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. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. RESULTS: We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. CONCLUSION: Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.

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. OBJECTIVE: The aim of this study was to see whether this very common clinical intervention induces significant changes in the gastric mucosal gene expression pattern. METHODS: Seven patients suffering from gastro-esophageal reflux disease were included in this study. Endoscopic biopsies were taken from the corpus mucosa before and toward the end of a 3-month treatment with the PPI esomeprazole. RESULTS: Microarray analysis identified 186 differentially expressed genes. A high proportion of genes with changed gene expression levels during PPI treatment are involved in proliferation, apoptosis, and stress response. CONCLUSION: This study identified many genes that were not previously known to be affected by inhibition of gastric acid secretion. Further characterization of the functional roles of genes whose expression is modulated by potent acid inhibition may give new insight into the biological responses to potent acid inhibition, including the mucosal response to the moderately increased gastrin levels encountered in clinical practice.

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. Our framework is based on three logically defined relations--validity, specificity, and relevance--used to link terms in the Gene Ontology with terms in the Taxonomy. The major advantages of this approach, as compared to the traditional GO slims methodology, are: unambiguous semantics of GO-TS annotations, significant reduction of the effort needed to manually select GO terms appropriate for a particular taxonomic context, ability to generate views of the GO even for taxa for which no explicit links with GO terms exist, logical consistency of such views, and automated updates of TS-dependent GO subsets. Incorporation of the proposed framework into the GO may improve the usability of the ontology for those scientists who focus their research on a particular species or a specific class of organisms.

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. Ciprofibrate changed the expression of many genes including previously known PPARalpha agonist-responsive genes involved in processes such as lipid metabolism and inflammatory responses. In addition, many novel candidate genes involved in sugar metabolism, transcription, signal transduction, cell proliferation, and stress responses appeared to be differentially regulated in ciprofibrate-dosed rats. Ciprofibrate also resulted in significant increases in liver weight and hepatocyte proliferation. The cDNA microarray results were confirmed by Northern blot analysis for selected genes. This study thus identifies many genes that appear to be differentially regulated in ciprofibrate-dosed rats, and some of these are potential targets of PPARalpha. The functional diversity of these candidate genes suggests that most of them are likely to be differentially regulated as indirect consequence of the many processes affected by ciprofibrate in rodent liver. Although caution is advisable in the interpretation of genome-wide expression data, the genes identified in the present study provide candidates for further studies that may give new insight into the mechanisms of action of peroxisome proliferators.