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Data Analysis and Knowledge Discovery  2018, Vol. 2 Issue (3): 79-86    DOI: 10.11925/infotech.2096-3467.2017.1047
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Using Text Mining to Discover Drug Side Effects: Case Study of PubMed
Fan Xinyue, Cui Lei()
School of Medical Informatics, China Medical University, Shenyang 110122, China
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Abstract  

[Objective] This paper finds the potential side effects of drugs with the help of text mining, aiming to improve the contents of existing databases and early prediction of drug side effects. [Methods] A total of 100, 873 articles were retrieved from the PubMed database for about five years (2011-2016). We generated the drug side effects co-occurrence matrix and conducted gCLUTO bi-clustering analysis with Perl’s segmentation technique, named entity recognition method based on the dictionary, as well as the R language. [Results] For one category of results, we found the precision rate of the proposed method reached 75.65%, and identified 13.91% potential side effects. [Limitations] Only used the dictionary-based named entity recognition method and did not consider grammatical or lexis factors, which yielded high false positive rates. [Conclusions] This paper proposes a new approach to detect the unannounced side effects of drugs automatically and effectively.
Key words： Drug-Side Effects      Text Mining      Named Entity Recognition      Cluster Analysis     
Received: 20 October 2017      Published: 03 April 2018
ZTFLH:  TP391 G353  
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Xinyue Fan
Lei Cui

Cite this article:

Fan Xinyue,Cui Lei. Using Text Mining to Discover Drug Side Effects: Case Study of PubMed. Data Analysis and Knowledge Discovery, 2018, 2(3): 79-86.

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https://manu44.magtech.com.cn/Jwk_infotech_wk3/EN/10.11925/infotech.2096-3467.2017.1047     OR     https://manu44.magtech.com.cn/Jwk_infotech_wk3/EN/Y2018/V2/I3/79

MeSH ID 药物MeSH词 药物款目词
D000935 Antifungal Agents Agents, Antifungal
Therapeutic Fungicides
Fungicides, Therapeutic
Antibiotics, Antifungal
Antifungal Antibiotics
D001569 Benzodiazepines Benzodiazepine Compounds
Benzodiazepine
D006493 Heparin Unfractionated Heparin
Heparin, Unfractionated
Heparinic Acid
Liquaemin
Sodium Heparin
Heparin, Sodium
Heparin Sodium
alpha-Heparin
alpha Heparin
… … …
PubMed MEDLINE SIDER
PMID: 24739449
TI
AB 1 Depression
AB 2
AB 3
AB 4
AB 5 Epilepsy
AB 6
AB 7
AB 8
AB 9
AB 10
AB 11
AB 12
PubMed MEDLINE Drug
PMID: 24739449
TI tianeptine
AB 1
AB 2
AB 3 tianeptine
AB 4 tianeptine
AB 5 tianeptine
AB 6 tianeptine
AB 7
AB 8
AB 9 tianeptine
AB 10 tianeptine
AB 11 tianeptine
AB 12 tianeptine
Lyme disease Polyps General Surgery Hypothermia
clarithromycin 1 0 0 0 …
ceftriaxone 1 0 0 0 …
doxycycline 1 0 0 0 …
erlotinib 0 1 0 0 …
thyroid 0 0 1 0 …
tyrosine 0 0 1 0 …
cabozantinib 0 0 1 0 …
morphine 0 0 1 1
Cluster 0 Pain Postoperative pain Rheumatism
disease		 Headache
ceftriaxone (+) (-) (-) (+)
hyaluronic acid — — — —
naloxone (-) (-) (-) (-)
fluconazole (+) (-) (-) (+)
ciclosporin (+) (-) (+) (+)
palonosetron (+) (-) (-) (+)
… … … … …
dinoprostone (+) (-) (-) (-)
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