Evolution of the Sequence Ontology terms and relationships

AbstractThe Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here, we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence

Corpora for the conceptualisation and zoning of scientific papers

We present two complementary annotation schemes for sentence based annotation of full scientific papers, CoreSC and AZ-II, which have been applied to primary research articles in chemistry. The AZ scheme is based on the rhetorical structure of a scientific paper and follows the knowledge claims made by the authors. It has been shown to be reliably annotated by independent human coders and has proven useful for various information access tasks. AZ-II is its extended version, which has been successfully applied to chemistry. The CoreSC scheme takes a different view of scientific papers, treating them as the humanly readable representations of scientific investigations. It therefore seeks to retrieve the structure of the investigation from the paper as generic high-level Core Scientific Concepts (CoreSC). CoreSCs have been annotated by 16 chemistry experts over a total of 265 full papers in physical chemistry and biochemistry. We describe the differences and similarities between the two schemes in detail and present the two corpora produced using each scheme. There are 36 shared papers in the corpora, which allows us to quantitatively compare aspects of the annotation schemes. We show the correlation between the two schemes, their strengths and weaknesses and discuss the benefits of combining a rhetorical based analysis of the papers with a content-based one

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared structural features, especially when these can be linked to specific functions. The RNAO is being developed in line with the developing standards of the Open Biomedical Ontologies (OBO) Consortium

ART: An ontology based tool for the translation of papers into Semantic Web format

The paper describes initial work on an ontology based tool, ART, for the semantic annotation of papers stored in digital repositories. ART is intended for the annotation not only of data and metadata about a paper, but also the main elements of the described scientific investigation, such as goals, hypotheses, and observations. ART will also be able to aid in the expression of research results directly in a semantic format, through the composition of text using ontology-based templates and stored typical key phrases for the description of basic elements of the research. ART's system design, its functionality, and related projects are discussed. An example annotated paper is presented in order to demonstrate the expected output of the tool.

Forces on a boiling bubble in a developing boundary layer, in microgravity with g-jitter and in terrestrial conditions

Terrestrial and microgravity flow boiling experiments were carried out with the same test rig, comprising a locally heated artificial cavity in the center of a channel near the frontal edge of an intrusive glass bubble generator. Bubble shapes were in microgravity generally not far from those of truncated spheres,which permitted the computation of inertial lift and drag from potential flow theory for truncated spheres approximating the actual shape. For these bubbles, inertial lift is counteracted by drag and both forces are of the same order of magnitude as g-jitter. A generalization of the Laplace equation is found which applies to a deforming bubble attached to a plane wall and yields the pressure difference between the hydrostatic pressures in the bubble and at the wall, p. A fully independent way to determine the overpressure p is given by a second Euler-Lagrange equation. Relative differences have been found to be about 5% for both terrestrial and microgravity bubbles. A way is found to determine the sum of the two counteracting major force contributions on a bubble in the direction normal to the wall from a single directly measurable quantity. Good agreement with expectation values for terrestrial bubbles was obtained with the difference in radii of curvature averaged over the liquid-vapor interface, (1/R2 − 1/R1), multiplied with the surface tension coefficient, σ. The new analysis methods of force components presented also permit the accounting for a surface tension gradient along the liquid-vapor interface. No such gradients were found for the present measurements

Characteristics of particle dispersion in the North Atlantic: An alternative interpretation of SOFAR float results

An analysis of published results on the dispersion behavior of SOFAR floats indicates a systematic depth dependence of the mixing length in the North Atlantic subtropical gyre. In contrast to the integral time scale, the length scale appears to be independent of eddy intensity in the thermocline (Lx, Ly ∼ 80, 45 km) and in the deep ocean (Lx ∼ Ly : 20 – 30 km). A similar decrease with depth is revealed by particle dispersion in an eddy-resolving circulation model and interpreted as an enhanced effect of wave behavior in the weaker, subthermocline flow. The only weak anisotropy of deep float dispersion suggests an influence of bottom roughness on the structure of eddy variability

A standard variation file format for human genome sequences

Here we describe the Genome Variation Format (GVF) and the 10Gen dataset. GVF, an extension of Generic Feature Format version 3 (GFF3), is a simple tab-delimited format for DNA variant files, which uses Sequence Ontology to describe genome variation data. The 10Gen dataset, ten human genomes in GVF format, is freely available for community analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon's EC2 cloud computing environment

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl