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.

MONDRIAN: Annotating and Querying Databases through Colors and Blocks

Abstract: Annotations play a central role in the curation of scientific databases. Despite their importance, data formats and schemas are not designed to manage the increasing variety of annotations. Moreover, DBMS’s often lack support for storing and querying annotations. Furthermore, annotations and data are only loosely coupled. This paper introduces an annotation-oriented data model for the manipulation and querying of both data and annotations. In particular, the model allows for the specification of annotations on sets of values and for effectively querying the information on their association. We use the concept of block to represent an annotated set of values. Different colors applied to the blocks represent different annotations. We introduce a color query language for our model and prove it to be both complete (it can express all possible queries over the class of annotated databases), and minimal (all the algebra operators are primitive). We present MONDRIAN, a prototype implementation of our annotation mechanism, and we conduct experiments that investigate the set of parameters which influence the evaluation cost for color queries.

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.

Abstract: The Institute for Genome Sciences (IGS) has developed a prokaryotic annotation pipeline that is used for coding gene/RNA prediction and functional annotation of Bacteria and Archaea. The fully automated pipeline accepts one or many genomic sequences as input and produces output in a variety of standard formats. Functional annotation is primarily based on similarity searches and motif finding combined with a hierarchical rule based annotation system. The output annotations can also be loaded into a relational database and accessed through visualization tools.

Genotator: A Workbench for Sequence Annotation

Abstract: Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signals such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching. [Further details for obtaining Genotator are available at http://www.cshl.org/gr.]

System and method for annotation on a moving image

Abstract: A system and method allows for the annotation of an image stream, which may be produced by, for example, an ingestible capsule. A workstation accepts images acquired by the capsule and displays the images on a monitor as a moving image. A user inputs an annotation which corresponds to a portion of the moving image, and the annotation is recorded in a database associated with the selected portion. The annotation may include, for example, textual notes regarding the image portion. The annotations may be displayed at a later time.

A Study of Multimedia Annotation of Web-Based Materials

Abstract: Web-based learning has become an important way to enhance learning and teaching, offering many learning opportunities. A limitation of current Web-based learning is the restricted ability of students to personalize and annotate the learning materials. Providing personalized tools and analyzing some types of learning behavior, such as students' annotation, has attracted attention as a means to enhance Web-based learning. We describe a Web-based tool for creating and sharing annotations and investigate the effect on learning of its use with college students. First, an annotation tool was designed and implemented for the research. Second, learning support mechanisms, including full and group annotation sharing, were developed to promote students' motivation for annotation. Lastly, experiments with individual and shared annotation were conducted and the results show that the influence of annotation on learning performance becomes stronger with the use of sharing mechanisms. We conclude that there is value in further study of collaborative learning through shared annotation.