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Ontology-based knowledge representation for bioinformatics
Much of biology works by applying prior knowledge ('what is known') to an unknown entity,
rather than the application of a set of axioms that will elicit knowledge. In addition, the …
rather than the application of a set of axioms that will elicit knowledge. In addition, the …
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The
software provides genome-informatics tools such as a genome browser, sequence …
software provides genome-informatics tools such as a genome browser, sequence …
The evolution of Protégé: an environment for knowledge-based systems development
The Protégé project has come a long way since Mark Musen first built the Protégé meta-tool
for knowledge-based systems in 1987. The original tool was a small application, aimed at …
for knowledge-based systems in 1987. The original tool was a small application, aimed at …
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Pathway Tools is a production-quality software environment for creating a type of model-
organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc …
organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc …
The pathway tools software
Motivation: Bioinformatics requires reusable software tools for creating model-organism
databases (MODs). Results: The Pathway Tools is a reusable, production-quality software …
databases (MODs). Results: The Pathway Tools is a reusable, production-quality software …
The knowledge model of Protege-2000: Combining interoperability and flexibility
Abstract Knowledge-based systems have become ubiquitous in recent years. Knowledge-
base developers need to be able to share and reuse knowledge bases that they build …
base developers need to be able to share and reuse knowledge bases that they build …
The ecocyc database
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and
signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its …
signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its …
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
Motivation: A critical element of the computational infrastructure required for functional
genomics is a shared language for communicating biological data and knowledge. The …
genomics is a shared language for communicating biological data and knowledge. The …
[HTML][HTML] XOL: An XML-based ontology exchange language
PD Karp, VK Chaudhri, J Thomere - 1999 - xml.coverpages.org
This document describes a language for ontology exchange. The language, called XOL, is
designed to provide a format for exchanging ontology definitions among a set of interested …
designed to provide a format for exchanging ontology definitions among a set of interested …
[HTML][HTML] An ontology of randomized controlled trials for evidence-based practice: content specification and evaluation using the competency decomposition method
Randomized controlled trials (RCTs) are one of the least biased sources of clinical research
evidence, and are therefore a critical resource for the practice of evidence-based medicine …
evidence, and are therefore a critical resource for the practice of evidence-based medicine …