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

Preliminary investigations into the use of the ancient pigments Han blue and Han purple as luminescent dusting powders for the detection of latent fingermarks

Here we present our preliminary studies into the inorganic pigments Han blue (BaCuSi4O10) and Han purple (BaCuSi2O6) as near-infrared luminescent fingerprint dusting powders. These pigments were developed in ancient China around 800 BCE and both show luminescence in the NIR region. There remains, however, ambiguity in the literature concerning their photophysical properties. Samples of Han blue and Han purple artist’s pigments were characterized by optical microscopy, infrared, ultraviolet-visible absorbance and luminescence spectroscopy. Their performance as fingerprint dusting powders, without any further treatment, on non-porous surfaces were compared to exfoliated lipophilic coated Egyptian blue and commercial fluorescent powders in a pilot study. These results demonstrate for the first time that both ancient pigments show promise as alternative dusting powders for latent fingermarks

Conocimiento sobre genética y confianza en pruebas genéticas en una ciudad de tamaño medio en Argentina

Public attitudes about genetics appear to depend on the local context. We analyzed survey responses obtained in 2015 from 293 residents of Luján, a city in the province of Buenos Aires, Argentina, who self-assessed their knowledge about genetics and their trust in genetic tests. The survey integrated a larger research project for which consenting adult participants shared demographic and genealogical information and provided saliva samples for genetic ancestry analyses. Participants reported little knowledge but high trust in genetic testing when questioned about knowledge and trust. Well-known media stories of DNA-based forensic genetic investigations to identify the victims of state repression during the military dictatorship may have contributed to the high self-assessment of their genetic knowledge expressed by some participants, regardless of educational attainment. Our analysis provides information that could be used as a baseline to begin unraveling the current level of public trust in genetics in a region of the Global South where genetic testing has become widespread, but people?s knowledge of and trust in genetics remain poorly studied.Las actitudes del público sobre la genética parecen depender del contexto local. Analizamos las respuestas de una encuesta suministrada en 2015 a 293 residentes de Luján, una ciudad de la provincia de Buenos Aires, Argentina, quienes autoevaluaron su conocimiento sobre genética y su confianza en las pruebas genéticas. La encuesta integraba un proyecto de investigación más amplio en el que los adultos participantes que dieron su consentimiento compartieron información demográfica y genealógica y proporcionaron muestras de saliva para un estudio de ancestría genética. Cuando se les preguntó sobre su conocimiento y confianza, los participantes informaron tener poco conocimiento sobre genética, pero mucha confianza en las pruebas genéticas. Historias muy conocidas de los medios de comunicación sobre investigaciones genéticas forenses basadas en el ADN para identificar a las víctimas de la represión estatal durante la dictadura militar pueden haber contribuido a la alta autoevaluación del propio conocimiento genético manifestado por algunos participantes, independientemente de su nivel educativo. Nuestro análisis proporciona información que podría utilizarse como base para comenzar a desentrañar los niveles actuales de confianza pública en la genética en una región del Sur Global donde las pruebas genéticas se han generalizado, pero el conocimiento y confianza de las personas sobre genética están poco estudiados.Fil: Mendoza, Marcela. University of Michigan; Estados UnidosFil: Mazza, Bárbara Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Secretaría de Cultura de la Nación. Dirección Nacional de Cultura y Museos. Instituto Nacional de Antropología y Pensamiento Latinoamericano; ArgentinaFil: Cabana, Graciela Susana. University of Tennessee; Estados UnidosFil: Smith, Lindsay. Arizona State University; Estados UnidosFil: Di Fabio Rocca, Francisco. Universidad Maimónides; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Delfino, Hugo. Universidad Nacional de Luján; ArgentinaFil: Martinez, C.. Universidad Nacional de Luján; Argentin

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Tidally induced radial-velocity variations in close binaries

A theoretical framework for the determination of tidally induced radial-velocity variations in a component of a close binary is presented. Both the free and the forced oscillations of the component are treated as linear, isentropic perturbations of a spherically symmetric star. Resonances between dynamic tides and free oscillation modes are taken into account by means of the formalism developed by Smeyers et al. (1998). The amplitude of the tidally induced radial-velocity variations seen by the observer depends on the orbital eccentricity and on the orbital inclination. The amplitude increases with increasing orbital eccentricity and is most sensitive to the value of the orbital inclination when 20 < i < 70. In the case of a 5 solar mass ZAMS star with a 1.4 solar mass compact companion, it is shown that resonant dynamic tides can lead to radial-velocity variations with amplitudes large enough to be detected in observations. The shape of the tidally induced radial-velocity curves varies from very irregular for orbital periods away from any resonances with free oscillation modes to sinusoidal for orbital periods close to a resonance with a free oscillation mode. Our investigation is concluded with an application to the slowly pulsating B star HD 177863 showing the possibility of resonant excitation of a high-order second-degree g-mode in this star.Comment: 11 pages, Accepted for publication in Astronomy and Astrophysic

