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OBML 2012 – 4. Workshop of Ontologies in Biomedicine and Life Sciences

September 27–28, Dresden, Germany



  • selected papers to be published in 

(see externer LinkVol. 2, Suppl. 4 for 2010; 2011 is in press)

Call for Participation

Where and when?

  • Technical University Dresden, Germany    
    • externer LinkBiotechnology Center (Bio Tec), Tatzberg 47/49, 01307 Dresden (externer Linkgoogle maps)
    • room: on 5th floor, there see pointers
    • Center for Regenerative Therapies Dresden (CRTD), entrance: Fetscherstraße 105, 01307 Dresden (externer Linkgoogle maps)
    • room: Auditorium (within CRTD, left entrance to the Auditorium only)
    [no longer valid as of Sep 25, 2012]
  • September 27–28, 2012

Important Dates

Submission of papers August 06, 2012
Author notification August 31, 2012
Submission of camera-ready manuscripts September 16, 2012
Registration to the workshop September 20, 2012
Deadline for payment September 20, 2012
Workshop September 27–28, 2012

NEW: Program & Report

The formal program of the workshop starts on Thu, Sep 27, at 13:00 (getting together 12:00) and is planned to end on Fri, Sep 28, at 15:00.

For details, please see: PDF DokumentOBML 2012 Program (PDF)

The workshop report is available since Sep 23, 2012: PDF DokumentOBML 2012 Report (PDF, ca. 5.5 MB)

Invited Speakers

Semantic Similarity in Biomedical Ontologies: measurement, assessment and applications
The analysis of complex biomedical entities and events, such as disease and epidemiological models, is challenging due to their multiple domain features, and thus to accurately describe them we need to use concepts from multiple biomedical ontologies, such as gene mutations, protein functions, anatomical parts and phenotypes. The usefulness of ontological annotations to interlink and interpret biomedical information is widely recognized, particularly for retrieving related information. This relatedness can be captured by semantic similarity measures that return a numerical value reflecting the closeness in meaning between two ontology concepts or two annotated entities. These measures have been successfully applied to biomedical ontologies, particularly to the Gene Ontology, for comparing proteins based on the similarity of their functions. This talk will discuss ongoing efforts to calculate semantic similarity, describe popular techniques used to calculate their effectiveness, and present existing biomedical applications that use semantic similarity measures to improve their performance.
Go Pub Med: Semantic search for the life sciences
In the talk I give an overview over recent work on ontology generation and semantic search with applications in drug discovery and trend analysis.
Pathology informatics; capturing and computing on pathology data

List of Accepted Papers

(Status according to author notification on Aug 31, 2012; ordered by surnames of first authors.)


Contribution towards Expenses

Account Data for Use from within Germany

EmpfängerUni Leipzig, Med. Fak.
Kontonr.132 345 001
Bankleitzahl860 700 00
FinanzinstitutDeutsche Bank Leipzig
VerwendungszweckProjekt 973000–103 (Angabe unbedingt erforderlich)
<<Name des Teilnehmers einsetzen>>
Unkostenbeitrag OBML 2012

Account Data for Use from Abroad

RecipientUni Leipzig, Med. Fak.
International Bank Account Number (IBAN)DE67 8607 0000 0132 3450 01
Bank Identification Code (BIC/SWIFT)DEUT DE 8LXXX
BankDeutsche Bank Leipzig
ReferenceProjekt 973000–103 (this is essential)
<<Provide the name of the participant>>
Unkostenbeitrag OBML 2012

Accommodation and Directions

hotel namespecial raterequired codes
externer LinkInnside Dresden
107,- EUR
tel.-code: biosaxony, web-code: biosinn
externer LinkSteigenberger Hotel de Saxe
109,- EUR
code: biosaxony
externer LinkIntercity Hotel Dresden
85,- EUR
code: biosaxony


Call for Papers

Goals of OBML

The workshop series on “Ontologies in Biomedicine and Life Sciences” (OBML workshop) was initiated by the working group for
OBML of the German Society for Computer Science in 2009. The OBML workshop aims to bring together scientists who are
working on all areas of ontologies applied to biomedicine and the life sciences to exchange ideas, discuss new results, start
collaborations and to initiate new projects. The OBML workshop is held annually and deals with all aspects of biomedical
ontologies as well as additional “hot” topics.

This year's “hot” topic is the representation of physiology. Physiology is the science of the functions and functionings of
biological systems, and significant resources have been invested in biology and medicine to describe and simulate physiological
processes. In particular, researchers in systems biology and systems medicine have generated a large number of computational
models to predict the outcome of physiological processes on a sub-cellular, cellular, tissue and organ-level scale, and projects
such as the Virtual Physiological Human aim to extend this work further and create a computational model of human physiology.
While ontologies are now widely applied to integrate biomedical data in many domains, the complexity of the physiology domain
has limited the success of ontologies so far. We aim to address this problem in the OBML workshop by organizing a special
session on the ontology of physiology. This session will bring together researchers in ontology, biomedicine, systems biology and
knowledge representation to present their solutions and requirements for the domain of physiology.


We invite submissions in all areas of biomedical ontology, including the following topics:

For the special session on “ontology of physiology”, we are particularly interested in 


Local Organization

Biotechnology Center, Technical University Dresden

Program Committee

Submission of Papers

Submissions to the workshop should comprise 2–4 pages and must be written in English.
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 DateiLaTeX template or the DateiMicrosoft Word template.
(NB: These are the same templates as used for OBML 2010 and 2011.)

Papers must be submitted via the Easy Chair conference system at externer Link .

Accepted papers will be printed in a proceedings volume (with ISSN) that will be distributed during the workshop.
A selection of these papers will be published in the externer LinkJournal of Biomedical Semantics.

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