Literature DB >> 29854221

The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps.

James C Schuler1, Werner M Ceusters1.   

Abstract

A requirement of realism-based ontology design is that classes denote exclusively entities that exist objectively in reality and that their definitions adhere to strict criteria to ensure that the classes are re-usable in other ontologies while preserving their ontological commitment. Building realism-based ontologies is therefore quite challenging and time-consuming, demanding considerable training. Although the top-level in the form of the Basic Formal Ontology (BFO) is worked out very well, and also the upper levels of certain domains, there is still a disconnect with the bottom- up or middle-out approach which is typical, and more practical, for application ontologies. Using the development of an application ontology for diabetes management in diabetes camps as an example, we present an overview of problems trainees in realism-based ontology design can be confronted with and offer some guidelines on how to deal with them in case no ideal solution is available.

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Mesh:

Year:  2018        PMID: 29854221      PMCID: PMC5977642     

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


  27 in total

1.  Ontological realism: A methodology for coordinated evolution of scientific ontologies.

Authors:  Barry Smith; Werner Ceusters
Journal:  Appl Ontol       Date:  2010-11-15       Impact factor: 1.115

2.  Discussion of "biomedical ontologies: toward scientific debate".

Authors:  M Brochhausen; A Burgun; W Ceusters; A Hasman; T Y Leong; M Musen; J L Oliveira; M Peleg; A Rector; S Schulz
Journal:  Methods Inf Med       Date:  2011       Impact factor: 2.176

3.  A fuzzy-ontology-oriented case-based reasoning framework for semantic diabetes diagnosis.

Authors:  Shaker El-Sappagh; Mohammed Elmogy; A M Riad
Journal:  Artif Intell Med       Date:  2015-08-14       Impact factor: 5.326

4.  Validating an ontology-based algorithm to identify patients with type 2 diabetes mellitus in electronic health records.

Authors:  Alireza Rahimi; Siaw-Teng Liaw; Jane Taggart; Pradeep Ray; Hairong Yu
Journal:  Int J Med Inform       Date:  2014-06-20       Impact factor: 4.046

5.  Competing interpretations of disorder codes in SNOMED CT and ICD.

Authors:  Stefan Schulz; Alan Rector; Jean-Marie Rodrigues; Kent Spackman
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

6.  Diabetes management at camps for children with diabetes.

Authors: 
Journal:  Diabetes Care       Date:  2012-01       Impact factor: 19.112

7.  Three ontologies to define phenotype measurement data.

Authors:  Mary Shimoyama; Rajni Nigam; Leslie Sanders McIntosh; Rakesh Nagarajan; Treva Rice; D C Rao; Melinda R Dwinell
Journal:  Front Genet       Date:  2012-05-28       Impact factor: 4.599

8.  Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Authors:  Warren A Kibbe; Cesar Arze; Victor Felix; Elvira Mitraka; Evan Bolton; Gang Fu; Christopher J Mungall; Janos X Binder; James Malone; Drashtti Vasant; Helen Parkinson; Lynn M Schriml
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

9.  The ontology of medically related social entities: recent developments.

Authors:  Amanda Hicks; Josh Hanna; Daniel Welch; Mathias Brochhausen; William R Hogan
Journal:  J Biomed Semantics       Date:  2016-07-12

10.  The Ontology for Biomedical Investigations.

Authors:  Anita Bandrowski; Ryan Brinkman; Mathias Brochhausen; Matthew H Brush; Bill Bug; Marcus C Chibucos; Kevin Clancy; Mélanie Courtot; Dirk Derom; Michel Dumontier; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Frank Gibson; Alejandra Gonzalez-Beltran; Melissa A Haendel; Yongqun He; Mervi Heiskanen; Tina Hernandez-Boussard; Mark Jensen; Yu Lin; Allyson L Lister; Phillip Lord; James Malone; Elisabetta Manduchi; Monnie McGee; Norman Morrison; James A Overton; Helen Parkinson; Bjoern Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Daniel Schober; Barry Smith; Larisa N Soldatova; Christian J Stoeckert; Chris F Taylor; Carlo Torniai; Jessica A Turner; Randi Vita; Patricia L Whetzel; Jie Zheng
Journal:  PLoS One       Date:  2016-04-29       Impact factor: 3.240

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  1 in total

1.  CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView.

Authors:  Asiyah Yu Lin; Stephan Gebel; Qingliang Leon Li; Sumit Madan; Johannes Darms; Evan Bolton; Barry Smith; Martin Hofmann-Apitius; Yongqun Oliver He; Alpha Tom Kodamullil
Journal:  CEUR Workshop Proc       Date:  2020-09
  1 in total

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