Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection

Objective

The US Vaccine Adverse Event Reporting System (VAERS) collects spontaneous reports of adverse events following vaccination. Medical officers review the reports and often apply standardized case definitions, such as those developed by the Brighton Collaboration. Our objective was to demonstrate a multi-level text mining approach for automated text classification of VAERS reports that could potentially reduce human workload.

Design

We selected 6034 VAERS reports for H1N1 vaccine that were classified by medical officers as potentially positive (N_pos=237) or negative for anaphylaxis. We created a categorized corpus of text files that included the class label and the symptom text field of each report. A validation set of 1100 labeled text files was also used. Text mining techniques were applied to extract three feature sets for important keywords, low- and high-level patterns. A rule-based classifier processed the high-level feature representation, while several machine learning classifiers were trained for the remaining two feature representations.

Measurements

Classifiers'' performance was evaluated by macro-averaging recall, precision, and F-measure, and Friedman''s test; misclassification error rate analysis was also performed.

Results

Rule-based classifier, boosted trees, and weighted support vector machines performed well in terms of macro-recall, however at the expense of a higher mean misclassification error rate. The rule-based classifier performed very well in terms of average sensitivity and specificity (79.05% and 94.80%, respectively).

Conclusion

Our validated results showed the possibility of developing effective medical text classifiers for VAERS reports by combining text mining with informative feature selection; this strategy has the potential to reduce reviewer workload considerably.     

Linguistic approach for identification of medication names and related information in clinical narratives

Background

Pharmacotherapy is an integral part of any medical care process and plays an important role in the medical history of most patients. Information on medication is crucial for several tasks such as pharmacovigilance, medical decision or biomedical research.

Objectives

Within a narrative text, medication-related information can be buried within other non-relevant data. Specific methods, such as those provided by text mining, must be designed for accessing them, and this is the objective of this study.

Methods

The authors designed a system for analyzing narrative clinical documents to extract from them medication occurrences and medication-related information. The system also attempts to deduce medications not covered by the dictionaries used.

Results

Results provided by the system were evaluated within the framework of the I2B2 NLP challenge held in 2009. The system achieved an F-measure of 0.78 and ranked 7th out of 20 participating teams (the highest F-measure was 0.86). The system provided good results for the annotation and extraction of medication names, their frequency, dosage and mode of administration (F-measure over 0.81), while information on duration and reasons is poorly annotated and extracted (F-measure 0.36 and 0.29, respectively). The performance of the system was stable between the training and test sets.     

Comprehensive temporal information detection from clinical text: medical events,time, and TLINK identification

Background

Temporal information detection systems have been developed by the Mayo Clinic for the 2012 i2b2 Natural Language Processing Challenge.

Objective

To construct automated systems for EVENT/TIMEX3 extraction and temporal link (TLINK) identification from clinical text.

Materials and methods

The i2b2 organizers provided 190 annotated discharge summaries as the training set and 120 discharge summaries as the test set. Our Event system used a conditional random field classifier with a variety of features including lexical information, natural language elements, and medical ontology. The TIMEX3 system employed a rule-based method using regular expression pattern match and systematic reasoning to determine normalized values. The TLINK system employed both rule-based reasoning and machine learning. All three systems were built in an Apache Unstructured Information Management Architecture framework.

Results

Our TIMEX3 system performed the best (F-measure of 0.900, value accuracy 0.731) among the challenge teams. The Event system produced an F-measure of 0.870, and the TLINK system an F-measure of 0.537.

Conclusions

Our TIMEX3 system demonstrated good capability of regular expression rules to extract and normalize time information. Event and TLINK machine learning systems required well-defined feature sets to perform well. We could also leverage expert knowledge as part of the machine learning features to further improve TLINK identification performance.     

Effects of personal identifier resynthesis on clinical text de-identification

Objective

De-identified medical records are critical to biomedical research. Text de-identification software exists, including “resynthesis” components that replace real identifiers with synthetic identifiers. The goal of this research is to evaluate the effectiveness and examine possible bias introduced by resynthesis on de-identification software.

