Search results for "Annotation"

The Multimodality of Digital Longform Journalism

2016

Digital longform journalism has recently attracted increased attention among both academics and professionals. This study contributes to the growing body of research by dissecting the multimodal structure of digital longform journalism, that is, how the emerging genre combines written language, photography, short videos, maps and other graphical elements, and joins them together into a seamless narrative using subtle transitions. The data consist of 12 longform articles published in 2012–2013, which have been annotated for their visual and verbal content, their underlying principle of organization and the transitions that hold between them. The annotation is stored into a digital corpus, wh…

Sa1611 Computer-Assisted Diagnosis of Confocal Laser Endomicroscopy (CLE) by a Novel Image Analysis and Semantic Annotation Method

2012

2004

The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions. We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general performance of the system was bench…

Impact of analytic provenance in genome analysis

2014

Background Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a direct impact on the biologically relevant products of a genomic analysis - for instance identification of common and differentiating regions among genomes in a comparison, or identification of enriched gene functional categories in a specific strain. Here, we examine the outcomes of different assembly and analysis steps in typical workflows in a comparison among strains of Vi…

How Does Tremblaya princeps Get Essential Proteins from Its Nested Partner Moranella endobia in the Mealybug Planoccocus citri?

2013

International audience; Many insects maintain intracellular mutualistic symbiosis with a wide range of bacteria which are considered essential for their survival (primary or P-endosymbiont) and typically suffer drastic genome degradation. Progressive loss of P-endosymbiont metabolic capabilities could lead to the recruitment of co-existent facultative endosymbiont (secondary or S-endosymbiont), thus adding more complexity to the symbiotic system. Planococcus citri, among other mealybug species, harbors an unconventional nested endosymbiotic system where every Tremblaya princeps cell (beta-proteobacterium) harbors many Moranella endobia cells (gamma-proteobacterium). In this system, T. princ…

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.

2019

Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…

Suitability of a content-based retrieval method in astronomical image databases

1996

Abstract Indexing and retrieval methods based on the image content are required to effectively use information from large repositories of digital images. Usually, the way to search for data and images in astronomical archives is via textual queries expressed in terms of constraints on observation parameters. In this paper we present a method for automatic extraction of images by using shape descriptions based on local symmetry. The proposed indexing methodology has been developed and tested inside JACOB, a prototypal system for content-based video database querying.

Co-occurrence of discourse markers in English : from juxtaposition to composition

2019

Abstract In this paper, we report on a qualitative analysis of co-occurring discourse markers, that is, sequences of adjacent discourse markers that belong to the same unit but may express different functions. We examine several formal and functional features of these co-occurring strings on the basis of corpus examples extracted from conversational data in English. In particular, we focus on scope, meaning-in-context (or functions), syntactic category and position. Our analysis reveals several degrees of integration: differences in scope allow us to differentiate juxtaposition and combination of markers. In the case of combination, difference in meaning integration allows us to distinguish…

Querying Dynamic and Context-Sensitive Metadata in Semantic Web

2005

RDF (core Semantic Web standard) is not originally appropriate for context representation, because of its initial focus on the ordinary Web resources, such as web pages, files, databases, services, etc., which structure and content are more or less stable. However, on the other hand, emerging industrial applications consider e.g. machines, processes, personnel, services for condition monitoring, remote diagnostics and maintenance, etc. to be specific classes of Web resources and thus a subject for semantic annotation. Such resources are naturally dynamic, not only from the point of view of changing values for some attributes (state of resource), but also from the point of view of changing “…

Sequencing, De Novo Assembly and Annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome

2012

Background. The Colorado potato beetle (Leptinotarsa decemlineata) is a major pest and a serious threat to potato cultivation throughout the northern hemisphere. Despite its high importance for invasion biology, phenology and pest management, little is known about L. decemlineata from a genomic perspective. We subjected European L. decemlineata adult and larval transcriptome samples to 454-FLX massively-parallel DNA sequencing to characterize a basal set of genes from this species. We created a combined assembly of the adult and larval datasets including the publicly available midgut larval Roche 454 reads and provided basic annotation. We were particularly interested in diapause-specific g…