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

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. 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. 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

Plans for the first balloon flight of the gamma-ray polarimeter experiment (GRAPE)

We have developed a design for a hard X-ray polarimeter operating in the energy range from 50 to 500 keV. This modular design, known as GRAPE (Gamma-Ray Polarimeter Experiment), has been successfully demonstrated in the lab using partially polarized gamma-ray sources and using fully polarized photon beams at Argonne National Laboratory. In June of 2007, a GRAPE engineering model, consisting of a single detector module, was flown on a high altitude balloon flight to further demonstrate the design and to collect background data. We are currently preparing a much larger balloon payload for a flight in the fall of 2011. Using a large (16-element) array of detector modules, this payload is being designed to search for polarization from known point sources of radiation, namely the Crab and Cygnus X-1. This first flight will not only provide a scientific demonstration of the GRAPE design (by measuring polarization from the Crab nebula), it will also lay the foundation for subsequent long duration balloon flights that will be designed for studying polarization from gamma-ray bursts and solar flares. Here we shall present data from calibration of the first flight module detectors, review the latest payload design and update the predicted polarization sensitivity for both the initial continental US balloon flight and the subsequent long-duration balloon flights

GRAPE: a balloon-borne gamma-ray polarimeter

The Gamma-RAy Polarimeter Experiment (GRAPE) is a concept for an astronomical hard X-ray Compton polarimeter operating in the 50 - 500 keV energy band. The instrument has been optimized for wide-field polarization measurements of transient outbursts from energetic astrophysical objects such as gamma-ray bursts and solar flares. The GRAPE instrument is composed of identical modules, each of which consists of an array of scintillator elements read out by a multi-anode photomultiplier tube (MAPMT). Incident photons Compton scatter in plastic scintillator elements and are subsequently absorbed in inorganic scintillator elements; a net polarization signal is revealed by a characteristic asymmetry in the azimuthal scattering angles. We have constructed a prototype GRAPE module that has been calibrated at a polarized hard X-ray beam and flown on an engineering balloon test flight. A full-scale scientific balloon payload, consisting of up to 36 modules, is currently under development. The first flight, a one-day flight scheduled for 2011, will verify the expected scientific performance with a pointed observation of the Crab Nebula. We will then propose long-duration balloon flights to observe gamma-ray bursts and solar flares

Simulations of a monolithic lanthanum bromide gamma-ray detector

We have been working on the development of a detector design for a large area coded aperture imaging system operating in the 10-600 keV energy range. The detector design is based on an array of Lanthanum Bromide (LaBr3) scintillators, each directly coupled to a Hamamatsu 64-channel multi-anode photomultiplier tube (MAPMT). This paper focuses on the development of the GEANT4-based simulations as an aid in the optimization of the detector design. The simulations have been validated by comparisons with various laboratory data sets. We will summarize the current status and latest findings from this study

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

PRIDE: a public repository of protein and peptide identifications for the proteomics community

PRIDE, the ‘PRoteomics IDEntifications database’ () is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. At the time of writing, PRIDE includes the full set of identifications as submitted by individual laboratories participating in the HUPO Plasma Proteome Project and a profile of the human platelet proteome submitted by the University of Ghent in Belgium. By late 2005 PRIDE is expected to contain the identifications and spectra generated by the HUPO Brain Proteome Project. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format if identifications are included or mzData format if the submitter is depositing mass spectra without identifications. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML

Three dimensional visualization of the World Wide Web

Although large-scale public hypermedia structures such as the World Wide Web are popularly referred to as "cyberspace", the extent to which they constitute a space in the everyday sense of the word is questionable. This paper reviews recent work in the area of three dimensional (3D) visualization of the Web that has attempted to depict it in the form of a recognizable space; in other words, as a navigable landscape that may be visibly populated by its users. Our review begins by introducing a range of visualizations that address different aspects of using the Web. These include visualizations of Web structure, especially of links, that act as 3D maps; browsing history; searches; evolution of the Web; and the presence and activities of multiple users. We then summarize the different techniques that are employed by these visualizations. We conclude with a discussion of key challenges for the future

