Did you evaluate your ontology? OOPS! (OntOlogy Pitfall Scanner!)

The application of methodologies for building ontologies can improve ontology quality. However, such quality is not guaranteed because of the difficulties involved in ontology modelling. These difficulties are related to the inclusion of anomalies or bad practices within the ontology development. In this context, our aim is to describe OOPS!(OntOlogy Pitfall Scanner!), a tool for detecting pitfalls in ontologies.

Role of surface trap states on two-dimensional electron gas density in InAlN/AlN/GaN heterostructures

In order to clarify the effect of charged dislocations and surface donor states on the transport mechanisms in polar AlInN/AlN/GaN heterostructures, we have studied the current-voltage characteristics of Schottky junctions fabricated on AlInN/AlN/GaN heterostructures. The reverse-bias leakage current behaviour has been interpreted with a Poole-Frenkel emission of electrons from trap states near the metal-semiconductor junction to dislocation induced states. The variation of the Schottky barrier height as a function of the AlN layer thickness has been measured and discussed, considering the role of the surface states in the formation of the two dimensional electron gas at AlN/GaN interface.

A correction to Whipple's law for ion-trap Current

We have analyzed a phenomenon heretofore ignored in the analyses of ion traps, which are used to determine ion temperature, among other plasma parameters, in planetary ionospheres: ions that are rejected by the trap perturb the plasma well ahead of the Debye sheath at the front of the trap.The determination of the perturbed plasma flow is found to depend on the fact that the ionospheric plasma be stable to quasineutral, ion-acoustic perturbations.

OOPS! (OntOlogy Pitfall Scanner!): a web-based tool for ontology evaluation

Presentación en Workshop EUON 2014

Ontology Evaluation: a pitfall-based approach to ontology diagnosis

La evaluación de ontologías, incluyendo diagnóstico y reparación de las mismas, es una compleja actividad que debe llevarse a cabo en cualquier proyecto de desarrollo ontológico para comprobar la calidad técnica de las ontologías. Sin embargo, existe una gran brecha entre los enfoques metodológicos sobre la evaluación de ontologías y las herramientas que le dan soporte. En particular, no existen enfoques que proporcionen guías concretas sobre cómo diagnosticar y, en consecuencia, reparar ontologías. Esta tesis pretende avanzar en el área de la evaluación de ontologías, concretamente en la actividad de diagnóstico. Los principales objetivos de esta tesis son (a) ayudar a los desarrolladores en el diagnóstico de ontologías para encontrar errores comunes y (b) facilitar dicho diagnóstico reduciendo el esfuerzo empleado proporcionando el soporte tecnológico adecuado. Esta tesis presenta las siguientes contribuciones: • Catálogo de 41 errores comunes que los ingenieros ontológicos pueden cometer durante el desarrollo de ontologías. • Modelo de calidad para el diagnóstico de ontologías alineando el catálogo de errores comunes con modelos de calidad existentes. • Diseño e implementación de 48 métodos para detectar 33 de los 41 errores comunes en el catálogo. • Soporte tecnológico OOPS!, que permite el diagnstico de ontologías de forma (semi)automática. De acuerdo con los comentarios recibidos y los resultados de los test de satisfacción realizados, se puede afirmar que el enfoque desarrollado y presentado en esta tesis ayuda de forma efectiva a los usuarios a mejorar la calidad de sus ontologías. OOPS! ha sido ampliamente aceptado por un gran número de usuarios de formal global y ha sido utilizado alrededor de 3000 veces desde 60 países diferentes. OOPS! se ha integrado en software desarrollado por terceros y ha sido instalado en empresas para ser utilizado tanto durante el desarrollo de ontologías como en actividades de formación. Abstract Ontology evaluation, which includes ontology diagnosis and repair, is a complex activity that should be carried out in every ontology development project, because it checks for the technical quality of the ontology. However, there is an important gap between the methodological work about ontology evaluation and the tools that support such an activity. More precisely, not many approaches provide clear guidance about how to diagnose ontologies and how to repair them accordingly. This thesis aims to advance the current state of the art of ontology evaluation, specifically in the ontology diagnosis activity. The main goals of this thesis are (a) to help ontology engineers to diagnose their ontologies in order to find common pitfalls and (b) to lessen the effort required from them by providing the suitable technological support. This thesis presents the following main contributions: • A catalogue that describes 41 pitfalls that ontology developers might include in their ontologies. • A quality model for ontology diagnose that aligns the pitfall catalogue to existing quality models for semantic technologies. • The design and implementation of 48 methods for detecting 33 out of the 41 pitfalls defined in the catalogue. • A system called OOPS! (OntOlogy Pitfall Scanner!) that allows ontology engineers to (semi)automatically diagnose their ontologies. According to the feedback gathered and satisfaction tests carried out, the approach developed and presented in this thesis effectively helps users to increase the quality of their ontologies. At the time of writing this thesis, OOPS! has been broadly accepted by a high number of users worldwide and has been used around 3000 times from 60 different countries. OOPS! is integrated with third-party software and is locally installed in private enterprises being used both for ontology development activities and training courses.

