My name is Paolo Ciccarese and I work at Massachusetts General Hospital and Harvard Medical School where I develop ontologies and knowledge management tools for biomedical scientists, publishers and pharmaceutical companies.
In the last year, I have dedicated a great deal of time on DOMEO [1], a web application for annotating online resources (text, images and data). DOMEO was developed in parallel with a model for exchanging annotation in RDF called Annotation Ontology (AO) [2]. One of the features of the tool is the support for automatic or semi-automatic annotation of text documents by leveraging text mining services. We therefore planned to integrate UIMA with our environment by writing code for translating the UIMA results into AO format. The interest for Clerezza came naturally. Thanks to a little introduction by Tommaso Teofili, in a few hours I was almost able to complete my own extensions for Clerezza for performing the AO serialization. The problem arose when I tried to bring URIs into the picture. Imagine an entity recognition service returning, for instance, the DBPedia URIs of cities extracted from a document. In our field, we have entity recognition services returning entities such as proteins, biological processes and genes. The way UIMA types work, I can create a field storing the URI and pass it along. That would be sufficient, however, it is going to be my personal way of dealing with URIs. As my goal is to integrate several entity recognition services through the UIMA platform, it would be more beneficial to establish a convention. For instance, we can ask all the developers that want to integrate with Linked Open Data to extend an abstract class that encodes the recommended way to take care of URIs (the URI of the entity and the related URIs). If you are not dealing with URI you can ignore the convention and keep doing exactly what you were doing before. For Semantic Web applications leveraging UIMA, not only in bio-medicine, this would be a big step forward. I am really interested in collecting your feedback on this topic. Best, Paolo [1] DOMEO http://vimeo.com/paolociccarese/videos [2] AO http://code.google.com/p/annotation-ontology/
