Biomedical Ontology in Action – [ Update: Accepted Papers ]

The accepted papers are listed here.

November 8, 2006, Baltimore, Maryland, USA

Workshop organized bythe National Center for Ontology Research (NCOR) and the Working Group on Formal (Bio-)Medical Knowledge Representation of the American Medical Informatics Association (AMIA)

Collocated with FOIS 2006

In recent years, a good deal of attention has been paid to the sorts of criteria that an ontology must satisfy if it is to ensure trueinformation integration and automatic reasoning across large-scale knowledge sources. Formal ontology is now an established field of research with conferences such as FOIS and organizations such as NCOR.The biomedical domain is at the leading edge of ontology research, as illustrated by the recent creation of the National Center for Biomedical Ontology, a NIH Roadmap center.

Standing on the foundations of biomedical ontologies are the many applications supported by these ontologies. For example, in health care, ontologies are an important component of an interoperable health information technology infrastructure. In biology, ontologies have become essential for annotating the literature and integrating the multiple, heterogeneous knowledge bases resulting from the analysis of high-throughput experiments.

This workshop aims at bringing together researchers from a broad range of fields that are related to formal ontology and medical informatics. The goal is to show how current research can be brought tobear on the practical problems associated with the development ofapplications supported by these ontologies, i.e., to show biomedical ontology "in action".

The scope of KR-MED 2006 includes the following areas:

Biomedical ontologies and electronic health records (EHRs)

Semantic Web applications in healthcare and life sciences

Use of ontologies in knowledge discovery, text analysis and data mining

Biomedical ontology evaluation

Temporal, spatial and causal knowledge reasoning in biomedical systems

Knowledge representation, acquisition, validation, visualization and maintenance in biomedical systems

Applications of knowledge representation languages, description logics for biomedical systems

Formal approaches to large biomedical controlled terminologies and vocabularies

Important dates

Paper submissions due: July 7, 2006

Notification of paper acceptance: August 18, 2006

Final paper deadline: September 15, 2006

Workshop: November 8, 2006

Submission information

Prospective authors are invited to submit papers in any of the areaslisted above. All papers must be written in English and the lengthshould not exceed 8 pages including figures, tables and references. Papers should be submitted electronically to

The final paper has to be delivered as PDF. The format corresponds tothat of the AMIA proceedings. Use 8.5 x 11 inch paper size with one inch margins left, right, top, and bottom. Place the title in 14 point Times Roman typeface, single-column, bolded, centered, initial capitals. Include the names, credentials, institutions and locations ofthe author(s) below the title using 12 point Times Roman typeface, single-column, bolded, centered, initial capitals. Include the main textof the submission single-spaced in 10 point Times Roman typeface,justified, two-column format with .5 inch between columns. Use the following reference format: Cite all references in the text, tables, orfigure legends. In the text, use 8 point superscript if possible toindicate reference numbers; if not possible, use 10 point numbers inbrackets. Under a centered heading References at the end of the submission, provide a list of references cited, in order of occurrencein the manuscript, and with titles using initial capitals only. List allauthors of any cited work when there are six or fewer authors; if morethan six, list only the first three followed by et al. Follow theVancouver Style (for further details, see LaTeX and MS Word document templates will be available shortly on the conference website:

The workshop proceedings will be published electronically on the workshop, the authors of the best submissions will be invitedto expand and refine their papers for possible publication in thejournal Applied Ontology (

Contact for additional information about papersubmission requirements.


Organizing Committee

Stefan Schulz (Freiburg University Hospital, Germany)

Barry Smith (State University of New York at Buffalo, USA)

Fabian Neuhaus (State University of New York at Buffalo, USA)

Scientific Program Committee

Olivier Bodenreider (chair, National Library of Medicine, USA)

Anita Burgun (University of Rennes, France)

Ronald Cornet (Amsterdam Academic Medical Center, The Netherlands)

Maureen Donnelly (State University of New York at Buffalo, USA)

Aldo Gangemi (ISTC Laboratory of Applied Ontology, Italy)

Michael Gruninger (University of Toronto, Canada)

Anand Kumar (IFOMIS, Germany)* Phillip Lord (University of Newcastle, UK)

Yves Lussier (University of Chicago, USA)

Onard Mejino (University of Washington, USA)

Peter Mork (Mitre Corporation, USA)

Fabian Neuhaus (National Center for Ontology Research, USA)

Daniel Rubin (National Center for Biomedical Ontology, USA)

Stefan Schulz (Freiburg University Hospital, Germany)

Lowell Vizenor (National Library of Medicine, USA)

Chris Welty (IBM T.J. Watson Research Center, USA)

Jennifer Williams (OntologyWorks, USA)


Inn at the Colonnade 4 West University Parkway Baltimore, Maryland 21218 Telephone: +1 410 235 5400 Fax: +1 410 235 5572

The Inn at the Colonnade is located across from Johns Hopkins University less than four miles from Baltimore’s CBD and historic Inner Harbor, and only 20 minutes from BWI International Airport.

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