Literature DB >> 23888086

CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY.

Barry Smith1.   

Abstract

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework.1.

Entities:  

Year:  2012        PMID: 23888086      PMCID: PMC3718480          DOI: 10.1111/j.1467-9329.2012.00557.x

Source DB:  PubMed          Journal:  Ratio (Oxf)        ISSN: 0034-0006


  11 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.  Bio-ontologies-fast and furious.

Authors:  Judith Blake
Journal:  Nat Biotechnol       Date:  2004-06       Impact factor: 54.908

3.  Identification of disease-causing genes using microarray data mining and Gene Ontology.

Authors:  Azadeh Mohammadi; Mohammad H Saraee; Mansoor Salehi
Journal:  BMC Med Genomics       Date:  2011-01-26       Impact factor: 3.063

4.  Modeling biomedical experimental processes with OBI.

Authors:  Ryan R Brinkman; Mélanie Courtot; Dirk Derom; Jennifer M Fostel; Yongqun He; Phillip Lord; James Malone; Helen Parkinson; Bjoern Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Larisa N Soldatova; Christian J Stoeckert; Jessica A Turner; Jie Zheng
Journal:  J Biomed Semantics       Date:  2010-06-22

5.  The Protein Ontology: a structured representation of protein forms and complexes.

Authors:  Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith A Blake; Carol J Bult; Michael Caudy; Harold J Drabkin; Peter D'Eustachio; Alexei V Evsikov; Hongzhan Huang; Jules Nchoutmboube; Natalia V Roberts; Barry Smith; Jian Zhang; Cathy H Wu
Journal:  Nucleic Acids Res       Date:  2010-10-08       Impact factor: 16.971

6.  Logical development of the cell ontology.

Authors:  Terrence F Meehan; Anna Maria Masci; Amina Abdulla; Lindsay G Cowell; Judith A Blake; Christopher J Mungall; Alexander D Diehl
Journal:  BMC Bioinformatics       Date:  2011-01-05       Impact factor: 3.169

7.  The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

Authors:  Bernard de Bono; Robert Hoehndorf; Sarala Wimalaratne; George Gkoutos; Pierre Grenon
Journal:  BMC Res Notes       Date:  2011-08-30

8.  Physical properties of biological entities: an introduction to the ontology of physics for biology.

Authors:  Daniel L Cook; Fred L Bookstein; John H Gennari
Journal:  PLoS One       Date:  2011-12-27       Impact factor: 3.240

9.  Relations in biomedical ontologies.

Authors:  Barry Smith; Werner Ceusters; Bert Klagges; Jacob Köhler; Anand Kumar; Jane Lomax; Chris Mungall; Fabian Neuhaus; Alan L Rector; Cornelius Rosse
Journal:  Genome Biol       Date:  2005-04-28       Impact factor: 13.583

10.  Gene Ontology annotations: what they mean and where they come from.

Authors:  David P Hill; Barry Smith; Monica S McAndrews-Hill; Judith A Blake
Journal:  BMC Bioinformatics       Date:  2008-04-29       Impact factor: 3.169

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  2 in total

1.  Development of an Ontology for Periodontitis.

Authors:  Asami Suzuki; Takako Takai-Igarashi; Jun Nakaya; Hiroshi Tanaka
Journal:  J Biomed Semantics       Date:  2015-07-01

2.  Process attributes in bio-ontologies.

Authors:  André Q Andrade; Ward Blondé; Janna Hastings; Stefan Schulz
Journal:  BMC Bioinformatics       Date:  2012-08-28       Impact factor: 3.169

  2 in total

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