Archive for the ‘Protégé’ Category

Semantator: annotating clinical narratives with semantic web ontologies

Thursday, July 12th, 2012

Semantator: annotating clinical narratives with semantic web ontologies by Dezhao Song, Christopher G. Chute, and Cui Tao. (AMIA Summits Transl Sci Proc. 2012;2012:20-9. Epub 2012 Mar 19.)


To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator.

If you are an AMIA member, see above for the paper. If not, see: Semantator: annotating clinical narratives with semantic web ontologies (PDF file). And the software/webpage: Semantator.

Software is a plugin for Protege 4.1 or higher.

Looking at the extensive screen shots at the website, which has good documentation, the first question I would ask a potential user is: “Are you comfortable with Protege?” If they aren’t I suspect you are going to invest a lot of time in teaching them ontologies and Protege. Just an FYI.

Complex authoring tools, particularly for newbies, seem like a non-starter to me. For example, why not have a standalone entity extractor (but don’t call it that, call it “I See You (ISY)) that uses a preloaded entity file to recognize entities in a text. Where there is uncertainty, those are displayed in a different color, with drop down options on possible other entities. User get to pick one from the list (no write in ballots). Performs a step towards getting clean data for a second round with another one-trick-pony tool. User contributes, we all benefit.

Which brings me to the common shortfall of annotation solutions: the requirement that the text to be annotated be in plain text.

There are lot of “text” documents but what of those in Word, PDF, Postscript, PPT, Excel, to say nothing of other formats?

The past will not disappear for want of a robust annotation solution.

Nor should it.

Advice regarding future directions for Protégé

Friday, September 30th, 2011

Advice regarding future directions for Protégé

Mark Munsen, Principal Investigator, The Protégé Project, posted the following request to the protege-users mailing list:

I am writing to seek your advice regarding future directions for the Protégé Project. As you know, all the work that we perform on the Protégé suite of tools is supported by external funding, nearly all from federal research grants. We currently are seeking additional grant support to migrate some of the features that are available in Protégé Version 3 to Protégé Version 4. We believe that this migration is important, as only Protégé 4 supports the full OWL 2 standard, and we appreciate that many members of our user community are asking to use certain capabilities currently unique to Protégé 3 with OWL 2 ontologies in Protégé 4.

To help the Protégé team in setting priorities, and to help us make the case to our potential funders that enhancement of Protégé 4 is warranted, we’d be grateful if you could please fill out the brief survey at the following URL:

It will not take more than a few minutes for you to give us feedback that will be influential in setting our future goals. If we can document strong community support for implementing certain Protégé 3 features in Protégé 4, then we will be in a much stronger position to make the case to our funders to initiate the required work.

The entire Protégé team is looking forward to your opinions. Please be sure to forward this message to colleagues who use Protégé who may not subscribe to these mailing lists so that we can obtain as much feedback as possible.

Many thanks for your help and support.

Please participate in this survey (there are only 7 questions, one of which is optional) and ask others to participate as well.