The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into
a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began
during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics...
WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we...
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
BACKGROUND: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a...
The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop,
maintain and use a set of structured, controlled
vocabularies for the annotation of genes, gene
products and sequences. The GO ontologies
are expanding both in content and in structure.
Several new relationship types have been introduced
and used, along with...