Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows
© Fu et al.; licensee BioMed Central. 2015
Received: 11 November 2014
Accepted: 22 February 2015
Published: 14 March 2015
Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare. Phenotypic information in electronic clinical records is essential in providing suitable personalised treatment to patients with COPD. However, as phenotypes are often “hidden” within free text in clinical records, clinicians could benefit from text mining systems that facilitate their prompt recognition. This paper reports on a semi-automatic methodology for producing a corpus that can ultimately support the development of text mining tools that, in turn, will expedite the process of identifying groups of COPD patients.
A corpus of 30 full-text papers was formed based on selection criteria informed by the expertise of COPD specialists. We developed an annotation scheme that is aimed at producing fine-grained, expressive and computable COPD annotations without burdening our curators with a highly complicated task. This was implemented in the Argo platform by means of a semi-automatic annotation workflow that integrates several text mining tools, including a graphical user interface for marking up documents.
When evaluated using gold standard (i.e., manually validated) annotations, the semi-automatic workflow was shown to obtain a micro-averaged F-score of 45.70% (with relaxed matching). Utilising the gold standard data to train new concept recognisers, we demonstrated that our corpus, although still a work in progress, can foster the development of significantly better performing COPD phenotype extractors.
We describe in this work the means by which we aim to eventually support the process of COPD phenotype curation, i.e., by the application of various text mining tools integrated into an annotation workflow. Although the corpus being described is still under development, our results thus far are encouraging and show great potential in stimulating the development of further automatic COPD phenotype extractors.
KeywordsCorpus annotation Phenotype curation Automatic annotation workflows Ontology linking Corpora for clinical text mining Chronic obstructive pulmonary disease
An umbrella term for a range of lung abnormalities, chronic obstructive pulmonary disease (COPD) pertains to medical conditions in which airflow from the lungs is repeatedly impeded. This life-threatening disease, known to be primarily caused by tobacco smoke, is not completely reversible and is incurable. COPD was ranked by the World Health Organization as the fifth leading cause of death worldwide in 2002, and is predicted to become the third by year 2030. Estimates have also shown that the mortality rate for COPD could escalate by at least 30% within the next decade if preventive measures are not implemented .
The disease and clinical manifestations of COPD are heterogeneous and widely vary from one patient to another. As such, its treatment needs to be highly personalised in order to ensure that the most suitable therapy is provided to a patient. COPD phenotyping allows for well-defined grouping of patients according to their prognostic and therapeutic characteristics, and thus informs the development and provision of personalised therapy .
The primary approach to recording phenotypic information is by means of electronic clinical records . However, as clinicians at the point of care use free text in describing phenotypes, such information can easily become obscured and inaccessible . In order to expedite the process of identifying a given patient’s COPD group, the phenotypic information locked away within these records needs to be automatically extracted and distilled for the clinicians’ perusal.
Capable of automatically distilling information expressed in natural language within documents, text mining can be applied on clinical records in order to efficiently extract COPD phenotypes of interest. However, the development of sophisticated text mining tools is reliant on the availability of gold standard annotated corpora, which serve as evaluation data as well as provide samples for training machine learning-based approaches.
This paper presents our ongoing efforts on the annotation of COPD phenotypes in a collection of scientific papers. In our previous publication  on which this work is built upon, we proposed to form a corpus of clinical records from the Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) Clinical Database [6,7]. However, our UK-based expert collaborators (i.e., stakeholders who will incorporate our text mining technology into their systems in the near future) recently pointed out that there are substantial discrepancies between the hospital system in the US (on which MIMIC II is focussed) and that in the UK. After considering their advice, we decided to utilise scientific articles from various COPD-relevant journals, rather than build a corpus of clinical records which are highly US-specific. As previous work demonstrated techniques which successfully extracted information from unseen data even if the training/development data used was of a different document type , we believe that a gold standard corpus of full scientific articles should still allow for the development of phenotype extraction tools for clinical records. Nevertheless, our collaborators are still currently working on obtaining a subset of clinical records from their own hospital, which will also be annotated to become part of an augmented version of our corpus.
