OnEX: Exploring changes in life science ontologies

<p>Abstract</p> <p>Background</p> <p>Numerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.</p> <p>Results</p> <p>We present <b>OnEX </b>(Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, <b>OnEX </b>provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the <b>OnEX </b>web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.</p> <p>Conclusion</p> <p><b>OnEX </b>provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at <url>http://www.izbi.de/onex</url>.</p

A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world.

Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management

A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter drier world

Crassulacean acid metabolism (CAM), a special mode of photosynthesis, features nocturnal CO2 uptake, which facilitates increased water-use efficiency (WUE) and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry rain forests. Human population growth in combination with global climate change now challenges agricultural production systems to increase food, feed, forage, fiber and fuel production by expanding into semi-arid, abandoned, marginal, or degraded agricultural lands. Such sustainable dryland production increases are envisioned by increased reliance on highly water-use efficient CAM crop species, such as Agave and Opuntia. Thus, major research efforts are now underway to provide detailed assessments of the productivity of major CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food and bioenergy crops. The gains in understanding CAM photosynthesis through an expanded research effort have potential for high returns on investment in the foreseeable future. To help realize this potential, it is necessary to address important scientific questions related to genomic features, regulatory mechanisms, CAM evolution, CAM-into-C3 engineering, and sustainable CAM crop production. Answering these questions requires collaborative efforts to build infrastructure for CAM model systems, field trials, mutant collections, and data management.status: publishe