Identification of genes required for Drosophila eye development using a phenotypic enhancer-trap

A novel method of P-element mutagenesis is described for the isolation of mutants affecting the development of the Drosophila compound eye. It exploits the interaction between the Bride of Sevenless (Boss) ligand and the Sevenless (Sev) receptor tyrosine kinase that triggers the formation of the UV-sensitive photoreceptor neuron, R7. Transposition of a boss cDNA transgene, in an otherwise boss mutant background, was used as a “phenotypic trap” in live flies to identify enhancers expressed during a narrow time window in eye development. Using a rapid behavioral screen, more than 400,000 flies were tested for restoration of R7. Some 1,800 R7-containing flies were identified. Among these, 21 independent insertions with expression of the boss reporter gene in the R8 cell were identified by a external eye morphology and staining with an antibody against Boss. Among 900 lines with expression of the boss reporter gene in multiple cells assessed for homozygous mutant phenotypes, insertions in the marbles, glass, gap1, and fasciclin II genes were isolated. This phenotypic enhancer-trap facilitates (i) the isolation of enhancer-traps with a specific expression pattern, and (ii) the recovery of mutants disrupting development of specific tissues. Because the temporal and tissue specificity of the phenotypic trap is dependent on the choice of the marker used, this approach can be extended to other tissues and developmental stages.

Paul–Straubel–Kingdon trap for true zero-point confinement of an individual ion and reservoir

A modification of the Paul–Straubel trap previously described by us may profitably be operated in a Paul–Straubel–Kingdon (PSK) mode during the initial loading of an individual ion into the trap. Thereby the coating of the trap ring electrode by the atomic beam directed upon it in earlier experiments is eliminated, as is the ionization of an already trapped ion. Coating created serious problems as it spot-wise changed the work function of the ring electrode, which caused large, uncontrolled dc fields in the trap center that prevented zero-point confinement. Operating the Paul–Straubel trap with a small negative bias on the ring electrode wire is all that is required to realize the PSK mode. In this mode the tiny ring trap in the center of the long, straight wire section is surrounded by a second trapping well shaped like a long, thin-walled cylindrical shell and extending to the end-caps. There, ions may be conveniently created in this well without danger of coating the ring with barium. In addition, the long second well is useful as a multi-ion reservoir.

Efficient gene tagging in Arabidopsis thaliana using a gene trap approach

Large quantities of DNA sequence information about plant genes are rapidly accumulating in public databases, but to progress from DNA sequence to biological function a mutant allele for each of the genes ideally should be available. Here we describe a gene trap construct that allowed us to disrupt transcribed genes with a high efficiency in Arabidopsis thaliana. In the T-DNA vector used, the expression of a bacterial reporter gene coding for neomycin phosphotransferase II (nptII) depends on the in vivo generation of a translation fusion upon the T-DNA integration into the Arabidopsis genome. Analysis of 20 selected transgenic lines showed that 12 lines are T-DNA insertion mutants. The disrupted genes analyzed encoded ribosomal proteins (three lines), aspartate tRNA synthase, DNA ligase, basic-domain leucine zipper DNA binding protein, ATP-binding cassette transporter, and five proteins of unknown function. Four tagged genes were new for Arabidopsis. The results presented here suggest that gene trapping, using nptII as a reporter gene, can be as high as 80% and opens novel perspectives for systematic gene tagging in A. thaliana.

Identification of genes induced by factor deprivation in hematopoietic cells undergoing apoptosis using gene-trap mutagenesis and site-specific recombination

A strategy employing gene-trap mutagenesis and site-specific recombination (Cre/loxP) has been developed to isolate genes that are transcriptionally activated during programmed cell death. Interleukin-3 (IL-3)-dependent hematopoietic precursor cells (FDCP1) expressing a reporter plasmid that codes for herpes simplex virus–thymidine kinase, neomycin phosphotransferase, and murine IL-3 were transduced with a retroviral gene-trap vector carrying coding sequences for Cre-recombinase (Cre) in the U3 region. Activation of Cre expression from integrations into active genes resulted in a permanent switching between the selectable marker genes that converted the FDCP1 cells to factor independence. Selection for autonomous growth yielded recombinants in which Cre sequences in the U3 region were expressed from upstream cellular promoters. Because the expression of the marker genes is independent of the trapped cellular promoter, genes could be identified that were transiently induced by IL-3 withdrawal.

Excitation transfer spectroscopy with two metastable 138Ba+ ions in same trap.

In the absence of lasers approaching trapped ion clock transitions in sharpness we propose to replace the 12.49 m laser field exciting the D3/2-D5/2 transition of the single Ba+ ion A in D3/2 with the near-field of a close by identical ion B in the excited D5/2 state. We tune the frequency of the near-field by the differential Stark shift generated when the center of mass of the tuned ions is slightly moved out of the trap center by a small bias voltage. We demonstrate that the resultant resonant energy exchange can be made considerably faster than the natural lifetime of either metastable level and show how it might be detected.

