<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>In general, it is not easy to specify a single sequence identity for each molecule name
that appears in a pathway in the scientific literature. A molecule name may stand
for concepts of various granularities, from concrete objects such as H-Ras and ERK1
to abstract concepts or categories such as Ras and MAPK. Typically, the relations
among molecule names derive a hierarchical structure; without a proper way to
handle this knowledge, it becomes ever more difficult to develop a reliable pathway
database. This paper describes an ontology that is designed to annotate molecules
in the scientific literature on signal transduction pathways.</p>
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Comp Funct Genomics. 2004 Aug-Oct; 5(6-7):528-536