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Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction.

Zhang Y, Soysal E, Moon S, Wang J, Tao C, Xu H - AMIA Jt Summits Transl Sci Proc (2015)

Bottom Line: LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase.Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%.Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book.

View Article: PubMed Central - PubMed

Affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

ABSTRACT
A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base.

No MeSH data available.


Venn diagrams of diseases, lab tests and relations extracted from LabTestsOnline, MedlinePlus and Wikipedia.
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Related In: Results  -  Collection


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f2-2094611: Venn diagrams of diseases, lab tests and relations extracted from LabTestsOnline, MedlinePlus and Wikipedia.

Mentions: Figure 2 illustrates the total numbers of diseases, lab tests and relations extracted from each resource and their overlaps. In total, 3,114 relation pairs consisting of 447 diseases and 300 lab tests were extracted from LabTestsOnline; 573 relation pairs consisting of 165 diseases and 193 lab tests were extracted from MedlinePlus; 2,023 relation pairs consisting of 604 diseases and 719 lab tests were extracted from Wikipedia. Examination of overlap among the three sources showed that 227 diseases, 238 lab tests, and 193 relations were extracted from at least two resources.


Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction.

Zhang Y, Soysal E, Moon S, Wang J, Tao C, Xu H - AMIA Jt Summits Transl Sci Proc (2015)

Venn diagrams of diseases, lab tests and relations extracted from LabTestsOnline, MedlinePlus and Wikipedia.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4525275&req=5

f2-2094611: Venn diagrams of diseases, lab tests and relations extracted from LabTestsOnline, MedlinePlus and Wikipedia.
Mentions: Figure 2 illustrates the total numbers of diseases, lab tests and relations extracted from each resource and their overlaps. In total, 3,114 relation pairs consisting of 447 diseases and 300 lab tests were extracted from LabTestsOnline; 573 relation pairs consisting of 165 diseases and 193 lab tests were extracted from MedlinePlus; 2,023 relation pairs consisting of 604 diseases and 719 lab tests were extracted from Wikipedia. Examination of overlap among the three sources showed that 227 diseases, 238 lab tests, and 193 relations were extracted from at least two resources.

Bottom Line: LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase.Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%.Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book.

View Article: PubMed Central - PubMed

Affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

ABSTRACT
A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base.

No MeSH data available.