Design

We evaluated the open-source MITRE Identification Scrubber Toolkit, which includes a resynthesis capability, with clinical text from Vanderbilt University Medical Center patient records. We investigated four record classes from over 500 patients'' files, including laboratory reports, medication orders, discharge summaries and clinical notes. We trained and tested the de-identification tool on real and resynthesized records.

Measurements

We measured performance in terms of precision, recall, F-measure and accuracy for the detection of protected health identifiers as designated by the HIPAA Safe Harbor Rule.

Results

The de-identification tool was trained and tested on a collection of real and resynthesized Vanderbilt records. Results for training and testing on the real records were 0.990 accuracy and 0.960 F-measure. The results improved when trained and tested on resynthesized records with 0.998 accuracy and 0.980 F-measure but deteriorated moderately when trained on real records and tested on resynthesized records with 0.989 accuracy 0.862 F-measure. Moreover, the results declined significantly when trained on resynthesized records and tested on real records with 0.942 accuracy and 0.728 F-measure.

Conclusion

The de-identification tool achieves high accuracy when training and test sets are homogeneous (ie, both real or resynthesized records). The resynthesis component regularizes the data to make them less “realistic,” resulting in loss of performance particularly when training on resynthesized data and testing on real data.     

Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries

Objective

A system that translates narrative text in the medical domain into structured representation is in great demand. The system performs three sub-tasks: concept extraction, assertion classification, and relation identification.

Design

The overall system consists of five steps: (1) pre-processing sentences, (2) marking noun phrases (NPs) and adjective phrases (APs), (3) extracting concepts that use a dosage-unit dictionary to dynamically switch two models based on Conditional Random Fields (CRF), (4) classifying assertions based on voting of five classifiers, and (5) identifying relations using normalized sentences with a set of effective discriminating features.

Measurements

Macro-averaged and micro-averaged precision, recall and F-measure were used to evaluate results.

Results

The performance is competitive with the state-of-the-art systems with micro-averaged F-measure of 0.8489 for concept extraction, 0.9392 for assertion classification and 0.7326 for relation identification.

Conclusions

The system exploits an array of common features and achieves state-of-the-art performance. Prudent feature engineering sets the foundation of our systems. In concept extraction, we demonstrated that switching models, one of which is especially designed for telegraphic sentences, improved extraction of the treatment concept significantly. In assertion classification, a set of features derived from a rule-based classifier were proven to be effective for the classes such as conditional and possible. These classes would suffer from data scarcity in conventional machine-learning methods. In relation identification, we use two-staged architecture, the second of which applies pairwise classifiers to possible candidate classes. This architecture significantly improves performance.     

A flexible framework for deriving assertions from electronic medical records

Objective

This paper describes natural-language-processing techniques for two tasks: identification of medical concepts in clinical text, and classification of assertions, which indicate the existence, absence, or uncertainty of a medical problem. Because so many resources are available for processing clinical texts, there is interest in developing a framework in which features derived from these resources can be optimally selected for the two tasks of interest.

Materials and methods

The authors used two machine-learning (ML) classifiers: support vector machines (SVMs) and conditional random fields (CRFs). Because SVMs and CRFs can operate on a large set of features extracted from both clinical texts and external resources, the authors address the following research question: Which features need to be selected for obtaining optimal results? To this end, the authors devise feature-selection techniques which greatly reduce the amount of manual experimentation and improve performance.

Results

The authors evaluated their approaches on the 2010 i2b2/VA challenge data. Concept extraction achieves 79.59 micro F-measure. Assertion classification achieves 93.94 micro F-measure.

Discussion

Approaching medical concept extraction and assertion classification through ML-based techniques has the advantage of easily adapting to new data sets and new medical informatics tasks. However, ML-based techniques perform best when optimal features are selected. By devising promising feature-selection techniques, the authors obtain results that outperform the current state of the art.

