Topic
Annotation
About: Annotation is a research topic. Over the lifetime, 6719 publications have been published within this topic receiving 203463 citations. The topic is also known as: note & markup.
Papers published on a yearly basis
Papers
More filters
TL;DR: A relational database representation is described that captures both the inter- and intra-layer dependencies and details of an object-oriented API for efficient, multi-tiered access to this data.
Abstract: The OntoNotes project is creating a corpus of large-scale, accurate, and integrated annotation of multiple levels of the shallow semantic structure in text. Such rich, integrated annotation covering many levels will allow for richer, cross-level models enabling significantly better automatic semantic analysis. At the same time, it demands a robust, efficient, scalable mechanism for storing and accessing these complex inter-dependent annotations. We describe a relational database representation that captures both the inter- and intra-layer dependencies and provide details of an object-oriented API for efficient, multi-tiered access to this data.
63 citations
Patent•
18 Aug 2004TL;DR: In this paper, the authors described a system and methods for managing annotations in pen-based computing systems, which can be used to collect, manage, search and share personal information entered by way of handwritten annotations.
Abstract: Systems and methods are described for managing annotations in pen-based computing systems The systems and methods described herein provide ways to collect, manage, search and share personal information entered by way of handwritten annotations Annotations are used to drive applications, serve as gestures, find related information and to further manage information Context information is obtained when a user enters an annotation, and is used to assist in determining and locating relevant content in which the user may be interested, whether in the same document or a different document located on a local computer or on the Internet or other network
63 citations
TL;DR: Jannovar, a stand‐alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis, uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society‐compliant annotations.
Abstract: Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar.
63 citations
Patent•
05 Oct 2012
TL;DR: In this article, an annotating method comprising of capturing data representing a light field with a plenoptic image capture device and matching the captured data with a corresponding reference data was proposed.
Abstract: The present invention relates to an annotating method comprising the steps of: capturing (100) data representing a light field with a plenoptic image capture device (4); matching (101) the captured data with a corresponding reference data; retrieving an annotation associated with an element of said reference data (102); rendering (103) a view generated from said captured data and including at least one annotation.
63 citations
TL;DR: A new online user-friendly metagenomics analysis server called MetaStorm is developed, which facilitates customization of computational analysis for metagenomic data sets and provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.
Abstract: Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.
63 citations