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| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Wang, Yipei Fan, Xingyu Chen, Luoxin Chang, Eric I-Chao Ananiadou, Sophia Tsujii, Junichi Xu, Yan |
| Abstract | * Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human body parts are crucial for building medical text mining applications. To achieve this, we establish a mapping system consisting of a Wikipedia-based scoring algorithm and a named entity normalization method (NEN). The mapping system makes full use of information available on Wikipedia, which is a comprehensive Internet medical knowledge base. We also built a new ontology, Tree of Human Body Parts (THBP), from core anatomical parts by referring to anatomical experts and Unified Medical Language Systems (UMLS) to make the mapping system efficacious for clinical treatments. * Result The gold standard is derived from 50 discharge summaries from our previous work, in which 2,224 anatomical entities are included. The F1-measure of the baseline system is 70.20%, while our algorithm based on Wikipedia achieves 86.67% with the assistance of NEN. * Conclusions We construct a framework to map anatomical entities to THBP ontology using normalization and a scoring algorithm based on Wikipedia. The proposed framework is proven to be much more effective and efficient than the main baseline system. |
| Related Links | https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-3005-0.pdf |
| Ending Page | 11 |
| Page Count | 11 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 14712105 |
| DOI | 10.1186/s12859-019-3005-0 |
| Journal | BMC Bioinformatics |
| Issue Number | 1 |
| Volume Number | 20 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2019-08-17 |
| Access Restriction | Open |
| Subject Keyword | Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Natural language processing Anatomical entity Human body parts Named entity normalization Wikipedia Computational Biology/Bioinformatics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology |
| Journal Impact Factor | 2.9/2023 |
| 5-Year Journal Impact Factor | 3.6/2023 |
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