Hematopoietic Cell Types: Prototype for a Revised Cell Ontology

The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology. A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL. The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL

Next-generation information systems for genomics

NIH Grant no. HG00739The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the translational potential of this technology we will need advanced information systems to integrate and interpret this deluge of data. These systems must be capable of extracting the location and function of genes and biological features from genomic data, requiring the coordinated parallel execution of multiple bioinformatics analyses and intelligent synthesis of the results. The resulting databases must be structured to allow complex biological knowledge to be recorded in a computable way, which requires the development of logic-based knowledge structures called ontologies. To visualise and manipulate the results, new graphical interfaces and knowledge acquisition tools are required. Finally, to help understand complex disease processes, these information systems must be equipped with the capability to integrate and make inferences over multiple data sets derived from numerous sources. RESULTS: Here I describe research, design and implementation of some of the components of such a next-generation information system. I first describe the automated pipeline system used for the annotation of the Drosophila genome, and the application of this system in genomic research. This was succeeded by the development of a flexible graphoriented database system called Chado, which relies on the use of ontologies for structuring data and knowledge. I also describe research to develop, restructure and enhance a number of biological ontologies, adding a layer of logical semantics that increases the computability of these key knowledge sources. The resulting database and ontology collection can be accessed through a suite of tools. Finally I describe how the combination of genome analysis, ontology-based database representation and powerful tools can be combined in order to make inferences about genotype-phenotype relationships within and across species. CONCLUSION: The large volumes of complex data generated by high-throughput genomic and systems biology technology threatens to overwhelm us, unless we can devise better computing tools to assist us with its analysis. Ontologies are key technologies, but many existing ontologies are not interoperable or lack features that make them computable. Here I have shown how concerted ontology, tool and database development can be applied to make inferences of value to translational research

Persistances, actualités et dynamiques du noir et blanc au cinéma dans les arts filmiques (1990-2010)

To work on cinematographic black and white is to enter an alternative temporality that incarnates itself on screen through an absence of mimetic colors. It is in theory a cinema rooted in the past and reclaiming it visually. Why do certain filmmakers persist in using black and white instead of following the course of evolution towards color ? Why do they reject the evolution of techniques ? How do they reflect on it, build new technical and esthetical frames ? Are there any styles of black and white which fully belong to the present and don't refer to past techniques and aesthetics ?In a time when color holds an economic supremacy on cinema, black and white films offer a form of technical criticism on the domination of an industry. Far from an bichromic old fashioned, why and how does others black and white become instruments of a new critical esthetics against industrial audiovisual representation ?Chosing black and white allows for a new, different cinema to break with the conventions of realism. This different cinema « reflects » on black and white, transcending it through holistic experiences, synesthetic and cognitive, redefining cinema as a broader act of creative art. This PhD attempts to map and analyse its richness and diversity.Travailler le noir et blanc au cinéma sous-entend une alternative temporelle qui s’inscrit à l’image par une absence de couleur mimétique. C’est un cinéma qui a priori puise aux sources d'un passé revendiqué visuellement. Pourquoi et dans quelles intentions certains cinéastes persistent-ils à utiliser le noir et blanc alors que l’évolution historique du média invite à utiliser la couleur ? Comment ce choix à contre-courant permet-il de penser l'histoire du média ? Quels en sont les enjeux matériels, esthétiques et réflexifs ? Existe-t-il des styles du noir et blanc ancrés dans le présent, sans références techniques et plastiques à une histoire univoque des formes ? À une époque de domination économique de la couleur, réaliser des films en noir et blanc serait-il porteur d’une réflexion critique sur les procédés cinématographiques actuels et sur l’industrie qui les impose ? Bien loin d’une bichromie passéiste, en quoi, pourquoi et comment d’autres noir et blanc deviennent-ils des outils de prédilection pour établir l’état des lieux d’une plasticité critique de la représentation de l’industrie audiovisuelle ?Nous verrons qu’en optant pour le noir et blanc, la palette chromatique construit un espace propice à un cinéma différent en rupture avec les conventions du réalisme audiovisuel. Ce cinéma différent « réfléchit » le noir et blanc qui devient une source d’expériences holistiques à l’origine d’un redéploiement élargi du cinéma comme geste et art plastique fondateurs. Ce Doctorat en cartographie et en analyse la richesse et la diversité

The Iowa Official Register, 1904

The Iowa Official Register, commonly known as the "Redbook," serves as a biographical and historical record of Iowa's leaders, government and people