Automatic categorization of diverse experimental information in the bioscience literature.

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming.

Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.

Background: Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis.

WormBase: a comprehensive resource for nematode research.

WormBase (http://www.wormbase.org) is a central data repository for nematode biology.

The Caenorhabditis elegans vulva: a post-embryonic gene regulatory network controlling organogenesis.

The Caenorhabditis elegans vulva is an elegant model for dissecting a gene regulatory network (GRN) that directs postembryonic organogenesis. The mature vulva comprises seven cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique pattern of spatial and temporal gene expression. The mechanisms that specify these cell types in a precise spatial pattern are not well understood.

WormBase 2007.

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research.

The tailless ortholog nhr-67 regulates patterning of gene expression and morphogenesis in the C. elegans vulva.

Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown.

Transcriptional network underlying Caenorhabditis elegans vulval development.

The vulval development of Caenorhabditis elegans provides an opportunity to investigate genetic networks that control gene expression during organogenesis. During the fourth larval stage (L4), seven vulval cell types are produced, each of which executes a distinct gene expression program. We analyze how the expression of cell-type-specific genes is regulated.

A reporter for amyloid precursor protein gamma-secretase activity in Drosophila.

A key event in the pathogenesis of Alzheimer's disease (AD) is the deposition of senile plaques consisting largely of a peptide known as beta-amyloid (Abeta) that is derived from the amyloid precursor protein (APP). A proteolytic activity called gamma-secretase cleaves APP in the transmembrane domain and is required for Abeta generation. Aberrant gamma-secretase cleavage of APP underlies the majority of early onset, familial AD.