Conclusion

This paper presents two ML-based approaches for processing language in the clinical texts evaluated in the 2010 i2b2/VA challenge. By using novel feature-selection methods, the techniques presented in this paper are unique among the i2b2 participants.     

Automatic extraction of medication information from medical discharge summaries

Objective

This article describes a system developed for the 2009 i2b2 Medication Extraction Challenge. The purpose of this challenge is to extract medication information from hospital discharge summaries.

Design

The system explored several linguistic natural language processing techniques (eg, term-based and token-based rule matching) to identify medication-related information in the narrative text. A number of lexical resources was constructed to profile lexical or morphological features for different categories of medication constituents.

Measurements

Performance was evaluated in terms of the micro-averaged F-measure at the horizontal system level.

Results

The automated system performed well, and achieved an F-micro of 80% for the term-level results and 81% for the token-level results, placing it sixth in exact matches and fourth in inexact matches in the i2b2 competition.

Conclusion

The overall results show that this relatively simple rule-based approach is capable of tackling multiple entity identification tasks such as medication extraction under situations in which few training documents are annotated for machine learning approaches, and the entity information can be characterized with a set of feature tokens.     

Finding falls in ambulatory care clinical documents using statistical text mining

Objective

To determine how well statistical text mining (STM) models can identify falls within clinical text associated with an ambulatory encounter.

Materials and Methods

2241 patients were selected with a fall-related ICD-9-CM E-code or matched injury diagnosis code while being treated as an outpatient at one of four sites within the Veterans Health Administration. All clinical documents within a 48-h window of the recorded E-code or injury diagnosis code for each patient were obtained (n=26 010; 611 distinct document titles) and annotated for falls. Logistic regression, support vector machine, and cost-sensitive support vector machine (SVM-cost) models were trained on a stratified sample of 70% of documents from one location (dataset A_train) and then applied to the remaining unseen documents (datasets A_test–D).

Results

All three STM models obtained area under the receiver operating characteristic curve (AUC) scores above 0.950 on the four test datasets (A_test–D). The SVM-cost model obtained the highest AUC scores, ranging from 0.953 to 0.978. The SVM-cost model also achieved F-measure values ranging from 0.745 to 0.853, sensitivity from 0.890 to 0.931, and specificity from 0.877 to 0.944.

Discussion

The STM models performed well across a large heterogeneous collection of document titles. In addition, the models also generalized across other sites, including a traditionally bilingual site that had distinctly different grammatical patterns.

Conclusions

The results of this study suggest STM-based models have the potential to improve surveillance of falls. Furthermore, the encouraging evidence shown here that STM is a robust technique for mining clinical documents bodes well for other surveillance-related topics.     

Hybrid methods for improving information access in clinical documents: concept,assertion, and relation identification

Objective

This paper describes the approaches the authors developed while participating in the i2b2/VA 2010 challenge to automatically extract medical concepts and annotate assertions on concepts and relations between concepts.

Design

The authors''approaches rely on both rule-based and machine-learning methods. Natural language processing is used to extract features from the input texts; these features are then used in the authors'' machine-learning approaches. The authors used Conditional Random Fields for concept extraction, and Support Vector Machines for assertion and relation annotation. Depending on the task, the authors tested various combinations of rule-based and machine-learning methods.

Results

The authors''assertion annotation system obtained an F-measure of 0.931, ranking fifth out of 21 participants at the i2b2/VA 2010 challenge. The authors'' relation annotation system ranked third out of 16 participants with a 0.709 F-measure. The 0.773 F-measure the authors obtained on concept extraction did not make it to the top 10.

Conclusion

On the one hand, the authors confirm that the use of only machine-learning methods is highly dependent on the annotated training data, and thus obtained better results for well-represented classes. On the other hand, the use of only a rule-based method was not sufficient to deal with new types of data. Finally, the use of hybrid approaches combining machine-learning and rule-based approaches yielded higher scores.     

