Information for Participants
Where and When?
- Medical Center – University of Freiburg, Freiburg im Breisgau, Germany
Main Campus, University Building 1, KG 1 cf. main campus map
- updated venue:
- rooms: HS / Konferenzraum IMBI at the first floor, i.e., workshop sessions are held in the lecture hall or the conference room at the IMBI building; further details are available on site.
- October 07–08, 2014 – time frame in CEST: Tue, Oct 7, 13:00 (get together) to Wed, Oct 8, afternoon
Schedule and Papers
Contribution towards Expenses
- Every participant is charged a contribution towards expenses for catering during the breaks of both days, excluding lunch and dinner.
- This amounts to
- 30 EUR regular,
- 25 EUR for members of IAOA or GI,
- 20 EUR for students.
- Payment by bank transfer: Account data for the payment
|Financial Institute||Deutsche Bank Freiburg|
|IBAN||DE22 6807 0030 0030148100|
|reason of payment||1028004001|
If you need any further information, please contact Monika Richards: email@example.com
Call for Update Talks and Participation
|Submission of contributions ||Tue, July 22, 2014 (strict!)|Tue, July 15, 2014
|Author notification ||Mon, August 25, 2014|
|Registration period opens ||Mon, September 08, 2014|
|Submission of update talk proposals ||Wed, September 10, 2014|
|Submission of camera-ready versions ||Sat, September 20, 2014|Wed, September 10, 2014
|Author Registration ||Sat, September 20, 2014|
|Regular Registration ||Tue, September 30, 2014|
|Late Registration ||Wed, October 08, 2014|
|Workshop ||Tue-Wed, October 07–08, 2014|
The projected time frame
for the workshop (in the CEST time zone) is Tue, Oct 07, 13:00 to Wed, Oct 08, afternoon
Update Session and OBML Workgroup Session
In addition to the technical program, an Update Session on selected ontologies, systems, and projects is being prepared.
We invite suggestions for update talks to be included in this session.
Please send your proposal(s) to firstname.lastname@example.org, thereby reaching the workshop organizers, by September 10, 2014 (Wed).
The workshop will further host an organizational meeting of the OBML workgroup.
List of Accepted Papers
(Status according to author notification on Aug 22, 2014; ordered by surnames of first authors.)
- A Proposal for an Ontology for the Tumor-Node-Metastasis Classification of Malignant Tumors: a Study on Breast Tumors. Martin Boeker, Rita Faria and Stefan Schulz
- OWL Patterns for Modeling the Change over Time exemplified by the Cell Tracking Ontology. Patryk Burek, Nico Scherf and Heinrich Herre
- Ontology for Molecular Structure. Henson Graves
- Butterflies and Embryos: The Ontology of Temporally Qualified Continuants. Ludger Jansen and Niels Grewe
- Entities with Genetic Information – An Initial Perspective from the Core Theme of Continuity and Change in Biology. Frank Loebe and Vinay K. Chaudhri
- Ontology usage in Omics Standards Initiatives: Pros and Cons of enriching XML data formats with controlled vocabulary terms. Daniel Schober, Michael Wilson, Daniel Jacob, Annick Moing, Gerhard Mayer, Martin Eisenacher, Reza M Salek and Steffen Neumann
- PEGASO: towards a teenager tailored ontology – Supporting inference about the obesity-related health status -. Aleksandra Sojic, Walter Terkaj, Giorgia Contini and Marco Sacco
- OntoStudyEdit: A new Approach for Ontology-Based Representation and Management of Metadata in Clinical and Epidemiological Research. Alexandr Uciteli and Heinrich Herre
- Biomedical Ethics Ontology, computers and moral reasoning. Paulina Wasilewska
- For registration please send an email to: email@example.com
- Therein one should be able to read / find the following information:
- first name, last name, and email address of the registrant(s)
- possibly a preferred shorthand of the affiliation (to be used at the name badge)
- if applicable, the title of the paper that the registrant presents
- joining the dinner on Tue, Oct 07: yes / maybe / no
- The registration period opens on Mon, September 08, 2014. Registrations and, if necessary, cancellation should be send until Tue, September 30, 2014 at the latest, please (= one week prior to the workshop start on Tue, October 07)
- Concerning the presentation of accepted submissions it is expected that at least one of the authors will participate in the workshop. Presenting authors should register as early as possible starting from September 08 and should specify which paper they will present.
- Interested parties (without contribution to any submission) are equally welcome.
