Linking science and semantics with the Annotation Ontology and the SWAN Annotation Tool




Annotation Ontology (AO) is an open ontology in OWL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation.

The SWAN Annotation Tool, recently renamed DOMEO (Document Metadata Exchange Organizer), is an extensible web application enabling users to visually and efficiently create and share ontology-based stand-off annotation metadata on HTML or XML document targets, using the Annotation Ontology RDF model. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control.




Paolo Ciccarese is Instructor at the Harvard Medical School and Assistant in Neurology at the Massachusetts General Hospital. After obtaining his MS in Computer Science, he started his career as a freelance consultant in knowledge management software development. Soon after, Paolo received a PhD in Bioengineering and Bioinformatics from the University of Pavia, Italy. Here, he was also a teaching assistant for five years in courses on the subjects of artificial intelligence in medicine and object orientation programming. Outside of his doctorate work, Paolo co-developed the RDF visualizer Welkin for the SIMILE project and founded the JDPF (Java Data Processing Framework) project, a modular and extendable open source infrastructure for processing big quantities of heterogeneous data.
Immediately following the completion of his PhD, Paolo became a research fellow in Department of Neurology at Massachusetts General Hospital where he co-developed the SWAN (Semantic Web Applications in Neuromedicine) platform. Paolo authored several ontologies including the SWAN Ontology, the PAV (Provenance, Authoring and Versioning) ontology and the Annotation Ontology (AO). Since 3 years, he also serves as coordinator of several subtasks of the Scientific Discourse task force at the W3C HCLS Interest Group. Currently, Paolo is focusing on the design and development of knowledge management tools leveraging Semantic Web technologies integrating the annotation of online resources.