Parthood as Spatial Inclusion - Evidence from biomedical Conceptualizations

Modeling complex compositional objects in the field of the life sciences requires to solve intricate ontological problems, especially those related to parts of a whole, space and location. For concrete physical entities, we here stipulate that the distinction between parthood and location can be abstracted away. We outline a logic-based reasoning framework in which taxonomic sub-sumption not only takes care of the propagation of roles across taxonomic hierarchies, but also across nontaxonomic, i.e., partonomic or spatial, ones.

[1]  Ian Horrocks,et al.  Decidability of SHIQ with Complex Role Inclusion Axioms , 2003, IJCAI.

[2]  Steffen Schulze-Kremer,et al.  The Ontology of the Gene Ontology , 2003, AMIA.

[3]  Roberto Casati,et al.  Parts And Places , 1999 .

[4]  Stefan Schulz,et al.  Logic-based Remodeling of the Digital Anatomist Foundational Model , 2003, AMIA.

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

[6]  Stefan Schulz,et al.  Mereotopological reasoning about parts and (w)holes in bio-ontologies , 2001, FOIS.

[7]  Cornelius Rosse,et al.  A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy , 2003 .

[8]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[9]  P. Simons Parts: A Study in Ontology , 1991 .

[10]  Stefan Schulz,et al.  Necessary Parts and Wholes in Bio-Ontologies , 2002, KR.

[11]  Nicola Guarino,et al.  Dwq : Esprit Long Term Research Project, No 22469 Part-whole Relations in Object-centered Systems: an Overview Part-whole Relations in Object-centered Systems: an Overview , 2022 .

[12]  Alan L. Rector,et al.  GALEN's model of parts and wholes: experience and comparisons , 2000, AMIA.

[13]  José L. V. Mejino,et al.  Research Paper: Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base , 1998, J. Am. Medical Informatics Assoc..

[14]  Martin Romacker,et al.  MedSynDikate - a natural language system for the extraction of medical information from findings reports , 2002, Int. J. Medical Informatics.

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

[16]  Werner Nutt,et al.  Basic Description Logics , 2003, Description Logic Handbook.

[17]  Barry Smith,et al.  The Role of Foundational Relations in the Alignment of Biomedical Ontologies , 2004, MedInfo.

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

[19]  Stefan Schulz,et al.  A knowledge representation view on biomedical structure and function , 2002, AMIA.

[20]  Robert M. MacGregor,et al.  A Description Classifier for the Predicate Calculus , 1994, AAAI.

[21]  D. Lindberg,et al.  Unified Medical Language System , 2020, Definitions.

[22]  P. F. PatelSchneider,et al.  What's inheritance got to do with knowledge representation , 1991 .

[23]  Stefan Schulz,et al.  Knowledge Engineering by Large-Scale Knowledge Reuse - Experience from the Medical Domain , 2000, KR.

[24]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[25]  Bonnie L. Webber,et al.  Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations , 2003, Pacific Symposium on Biocomputing.

[26]  Volker Haarslev,et al.  Description of the RACER System and its Applications , 2001, Description Logics.

[27]  Maureen Donnelly,et al.  On Parts and Holes: The Spatial Structure of the Human Body , 2004, MedInfo.

[28]  Roberto Casati,et al.  Parts and Places: The Structures of Spatial Representation , 1999 .

[29]  Ian Horrocks,et al.  A Description Logic Based Schema for the Classification of Medical Data , 1996, KRDB.

[30]  Alan L. Rector Analysis of propagation along transitive roles: Formalisation of the GALEN experience with Medical Ontologies , 2002, Description Logics.