Survey-based naming conventions for use in OBO Foundry ontology development.

Background: A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration.

Changes in gene expression of gastric mucosa during therapeutic acid inhibition.

Background: Long-term therapy with potent acid inhibitors is a common treatment for gastro-esophageal reflux disease. Administration of proton pump inhibitors (PPIs) causes profound and continuous hypochlorhydria by inhibition of the proton pump in gastric parietal cells. Long-term hypergastrinaemia increases mucosal thickness and enterochromaffin-like cell density in oxyntic mucosa.

Taxonomy-based partitioning of the Gene Ontology.

The Gene Ontology (GO) project is a collaborative effort to construct ontologies which facilitate biologically meaningful annotation of gene products. In some situations, only a generic or a species-specific subset of all GO terms is required to annotate and analyze the results of a particular biomedical experiment. We show that by defining explicit links between terms in the GO and terms in the Taxonomy of Species (TS) it is possible to automatically create partitions of the GO according to various taxonomic criteria.

Identification of novel growth factor-responsive genes in neuroendocrine gastrointestinal tumour cells.

Targeting growth-regulatory pathways is a promising approach in cancer treatment. A prerequisite to the development of such therapies is characterisation of tumour growth regulation in the particular tumour cell type of interest. In order to gain insight into molecular mechanisms underlying proliferative responses in neuroendocrine (NE) gastrointestinal (GI) tumours, we investigated gene expression in human carcinoid BON cells after exposure to gastrin, hepatocyte growth factor (HGF), pituitary adenylate cyclase-activating polypeptide or epidermal growth factor.

Liver gene expression in rats in response to the peroxisome proliferator-activated receptor-alpha agonist ciprofibrate.

Fibrate class hypolipidemic drugs such as ciprofibrate activate the peroxisome proliferator-activated receptor-alpha (PPARalpha), which is involved in processes including lipid metabolism and hepatocyte proliferation in rodents. We examined the effects of ciprofibrate (50 mg/kg body wt per day for 60 days) on liver gene expression in rats using cDNA microarrays. The 60-day dosing period was chosen to elucidate both the metabolic and proliferative actions of this substance, while avoiding confounding effects from the hepatic carcinogenesis seen during more long-term stimulation.