Database Open Access

CUILESS2016

Published: Jan. 24, 2018. Version: 1.0.0


When using this resource, please cite the original publication:

John D. Osborne, Matthew B. Neu, Maria I. Danila, Thamar Solorio and Steven J. Bethard. CUILESS2016: a clinical corpus applying compositional normalization of text mentions. Journal of Biomedical Semantics 2018 9:2. doi:10.1186/s13326-017-0173-6

Please include the standard citation for PhysioNet:

Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals (2003). Circulation. 101(23):e215-e220.

Introduction

The Concept Unique Identifier (CUI)-less database contains a corpus of "CUI-less" concepts taken from the SemEval2015 Task 14 that have been assigned CUIs. The annotation process allows assignment of CUIS from any Unified Medical Language System (UMLS) semantic group and compositional normalization using more than one CUI per disease entity. Concepts are mapped to SNOMED CT as represented in the September 2016 version found in Unified Medical Language System (UMLS) 2016AB.

Data Collection

We annotated 5397 disorder mentions from the ShARe corpus to SNOMED CT that were previously normalized as “CUI-less” in the “SemEval-2015 Task 14” shared task because they lacked a pre-coordinated mapping. Unlike the previous normalization method, we do not restrict concept mappings to a particular set of the Unified Medical Language System (UMLS) semantic types and allow normalization to occur to multiple UMLS Concept Unique Identifiers (CUIs). We computed annotator agreement and assessed semantic coverage with this method. See the referenced paper for more details.

Files

The development CUILESS_DEV.tar.gz and training CUILESS_TRAIN.tar.gz data sets consist of pipe delimited data files in the same format as the SemEval2015-Task 14 (http://alt.qcri.org/semeval2015/task14/index.php?id=data-and-tools) and shown below:

    report name|disorder-span|cui|Norm_NI|Cue_NI|Norm_SC|Cue_SC|Norm_UI|Cue_UI|
    Norm_CC|Cue_CC|Norm_SV|Cue_SV|Norm_CO|Cue_CO|Norm_GC|Cue_GC|Norm_BL|Cue_BL|
    Norm_DT|Norm_TE|Cue_TE

The only difference is that the "cui" column can consist of one or more cuis separated by spaces.

Clinical text is not distributed in this corpus. Interested parties can download the original clinical text and sign the Data Usage Agreement as outlined in: http://alt.qcri.org/semeval2015/task14/index.php?id=data-and-tools. This dataset is free to download provide by interested parties provided the interested agrees not to redistribute the data or attempt to re-identify patients in the dataset.

Contributors

John D. Osborne
Assistant Professor
Informatics Institute (General Medicine)
University of Alabama at Birmingham

 


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License (for files):
Open Data Commons Attribution License v1.0

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Files

Total uncompressed size: 148.3 KB.

Access the files

Folder Navigation: <base>
Name Size Modified
CUILESS_DEV.tar.gz (download) 39.0 KB 2018-01-19
CUILESS_TRAIN.tar.gz (download) 75.5 KB 2018-01-19
SHA256SUMS.txt (download) 272 B 2019-02-20
semanticly_similiar_concept_sets.txt (download) 33.6 KB 2018-01-19