In embarking on this effort, we are building a resource that will support the development of text mining methods for the automatic extraction of COPD phenotypes from free text. We envisage that such methods will ultimately foster the development of applications which will enable point-of-care clinicians to more easily and confidently identify a given COPD patient’s group, potentially leading to the provision of the most appropriate personalised treatment. Furthermore, text mining methods can be employed in order to facilitate the linking of COPD phenotypes with genotypic information contained in published scientific literature.
In the remainder of this paper, we firstly provide a review of the state of the art (Related Work). We proceed to describing our methods for corpus development (Methods), including our strategy for document selection followed by our proposed annotation scheme. A discussion of our text mining-assisted annotation workflow is also provided. We then share the results and analysis of our evaluation (Results and Discussion). Lastly, we conclude the paper with a summary of our contributions and an overview of ongoing and future work.
Various corpora have been constructed to support the development of clinical natural language processing (NLP) methods. Some contain annotations formed on the basis of document-level tags indicating the specific diseases that clinical reports pertain to. In the 2007 Computational Medicine Challenge data set , radiology reports were assigned codes from the ninth revision of the International Classification of Diseases-Clinical Modification (ICD-9-CM) terminology . In similar corpora, chest X-ray reports were manually labelled with any of four pneumonia-related concepts  whilst any of 80 possible disease names were assigned to documents in another collection of clinical records  with the assistance of automatic tools MetaMap Transfer (MMTx)  for concept recognition and NegEx  for negation detection. Whilst suitable for evaluating information retrieval methods, such document-level annotations cannot sufficiently support the extraction of phenotypic concepts which are described in clinical records in largely variable ways, making it necessary for automated methods to perform analysis by looking at their actual mentions within text.
Several other clinical corpora were thus enriched with text-bound annotations, which serve as indicators of specific locations of phenotypic concept mentions within text. For instance, all mentions of signs or symptoms, medications and procedures relevant to inflammatory bowel disease were marked up in the corpus developed by South et al . Specific mentions of diseases and signs or symptoms were similarly annotated under the ShARe scheme [16,17] and additionally linked to terms in the SNOMED Clinical Terms vocabulary . Whilst the scheme developed by  had similar specifications, it is unique in terms of its employment of an automatic tool to accelerate the annotation process. One difficulty encountered by annotators following such scheme, however, is with manually mapping mentions of phenotypic concepts to vocabulary terms, owing to the high degree of variability in which these concepts are expressed in text. For instance, many signs or symptoms (e.g., gradual progressive breathlessness), cannot be fully mapped to any of the existing terms in vocabularies.
Alleviating this issue are schemes which were designed to enrich corpora with finer-grained text-bound annotations. The Clinical e-Science Framework (CLEF) annotation scheme  which defined several clinical concept types and relationships, required the decomposition of phrases into their constituent concepts which were then individually assigned concept type labels and linked using any of their defined relationships. Also based on a fine-grained annotation approach is the work by Mungall et al.  on the ontology-driven annotation of inter-species phenotypic information based on the EQ model . Although their work was carried out with the help of the Phenote software  for storing, managing and visualising annotations, the entire curation process was done manually, i.e., without the support of any NLP tools. The effort we have undertaken, in contrast, can be considered as a step towards automating such EQ model-based fine-grained annotation of phenotypic information.
In this regard, our work is unique amongst annotation efforts within the clinical NLP community, but shares similarities with some phenotype curation pipelines employed in the domain of biological systematics. Curators of the Phenoscape project  manually link EQ-encoded phenotypes of fishes to the Zebrafish Model Organism Database using Phenex  which is a tool for managing character-by-taxon matrices, a formal approach used by evolutionary biologists. To accelerate this process, Phenex has been recently enhanced with NLP capabilities  upon the integration of a text analytic known as CharaParser . Based on a combination of bootstrapping and syntactic parsing approaches , CharaParser can automatically annotate structured characteristics of organisms (i.e., phenotypes) in text, but currently does not have full support for linking concepts to ontologies . Also facilitating the semi-automatic curation of systematics literature is GoldenGATE , a stand-alone application modelled after the GATE framework , which allows for the combination of various NLP tools into text processing pipelines. It is functionally similar to our Web-based annotation platform Argo  in terms of its support for NLP workflow management and manual validation of automatically generated annotations. However, the latter fosters interoperability to a higher degree by conforming to the industry-supported Unstructured Management Information Architecture  and allowing workflows to be invoked as Web services .
