Enhancing GO for the sake of clinical bioinformatics

Download Edit this record How to cite View on PhilPapers
Abstract
Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved.
PhilPapers/Archive ID
KUMEGF
Revision history
Archival date: 2017-12-09
View upload history
References found in this work BETA

Add more references

Citations of this work BETA

No citations found.

Add more citations

Added to PP index
2017-11-05

Total views
30 ( #37,829 of 42,168 )

Recent downloads (6 months)
7 ( #40,158 of 42,168 )

How can I increase my downloads?

Downloads since first upload
This graph includes both downloads from PhilArchive and clicks to external links.