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http://dx.doi.org/10.5808/gi.21016

Visualizing the phenotype diversity: a case study of Alexander disease  

Dohi, Eisuke (Department of Neuroscience of Disease, Brain Research Institute, Niigata University)
Bangash, Ali Haider (Shifa College of Medicine, Shifa Tameer-e-Millat University)
Abstract
Since only a small number of patients have a rare disease, it is difficult to identify all of the features of these diseases. This is especially true for patients uncommonly presenting with rare diseases. It can also be difficult for the patient, their families, and even clinicians to know which one of a number of disease phenotypes the patient is exhibiting. To address this issue, during Biomedical Linked Annotation Hackathon 7 (BLAH7), we tried to extract Alexander disease patient data in Portable Document Format. We then visualized the phenotypic diversity of those Alexander disease patients with uncommon presentations. This led to us identifying several issues that we need to overcome in our future work.
Keywords
annotation; biomedical text mining; case reports; phenotype; rare diseases; symptoms;
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1 Faviez C, Chen X, Garcelon N, Neuraz A, Knebelmann B, Salomon R, et al. Diagnosis support systems for rare diseases: a scoping review. Orphanet J Rare Dis 2020;15:94.   DOI
2 Fujiwara T, Yamamoto Y, Kim JD, Buske O, Takagi T. PubCaseFinder: a case-report-based, phenotype-driven differential-diangnosis system for rare diseases. Am J Hum Genet 2018;103:389-399.   DOI
3 Srivastava S, Waldman A, Naidu S. Alexander disease. GeneReviews. Seattle: University of Washington, 1993-2021. Accessed 2021 Jan 20. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1172/.
4 MeSH Browser. Bethesda: National Library of Medicine, 2021. Accessed 2021 Mar 11. Available from: https://meshb.nlm.nih.gov/search.
5 Advanced Search Results - PubMed. Bethesda: National Library of Medicine, 2021. Accessed 2021 Mar 11. Available from: https://pubmed.ncbi.nlm.nih.gov/advanced.
6 Apowersoft PDF converter. Hong Kong: Wangxu Ltd., 2021.
7 PubAnnotation. Bethesda: Database Center for Life Science, 2021. Accessed 2021 Mar 11. Available from: https://pubannotation.org/.
8 Pubdictionaries. Kashiwa: Database Center for Life Science, 2021. Accessed 2021 Mar 11. Available from: http://pubdictionaries.org/.
9 Funk C, Baumgartner W Jr, Garcia B, Roeder C, Bada M, Cohen KB, et al. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics 2014;15:59.   DOI
10 Barkovich AJ, Messing A. Alexander disease: not just a leukodystrophy anymore. Neurology 2006;66:468-469.   DOI
11 Bast H, Korzen C. A benchmark and evaluation for text extraction from PDF. In: ACM/IEEE Joint Conference on Digital Libraries (JCDL), 2017 Jun 19-23, Toronto, ON, Canada.