PMID- 30195820
OWN - NLM
STAT- MEDLINE
DCOM- 20190925
LR  - 20190925
IS  - 1879-0534 (Electronic)
IS  - 0010-4825 (Linking)
VI  - 101
DP  - 2018 Oct 1
TI  - Disease Specific Ontology of Adverse Events: Ontology extension and adaptation 
      for Chronic Kidney Disease.
PG  - 210-217
LID - S0010-4825(18)30250-6 [pii]
LID - 10.1016/j.compbiomed.2018.08.024 [doi]
AB  - BACKGROUND: Adverse Event (AE) ontology can be used to support interoperability 
      and computer-assisted reasoning of AEs. Despite significant progress in 
      developing biomedical ontologies, they are facing the obstacle of adoption partly 
      because those ontologies are too general to meet the requirements of a specific 
      domain. Understanding and representing of AEs for a specific domain such as 
      Chronic Kidney Disease (CKD) has both theoretical and clinical significance. CKD 
      patients are at a high risk for an array of disease-intervention specific AEs, 
      and these in turn can contribute to disease progression unlike other diseases. 
      This study proposes Disease Specific Ontology of Adverse Events (DSOAE) to 
      address specific requirements of CKD, and applies it to different usage scenarios 
      with real data. METHODS: We introduce a method for developing DSOAE through the 
      extension and adaption of general ontologies by incorporating domain-specific 
      information and usage requirements. It starts with specifying the goal and scope 
      of a target domain (i.e. selecting seed ontologies), followed by identifying main 
      AE classes and relations, extracting and creating classes and relations, aligning 
      and identifying upper-level classes and lower-level classes, and finally 
      populating the ontology with instances. Any of these steps may be repeated to 
      refine the ontology. RESULTS: DSOAE contains 22 CKD-specific AE classes, which 
      are grouped into two general categories: patient-reported AEs and 
      biochemical/laboratory-related AEs. In addition, disease history and comorbidity 
      classes as introduced in this study help model patient-related risk factors for 
      AEs. With the support of DSOAE, we build a knowledge base of CKD-specific AEs 
      using data from different sources (e.g. patient cohort data and social media), 
      and apply the knowledge base to data analysis and data integration. CONCLUSIONS: 
      DSOAE enables the interoperability of AEs across different sources and supports 
      the development of a knowledge base of domain-specific AEs. DSOAE can also meet 
      the needs of different usage scenarios. The approach to constructing DSOAE is 
      generalizable and can be used to develop AE ontology in other domains.
CI  - Copyright (c) 2018. Published by Elsevier Ltd.
FAU - Kang, Yin
AU  - Kang Y
AD  - Department of Information Systems, University of Maryland, Baltimore County, 1000 
      Hilltop Circle, Baltimore, MD, 21250, USA. Electronic address: ky6@umbc.edu.
FAU - Fink, Jeffrey C
AU  - Fink JC
AD  - Department of Medicine, University of Maryland, Baltimore, 22 S Greene St 
      Baltimore, MD, 21201, USA. Electronic address: Jfink@medicine.umaryland.edu.
FAU - Doerfler, Rebecca
AU  - Doerfler R
AD  - Department of Medicine, University of Maryland, Baltimore, 22 S Greene St 
      Baltimore, MD, 21201, USA. Electronic address: rdoerfler@medicine.umaryland.edu.
FAU - Zhou, Lina
AU  - Zhou L
AD  - Business Information Systems and Operations Management, The University of North 
      Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. 
      Electronic address: lzhou8@uncc.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20180828
PL  - United States
TA  - Comput Biol Med
JT  - Computers in biology and medicine
JID - 1250250
SB  - IM
MH  - *Artificial Intelligence
MH  - *Biological Ontologies
MH  - Female
MH  - Humans
MH  - Male
MH  - *Models, Biological
MH  - *Renal Insufficiency, Chronic/pathology/physiopathology/therapy
OTO - NOTNLM
OT  - Adverse event ontology
OT  - Chronic kidney disease
OT  - Disease specific adverse event
OT  - Ontology extension and adaptation
EDAT- 2018/09/10 06:00
MHDA- 2019/09/26 06:00
CRDT- 2018/09/10 06:00
PHST- 2018/04/11 00:00 [received]
PHST- 2018/08/22 00:00 [revised]
PHST- 2018/08/22 00:00 [accepted]
PHST- 2018/09/10 06:00 [pubmed]
PHST- 2019/09/26 06:00 [medline]
PHST- 2018/09/10 06:00 [entrez]
AID - S0010-4825(18)30250-6 [pii]
AID - 10.1016/j.compbiomed.2018.08.024 [doi]
PST - ppublish
SO  - Comput Biol Med. 2018 Oct 1;101:210-217. doi: 10.1016/j.compbiomed.2018.08.024. 
      Epub 2018 Aug 28.