA) [5].
Scientific Co-organizers:
* Martin Boeker, University of Freiburg
* Heinrich Herre, University of Leipzig
* Ludger Jansen, University of Rostock
* Frank Loebe, University of Leipzig <-- main contact [6]
* Daniel Schober, Leibniz Institute of Plant Biochemistry,
Halle (Saale)
Location and Local Organization
-------------------------------
The workshop is hosted by the
Leibniz Institute of Plant Biochemistry (IPB) [7]
in Halle (Saale), Germany.
Local Co-organizers:
* Daniel Schober, <-- main local contact [8]
AG Bioinformatics & Mass Spectrometry, IPB
* Steffen Neumann, AG Bioinformatics & Mass Spectrometry, IPB
* Stefan Brass, Institute for Computer Science,
Martin-Luther-University of Halle-Wittenberg
Sponsor
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The organizers acknowledge generous sponsorship by
OntoChem IT Solutions [9], Halle (Saale), Germany.
Links
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[1] Workshop website
https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2016-ODLS
http://tinyurl.com/odls-2016
[2] Program (direct link, otherwise see [1])
http://www.onto-med.de/obml/ws2016/odls2016program.pdf
[3] Registration (and overall event) email address
odls2016 at ipb-halle.de
[4] OBML website
https://wiki.imise.uni-leipzig.de/Gruppen/OBML
[5] IAOA website
http://iaoa.org/
[6] Main contact: Frank Loebe
https://wiki.imise.uni-leipzig.de/FrankLoebe
[7] Local organization website
http://www.ipb-halle.de/en/
[8] Local main contact: Daniel Schober
http://www.ipb-halle.de/en/employee/daniel-schober/
[9] OntoChem IT Solutions (Sponsor) website
http://www.ontochem.de/
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