Open semantic annotation of scientific publications using DOMEO

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.

Assisted editing in the biomedical domain

“…It can be operated either through a browser plugin or remotely via web interface. DOMEO [1] is a more recent literature curation tools which supports several types of curation paradigms (e.g. highlighting, adding notes, adding semantic tags).…”

Data Citation as a Bibliometric Oxymoron

“…Discovery can be improved by more extensive description of data, figures, tables, and other elements in publications. Such descriptions can be accommodated by open annotation systems that facilitate interoperability across systems, which includes synchronizing links to related resources (Ciccarese, Ocana, & Clark, 2012;Das et al, 2009;Foster & Moreau, 2006;Hunter, 2009;Van de Sompel et al, 2012). These approaches may be effective to the extent that document enrichment survives the publication process.…”

Theophrastus: On demand and real-time automatic annotation and exploration of (web) documents using open linked data

“…The user can select the preferred organism whose protein aliases will be used for the tagging and network generation. Domeo Annotation Toolkit [11] is a collection of software components that enables users to create, share and curate ontology-based annotations for online documents. It supports fully automated, semi-automated, and manual biomedical annotation with full representation of the provenance of annotations, as well as personal or community annotations with authorization and access control.…”