By producing our proposed fine-grained phenotype annotations which are linked to ontological concepts, we are representing them in a computable form thus making them suitable for computational applications such as inferencing and semantic search. The Phenomizer tool , for instance, has demonstrated the benefits of encoding phenotypic information in a computable format. Leveraging the Human Phenotype Ontology (HPO)  whose terms are linked to diseases in the Online Mendelian Inheritance in Man (OMIM) vocabulary , it supports clinicians in making diagnoses by semantically searching for the medical condition that best matches the HPO signs or symptoms given in a query. We envisage that such an application, when integrated with a repository of phenotypes and corresponding clinical recommendations, e.g., Phenotype Portal  and the Phenotype KnowledgeBase , can ultimately assist point-of-care clinicians in more confidently providing personalised treatment to patients. Our work on the annotation of COPD phenotypes aims to support the development of similar applications in the future.
We describe in this section our strategies for collecting documents for the corpus and our proposed annotation scheme. We also elaborate on the technology behind our text mining-assisted annotation methodology.
Upon consideration of our constraints in terms of resources such as time and personnel, we decided to trim down the document set to 30 full articles. This was carried out by compiling a list of COPD phenotypes based on the combination of terms given by our domain experts and those automatically extracted by Termine  from the COPD guidelines published jointly by the American Thoracic Society and the European Respiratory Society in 2004 . The resulting term list (provided as Additional file 1) contains 1,925 COPD phenotypes which were matched against the content of the initial set of 974 articles. In order to ensure that the documents in our corpus is representative of the widest possible range of COPD phenotypes, we ranked the documents according to decreasing number of their contained unique matches. We then selected the 30 top-ranked articles as the final document set for our corpus.
A simple yet expressive annotation scheme
The proposed typology for capturing COPD phenotypes
an overall category for any COPD indications of concern
any disease or medical condition; includes COPD comorbidities
emphysema, pulmonary vascular disease, asthma, congestive heart failure
a phenotype signifying a patient’s increased chances of having COPD
increased levels of the c-reactive protein, alpha1 antitrypsin deficiency
an observable irregularity manifested by a COPD patient
chronic cough, shortness of breath, purulent sputum production
a patient’s habits leading to susceptibility of having COPD
smoking for 25 years
findings based on COPD-relevant examinations
increased white blood cell counts, FEV1 45% predicted
any medication, therapy or program for treating COPD
oxygen therapy, pulmonary rehabilitation, pursed lips breathing
an overall category for any COPD-relevant examinations or measures/parameters
increased compliance of the lung, FEV1, FEV1/FVC ratio
any of the radiological tests for detecting COPD
computed tomography scanning, high resolution computed tomography
an examination of a COPD- relevant specimen
complete blood count
a measurement of a COPD patient’s capacity to exercise
6-min walking distance
Examples of phenotypic information represented using our proposed annotation scheme
Automatically recognized underlying concepts
Automatically linked ontological concepts
chronic airways obstruction
chronic airways obstruction
chronic (PATO:0001863) respiratory airway (UBERON:0001005) obstructed (PATO:0000648)
parenchyma (UBERON:0000353) damaged (PATO:0001167)
decrease in rate of lung function
decrease in rate lung function
decreased rate (PATO:0000911) lung (UBERON:0002048) function (PATO:0000173)
chronic bronchitis (DOID:6132)
myocardial infarction (DOID:5844)
enhanced response to inhaled corticosteroids
enhanced response to corticosteroids
enhanced (PATO:0001589) response to (PATO:0000077) corticosteroid (ChEBI:50858)
FEV1 45% predicted
Forced Expiratory Volume 1 Test (NCIT:C38084)
alpha1 antitrypsin deficiency
alpha1 antitrypsin deficiency
alpha-1-antitrypsin (PR:000014678) decreased amount (PATO:0001997)
