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.

A method and system for organizing documents based upon annotations in context

Abstract: A document organizing system extracts annotations made to a document along with the context surrounding each annotation and organizes the annotations based upon the annotation attributes and/or context. The annotations are created by grouping marks based upon their proximity in time and space. The document is segmented to determine a minimum context associated with each annotation. A list of the annotations sorted by the attributes are then displayed to the user. The context provided by the invention for each annotation allows the user to fully understand the annotation.

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Abstract: Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5). Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.

Semantic Instance Annotation of Street Scenes by 3D to 2D Label Transfer

Abstract: Semantic annotations are vital for training models for object recognition, semantic segmentation or scene understanding. Unfortunately, pixelwise annotation of images at very large scale is labor-intensive and only little labeled data is available, particularly at instance level and for street scenes. In this paper, we propose to tackle this problem by lifting the semantic instance labeling task from 2D into 3D. Given reconstructions from stereo or laser data, we annotate static 3D scene elements with rough bounding primitives and develop a model which transfers this information into the image domain. We leverage our method to obtain 2D labels for a novel suburban video dataset which we have collected, resulting in 400k semantic and instance image annotations. A comparison of our method to state-of the-art label transfer baselines reveals that 3D information enables more efficient annotation while at the same time resulting in improved accuracy and time-coherent labels.

Measuring Agreement on Set-valued Items (MASI) for Semantic and Pragmatic Annotation

Abstract: Annotation projects dealing with complex semantic or pragmatic phenomena face the dilemma of creating annotation schemes that oversimplify the phenomena, or that capture distinctions conventional reliability metrics cannot measure adequately. The solution to the dilemma is to develop metrics that quantify the decisions that annotators are asked to make. This paper discusses MASI, distance metric for comparing sets, and illustrates its use in quantifying the reliability of a specific dataset. Annotations of Summary Content Units (SCUs) generate models referred to as pyramids which can be used to evaluate unseen human summaries or machine summaries. The paper presents reliability results for five pairs of pyramids created for document sets from the 2003 Document Understanding Conference (DUC). The annotators worked independently of each other. Differences between application of MASI to pyramid annotation and its previous application to co-reference annotation are discussed. In addition, it is argued that a paradigmatic reliability study should relate measures of inter-annotator agreement to independent assessments, such as significance tests of the annotated variables with respect to other phenomena. In effect, what counts as sufficiently reliable intera-annotator agreement depends on the use the annotated data will be put to.

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.

Abstract: Using the Pseudomonas aeruginosa Genome Project as a test case, we have developed a database and submission system to facilitate a community-based approach to continually updated genome annotation (http://www.pseudomonas.com). Researchers submit proposed annotation updates through one of three web-based form options which are then subjected to review, and if accepted, entered into both the database and log file of updates with author acknowledgement. In addition, a coordinator continually reviews literature for suitable updates, as we have found such reviews to be the most efficient. Both the annotations database and updates-log database have Boolean search capability with the ability to sort results and download all data or search results as tab-delimited files. To complement this peer-reviewed genome annotation, we also provide a linked GBrowse view which displays alternate annotations. Additional tools and analyses are also integrated, including PseudoCyc, and knockout mutant information. We propose that this database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach. The source code is freely available under GNU General Public Licence.