Automated concept-level information extraction to reduce the need for custom software and rules development

Objective

Despite at least 40 years of promising empirical performance, very few clinical natural language processing (NLP) or information extraction systems currently contribute to medical science or care. The authors address this gap by reducing the need for custom software and rules development with a graphical user interface-driven, highly generalizable approach to concept-level retrieval.

Materials and methods

A ‘learn by example’ approach combines features derived from open-source NLP pipelines with open-source machine learning classifiers to automatically and iteratively evaluate top-performing configurations. The Fourth i2b2/VA Shared Task Challenge''s concept extraction task provided the data sets and metrics used to evaluate performance.

Results

Top F-measure scores for each of the tasks were medical problems (0.83), treatments (0.82), and tests (0.83). Recall lagged precision in all experiments. Precision was near or above 0.90 in all tasks.

Discussion

With no customization for the tasks and less than 5 min of end-user time to configure and launch each experiment, the average F-measure was 0.83, one point behind the mean F-measure of the 22 entrants in the competition. Strong precision scores indicate the potential of applying the approach for more specific clinical information extraction tasks. There was not one best configuration, supporting an iterative approach to model creation.

Conclusion

Acceptable levels of performance can be achieved using fully automated and generalizable approaches to concept-level information extraction. The described implementation and related documentation is available for download.     

Research and applications: Learning regular expressions for clinical text classification

Objectives

Natural language processing (NLP) applications typically use regular expressions that have been developed manually by human experts. Our goal is to automate both the creation and utilization of regular expressions in text classification.

Methods

We designed a novel regular expression discovery (RED) algorithm and implemented two text classifiers based on RED. The RED+ALIGN classifier combines RED with an alignment algorithm, and RED+SVM combines RED with a support vector machine (SVM) classifier. Two clinical datasets were used for testing and evaluation: the SMOKE dataset, containing 1091 text snippets describing smoking status; and the PAIN dataset, containing 702 snippets describing pain status. We performed 10-fold cross-validation to calculate accuracy, precision, recall, and F-measure metrics. In the evaluation, an SVM classifier was trained as the control.

Results

The two RED classifiers achieved 80.9–83.0% in overall accuracy on the two datasets, which is 1.3–3% higher than SVM''s accuracy (p<0.001). Similarly, small but consistent improvements have been observed in precision, recall, and F-measure when RED classifiers are compared with SVM alone. More significantly, RED+ALIGN correctly classified many instances that were misclassified by the SVM classifier (8.1–10.3% of the total instances and 43.8–53.0% of SVM''s misclassifications).

Conclusions

Machine-generated regular expressions can be effectively used in clinical text classification. The regular expression-based classifier can be combined with other classifiers, like SVM, to improve classification performance.     

A sequence labeling approach to link medications and their attributes in clinical notes and clinical trial announcements for information extraction

Objective

The goal of this work was to evaluate machine learning methods, binary classification and sequence labeling, for medication–attribute linkage detection in two clinical corpora.

Data and methods

We double annotated 3000 clinical trial announcements (CTA) and 1655 clinical notes (CN) for medication named entities and their attributes. A binary support vector machine (SVM) classification method with parsimonious feature sets, and a conditional random fields (CRF)-based multi-layered sequence labeling (MLSL) model were proposed to identify the linkages between the entities and their corresponding attributes. We evaluated the system''s performance against the human-generated gold standard.

Results

The experiments showed that the two machine learning approaches performed statistically significantly better than the baseline rule-based approach. The binary SVM classification achieved 0.94 F-measure with individual tokens as features. The SVM model trained on a parsimonious feature set achieved 0.81 F-measure for CN and 0.87 for CTA. The CRF MLSL method achieved 0.80 F-measure on both corpora.