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

Pattern of gray matter volumes related to retinal thickness and its association with cognitive function in relapsing–remitting MS

Background Neurodegeneration in multiple sclerosis (MS) may be investigated in the visual system as optical coherence tomography (OCT) and magnetic resonance imaging (MRI) allows examining structural integrity in detail. The association between thickness of retinal layers and focal cortical volumes beyond the primary visual system has not been thoroughly investigated. Objective To investigate the association between focal cortical volume and thickness of retinal layers. Methods Fifty-four patients (relapsing–remitting MS, mean age 40.5 years, mean disease duration 7.6 years, median EDSS 2) underwent OCT and MRI. The association between focal cortical volume and OCT measurements was investigated with voxel-based morphometry (VBM). Patterns of association were determined with Yeo's functional network atlas and the Harvard-Oxford cortical atlas. We used GEE models with cortical volumes from the FreeSurfer parcellation to confirm VBM results. Post hoc, we analyzed the association between OCT, focal cortical volumes, and an extended neuropsychological assessment in a subgroup of 14 patients. Results Macular retinal nerve fiber layer (mRNFL) and ganglion cell /inner plexiform layer (GCIPL) showed a robust association with mainly the insular cortex and the cingulate cortex. VBM findings were confirmed with FreeSurfer volumes. The post hoc analysis detected significant correlations between both OCT outcomes and cognition. Conclusion Besides the primary visual system, OCT outcomes show a correlation pattern with cortical regions that are known to be important for cognitive performance, predominantly the insula in both hemispheres. Thus, OCT should be further investigated as a marker for neurodegeneration in MS

Ab-initio density functional study of O on the Ag(001) surface

The adsorption of oxygen on the Ag(001) is investigated by means of density functional techniques. Starting from a characterization of the clean silver surfaces oxygen adsorption in several modifications (molecularly, on-surface, sub-surface, Ag$_2$O) for varying coverage was studied. Besides structural parameters and adsorption energies also work-function changes, vibrational frequencies and core level energies were calculated for a better characterization of the adsorption structures and an easier comparison to the rich experimental data.Comment: 26 pages, 8 figures, Surf. Sci. accepte

The Stellar Content of the Post-Starburst S0 Galaxy NGC 5102

The stellar content of the S0 galaxy NGC 5102 is investigated. A modest population of bright main sequence stars and red supergiants (RSGs) is detected throughout the western portion of the disk, and the star formation rate (SFR) during the past ten million years is estimated to have been 0.02 solar masses per year. RGB stars are traced out to galactocentric distances of 10 kpc, which corresponds to ~ 14 disk scale lengths. A large population of bright asymptotic giant branch (AGB) stars are seen throughout the western portion of the disk, and it is concluded that (1) stars that formed within the past Gyr comprise ~ 20% of the total stellar disk mass, and (2) the SFR during intermediate epochs in the disk of NGC 5102 was at least 1.4 solar masses per year. It is suggested that NGC 5102 was a spiral galaxy that experienced a galaxy-wide episode of enhanced star formation that terminated a few hundred Myr in the past, and that much of its interstellar medium was ejected in an outflow.Comment: To appear in the Astronomical Journa

The XMM-Newton serendipitous ultraviolet source survey catalogue

The XMM-Newton Serendipitous Ultraviolet Source Survey (XMM-SUSS) is a catalogue of ultraviolet (UV) sources detected serendipitously by the Optical Monitor (XMM-OM) on-board the XMM-Newton observatory. The catalogue contains ultraviolet-detected sources collected from 2,417 XMM-OM observations in 1-6 broad band UV and optical filters, made between 24 February 2000 and 29 March 2007. The primary contents of the catalogue are source positions, magnitudes and fluxes in 1 to 6 passbands, and these are accompanied by profile diagnostics and variability statistics. The XMM-SUSS is populated by 753,578 UV source detections above a 3 sigma signal-to-noise threshold limit which relate to 624,049 unique objects. Taking account of substantial overlaps between observations, the net sky area covered is 29-54 square degrees, depending on UV filter. The magnitude distributions peak at 20.2, 20.9 and 21.2 in UVW2, UVM2 and UVW1 respectively. More than 10 per cent of sources have been visited more than once using the same filter during XMM-Newton operation, and > 20 per cent of sources are observed more than once per filter during an individual visit. Consequently, the scope for science based on temporal source variability on timescales of hours to years is broad. By comparison with other astrophysical catalogues we test the accuracy of the source measurements and define the nature of the serendipitous UV XMM-OM source sample. The distributions of source colours in the UV and optical filters are shown together with the expected loci of stars and galaxies, and indicate that sources which are detected in multiple UV bands are predominantly star-forming galaxies and stars of type G or earlier.Comment: Accepted for publication in MNRA