Annotation Layers Research Articles

Anaphora as an Indicator of Elaboration: A Corpus Study

This article describes an investigation of the relationship between anaphora and relational discourse structure, notably the Elaboration relation known from theories like RST. A corpus was annotated on the levels of anaphoric structure and rhetorical structure. The statistical analysis of interrelations between the two annotation layers revealed correlations between specific subtypes of anaphora and Elaboration, indicating that anaphora can function as a cue for Elaboration. 1

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

BackgroundSeveral biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds.ResultsWe have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization.ConclusionEST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials

An Internet browser-based annotation system can be used to identify and describe features in digitalized retinal images, in multicentric clinical trials, in real time. In this web-based annotation system, the user employs a mouse to draw and create annotations on a transparent layer, that encapsulates the observations and interpretations of a specific image. Multiple annotation layers may be overlaid on a single image. These layers may correspond to annotations by different users on the same image or annotations of a temporal sequence of images of a disease process, over a period of time. In addition, geometrical properties of annotated figures may be computed and measured. The annotations are stored in a central repository database on a server, which can be retrieved by multiple users in real time. This system facilitates objective evaluation of digital images and comparison of double-blind readings of digital photographs, with an identifiable audit trail. Annotation of ophthalmic images allowed clinically feasible and useful interpretation to track properties of an area of fundus pathology. This provided an objective method to monitor properties of pathologies over time, an essential component of multicentric clinical trials. The annotation system also allowed users to view stereoscopic images that are stereo pairs. This web-based annotation system is useful and valuable in monitoring patient care, in multicentric clinical trials, telemedicine, teaching and routine clinical settings.

Unification of XML Documents with Concurrent Markup

An approach to the unification of XML (Extensible Markup Language) documents with identical textual content and conc irrent markup in the framework of XML-based multi-layer annotation is introduced. A Prolog program allows the possible relationships between element instances on two annotation layers that share PCDATA to be explored and also the computing of a target node hierarchy for a well-formed, merged XML document. Special attention is paid to identity conflicts between element instances, for which a default solution that takes into account metarelations that hold between element types on the different annotation layers is provided. In addition, rules can be specified by a user to prescribe how identity conflicts should be solved for certain element types.

A formal concurrency model based architecture description language for synthesis of software development tools

Rapidly increasing design and manufacturing non-recurring engineering (NRE) costs are prompting a shift in electronic design from hardwired application specific integrated circuits (ASICs) to the use of software on programmable platforms. However, in order to minimize the power and performance overhead of such processors, we are seeing the introduction of domain or application specific processors such as network and communication processors. The design of such specialized processors requires software development tools such as simulators and compilers. In order to quickly develop these tools for multiple design points under consideration, it is highly desirable to have them synthesized from formal processor descriptions written in Architecture Description Languages (ADLs). In this paper, we present the Mescal Architecture Description Language (MADL). MADL features a two-layer structure, a core layer and an annotation layer. The core layer is based on a formal and flexible microprocessor model -- the operation state machine (OSM), which enables MADL to express the concurrency at the operation execution level for a wide range of architectures. We address the challenges faced in designing the core layer to combine the OSM model with techniques for achieving compact processor descriptions. The annotation layer features a generic syntax that allows creating annotation schemes to specify implementation dependent or tool specific information. To show the effectiveness of MADL, we present an MADL-based simulator synthesis framework that has been used to generate efficient cycle accurate simulators and instruction set simulators with very low development effort. We also describe our annotation schemes that enable the extraction of architecture properties for use in instruction scheduling and integer-linear-programming based register allocation. Our experimental results demonstrate the efficacy of MADL as a practical and promising language for the development of programmable platforms.