Untangling taxonomies and relationships: personal and practical problems in loosely coupled development of large ontologies

The GALEN programme has been developing medical ontologies collaboratively for nearly a decade. The ontologies are large and formulated in a specialised description logic, GRAIL. The programme is a broad collaboration of over a dozen groups, most with no prior experience of developing formal ontologies. The programme has developed a methodology for loosely coupled development using layers of intermediate representations, guidelines and tools which minimises training requirements for domain experts and effort by central knowledge engineers. Issues arise both from problems in formal representations and from the idiosyncrasies of the medical domain. Issues dealt with include 'tangled' taxonomies, part-whole and locative relationships, defaults and exceptions, semantic normalisation, and the difference between medical convention and strict logical criteria for correctness.

[1]  Michael Uschold,et al.  Ontologies: principles, methods and applications , 1996, The Knowledge Engineering Review.

[2]  E H Shortliffe,et al.  Scalable Methodologies for Distributed Development of Logic-Based Convergent Medical Terminology , 1998, Methods of Information in Medicine.

[3]  Ramanathan V. Guha,et al.  Building Large Knowledge-Based Systems: Representation and Inference in the Cyc Project , 1990 .

[4]  Ian Horrocks,et al.  Practical Reasoning for Very Expressive Description Logics , 2000, Log. J. IGPL.

[5]  Ian Horrocks,et al.  Using an Expressive Description Logic: FaCT or Fiction? , 1998, KR.

[6]  V. Rich.  Personal communication , 1989, Nature.

[7]  Nicola Guarino,et al.  Open Problems with Part-Whole Relations , 1996, Description Logics.

[8]  Michael Wessel,et al.  Obstacles on the Way to Spatial Reasoning with Description Logics: Undecidability of. . , 2000 .

[9]  Alan L. Rector,et al.  Integrating existing drug formulation terminologies into an HL7 standard classification using OpenGALEN , 2001, AMIA.

[10]  Martin Romacker,et al.  Partonomic Reasoning as Taxonomic Reasoning in Medicine , 1999, AAAI/IAAI.

[11]  Ian Horrocks,et al.  The GRAIL concept modelling language for medical terminology , 1997, Artif. Intell. Medicine.

[12]  Mark A. Musen,et al.  Modern architectures for intelligent systems: reusable ontologies and problem-solving methods , 1998, AMIA.

[13]  Drew McDermott,et al.  D. B. Lenat and R. V. Guha, Building Large Knowledge-Based Systems: Representation and Inference in the Cyc Project , 1993, Artif. Intell..

[14]  Aldo Gangemi,et al.  An Ontological Analysis of Surgical Deeds , 1997, AIME.

[15]  W A Nowlan,et al.  Clinical workstations: identifying clinical requirements and understanding clinical information. , 1994, International journal of bio-medical computing.

[16]  Alan L. Rector,et al.  Inheritance of Drug Information , 2000, AMIA.

[17]  Brian R. Gaines,et al.  Knowledge Acquisition Tools for Expert Systems , 1988 .

[18]  A. L. Rector.  Clinical terminology : Why is it so hard? : Challenges to Progresses , 1999 .

[19]  Kent A. Spackman,et al.  SNOMED RT: a reference terminology for health care , 1997, AMIA.

[20]  Alan L. Rector,et al.  Having our cake and eating it too: how the GALEN Intermediate Representation reconciles internal complexity with users' requirements for appropriateness and simplicity , 2000, AMIA.

[21]  Yuval Shahar,et al.  Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support , 1995, Artif. Intell. Medicine.

[22]  Werner Ceusters,et al.  Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine , 1998, IEEE Transactions on Information Technology in Biomedicine.

[23]  Douglas Herrmann,et al.  A Taxonomy of Part-Whole Relations , 1987, Cogn. Sci..

[24]  Linda G. Shapiro,et al.  The digital anatomist foundational model: principles for defining and structuring its concept domain , 1998, AMIA.

[25]  Steffen Staab,et al.  Ontology Engineering beyond the Modeling of Concepts and Relations , 2000 .

[26]  Nick Booth,et al.  Using scenarios in chronic disease management guidelines for primary care , 2000, AMIA.

[27]  J. M. Akkermans,et al.  The KADS Knowledge Modelling Approach , 1992 .

[28]  Samson W. Tu,et al.  A flexible approach to guideline modeling , 1999, AMIA.

[29]  Paul Smaglik,et al.  Fact or fiction? , 2003, Nature.

[30]  Carole A. Goble,et al.  Supporting a humanly impossible task: The clinical human computer environment , 1990, INTERACT.

[31]  A. Rector.  Clinical Terminology: Why Is it so Hard? , 1999, Methods of Information in Medicine.

[32]  Alan L. Rector,et al.  A reference terminology for drugs , 1999, AMIA.