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Biomedical question answering using semantic relations.

Hristovski D, Dinevski D, Kastrin A, Rindflesch TC - BMC Bioinformatics (2015)

Bottom Line: The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions.A typical question is answered within a few seconds.The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

View Article: PubMed Central - PubMed

Affiliation: Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1104, Ljubljana, Slovenia. dimitar.hristovski@mf.uni-lj.si.

ABSTRACT

Background: The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature.

Results: We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si ). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%).

Conclusions: In this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

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The first few instances of the semantic relation “Donepezil-TREATS-Alzheimer’s disease” shown as highlighted sentences.
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Fig3: The first few instances of the semantic relation “Donepezil-TREATS-Alzheimer’s disease” shown as highlighted sentences.

Mentions: In the question processing phase the question entered by the user is interpreted depending on user-selected options; then it is executed. Answers are presented in a top-down fashion, semantic relations first, then, on demand, semantic relation instances, and finally, MEDLINE citations. In Figures 2 and 3 in the lower right is the list of semantic relations, which are presented first. In addition to the subject, relation and object fields, the table also contains a “Frequency” field which is the number of instances of each relation in the table. The relations in the answer list are sorted by frequency of descending relation instance. In other words, the most frequent relation is at the top of the list.Figure 3


Biomedical question answering using semantic relations.

Hristovski D, Dinevski D, Kastrin A, Rindflesch TC - BMC Bioinformatics (2015)

The first few instances of the semantic relation “Donepezil-TREATS-Alzheimer’s disease” shown as highlighted sentences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307891&req=5

Fig3: The first few instances of the semantic relation “Donepezil-TREATS-Alzheimer’s disease” shown as highlighted sentences.
Mentions: In the question processing phase the question entered by the user is interpreted depending on user-selected options; then it is executed. Answers are presented in a top-down fashion, semantic relations first, then, on demand, semantic relation instances, and finally, MEDLINE citations. In Figures 2 and 3 in the lower right is the list of semantic relations, which are presented first. In addition to the subject, relation and object fields, the table also contains a “Frequency” field which is the number of instances of each relation in the table. The relations in the answer list are sorted by frequency of descending relation instance. In other words, the most frequent relation is at the top of the list.Figure 3

Bottom Line: The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions.A typical question is answered within a few seconds.The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

View Article: PubMed Central - PubMed

Affiliation: Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1104, Ljubljana, Slovenia. dimitar.hristovski@mf.uni-lj.si.

ABSTRACT

Background: The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature.

Results: We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si ). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%).

Conclusions: In this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

Show MeSH