• Ford E, Oswald M, Hassan L, Bozentko K, Nenadic G, Cassell J: Should free-text data in electronic medical records be shared for research? A citizens’ jury study in the UK. Journal of Medical Ethics 2020;46:367-377 (link)
• Jones KH, Ford EM, Lea N, Griffiths L, Hassan L, Heys S, Squires E, Nenadic G: Towards the development of data governance standards for using clinical free-text data in health research: a position paper. Journal of Medical Internet Research. 23/03/2020:16760, DOI: 10.2196/16760 (link)

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As part of the NIHR-funded project Developing and Enhancing the Usefulness of Patient Experience and Narrative Data (DEPEaND), we have developed a text mining software to analyse themes and sentiment expressed in free-text patient service feedback comments (e.g. Family and Friends Test).

The topic-specific opinion mining techniques have been applied to extract commonly mentioned themes from patient comments and to detect the polarity related to each theme. Following an initial manual inspection of a small sample, we focused on four main themes (staff attitude, quality of care, waiting time and environment) and associated sentiment (positive and negative/neutral). Two machine-learning methods have been developed (using Python and R), focusing on the segmentation of patient comments, and then prediction of the themes (and sentiment) using various machine learning algorithms look answer to the question. The system can also combine outputs of the two systems using a probability-threshold technique, and show top comments for each of the themes, for which the system is most confident (i.e. have the most confident prediction). The approach has been tested in two clinical settings – a general hospital and a mental health trust.

The methodology is explained in the paper “Segmentation-based mining of free-text patient feedback comments” (in preparation).

The code to train the software is available at here. The user manual is available here. Note that an annotated corpus is needed to generate the models.

The output of the software can be further analysed (using Stata) and visualised (using LaTeX) to automatically generate reports containing main themes, sentiment and most representative comments over a period of time. The software for this is available here (Stata code) and here (LaTeX). We note that Stata does require a licence.

Funded by:  

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CliNER is a command line tool for identification of mentions of four categories of clinically relevant events: Problems, Tests, Treatments and Clinical Departments. It also recognises and normalises clinical temporal expressions. It was developed as part of the i2b2 2012 text mining challenge and therefore has been trained and optimised on the i2b2 data.

For example, for input:

He had surgery about 3 weeks ago and had the lining cleaned and a biopsy was performed.

CliNER will produce the following output (stand-off):

<?xml version="1.0" encoding="UTF-8" ?>
<ClinicalNarrativeTemporalAnnotation>
<TEXT><![CDATA[
He had surgery about 3 weeks ago and had the lining cleaned and a biopsy was performed.
]]></TEXT>
<TAGS>
<EVENT id="E1" start="65" end="73" text="a biopsy" modality="FACTUAL" polarity="POS" type="TEST" />
<EVENT id="E1" start="8" end="15" text="surgery" modality="FACTUAL" polarity="POS" type="TREATMENT" />
<TIMEX3 id="T1" start="22" end="33" text="3 weeks ago" type="DATE" val="2014-07-29" mod="NA" />
</TAGS>

System Architecture

• Implemented in Java, using cTAKES, CRF++ and Clinical NorMA
• Support for multiple formats, currently supporting:
  • standoff XML
  • character offset-based format

Algorithm details
Conditional random fields with IO scheme and five groups of features:

• Lexical features included the token itself, its lemma, and POS tag, as well as lemmas and POS tags of the surrounding tokens. Each token was also assigned features from its associated chunk (phrase): the type of phrase (nominal, verbal, etc), tense and aspect (if the phrase was verbal), the location of the token within the chunk (beginning or inside), and the presence of negation.
• Domain features capture mentions of specific clinical/healthcare concepts. Mentions of Problem, Test, and Treatment (as generated by cTAKES) were assigned to the token.
• Semantic role features model dependencies between the token and associated verb. Each token is assigned the role, the verb, and their combination (eg, ‘object+perform’) in order to capture particular verb–role preferences.
• Section type feature represents the section type in which the token appeared.
• Temporal expression (TE) features represent five features that indicated the presence of the five common types of constituents of TEs in a given token.

More details on the architecture and the performance of the tool can be found in the paper below. Please cite this publication if you use CliNER:

Kovačević, A., Dehghan, A., Filannino, M., Keane, J. A., & Nenadic, G. (2013). Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. Journal of the American Medical Informatics Association, 20(5), 859-866.

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DOSES (DOSage Extraction System) extracts and represents free-text medication prescription instruction information in a structured form. In particular, it represents the variability and flexibility in drug directions by including minimum and maximum values for drug dosage, frequency and interval of administration, as well as optional choices. In order to comprehensively represent the information in medication prescriptions, DOSES identifies and represents in structure the following medication prescription dosage attributes:

• min/max dose number
• min/max dose frequency
• min/max dose interval
• dose unit
• optional dose

DOSES is implemented in MinorThird for the identification of the targeted dosage attributes, and Python for result post-processing and structured representation.

Currently, two versions are available for DOSES:

In DOSES v.1, the performance has been evaluated on a subset of CPRD (Clinical Practice Research Database) prescription records.

More details on the architecture and the performance can be found in.

• Karystianis, George, et al. “Modelling and extraction of variability in free-text medication prescriptions from an anonymised primary care electronic medical record research database.” BMC medical informatics and decision making 16.1 (2016): 1.

DOSES v.2 has been tailored and evaluated on a collection of patient records acquired from the UK Renal Registry (UKRR).

More details on the tailored version can be found in.

• Alfattni, Ghada, et al. “Integrating text analytics and statistical modelling to analyse the UK Renal Registry data.” Poster presented at: International Population Data Linkage Conference; 2016 AUGUST 24-26; Swansea, United Kingdom.

Contact George Christopher Karystianis, (karystianis@gmail) regarding any questions, bugs and/or suggestions.

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