Search results for "ANNOTATION"
showing 10 items of 161 documents
De l'usage des logiques modales pour la gestion de l'incertitude des données : application en archéologie
2015
Archaeological information systems offer methods and tools for representing collected data and performing analyses with which taking into account imperfect data is often hard to please. Our contribution describes the use of several modal logics to model and verify the effects of the consideration of uncertain data, but also to check the quality of a corpus in an in-terdisciplinary collaborative environment. The modelling and the reasoning based on uncertain data, which are studied in this article, are integrated open and extensible platform allowing to manage archaeological data. From the computing point of view, the reasoner used, based on the first order logic, provides the archaeologists…
In Search of Pathogens: Transcriptome-Based Identification of Viral Sequences from the Pine Processionary Moth (Thaumetopoea pityocampa)
2015
Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. pityocampa occurrence is also an issue for public and animal health, as it is responsible for dermatological reactions in humans and animals by contact with its irritating hairs. High throughput sequencing technologies have allowed the fast and cost-effective generation of genetic information of interest to understand different biological aspects of non-model organisms as well as the identification of potential pathogens. Using these technologies, we have o…
unitas: the universal tool for annotation of small RNAs
2017
AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, …
Toward completion of the Earth’s proteome: an update a decade later
2017
Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy. While the SwissProt database has decelerated its growth mostly because of a focus on i…
BAG3 Proteomic Signature under Proteostasis Stress
2020
The multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3) represents a key player in the quality control of the cellular proteostasis network. In response to stress, BAG3 specifically targets aggregation-prone proteins to the perinuclear aggresome and promotes their degradation via BAG3-mediated selective macroautophagy. To adapt cellular homeostasis to stress, BAG3 modulates and functions in various cellular processes and signaling pathways. Noteworthy, dysfunction and deregulation of BAG3 and its pathway are pathophysiologically linked to myopathies, cancer, and neurodegenerative disorders. Here, we report a BAG3 proteomic signature under proteostasis stress. To elucidat…
Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases
2009
Abstract Background Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity. Results In this paper, we…
Brima: Low-Overhead Browser-Only Image Annotation Tool (Preprint)
2021
Image annotation and large annotated datasets are crucial parts within the Computer Vision and Artificial Intelligence this http URL the same time, it is well-known and acknowledged by the research community that the image annotation process is challenging, time-consuming and hard to scale. Therefore, the researchers and practitioners are always seeking ways to perform the annotations easier, faster, and at higher quality. Even though several widely used tools exist and the tools' landscape evolved considerably, most of the tools still require intricate technical setups and high levels of technical savviness from its operators and crowdsource contributors. In order to address such challenge…
High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
2020
Abstract The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. R…
Pini Language and PiniTree Ontology Editor: Annotation and Verbalisation for Atomised Journalism
2020
We present a new ontology language Pini and the PiniTree ontology editor supporting it. Despite Pini language bearing lot of similarities with RDF, UML class diagrams, Property Graphs and their frontends like Google Knowledge Graph and Protege, it is a more expressive language enabling FrameNet-style natural language annotation for Atomised journalism use case.
Discourse Markers in Speech: Distinctive Features and Corpus Annotation
2017
It is generally acknowledged that discourse markers are used differently in speech and writing, yet many general descriptions and most annotation frameworks are written-based, thus partially unfit to be applied in spoken corpora. This paper identifies the major distinctive features of discourse markers in spoken language, which can be associated with problems related to their scope and structure, their meaning and their tendency to co-occur. The description is based on authentic examples and is followed by methodological recommendations on how to deal with these phenomena in more exhaustive, speech-friendly annotation models.