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KneeTex: an ontology-driven system for information extraction from MRI reports.

Spasić I, Zhao B, Jones CB, Button K - J Biomed Semantics (2015)

Bottom Line: Therefore, clinical narratives found in MRI reports convey valuable diagnostic information.Information extraction results were evaluated on a test set of 100 MRI reports.As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK.

ABSTRACT

Background: In the realm of knee pathology, magnetic resonance imaging (MRI) has the advantage of visualising all structures within the knee joint, which makes it a valuable tool for increasing diagnostic accuracy and planning surgical treatments. Therefore, clinical narratives found in MRI reports convey valuable diagnostic information. A range of studies have proven the feasibility of natural language processing for information extraction from clinical narratives. However, no study focused specifically on MRI reports in relation to knee pathology, possibly due to the complexity of knee anatomy and a wide range of conditions that may be associated with different anatomical entities. In this paper we describe KneeTex, an information extraction system that operates in this domain.

Methods: As an ontology-driven information extraction system, KneeTex makes active use of an ontology to strongly guide and constrain text analysis. We used automatic term recognition to facilitate the development of a domain-specific ontology with sufficient detail and coverage for text mining applications. In combination with the ontology, high regularity of the sublanguage used in knee MRI reports allowed us to model its processing by a set of sophisticated lexico-semantic rules with minimal syntactic analysis. The main processing steps involve named entity recognition combined with coordination, enumeration, ambiguity and co-reference resolution, followed by text segmentation. Ontology-based semantic typing is then used to drive the template filling process.

Results: We adopted an existing ontology, TRAK (Taxonomy for RehAbilitation of Knee conditions), for use within KneeTex. The original TRAK ontology expanded from 1,292 concepts, 1,720 synonyms and 518 relationship instances to 1,621 concepts, 2,550 synonyms and 560 relationship instances. This provided KneeTex with a very fine-grained lexico-semantic knowledge base, which is highly attuned to the given sublanguage. Information extraction results were evaluated on a test set of 100 MRI reports. A gold standard consisted of 1,259 filled template records with the following slots: finding, finding qualifier, negation, certainty, anatomy and anatomy qualifier. KneeTex extracted information with precision of 98.00 %, recall of 97.63 % and F-measure of 97.81 %, the values of which are in line with human-like performance.

Conclusions: KneeTex is an open-source, stand-alone application for information extraction from narrative reports that describe an MRI scan of the knee. Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects. The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions. As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions.

No MeSH data available.


Related in: MedlinePlus

A manually annotated MRI report. A screenshot of the BRAT interface
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Fig2: A manually annotated MRI report. A screenshot of the BRAT interface

Mentions: For training and testing purposes, the data were manually annotated with labels that correspond to slots and their relationships from the IE template (see Fig. 1). The annotation was performed using BRAT, a web–based tool for text annotation [32]. The process involved annotating text spans with slot names (e.g. finding or anatomy) as well as annotating dependencies between them (e.g. observed_in). Figure 2 provides a visualisation of an annotated example. A total of 100 training documents and 100 testing documents were annotated independently by two annotators.Fig. 2


KneeTex: an ontology-driven system for information extraction from MRI reports.

Spasić I, Zhao B, Jones CB, Button K - J Biomed Semantics (2015)

A manually annotated MRI report. A screenshot of the BRAT interface
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4561435&req=5

Fig2: A manually annotated MRI report. A screenshot of the BRAT interface
Mentions: For training and testing purposes, the data were manually annotated with labels that correspond to slots and their relationships from the IE template (see Fig. 1). The annotation was performed using BRAT, a web–based tool for text annotation [32]. The process involved annotating text spans with slot names (e.g. finding or anatomy) as well as annotating dependencies between them (e.g. observed_in). Figure 2 provides a visualisation of an annotated example. A total of 100 training documents and 100 testing documents were annotated independently by two annotators.Fig. 2

Bottom Line: Therefore, clinical narratives found in MRI reports convey valuable diagnostic information.Information extraction results were evaluated on a test set of 100 MRI reports.As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK.

ABSTRACT

Background: In the realm of knee pathology, magnetic resonance imaging (MRI) has the advantage of visualising all structures within the knee joint, which makes it a valuable tool for increasing diagnostic accuracy and planning surgical treatments. Therefore, clinical narratives found in MRI reports convey valuable diagnostic information. A range of studies have proven the feasibility of natural language processing for information extraction from clinical narratives. However, no study focused specifically on MRI reports in relation to knee pathology, possibly due to the complexity of knee anatomy and a wide range of conditions that may be associated with different anatomical entities. In this paper we describe KneeTex, an information extraction system that operates in this domain.

Methods: As an ontology-driven information extraction system, KneeTex makes active use of an ontology to strongly guide and constrain text analysis. We used automatic term recognition to facilitate the development of a domain-specific ontology with sufficient detail and coverage for text mining applications. In combination with the ontology, high regularity of the sublanguage used in knee MRI reports allowed us to model its processing by a set of sophisticated lexico-semantic rules with minimal syntactic analysis. The main processing steps involve named entity recognition combined with coordination, enumeration, ambiguity and co-reference resolution, followed by text segmentation. Ontology-based semantic typing is then used to drive the template filling process.

Results: We adopted an existing ontology, TRAK (Taxonomy for RehAbilitation of Knee conditions), for use within KneeTex. The original TRAK ontology expanded from 1,292 concepts, 1,720 synonyms and 518 relationship instances to 1,621 concepts, 2,550 synonyms and 560 relationship instances. This provided KneeTex with a very fine-grained lexico-semantic knowledge base, which is highly attuned to the given sublanguage. Information extraction results were evaluated on a test set of 100 MRI reports. A gold standard consisted of 1,259 filled template records with the following slots: finding, finding qualifier, negation, certainty, anatomy and anatomy qualifier. KneeTex extracted information with precision of 98.00 %, recall of 97.63 % and F-measure of 97.81 %, the values of which are in line with human-like performance.

Conclusions: KneeTex is an open-source, stand-alone application for information extraction from narrative reports that describe an MRI scan of the knee. Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects. The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions. As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions.

No MeSH data available.


Related in: MedlinePlus