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.

Apparatus and method for collaborative dynamic video annotation

Abstract: A method for dynamic video annotation among a plurality of users utilizes a programmable computer and comprises the steps of: selecting a network service coupled to the computer; performing one of (a) starting and (b) joining a collaborative session among the users; loading one of (a) a video and (b) a recorded annotation file; performing annotation of at least one of graphical, text, and audio annotation; and storing said collaborative session.

JAMS: A JSON annotated music specification for reproducible MIR research

Abstract: The continued growth of MIR is motivating more complex annotation data, consisting of richer information, multiple annotations for a given task, and multiple tasks for a given music signal. In this work, we propose JAMS, a JSON-based music annotation format capable of addressing the evolving research requirements of the community, based on the three core principles of simplicity, structure and sustainability. It is designed to support existing data while encouraging the transition to more consistent, comprehensive, well-documented annotations that are poised to be at the crux of future MIR research. Finally, we provide a formal schema, software tools, and popular datasets in the proposed format to lower barriers to entry, and discuss how now is a crucial time to make a concerted effort toward sustainable annotation standards.

Anafora: A Web-based General Purpose Annotation Tool

Abstract: Anafora is a newly-developed open source web-based text annotation tool built to be lightweight, flexible, easy to use and capable of annotating with a variety of schemas, simple and complex. Anafora allows secure web-based annotation of any plaintext file with both spanned (e.g. named entity or markable) and relation annotations, as well as adjudication for both types of annotation. Anafora offers automatic set assignment and progress-tracking, centralized and human-editable XML annotation schemas, and file-based storage and organization of data in a human-readable single-file XML format.

Genome annotation for clinical genomic diagnostics: strengths and weaknesses.

Abstract: The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Abstract: Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies—as well as in somatic and germline mutation studies. The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called and anchored against a reference genome. Here we present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, we wrote and made available through the multiple vcflib, bio-vcf, cyvcf2, hts-nim and slivar projects. These tools are applied for comparison, filtering, normalisation, smoothing and annotation of VCF, as well as output of statistics, visualisation, and transformations of files variants. These tools run everyday in critical biomedical pipelines and countless shell scripts. Our tools are part of the wider bioinformatics ecosystem and we highlight best practices. We shortly discuss the design of VCF, lessons learnt, and how we can address more complex variation through pangenome graph formats, variation that can not easily be represented by the VCF format.