Discussion and conclusions

We compared the novel MLSL method with a binary classification and a rule-based method. The MLSL method performed statistically significantly better than the rule-based method. However, the SVM-based binary classification method was statistically significantly better than the MLSL method for both the CTA and CN corpora. Using parsimonious feature sets both the SVM-based binary classification and CRF-based MLSL methods achieved high performance in detecting medication name and attribute linkages in CTA and CN.     

High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge

Objective

Medication information comprises a most valuable source of data in clinical records. This paper describes use of a cascade of machine learners that automatically extract medication information from clinical records.

Design

Authors developed a novel supervised learning model that incorporates two machine learning algorithms and several rule-based engines.

Measurements

Evaluation of each step included precision, recall and F-measure metrics. The final outputs of the system were scored using the i2b2 workshop evaluation metrics, including strict and relaxed matching with a gold standard.

Results

Evaluation results showed greater than 90% accuracy on five out of seven entities in the name entity recognition task, and an F-measure greater than 95% on the relationship classification task. The strict micro averaged F-measure for the system output achieved best submitted performance of the competition, at 85.65%.

Limitations

Clinical staff will only use practical processing systems if they have confidence in their reliability. Authors estimate that an acceptable accuracy for a such a working system should be approximately 95%. This leaves a significant performance gap of 5 to 10% from the current processing capabilities.

Conclusion

A multistage method with mixed computational strategies using a combination of rule-based classifiers and statistical classifiers seems to provide a near-optimal strategy for automated extraction of medication information from clinical records.Many of the potential benefits of the electronic medical record (EMR) rely significantly on our ability to automatically process the free-text content in the EMR. To understand the limitations and difficulties of exploiting the EMR we have designed an information extraction engine to identify medication events within patient discharge summaries, as specified by the i2b2 medication extraction shared task.     

Automated identification of drug and food allergies entered using non-standard terminology

Objective

An accurate computable representation of food and drug allergy is essential for safe healthcare. Our goal was to develop a high-performance, easily maintained algorithm to identify medication and food allergies and sensitivities from unstructured allergy entries in electronic health record (EHR) systems.

Materials and methods

An algorithm was developed in Transact-SQL to identify ingredients to which patients had allergies in a perioperative information management system. The algorithm used RxNorm and natural language processing techniques developed on a training set of 24 599 entries from 9445 records. Accuracy, specificity, precision, recall, and F-measure were determined for the training dataset and repeated for the testing dataset (24 857 entries from 9430 records).

Results

Accuracy, precision, recall, and F-measure for medication allergy matches were all above 98% in the training dataset and above 97% in the testing dataset for all allergy entries. Corresponding values for food allergy matches were above 97% and above 93%, respectively. Specificities of the algorithm were 90.3% and 85.0% for drug matches and 100% and 88.9% for food matches in the training and testing datasets, respectively.

Discussion

The algorithm had high performance for identification of medication and food allergies. Maintenance is practical, as updates are managed through upload of new RxNorm versions and additions to companion database tables. However, direct entry of codified allergy information by providers (through autocompleters or drop lists) is still preferred to post-hoc encoding of the data. Data tables used in the algorithm are available for download.

Conclusions

A high performing, easily maintained algorithm can successfully identify medication and food allergies from free text entries in EHR systems.     

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010

Objective

As clinical text mining continues to mature, its potential as an enabling technology for innovations in patient care and clinical research is becoming a reality. A critical part of that process is rigid benchmark testing of natural language processing methods on realistic clinical narrative. In this paper, the authors describe the design and performance of three state-of-the-art text-mining applications from the National Research Council of Canada on evaluations within the 2010 i2b2 challenge.

Design

The three systems perform three key steps in clinical information extraction: (1) extraction of medical problems, tests, and treatments, from discharge summaries and progress notes; (2) classification of assertions made on the medical problems; (3) classification of relations between medical concepts. Machine learning systems performed these tasks using large-dimensional bags of features, as derived from both the text itself and from external sources: UMLS, cTAKES, and Medline.

