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.

Method for associating annotations with document families

Abstract: The present invention generally provides methods, systems, and articles of manufacture for managing an annotation system that includes storing annotations for a document family, i.e., a series of versions of a data source. Annotations created for one version of the data source may be viewed in context from both subsequent and prior versions of the same data source. Embodiments of the invention associate annotations with both a data source “family identifier” as well as a “version identifier.” Other than adding a family ID to the data source, the data source remains unchanged. The family ID is maintained across different versions of the data source, whereas version IDs are determined for a specific version of the data source. Version IDs can be constructed from each data source directly, and do not need to be stored.

GATE Teamware: a web-based, collaborative text annotation framework

Abstract: This paper presents GATE Teamware--an open-source, web-based, collaborative text annotation framework. It enables users to carry out complex corpus annotation projects, involving distributed annotator teams. Different user roles are provided (annotator, manager, administrator) with customisable user interface functionalities, in order to support the complex workflows and user interactions that occur in corpus annotation projects. Documents may be pre-processed automatically, so that human annotators can begin with text that has already been pre-annotated and thus making them more efficient. The user interface is simple to learn, aimed at non-experts, and runs in an ordinary web browser, without need of additional software installation. GATE Teamware has been evaluated through the creation of several gold standard corpora and internal projects, as well as through external evaluation in commercial and EU text annotation projects. It is available as on-demand service on GateCloud.net, as well as open-source for self-installation.

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

Abstract: Background The Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) is a set of guidelines for the annotation and curation processes of computational models, in order to facilitate their exchange and reuse. An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs.

Knowledge extraction by using an ontology-based annotation tool

Abstract: This paper describes a Semantic Annotation Tool for extraction of knowledge structures from web pages through the use of simple user-defined knowledge extraction patterns. The semantic annotation tool contains: an ontology-based mark-up component which allows the user to browse and to mark-up relevant pieces of information; a learning component (Crystal from the University of Massachusetts at Amherst) which learns rules from examples and an information extraction component which extracts the objects and relation between these objects. Our final aim is to provide support for ontology population by using the information extraction component. Our system uses as domain of study “KMi Planet”, a Webbased news server that helps to communicate relevant information between members in our institute.

GOblet: a platform for Gene Ontology annotation of anonymous sequence data

Abstract: GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms. It uses a variety of different protein databases (human, murines, invertebrates, plants, sp-trembl) and their respective GO mappings. The user selects the appropriate database and alignment threshold and thereafter submits single or multiple nucleotide or protein sequences. Results are shown in different ways, e.g. as survey statistics for the main GO categories for all sequences or as detailed results for each single sequence that has been submitted. In its newest version, GOblet allows the batch submission of sequences and provides an improved display of results with the aid of Java applets. All output data, together with the Java applet, are packed to a downloadable archive for local installation and analysis. GOblet can be accessed freely at http://goblet.molgen.mpg.de.