A method for the graphical modeling of relative temporal constraints

Mate S, Bürkle T, Kapsner L, Toddenroth D, Kampf M, Sedlmayr M, Castellanos I, Prokosch HU, Kraus S (2019)

Publication Type: Journal article

Publication year: 2019

Journal

Book Volume: 100

Article Number: 103314

DOI: 10.1016/j.jbi.2019.103314

Abstract

Searching for patient cohorts in electronic patient data often requires the definition of temporal constraints between the selection criteria. However, beyond a certain degree of temporal complexity, the non-graphical, form-based approaches implemented in current translational research platforms may be limited when modeling such constraints. In our opinion, there is a need for an easily accessible and implementable, fully graphical method for creating temporal queries. We aim to respond to this challenge with a new graphical notation. Based on Allen's time interval algebra, it allows for modeling temporal queries by arranging simple horizontal bars depicting symbolic time intervals. To make our approach applicable to complex temporal patterns, we apply two extensions: with duration intervals, we enable the inference about relative temporal distances between patient events, and with time interval modifiers, we support counting and excluding patient events, as well as constraining numeric values. We describe how to generate database queries from this notation. We provide a prototypical implementation, consisting of a temporal query modeling frontend and an experimental backend that connects to an i2b2 system. We evaluate our modeling approach on the MIMIC-III database to demonstrate that it can be used for modeling typical temporal phenotyping queries. Data availability statement The source code (licensed under the GNU General Public License v3.0) is available on GitHub (https://github.com/sebmate/AllenGUI and https://github.com/sebmate/AllenSPARQL). Also supplied are the development i2b2 dataset (with the 13 artificial patients) and the SQL scripts to populate the i2b2 system with the MIMIC-III data. Please note that the software is of prototypical character and provided “as is”, without any warranties.

Authors with CRIS profile

Involved external institutions

Berner Fachhochschule (BFH) Switzerland (CH) Universitätsklinikum Carl Gustav Carus Dresden Germany (DE)

How to cite

APA:

Mate, S., Bürkle, T., Kapsner, L., Toddenroth, D., Kampf, M., Sedlmayr, M.,... Kraus, S. (2019). A method for the graphical modeling of relative temporal constraints. Journal of Biomedical Informatics, 100. https://doi.org/10.1016/j.jbi.2019.103314

MLA:

Mate, Sebastian, et al. "A method for the graphical modeling of relative temporal constraints." Journal of Biomedical Informatics 100 (2019).

BibTeX: Download