Literature DB >> 16779026

Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study.

Olivier Dameron1, Daniel L Rubin, Mark A Musen.   

Abstract

A description logics representation of the Foundational Model of Anatomy (FMA) in the Web Ontology Language (OWL-DL) would allow developers to combine it with other OWL ontologies, and would provide the benefit of being able to access generic reasoning tools. However, the FMA is currently represented in a frame language. The differences between description logics and frames are not only syntactic, but also semantic. We analyze some theoretical and computational limitations of converting the FMA into OWL-DL. Namely, some of the constructs used in the FMA do not have a direct equivalent in description logics, and a complete conversion of the FMA in description logics is too large to support reasoning. Therefore, an OWL-DL representation of the FMA would have to be optimized for each application. We propose a solution based on OWL-Full, a superlanguage of OWL-DL, that meets the expressiveness requirements and remains application-independent. Specific simplified OWL-DL representations can then be generated from the OWL-Full model by applications. We argue that this solution is easier to implement and closer to the application needs than an integral translation, and that the latter approach would only make the FMA maintenance more difficult.

Mesh:

Year:  2005        PMID: 16779026      PMCID: PMC1560487     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN: 1559-4076


  3 in total

1.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy.

Authors:  Cornelius Rosse; José L V Mejino
Journal:  J Biomed Inform       Date:  2003-12       Impact factor: 6.317

2.  Use of description logic classification to reason about consequences of penetrating injuries.

Authors:  Daniel L Rubin; Olivier Dameron; Mark A Musen
Journal:  AMIA Annu Symp Proc       Date:  2005

3.  Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base.

Authors:  C Rosse; J L Mejino; B R Modayur; R Jakobovits; K P Hinshaw; J F Brinkley
Journal:  J Am Med Inform Assoc       Date:  1998 Jan-Feb       Impact factor: 4.497

  3 in total
  11 in total

1.  Use of description logic classification to reason about consequences of penetrating injuries.

Authors:  Daniel L Rubin; Olivier Dameron; Mark A Musen
Journal:  AMIA Annu Symp Proc       Date:  2005

2.  Experience in reasoning with the foundational model of anatomy in OWL DL.

Authors:  Songmao Zhang; Olivier Bodenreider; Christine Golbreich
Journal:  Pac Symp Biocomput       Date:  2006

3.  Translating the Foundational Model of Anatomy into OWL.

Authors:  Natalya F Noy; Daniel L Rubin
Journal:  Web Semant       Date:  2008       Impact factor: 1.897

4.  The foundational model of anatomy in OWL: Experience and perspectives.

Authors:  Christine Golbreich; Songmao Zhang; Olivier Bodenreider
Journal:  Web Semant       Date:  2006       Impact factor: 1.897

5.  Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.

Authors:  Natalya F Noy; Sherri de Coronado; Harold Solbrig; Gilberto Fragoso; Frank W Hartel; Mark A Musen
Journal:  Appl Ontol       Date:  2008-01-01       Impact factor: 1.115

6.  An analysis of multi-type relational interactions in FMA using graph motifs with disjointness constraints.

Authors:  Guo-Qiang Zhang; Lingyun Luo; Chime Ogbuji; Cliff Joslyn; Jose Mejino; Satya S Sahoo
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

7.  OntoVIP: an ontology for the annotation of object models used for medical image simulation.

Authors:  Bernard Gibaud; Germain Forestier; Hugues Benoit-Cattin; Frédéric Cervenansky; Patrick Clarysse; Denis Friboulet; Alban Gaignard; Patrick Hugonnard; Carole Lartizien; Hervé Liebgott; Johan Montagnat; Joachim Tabary; Tristan Glatard
Journal:  J Biomed Inform       Date:  2014-07-16       Impact factor: 6.317

8.  From frames to OWL2: Converting the Foundational Model of Anatomy.

Authors:  Landon T Detwiler; Jose L V Mejino; James F Brinkley
Journal:  Artif Intell Med       Date:  2016-04-27       Impact factor: 5.326

9.  Alignment of the UMLS semantic network with BioTop: methodology and assessment.

Authors:  Stefan Schulz; Elena Beisswanger; László van den Hoek; Olivier Bodenreider; Erik M van Mulligen
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

10.  Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study.

Authors:  Tristan Moreau; Bernard Gibaud
Journal:  Front Neuroinform       Date:  2015-04-10       Impact factor: 4.081

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