Response of triploid Atlantic salmon (Salmo salar) to commercial vaccines

While triploid Atlantic salmon represent a practical and affordable solution to the issues associated with sexual maturation in the salmonid aquaculture industry, empirical evidence suggests triploids are more susceptible to disease and vaccine side-effects than diploids. With vaccination now part of routine husbandry, it is essential their response be studied to confirm their suitability for commercial production. This study tested the response of triploid and diploid Atlantic salmon to vaccination with commercially available vaccines. Triploid and diploid Atlantic salmon siblings were injected with one of three commercial vaccines (or sham-vaccinated) and monitored for performance throughout a commercial production cycle. Sampling at smolt and harvest was undertaken along with individual weight and length assessments through the cycle. Antibody response to Aeromonas salmonicida vaccination was similar in both ploidy, with a positive response in vaccine-injected fish. For both adhesions and melanin, analysis found that higher scores were more likely to occur as the anticipated severity of the vaccine increased. In addition, for adhesion scores at smolt and melanin scores at smolt and harvest, triploids were statistically more likely to exhibit high scores than diploids. Triploids maintained a significantly higher body weight during freshwater and until 11 months post-seawater transfer, with diploids weighing significantly more at harvest. Growth, represented by thermal growth coefficient (TGC), decreased in both ploidy as the severity of adhesions increased, and regression patterns did not differ significantly between ploidy. Vertebral deformity prevalence was consistently higher in triploids (smolt 12.3 ± 4.5%; harvest 34.9 ± 5.9%) than diploids (smolt 0.8 ± 0.5%; harvest 15.9 ± 1.9%), with no significant difference between vaccine groups in each ploidy. This study demonstrates that triploids respond as well to vaccination as diploids and provides further supporting evidence of triploid robustness for commercial aquaculture

Double Neutron Star Systems and Natal Neutron Star Kicks

We study the four double neutron star systems found in the Galactic disk in terms of the orbital characteristics of their immediate progenitors and the natal kicks imparted to neutron stars. Analysis of the effect of the second supernova explosion on the orbital dynamics, combined with recent results from simulations of rapid accretion onto neutron stars lead us to conclude that the observed systems could not have been formed had the explosion been symmetric. Their formation becomes possible if kicks are imparted to the radio-pulsar companions at birth. We identify the constraints imposed on the immediate progenitors of the observed double neutron stars and calculate the ranges within which their binary characteristics (orbital separations and masses of the exploding stars) are restricted. We also study the dependence of these limits on the magnitude of the kick velocity and the time elapsed since the second explosion. For each of the double neutron stars, we derive a minimum kick magnitude required for their formation, and for the two systems in close orbits we find it to exceed 200km/s. Lower limits are also set to the center-of-mass velocities of double neutron stars, and we find them to be consistent with the current proper motion observations.Comment: 25 pages, 6 figs (9 parts), 4 tables, AASTeX, Accepted in Ap

Simple strategy for simulation of large area of axially symmetric metasurfaces

Metalenses are composed of nanostructures for focusing light and have been widely explored in many exciting applications. However, their expanding dimensions pose simulation challenges. We propose a method to simulate metalenses in a timely manner using vectorial wave and ray tracing models. We sample the metalens' radial phase gradient and locally approximate it by a linear phase response. Each sampling point is modeled as a binary blazed grating, employing the chosen nanostructure, to build a transfer function set. The metalens transmission or reflection is then obtained by applying the corresponding transfer function to the incoming field on the regions surrounding each sampling point. Fourier optics is used to calculate the scattered fields under arbitrary illumination for the vectorial wave method and a Monte Carlo algorithm is used in the ray tracing formalism. We validated our method against finite difference time domain simulations at 632 nm and we were able to simulate metalenses larger than 3000lambda0 in diameter on a personal computer.Comment: 10 page