Using multiple reference ontologies: Managing composite annotations

There are a growing number of reference ontologies available across a variety of biomedical domains and current research focuses on their construction, organization and use. An important use case for these ontologies is annotation—where users create metadata that access concepts and terms in reference ontologies. We draw on our experience in physiological modeling to present a compelling use case that demonstrates the potential complexity of such annotations. In the domain of physiological biosimulation, we argue that most annotations require the use of multiple reference ontologies. We suggest that these “composite” annotations should be retained as a repository of knowledge about post-coordination that promotes sharing and interoperation across biosimulation models

The TNG Near Infrared Camera Spectrometer

NICS (acronym for Near Infrared Camera Spectrometer) is the near-infrared cooled camera-spectrometer that has been developed by the Arcetri Infrared Group at the Arcetri Astrophysical Observatory, in collaboration with the CAISMI-CNR for the TNG (the Italian National Telescope Galileo at La Palma, Canary Islands, Spain). As NICS is in its scientific commissioning phase, we report its observing capabilities in the near-infrared bands at the TNG, along with the measured performance and the limiting magnitudes. We also describe some technical details of the project, such as cryogenics, mechanics, and the system which executes data acquisition and control, along with the related software.Comment: 7 pages, 5 figures, compiled with A&A macros. A&A in pres

The Messinian "Calcare di Base" (Sicily, Italy) revisited

Three different types of carbonate deposits are included within the "Calcare di Base",commonly envisaged to record the Messinian salinity crisis onset: type 1 consists of sulphur-bearinglimestones, representing the biogenic product of bacterial sulphate reduction after original gypsum;type 2 comprises dm-thick laminated dolomitic limestones interbedded with diatomites, sapropels andmarls found at the top the Tripoli Formation; type 3, the most common variety, consists of m-thickbrecciated limestones interbedded with shales and clastic gypsum.Type 3 shows sedimentary features suggesting a clastic origin and deposition from high- to lowdensitygravity flows; thus, these deposits can be regarded as an end-member of a large variety ofevaporite-bearing gravity flow deposits, with a dominant carbonate component.The genetic and stratigraphic characterization of these carbonates has strong implications for a bettercomprehension of Messinian events; the three types of Calcare di Base seem to have formed duringdifferent stages of the Messinian salinity crisis (MSC). Type 2 formed in the first stage (5.96-5.60 Ma),and is the only type that can be regarded as the Lower Gypsum time-equivalent. Type 3 was depositedin the second stage (5.60-5.55 Ma) and its base is associated with a regional-scale hiatus and erosion(Messinian erosional surface). Type 1 formed even later, likely in post-Messinian time, throughdiagenetic processes affecting resedimented gypsum deposited during the second stage of the MSC.It follows that not all the Calcare di Base deposits record the onset of the Messinian salinity crisis, ascommonly thought. Thus, a detailed facies characterization of these carbonate deposits is fundamental for both stratigraphic reconstructions and a better comprehension of Messinian events

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology

We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformatics modeling of biological structures and the biosimulation modeling of biological processes. Whereas modeling anatomical entities is relatively wellstudied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap--linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies

Abstract—Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative “virtual human” projects. For such integrative challenges, we describe a “composite annotation” schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies

Radiation test and application of FPGAs in the ATLAS Level 1 Trigger

The front-end system of the Silicon Drift Detectors (SDDs) of the ALICE experiment is made of two ASICs. The first chip performs the preamplification, temporary analogue storage and analogue-to-digital conversion of the detector signals. The second chip is a digital buffer that allows for a significant reduction of the connection from the front-end module to the outside world. In this paper, the results achieved on the first complete prototype of the front-end system for the SDDs of ALICE are presented

Desarrollo de un chip de DNA para la detección de dianas génicas bacterianas de interés en el campo de la acuicultura

La adquisición bacteriana de multiresistencias frente a antimicrobianos es un fenómeno cada vez más preocupante, con gran repercusión para la salud pública, pero también con impacto en sectores de la producción animal, como es el caso particular de la acuicultura. Entre los años 2010-2012, como objetivo de un Proyecto de Investigación Italiano (Progetti d’interesse Nazionale, PRIN), se realizaron diferentes campañas de muestreo a lo largo de la costa del mar Adriático, en centros dedicados a la acuicultura y áreas costeras, estudiando la incidencia de bacterias multiresistentes, así como de los elementos genéticos móviles responsables de su adquisición, desarrollando además una herramienta biotecnológica que agiliza este tipo de estudios permitiendo detectar 164 dianas génicas en un único soporte. Se obtuvo una colección de 1274 aislados bacterianos, a partir de muestras de agua, sedimento y biofilm, resistentes a las distintas combinaciones de antibióticos utilizados según la legislación italiana. Del total, 105 (8,25%) aislados resultaron ser multiresistentes, detectándose en el 13,59% el integrón de clase I, en el 14,56% el plásmido pAb5s9, en el 5,82% el elemento SXT/R391, y en el 15,52% diferentes combinaciones de estos elementos genéticos. Basándonos en estos resultados, se ha desarrollado y validado un chip de DNA que permite detectar en un mismo soporte, genes que codifican para determinantes de resistencia a antimicrobianos, elementos genéticos móviles (MGE), genes para la detección de especies bacterianas patógenas con repercusión en acuicultura y para la salud del hombre, e indicadores de contaminación fecal.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech