Annotating Temporal Information in Clinical Notes for Timeline Reconstruction: Towards the Definition of Calendar Expressions

Natalia Viani, Hegler Tissot, Ariane Bernardino, Sumithra Velupillai

Abstract
To automatically analyse complex trajectory information enclosed in clinical text (e.g. timing of symptoms, duration of treatment), it is important to understand the related temporal aspects, anchoring each event on an absolute point in time. In the clinical domain, few temporally annotated corpora are currently available. Moreover, underlying annotation schemas - which mainly rely on the TimeML standard - are not necessarily easily applicable for applications such as patient timeline reconstruction. In this work, we investigated how temporal information is documented in clinical text by annotating a corpus of medical reports with time expressions (TIMEXes), based on TimeML. The developed corpus is available to the NLP community. Starting from our annotations, we analysed the suitability of the TimeML TIMEX schema for capturing timeline information, identifying challenges and possible solutions. As a result, we propose a novel annotation schema that could be useful for timeline reconstruction: CALendar EXpression (CALEX).
Anthology ID:
W19-5021
Volume:
Proceedings of the 18th BioNLP Workshop and Shared Task
Month:
August
Year:
2019
Address:
Florence, Italy
Editors:
Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii
Venue:
BioNLP
SIG:
SIGBIOMED
Publisher:
Association for Computational Linguistics
Note:
Pages:
201–210
Language:
URL:
https://aclanthology.org/W19-5021
DOI:
10.18653/v1/W19-5021
Bibkey:
Cite (ACL):
Natalia Viani, Hegler Tissot, Ariane Bernardino, and Sumithra Velupillai. 2019. Annotating Temporal Information in Clinical Notes for Timeline Reconstruction: Towards the Definition of Calendar Expressions. In Proceedings of the 18th BioNLP Workshop and Shared Task, pages 201–210, Florence, Italy. Association for Computational Linguistics.
Cite (Informal):
Annotating Temporal Information in Clinical Notes for Timeline Reconstruction: Towards the Definition of Calendar Expressions (Viani et al., BioNLP 2019)
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PDF:
https://preview.aclanthology.org/emnlp-22-attachments/W19-5021.pdf
Code
 medesto/timeline-reconstruction
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