Abstract
BackgroundOur group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model.MethodsThe Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms.ResultsWe report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF’s next full release.Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.
Highlights
Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model
The Domeo Toolkit was developed in parallel with the Annotation Ontology (AO), an OWL ontology providing a model for creating ‘stand-off’ annotation anchored to online resources such as documents, images and databases and their fragments [21,22]
As the Google Web Toolkit (GWT) code is eventually compiled into JavaScript, the final product consists of a JavaScript file to be imported by the hosting page
Summary
Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Annotation is a fundamental activity in biomedical research and in scholarship generally. It associates a commentary or formal judgment (textual comment, revision, citation, classification, or other related object) to a target of annotation, such as a text or image. It can be created for personal use, as in note-taking and personal classification of documents. On the Web, a target or subject of annotation necessarily means a digital artifact – that is, a Web document, or more technically, an “information resource” [1]. Multiple systems and technical approaches are used today for annotating information resources on the Web and for viewing the annotations in context
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