Open semantic annotation of scientific publications using DOMEO

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Authors: Ciccarese, Paolo

Ocana, Marco

Clark, Tim

Background

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.

Methods

The 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.

Results

We 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 webcite) 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.

Journal: Journal of Biomedical Semantics 2012 vol 3 (Suppl 1) start pg I1