Gathering annotations from non-expert online raters is an attractive method for quickly completing large-scale annotation tasks, but the increased possibility of unreliable annotators and diminished work quality remains a cause for concern. In the context of information retrieval, where human-encoded relevance judgments underlie the evaluation of new systems and methods, the ability to quickly ...

This paper presents rstWeb, a new browserbased interface for Rhetorical Structure Theory and other discourse relation annotations. Expanding on previous tools for RST, rstWeb allows annotators to work online using only a browser. Project administrators can easily collect multiple annotations of the same documents on a central server, keep track of annotation processes and assign tasks and annot...

SUMMARY Systems Biology Markup Language (SBML) is the leading exchange format for mathematical models in Systems Biology. Semantic annotations link model elements with external knowledge via unique database identifiers and ontology terms, enabling software to check and process models by their biochemical meaning. Such information is essential for model merging, one of the key steps towards the ...

This paper describes the results of a collaborative effort that has reconciled the Open Annotation Collaboration (OAC) ontology and the Annotation Ontology (AO) to produce a merged data model [the Open Annotation (OA) data model] to describe Web-based annotations—and hence facilitate the discovery, sharing and re-use of such annotations. Using a number of case studies that include digital schol...

Resampling algorithms provide an empirical, non-parametric approach to determine the statistical significance of annotations in different experimental settings. ResA(3) (Resampling Analysis of Arbitrary Annotations, short: ResA) is a novel tool to facilitate the analysis of enrichment and regulation of annotations deposited in various online resources such as KEGG, Gene Ontology and Pfam or any...

This paper describes the NEAR (Navigating Exhibitions, Annotations and Resources) panel, a novel interactive visualization technique designed to help people navigate and interpret groups of resources, exhibitions and annotations by revealing hidden relations such as similarities and references. NEAR is implemented on A•VI•RE, an extended online information repository. A•VI•RE supports a semi-st...

MOTIVATION In general, most accurate gene/protein annotations are provided by curators. Despite having lesser evidence strengths, it is inevitable to use computational methods for fast and a priori discovery of protein function annotations. This paper considers the problem of assigning Gene Ontology (GO) annotations to partially annotated or newly discovered proteins. RESULTS We present a dat...