Detection of sub-8-nm movements of kinesin by high-resolution optical-trap microscopy.

Kinesin is a molecular motor that transports organelles along microtubules. This enzyme has two identical 7-nm-long motor domains, which it uses to move between consecutive tubulin binding sites spaced 8 nm apart along a microtubular protofilament. The molecular mechanism of this movement, which remains to be elucidated, may be common to all families of motor proteins. In this study, a high-resolution optical-trap microscope was used to measure directly the magnitude of abrupt displacements produced by a single kinesin molecule transporting a microscopic bead. The distribution of magnitudes reveals that kinesin not only undergoes discrete 8-nm movements, in agreement with previous work [Svoboda, K., Schmidt, C. F., Schnapp, B. J. & Block, S.M. (1993) Nature (London) 365, 721-727], but also frequently exhibits smaller movements of about 5 nm. A possible explanation for these unexpected smaller movements is that kinesin's movement from one dimer to the next along a protofilament involves at least two distinct events in the mechanical cycle.

An induction gene trap screen in embryonic stem cells: Identification of genes that respond to retinoic acid in vitro.

We have developed a novel induction gene trap approach that preselects in vitro for integrations into genes that lie downstream of receptor/ligand-mediated signaling pathways. Using this approach, we have identified 20 gene trap integrations in embryonic stem cells, 9 of which were induced and 11 of which were repressed after exposure to exogenous retinoic acid (RA). All but one of these integrations showed unique spatially restricted or tissue-specific patterns of expression between 8.5 and 11.5 days of embryogenesis. Interestingly, expression was observed in tissues that are affected by alterations in RA levels during embryogenesis. Sequence analysis of fusion transcripts from six integrations revealed five novel gene sequences and the previously identified protooncogene c-fyn. To date, germ-line transmission and breeding has uncovered one homozygous embryonic lethal and three homozygous viable insertions. These studies demonstrate the potential of this induction gene trap approach for identifying and mutating genes downstream of signal transduction pathways.

TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a toroid-shaped molecule that binds transcripts containing GAG or UAG repeats separated by two nucleotides.

The trp RNA-binding attenuation protein of Bacillus subtilis, TRAP, regulates both transcription and translation by binding to specific transcript sequences. The optimal transcript sequences required for TRAP binding were determined by measuring complex formation between purified TRAP protein and synthetic RNAs. RNAs were tested that contained repeats of different trinucleotide sequences, with differing spacing between the repeats. A transcript containing GAG repeats separated by two-nucleotide spacers was bound most tightly. In addition, transmission electron microscopy was used to examine the structure of TRAP and the TRAP-transcript complex. TRAP was observed to be a toroid-shaped oligomer when free or when bound to either a natural or a synthetic RNA.

CuH-ZSM-5 as Hydrocarbon Trap under Cold Start Conditions

Cold start tests are carried out to evaluate the performance of copper-exchanged zeolites as hydrocarbon traps under simulated gasoline car exhaust gases, paying special attention to the role of copper in the performance of these zeolites. It is concluded that the partial substitution of the protons in the parent H-ZSM-5 zeolite is highly beneficial for hydrocarbon trapping due to the formation of selective adsorption sites with specific affinity for the different exhaust components. However, it is also observed that uncontrolled exchanging process conditions could lead to the presence of CuO nanoparticles in the zeolite surface, which seem to block the pore structure of the zeolite, decreasing the hydrocarbon trap efficiency. Among all the zeolites studied, the results point out that a CuH-ZSM-5 with a partial substitution of extra-framework protons by copper cations and without any detectable surface CuO nanoparticles is the zeolite that showed the best performance under simulated cold start conditions due to both the high stability and the hydrocarbon retaining capacity of this sample during the consecutive cycles.

Advances in camera trap data management tools: Towards collaborative development and integration with GIS

Camera traps have become a widely used technique for conducting biological inventories, generating a large number of database records of great interest. The main aim of this paper is to describe a new free and open source software (FOSS), developed to facilitate the management of camera-trapped data which originated from a protected Mediterranean area (SE Spain). In the last decade, some other useful alternatives have been proposed, but ours focuses especially on a collaborative undertaking and on the importance of spatial information underpinning common camera trap studies. This FOSS application, namely, “Camera Trap Manager” (CTM), has been designed to expedite the processing of pictures on the .NET platform. CTM has a very intuitive user interface, automatic extraction of some image metadata (date, time, moon phase, location, temperature, atmospheric pressure, among others), analytical (Geographical Information Systems, statistics, charts, among others), and reporting capabilities (ESRI Shapefiles, Microsoft Excel Spreadsheets, PDF reports, among others). Using this application, we have achieved a very simple management, fast analysis, and a significant reduction of costs. While we were able to classify an average of 55 pictures per hour manually, CTM has made it possible to process over 1000 photographs per hour, consequently retrieving a greater amount of data.