Measurements

Performance was measured per subtask, using micro-averaged F-scores, as calculated by comparing system annotations with ground-truth annotations on a test set.

Results

The systems ranked high among all submitted systems in the competition, with the following F-scores: concept extraction 0.8523 (ranked first); assertion detection 0.9362 (ranked first); relationship detection 0.7313 (ranked second).

Conclusion

For all tasks, we found that the introduction of a wide range of features was crucial to success. Importantly, our choice of machine learning algorithms allowed us to be versatile in our feature design, and to introduce a large number of features without overfitting and without encountering computing-resource bottlenecks.     

Integrating existing natural language processing tools for medication extraction from discharge summaries

Objective

To develop an automated system to extract medications and related information from discharge summaries as part of the 2009 i2b2 natural language processing (NLP) challenge. This task required accurate recognition of medication name, dosage, mode, frequency, duration, and reason for drug administration.

Design

We developed an integrated system using several existing NLP components developed at Vanderbilt University Medical Center, which included MedEx (to extract medication information), SecTag (a section identification system for clinical notes), a sentence splitter, and a spell checker for drug names. Our goal was to achieve good performance with minimal to no specific training for this document corpus; thus, evaluating the portability of those NLP tools beyond their home institution. The integrated system was developed using 17 notes that were annotated by the organizers and evaluated using 251 notes that were annotated by participating teams.

Measurements

The i2b2 challenge used standard measures, including precision, recall, and F-measure, to evaluate the performance of participating systems. There were two ways to determine whether an extracted textual finding is correct or not: exact matching or inexact matching. The overall performance for all six types of medication-related findings across 251 annotated notes was considered as the primary metric in the challenge.

Results

Our system achieved an overall F-measure of 0.821 for exact matching (0.839 precision; 0.803 recall) and 0.822 for inexact matching (0.866 precision; 0.782 recall). The system ranked second out of 20 participating teams on overall performance at extracting medications and related information.

Conclusions

The results show that the existing MedEx system, together with other NLP components, can extract medication information in clinical text from institutions other than the site of algorithm development with reasonable performance.     

Extracting medical information from narrative patient records: the case of medication-related information

Objective

While essential for patient care, information related to medication is often written as free text in clinical records and, therefore, difficult to use in computerized systems. This paper describes an approach to automatically extract medication information from clinical records, which was developed to participate in the i2b2 2009 challenge, as well as different strategies to improve the extraction.

Design

Our approach relies on a semantic lexicon and extraction rules as a two-phase strategy: first, drug names are recognized and, then, the context of these names is explored to extract drug-related information (mode, dosage, etc) according to rules capturing the document structure and the syntax of each kind of information. Different configurations are tested to improve this baseline system along several dimensions, particularly drug name recognition—this step being a determining factor to extract drug-related information. Changes were tested at the level of the lexicons and of the extraction rules.

Results

The initial system participating in i2b2 achieved good results (global F-measure of 77%). Further testing of different configurations substantially improved the system (global F-measure of 81%), performing well for all types of information (eg, 84% for drug names and 88% for modes), except for durations and reasons, which remain problematic.

Conclusion

This study demonstrates that a simple rule-based system can achieve good performance on the medication extraction task. We also showed that controlled modifications (lexicon filtering and rule refinement) were the improvements that best raised the performance.     

A classification approach to coreference in discharge summaries: 2011 i2b2 challenge

Objective

To create a highly accurate coreference system in discharge summaries for the 2011 i2b2 challenge. The coreference categories include Person, Problem, Treatment, and Test.

Design

An integrated coreference resolution system was developed by exploiting Person attributes, contextual semantic clues, and world knowledge. It includes three subsystems: Person coreference system based on three Person attributes, Problem/Treatment/Test system based on numerous contextual semantic extractors and world knowledge, and Pronoun system based on a multi-class support vector machine classifier. The three Person attributes are patient, relative and hospital personnel. Contextual semantic extractors include anatomy, position, medication, indicator, temporal, spatial, section, modifier, equipment, operation, and assertion. The world knowledge is extracted from external resources such as Wikipedia.