We can offer you booking possibilities in two hotels directly in resp. at the city center for a special price on Tue-Wed, Oct 07–08
Call for Papers
Goals of the Workshop
Medicine, biology and life sciences produce hardly manageable and comprehensible amounts of data, information, and knowledge. Their computer-based processing, integration, as well as their conceptual foundation 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 processing, from experimental data acquisition and data management, across analysis, structuring and interpretation of data, up to the development of structures of knowledge in the form of ontologies with their various applications. The workshop pursues the aim to gather scientists that work in these fields in order to exchange ideas, to discuss new results and to inspire collaborations. 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.
The following topics are relevant, yet others related to these basic topics are likewise welcome:
- Integration, management and retrieval of big data and/or complex data sets
- Heterogeneity and integration of big data
- Integrative data semantics
- Curation of data in life sciences
- Visualization of data in life sciences
- Generic transformation of clinical data into Semantic Web standards
- Data protection of clinical data
- Omics-data for diagnosis and therapy
- Ontologies in the field of biology, medicine and clinical research, for example
- Ontologies for the specification of clinical trials and medical phenotypes
- Process ontologies in systems biology and in medicine
- Ontologies in neuro-biology
- Ontologies in knowledge representation
for example, formal ontology of time and space, formal ontology of properties, roles and functions
- Methods and tools for development, management and application of ontologies
- Quality assurance and evaluation of ontologies
- Applications in the fields of Semantic Web, Linked Open Data, and Big Data
- Martin Boeker, University of Freiburg (general & local chair)
- Ludger Jansen, University of Muenster (PC chair)
- Heinrich Herre, University of Leipzig (speaker of OBML & co-organizer)
- Frank Loebe, University of Leipzig (co-organizer)
The workshop is hosted by the Center for Medical Biometry and Medical Informatics
, Medical Center – University of Freiburg.
- Patryk Burek, University of Leipzig
- Jesualdo Tomás Fernández-Breis, University of Murcia, Spain
- George Gkoutos, Aberystwyth University, UK
- Heinrich Herre, University of Leipzig
- Robert Hoehndorf, University of Cambridge, UK
- Toralf Kirsten, University of Leipzig
- Oliver Kutz, Otto von Guericke University Magdeburg
- Wolfgang Müller, HITS gGmbH, Heidelberg
- Axel Ngonga-Ngomo, University of Leipzig
- Anika Oellrich, European Bioinformatics Institute (EBI), Hinxton, UK
- Dietrich Rebholz-Schuhmann, University of Zurich, Switzerland
- Peter Robinson, Charité Berlin
- Daniel Schober, Leibniz Institute of Plant Biochemistry (IPB), Halle
- Falk Schreiber, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben
- Stefan Schulz, Medical University of Graz, Austria
- Aleksandra Sojic, Institute of Industrial Technologies and Automation (ITIA-CNR), Milan, Italy
- George Tsatsaronis, Technical University Dresden
- Dagmar Waltemath, University of Rostock
Submissions to the workshop can be extended abstracts of 2 pages
or papers of 4–6 pages
(any such length is equally welcome; 6 pages is the strict maximum).
Contributions in English
are highly recommended, but submissions in German can also be accepted.
The preferred file format for submissions is PDF
, other admitted formats are Microsoft Word (DOC and DOCX) and Postscript (PS).
Please use the corresponding template
for submissions, either the Microsoft Word template
or the LaTeX template
, for which there is a sample file
(NB: These are the same templates as used for OBML 2010–201
2. The templates were adopted with minor modifications from Bioinformatics
, whose original ZIP archives of both templates comprise further files (a sample PDF and, for LaTeX, a sample TEX file and additional style files (STY)), cf. wordtemplate.zip
(for LaTeX). Please ensure that you use one of the modified template files linked above – the ZIP archives contain unmodified versions, also those linked here.)
Contributions must be submitted via the EasyChair conference system at https://www.easychair.org/conferences/?conf=odls2014
Accepted abstracts and papers will be
printed in a proceedings volume (with ISSN) that will be distributed during the workshop
integrated into a proceedings volume (with ISSN) that will be available electronically until the beginning of the workshop.
After the workshop authors of selected papers
will be invited to submit extended versions to the Journal of Biomedical Semantics
(JBMS). These manuscripts must then be written in English and will be re-reviewed. (Since 2012 invited papers appear separately in JBMS, e.g. in the series Biomedical Ontologies