We therefore propose an annotation methodology that strikes a balance between simplicity and granularity of annotations. On the one hand, our scheme renders the annotation task highly intuitive by asking for only simple text span selections, and not requiring the creation of relations nor the filling in of template slots. On the other hand, we also introduce granularity into the annotations by exploiting various semantic analytic tools, described in the next section, which automatically identify constituent ontological concepts. The contribution of applying automated concept identifiers is two-fold. Firstly, automatic concept identification as a pre-annotation step helps accelerate the manual annotation process by supplying visual cues to the annotators. For instance, the symptom expressed within text as increased resistance of the small airways becomes easier for an annotator to recognise, seeing that the elementary concepts resistance and airways have been pre-annotated. Secondly, as the constituent concepts will be linked to pertinent ontologies, the semantics of the expression signifying the symptom, which will be manually annotated as a simple text span, is nevertheless encoded in a fine-grained and computable manner. Shown in Table 2 are some examples of annotated phenotypes resulting from the application of our scheme.
Text mining-assisted annotation with Argo
Our proposed methodology employs a number of text analytics to realise its aims of reducing the manual effort required from annotators and providing granular computable annotations of COPD phenotypes. After analysing several documents, we established that treatments are often composed of drug names (e.g., Coumadin in Coumadin dosing) whilst problems typically contain mentions of diseases/medical conditions (e.g., myocardial infarction), anatomical concepts (e.g., airways in chronic airways obstruction), proteins (e.g., alpha1 antitrypsin in alpha1 antitrypsin deficiency), qualities (e.g., destruction in parenchymal destruction) and tests (e.g., FEV1 in FEV1 45% predicted). These observations, confirmed by COPD experts, guided us in selecting the automatic tools for recognising the above-mentioned types and for linking them to relevant ontologies.
Finally, the workflow’s last component, the XMI Writer, stores the annotated documents in the XML Metadata Interchange standard format, which allows us to reuse the output in other workflows if necessary. Eventually, the annotations can be made available in several other standard formats, such as RDF and BioC , which will be accomplished directly in Argo through its various serialisation components. We note that the automatic tool for recognising qualities is still under development, as are the components for linking mentions to concepts in ontologies. Nevertheless, we describe below our proposed strategy for ontological concept identification.
Linking phenotypic mentions to ontologies
In order to identify the ontological concepts underlying COPD phenotypic information, the mentions automatically annotated by our concept recognisers will be normalised to entries in various ontologies, namely, the Phenotype and Trait Ontology (PATO)  for qualities, Human Disease Ontology (DO)  for medical conditions, Uber Anatomy Ontology (UBERON)  for anatomical entities, Chemical Entities of Biological Interest (ChEBI)  for drugs, Protein Ontology (PRO)  for proteins and the National Cancer Institute Thesaurus (NCIT)  for tests/measures.
The NCBO Annotator , formerly Open Biomedical Annotator, offers a solution to this problem by employing a Web service that automatically matches text against specific ontologies. It is, however, not sufficient for the requirements of our task as it is very limited in terms of variant-matching , obtaining only exact string matches against terms and synonyms contained in ontologies. As observed from the examples in Table 2, there is a large variation in the expressions comprising COPD phenotypes. Consequently, many of these expressions do not exist in ontologies in the same form. More suitable, therefore, is a sophisticated normalisation method that takes into consideration morphological variations (e.g., alpha1 antitrypsin vs. alpha-1-antitrypsin), inflections (e.g., obstruction vs. obstructed), syntactic variations (e.g., decrease in rate vs. decreased rate) and synonym sets (e.g., deficiency vs. decreased amount and destruction vs. damage).