Measurements

Micro-averaged precision, recall and F-measure in MUC, BCubed and CEAF were used to evaluate results.

Results

The system achieved an overall micro-averaged precision, recall and F-measure of 0.906, 0.925, and 0.915, respectively, on test data (from four hospitals) released by the challenge organizers. It achieved a precision, recall and F-measure of 0.905, 0.920 and 0.913, respectively, on test data without Pittsburgh data. We ranked the first out of 20 competing teams. Among the four sub-tasks on Person, Problem, Treatment, and Test, the highest F-measure was seen for Person coreference.

Conclusions

This system achieved encouraging results. The Person system can determine whether personal pronouns and proper names are coreferent or not. The Problem/Treatment/Test system benefits from both world knowledge in evaluating the similarity of two mentions and contextual semantic extractors in identifying semantic clues. The Pronoun system can automatically detect whether a Pronoun mention is coreferent to that of the other four types. This study demonstrates that it is feasible to accomplish the coreference task in discharge summaries.     

Integrated gene network analysis and text mining revealing PIK3R1 regulated by miR-127 in human bladder cancer

Background

Cancer is the result of a complex multistep process that involves the accumulation of sequential alterations of several genes, including those encoding microRNAs (miRNAs) that have critical roles in the regulation of gene expression.In this study, we aimed to predict potential mechanisms of bladder cancer related miRNAs and target genes by bioinformatics analyses.

Methods

Here we used the method of text mining to identify nine miRNAs in bladder cancer and adopted protein-protein interaction analysis to identify interaction sites between these miRNAs and related-target genes.

Results

There are two relationship types between bladder cancer and its related miRNAs: causal and unspecified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment test showed that there were three pathways related to four miRNA targeted genes. The remaining five miRNAs annotated to disease are not enriched in the KEGG pathways. Of these, PIK3R1 is the overlapping gene among 38 genes in the cancer and bladder cancer pathways.

Conclusions

These findings provide new insights into the role of miRNAs in the pathway of cancer and give us a hypothesis that miR-127 might play a similar role in regulation and control of PIK3R1.     

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences

Objective

To develop, evaluate, and share: (1) syntactic parsing guidelines for clinical text, with a new approach to handling ill-formed sentences; and (2) a clinical Treebank annotated according to the guidelines. To document the process and findings for readers with similar interest.

Methods

Using random samples from a shared natural language processing challenge dataset, we developed a handbook of domain-customized syntactic parsing guidelines based on iterative annotation and adjudication between two institutions. Special considerations were incorporated into the guidelines for handling ill-formed sentences, which are common in clinical text. Intra- and inter-annotator agreement rates were used to evaluate consistency in following the guidelines. Quantitative and qualitative properties of the annotated Treebank, as well as its use to retrain a statistical parser, were reported.

Results

A supplement to the Penn Treebank II guidelines was developed for annotating clinical sentences. After three iterations of annotation and adjudication on 450 sentences, the annotators reached an F-measure agreement rate of 0.930 (while intra-annotator rate was 0.948) on a final independent set. A total of 1100 sentences from progress notes were annotated that demonstrated domain-specific linguistic features. A statistical parser retrained with combined general English (mainly news text) annotations and our annotations achieved an accuracy of 0.811 (higher than models trained purely with either general or clinical sentences alone). Both the guidelines and syntactic annotations are made available at https://sourceforge.net/projects/medicaltreebank.

Conclusions

We developed guidelines for parsing clinical text and annotated a corpus accordingly. The high intra- and inter-annotator agreement rates showed decent consistency in following the guidelines. The corpus was shown to be useful in retraining a statistical parser that achieved moderate accuracy.