Ontology-based knowledge representation for bioinformatics

R Stevens, CA Goble, S Bechhofer - Briefings in bioinformatics, 2000‏ - academic.oup.com
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 …

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PD Karp, M Latendresse, SM Paley… - Briefings in …, 2016‏ - academic.oup.com
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 …

The evolution of Protégé: an environment for knowledge-based systems development

JH Gennari, MA Musen, RW Fergerson… - International Journal of …, 2003‏ - Elsevier
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 …

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PD Karp, SM Paley, M Krummenacker… - Briefings in …, 2010‏ - academic.oup.com
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 …

The pathway tools software

PD Karp, S Paley, P Romero - Bioinformatics, 2002‏ - academic.oup.com
Motivation: Bioinformatics requires reusable software tools for creating model-organism
databases (MODs). Results: The Pathway Tools is a reusable, production-quality software …

The knowledge model of Protege-2000: Combining interoperability and flexibility

NF Noy, RW Fergerson, MA Musen - International Conference on …, 2000‏ - Springer
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 …

The ecocyc database

PD Karp, M Riley, M Saier, IT Paulsen… - Nucleic acids …, 2002‏ - academic.oup.com
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 …

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)

I Yeh, PD Karp, NF Noy, RB Altman - Bioinformatics, 2003‏ - academic.oup.com
Motivation: A critical element of the computational infrastructure required for functional
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 …

[HTML][HTML] An ontology of randomized controlled trials for evidence-based practice: content specification and evaluation using the competency decomposition method

I Sim, B Olasov, S Carini - Journal of Biomedical Informatics, 2004‏ - Elsevier
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 …