Semantic-Web based Annotation and Reasoning for Temporal Information in Clinical Narratives

drillchinchillaInternet και Εφαρμογές Web

21 Οκτ 2013 (πριν από 3 χρόνια και 5 μήνες)

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Web based Annotation

and Reasoning for Temporal Information in

Clinical Narratives

The temporal dimension in medical data is essential in clinical research. Efficient and timely dissemination
and analysis of the temporal aspects could boost an
array of clinical translational research such as disease
progression studies, disease support systems, and personalized medicine. Time aspects that are important
for clinical findings, however, are often embedded in clinical narratives. This makes it chall
enging to
retrieve temporal relations and reason about them, especially when it involves multiple patients across
different sites. In order to facilitate clinical researchers to expose the temporal dimension in medical data
analysis, scalable software plat
forms that allow users to ask time
oriented questions and retrieve temporal
information automatically from large volumes of clinical records are highly desired. Toward this goal, we
have designed a framework where temporal information in narratives can be

annotated with respect to an
OWL ontology, and annotated data can be queried and reasoned.

The system is centered by a Semantic
Web ontology, CNTRO


(Clinical Narrative Temporal Relation
for modeling temporal information and relat
ions in the clinical domain. It models
clinical events, different kinds of temporal expressions (such as time instants, time intervals, repeated time
periods, and durations), different levels of time granularity, temporal relations, and time uncertainties.

have also conducted analyses for limitations and possible improvements of CNTRO, based on which, a
newer version of CNTRO is under development with finer levels of classifications, more robust coverage,
and more formal semantic definitions


With re
spect to CNTRO, temporal data in clinical narratives can be annotated and represented in RDF. A
Protégé plug
in is being implemented for annotating events and time
related information. This GUI is built
upon the Knowtator [
], an annotation interface devel
oped in Mayo Clinic for manual text annotation to
XML files based on a pre
defined schema. The new interface makes it work with the Semantic Web, so that
users can annotate information of interested with respect to CNTRO, the annotated information can be
tored as RDF files, and queried by SPARQL.

We have also developed a prototype framework for querying and inferring temporal information [
]. This
framework combines DL
based reasoning, SWRL
based reasoning, and SWRL Built
Ins library. It
provides basic fun
ctions for answering a list of time
related questions. We evaluated the feasibility of using
CNTRO with existing Semantic
Web technologies and discussed possible limitations and extensions that
we found necessary or desirable to achieve the purposes of que
rying time
oriented data from real
clinical narratives.

For detailed inform
ation about CNTRO, please visit
, or contact Dr. Cui Tao


Tao C, et al, A Semantic Web Ontology for Temporal

Relation Inferencing in Clinical Narratives. AMIA 2010
Annual Symposium.


Tao C, et al,
A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives
CRI 2011.


Ogren PV. Knowtator: a Protégé plug
in for annotated corpu
s construction. HLT
NAACL 2006.


Tao C, et al, Time
Oriented Question Answering from Clinical Narratives Using Semantic
Web Techniques.
ISWC 2010.