Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

SNP2GO: functional analysis of genome-wide association studies.

Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.

Paikkatiedon perustukset puntarissa

Kokouksen esitysten verkko-osoite: http://www.geoinfo.tuwien.ac.at/events/Euresco2000/gdgis.htm

Ontología y conocimiento en M. Merleau-Ponty

Se ofrece aquí una revisión de la filosofía de Merleau-Ponty atendiendo a la estructura básica desde la que se conforma tanto temporal como sistemáticamente: La coimplicación radical entre la vertiente metafísica y ontológica con la gnoseológica y crítica, en cuyo seno aparece una singular filosofía antropológica de la ambigüedad». El hilo conductor es el análisis del binomio conducta humana-existencia humana» del hombre-mundo como fenómeno unitario, lo que lleva a su autor a proyectar un monismo integrador que se desarrolla bajo el postulado de una síntesis inacabada de corte fluido y ambiguo.

La inversión ontológica de la crítica en Spinoza

El presente trabajo pretende poner de relieve los rasgos esenciales que configuran la sistematización spinozista del racionalismo heredado de Descartes, analizando las diferencias abismales que separan la actitud subjetual y antropológica de la crítica cartesiana, defensora de la categoría de "individualidad", frente a la de "totalidad" preconizada por Spinoza. La tarea se lleva a cabo, concretamente, contraponiendo las nociones de "método","razón" e "ideas", tal como se entienden en uno y otro sistema.

M.Merleau-Ponty: El hombre como unidad ontológica proyectiva

Este trabajo es un intento de retomar sistemáticamente el problema de la estructuraontológica unitaria del hombre, con su dinamicidad propia, partiendo de la temáticaexpuesta en la "Estructura del comportamiento ", con lo que se pone de relieve su unidad significativa para responder de forma nueva al clásico problema de las relaciones entre el alma y el cuerpo. La respuesta merleau-pontyana implica un monismo superador de exclusivismosreductivistas por los que se habían decantado soluciones históricas a las que hay que responder, sin recaer ni en el idealismo ni en el empirismo que desconocen el significado exacto del problema, y no ofrecen ninguna respuesta aceptable al problema de la percepción.En conclusión, lo que se pretende es llevar a cabo una reconstrucción de la antropologíafenomenológica del autor, con miras a mostrar la estructura ontológica que le sirve de fundamento.

La paciente embarazada: repercusión en la cavidad bucal y consideraciones respecto al tratamiento odontológico

El embarazo conlleva una serie de cambios orgánicos, fisiológicos (del sistema cardiovascular y gastrointestinal, de la función pulmonar, hematológicos...) y de conducta que pueden repercutir en la cavidad bucal. El granuloma gravídico se considera una entidad patológica propia del embarazo. Podremos observar también en las pacientes gestantes un aumento en la incidencia de caries, asociado fundamentalmente a un incremento de Jos factores locales cariogénicos (descuido de la higiene bucal, cambio de Jos hábitos dietéticos y horarios...), y un posible empeoramiento de la patología gingival y periodontal asociado a las variaciones hormonales que acompañan al embarazo y a factores locales irritativos. El segundo trimestre de gestación será el momento ideal para llevar a cabo cualquier tratamiento dental rutinario. Deberemos ir con sumo cuidado en lo que se refiere a la administración de fármacos (penicilina, eritromicina, cefalosporinas de primera generación, paracetamol y lidocaína con vasoconstrictor se consideran fármacos de prescripción segura durante el embarazo) y la realización de radiografías dentales (es imprescindible colocar un delantal plomado a la paciente).

EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

Comparativa entre dues BD semàntiques : OWLIM-Lite i Virtuoso

L'objectiu fonamental d'aquest treball és estudiar els conceptes bàsics de la web semàntica mitjançant l'estudi de dos sistemes de gestió de bases de dades (SGBD) utilitzats en el context de la web semàntica, OWLIM-Lite i Virtuoso, que ens permetran dissenyar i implementar una ontologia.

Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis

Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses.

ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

Ontologia de Twitter : El primer pas per inferir informació dels tweets

La web semàntica ens pot facilitar i agilitzar l'aprenentatge o recerca d'informació a través de les relacions de conceptes que ens aporta gràcies a la utilització de les ontologies. Per a la creació de la nostra ontologia hem utilitzat el programa Protégé. Per al disseny de l'ontologia ens hem basat en les funcionalitats bàsiques del Twitter.

Creació d'una aplicació col·laborativa orientada a web semàntica

L'objectiu d'aquest projecte es la creació d'una plataforma que ofereix un nou format per a presentar aquest tipus d'informació, i que a mes permet la integració d'ontologies per a poder classificar les diferents noticies que s'afegeixin al sistema.

XML y web semántica diseño y populación semiautomático de ontologías

El objetivo de este proyecto es familiarizarse con las tecnologías de Semántica, entender que es una ontología y aprender a modelar una en un dominio elegido por nosotros. Realizar un parser que conectándose a la la Wikipedia y/o DBpedia rellene dicha ontología permitiendo al usuario navegar por sus conceptos y estudiar sus relaciones.