A plant disease extension of the Infectious Disease Ontology

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism

Ontological Reengineering for Reuse

This paper presents the concept of Ontological Reengineering as the process of retrieving and transforming a conceptual model of an existing and implemented ontology into a new, more correct and more complete conceptual model which is reimplemented. Three activities have been identified in this process: reverse engineering, restructuring and forward engineering. The aim of Reverse Engineering is to output a possible conceptual model on the basis of the code in which the ontology is implemented. The goal of Restructuring is to reorganize this initial conceptual model into a new conceptual model, which is built bearing in mind the use of the restructured ontology by the ontology/application that reuses it. Finally, the objective of Forward Engineering is output a new implementation of the ontology. The paper also discusses how the ontological reengineering process has been applied to the Standard-Units ontology [18], which is included in a Chemical-Elements [12] ontology. These two ontologies will be included in a Monatomic-Ions and Environmental-Pollutants ontologies

Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

Shelf and coastal sea processes extend from the atmosphere through the water column and into the sea bed. These processes are driven by physical, chemical, and biological interactions at local scales, and they are influenced by transport and cross strong spatial gradients. The linkages between domains and many different processes are not adequately described in current model systems. Their limited integration level in part reflects lacking modularity and flexibility; this shortcoming hinders the exchange of data and model components and has historically imposed supremacy of specific physical driver models. We here present the Modular System for Shelves and Coasts (MOSSCO, http://www.mossco.de), a novel domain and process coupling system tailored---but not limited--- to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the existing coupling technology Earth System Modeling Framework and on the Framework for Aquatic Biogeochemical Models, thereby creating a unique level of modularity in both domain and process coupling; the new framework adds rich metadata, flexible scheduling, configurations that allow several tens of models to be coupled, and tested setups for coastal coupled applications. That way, MOSSCO addresses the technology needs of a growing marine coastal Earth System community that encompasses very different disciplines, numerical tools, and research questions.Comment: 30 pages, 6 figures, submitted to Geoscientific Model Development Discussion

htsint: a Python library for sequencing pipelines that combines data through gene set generation

Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. Conclusion: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint

The Semantic Web Revisited

The original Scientific American article on the Semantic Web appeared in 2001. It described the evolution of a Web that consisted largely of documents for humans to read to one that included data and information for computers to manipulate. The Semantic Web is a Web of actionable information--information derived from data through a semantic theory for interpreting the symbols.This simple idea, however, remains largely unrealized. Shopbots and auction bots abound on the Web, but these are essentially handcrafted for particular tasks; they have little ability to interact with heterogeneous data and information types. Because we haven't yet delivered large-scale, agent-based mediation, some commentators argue that the Semantic Web has failed to deliver. We argue that agents can only flourish when standards are well established and that the Web standards for expressing shared meaning have progressed steadily over the past five years. Furthermore, we see the use of ontologies in the e-science community presaging ultimate success for the Semantic Web--just as the use of HTTP within the CERN particle physics community led to the revolutionary success of the original Web. This article is part of a special issue on the Future of AI

Narratives and the Ethics and Politics of Environmentalism: The Transformative Power of Stories

By revealing the centrality of stories to action, to social life and to inquiry together with the implicit assumptions in polyphonic stories about the nature of humans, of life and of physical reality, this paper examines the potential of stories to transform civilization. Focussing on the failure of environmentalists so far in the face of the global ecological crisis, it is shown how ethics and political philosophy could be reconceived and radical ecology reformulated and reinvigorated by appreciating and exploiting the potential of stories. This could enable radical ecologists to effect the major social and economic changes necessary to meet the global ecological crisis. What we need, it is argued, is a new, polyphonic grand narrative