Results and discussion
Number of unique concepts for each type, based on the nine manually annotated articles
Number of unique concepts
Evaluation of annotations automatically generated by the text mining-assisted workflow against gold standard data
It is obviously more desirable for a semi-automatic workflow to approximate the gold standard annotations (i.e., to produce exact matches rather than partial ones). Nevertheless, Argo’s automatically generated annotations proved to be helpful in a number of cases. For example, the automatic workflow was able to correctly annotate partially correct annotations such as sputum (for sputum smear), pulmonary (for pulmonary TB) and COPD-staging (for COPD) served as visual cues to the annotator. Based on her experience in annotating our corpus, she feels that having pre-supplied annotations, albeit incomplete or incorrect, is preferable over not having any annotations at all. We are, however, aware of the potential bias that having pre-supplied annotations may bring about, i.e., failure to annotate concepts completely missed by automatic annotation due to reliance on visual cues. To avoid this scenario, the annotator has been asked to read all of the sentences thoroughly and to keep in mind that the cues are not to be relied on. She has adhered to this guideline throughout her annotations.
Results of 10-fold cross validation of concept recognisers, using exact matching
Concept recognisers currently in Argo
Concept recognisers trained on our corpus
Results of evaluation using a fixed split over 381 paragraphs (training set: 75% or 286 paragraphs; held-out set: 25% or 95 paragraphs), using exact matching
Concept recognisers currently in Argo
Concept recognisers trained on our corpus
We show that by using our gold standard annotations as training data, we were able to develop concept recognisers whose performance is drastically better than those we employed in our semi-automatic workflow. This significant improvement ranged from 24.84 (for AnatomicalConcept) to 40.43 (for TestOrMeasure) percentage points according to 10-fold cross validation, and from 19.49 (for AnatomicalConcept) to 40.45 (for TestOrMeasure) according to the fixed split evaluation. This implies that our corpus can stimulate the development of more suitable automatic COPD phenotype extractors. We expect that as more gold standard annotations become available to us (i.e., as our domain expert completes the validation of more documents in our corpus), the better equipped we will be in boosting the performance of our automatic COPD concept recognisers.
In this paper, we elucidate our proposed text mining-assisted methodology for the gold-standard annotation of COPD phenotypes in a corpus of full-text scientific articles. We demonstrate with the proposed scheme that the annotation task can be kept simple for curators whilst producing expressive and computable annotations. By constructing a semi-automatic annotation workflow in Argo, we seamlessly integrate and take advantage of several automatic NLP tools for the task. Furthermore, we are providing the domain experts with a highly intuitive interface for creating and manipulating annotations. The comparison of annotations automatically generated by the workflow against manually validated ones (i.e., gold standard) reveals an F-score of 45.70% using relaxed matching. New concept recognisers trained on these gold standard annotations demonstrate dramatically better performance (i.e., with a 20- to 30-percentage point margin in terms of F-scores) over the off-the-shelf components used in the Argo workflow.
Manual expert validation of the text mining-generated annotations on the remaining 21 papers in the corpus is still ongoing. In the meantime, we are enhancing our ontology concept linkers, which, once ready, will be applied on the gold standard concepts to enrich our corpus with computable annotations. Our expert collaborators are also working hard on obtaining a subset of clinical records from their hospital, which will then be used to augment our corpus. With the resulting resource, which will be made publicly available upon completion, we aim to support the development and evaluation of text mining systems that can ultimately be applied to evidence-based healthcare and clinical decision support systems.
The authors would like to thank Drs. Nawar Bakerly and Andrea Short of the Salford Royal NHS Foundation Trust and University of Manchester, who have provided their expertise on COPD to guide the clinical aspects of this work. Special mention goes to Andrea who has graciously contributed a significant amount of her time to provide us with annotations.
The first author is financially supported by the University of Manchester’s 2013 President's Doctoral Scholar Award. This work is also partially supported by the Medical Research Council (Supporting Evidence-based Public Health Interventions using Text Mining [Grant MR/L01078X/1]) and by the Defense Advanced Research Projects Agency (Big Mechanism [Grant DARPA-BAA-14-14]).
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