Using mobile technology to create flexible learning contexts

This paper discusses the importance of learning context with a particular focus upon the educational application of mobile technologies. We suggest that one way to understand a learning context is to perceive it as a Learner Centric Ecology of Resources. These resources can be deployed variously but with a concern to promote and support different kinds of mediations, including those of the teacher and learner. Our approach is informed by sociocultural theory and is used to construct a framework for the evaluation of learning experiences that encompass various combinations of technologies, people, spaces and knowledge. The usefulness of the framework is tested through two case studies that evaluate a range of learning contexts in which mobile technologies are used to support learning. We identify the benefits and challenges that arise when introducing technology across multiple locations. An analytical technique mapped from the Ecology of Resources framework is presented and used to identify the ways in which different technologies can require learners to adopt particular roles and means of communication. We illustrate how we involve participants in the analysis of their context and highlight the extent to which apparently similar contexts vary in ways that are significant for learners. The use of the Ecology of Resources framework to evaluate a range of learning contexts has demonstrated that technology can be used to provide continuity across locations: the appropriate contextualization of activities across school and home contexts, for example. It has also provided evidence to support the use of technology to identify ways in which resources can be adapted to meet the needs of a learner

Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster group

Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include UTRs and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. Using these revised annotations, we perform differential expression testing using the cufflinks suite to provide a broad overview of differential expression between reproductive tissues and the carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify several cases of putative polycistronic transcripts, pointing to a combination of transcriptional read-through in the genome as well as putative gene fusion and fission events across taxa. We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and a potential source of genetic novelty.Comment: Revised manuscript, also available online preprint at G3: Genes, Genomes, Genetics. Gene models, ortholog calls, and tissue specific expression results are available at http://github.com/ThorntonLab/GFF or the UCSC browser on the Thornton Lab public track hub at http://genome.ucsc.ed

Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation

Phytoplankton growth rates are limited by the supply of iron (Fe) in approximately one third of the open ocean, with major implications for carbon dioxide sequestration and carbon (C) biogeochemistry. To date, understanding how alteration of Fe supply changes phytoplankton physiology has focused on traditional metrics such as growth rate, elemental composition, and biophysical measurements such as photosynthetic competence (Fv/Fm). Researchers have subsequently employed transcriptomics to probe relationships between changes in Fe supply and phytoplankton physiology. Recently, studies have investigated longer-term (i.e. following acclimation) responses of phytoplankton to various Fe conditions. In the present study, the coastal diatom, Thalassiosira pseudonana, was acclimated (10 generations) to either low or high Fe conditions, i.e. Fe-limiting and Fe-replete. Quantitative proteomics and a newly developed proteomic profiling technique that identifies low abundance proteins were employed to examine the full complement of expressed proteins and consequently the metabolic pathways utilized by the diatom under the two Fe conditions. A total of 1850 proteins were confidently identified, nearly tripling previous identifications made from differential expression in diatoms. Given sufficient time to acclimate to Fe limitation, T. pseudonana up-regulates proteins involved in pathways associated with intracellular protein recycling, thereby decreasing dependence on extracellular nitrogen (N), C and Fe. The relative increase in the abundance of photorespiration and pentose phosphate pathway proteins reveal novel metabolic shifts, which create substrates that could support other well-established physiological responses, such as heavily silicified frustules observed for Fe-limited diatoms. Here, we discovered that proteins and hence pathways observed to be down-regulated in short-term Fe starvation studies are constitutively expressed when T. pseudonana is acclimated (i.e., nitrate and nitrite transporters, Photosystem II and Photosystem I complexes). Acclimation of the diatom to the desired Fe conditions and the comprehensive proteomic approach provides a more robust interpretation of this dynamic proteome than previous studies.This work was supported by National Science Foundation grants OCE1233014 (BLN) and the Office of Polar Programs Postdoctoral Fellowship grant 0444148 (BLN). DRG was supported by National Institutes of Health 5P30ES007033-10. AH and MTM were supported by Natural Sciences and Engineering Research Council of Canada. RFS and PWB were supported by the New Zealand Royal Society Marsden Fund and the Ministry of Science. This work is supported in part by the University of Washington's Proteomics Computer Resource Centre (UWPR95794). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics