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Context-based resolution of semantic conflicts in biological pathways

Authors
 Seyeol Yoon  ;  Jinmyung Jung  ;  Hasun Yu  ;  Mijin Kwon  ;  Sungji Choo  ;  Kyunghyun Park  ;  Dongjin Jang  ;  Sangwoo Kim  ;  Doheon Lee 
Citation
 BMC MEDICAL INFORMATICS AND DECISION MAKING, Vol.15(Suppl1) : 3, 2015 
Journal Title
 BMC MEDICAL INFORMATICS AND DECISION MAKING 
Issue Date
2015
MeSH
Animals ; Biochemical Phenomena* ; Data Mining ; Databases, Factual/standards* ; Humans ; Medical Informatics/methods* ; Natural Language Processing ; Semantics*
Keywords
Pituitary Adenoma ; Acromegaly ; Context Information ; Biomedical Literature ; Pathway Database
Abstract
BACKGROUND: Interactions between biological entities such as genes, proteins and metabolites, so called pathways, are key features to understand molecular mechanisms of life. As pathway information is being accumulated rapidly through various knowledge resources, there are growing interests in maintaining the integrity of the heterogeneous databases. METHODS: Here, we defined conflict as a status where two contradictory pieces of evidence (i.e. 'A increases B' and 'A decreases B') coexist in a same pathway. This conflict damages unity so that inference of simulation on the integrated pathway network might be unreliable. We defined rule and rule group. A rule consists of interaction of two entities, meta-relation (increase or decrease), and contexts terms about tissue specificity or environmental conditions. The rules, which have the same interaction, are grouped into a rule group. If the rules don't have a unanimous meta-relation, the rule group and the rules are judged as being conflicting. RESULTS: This analysis revealed that almost 20% of known interactions suffer from conflicting information and conflicting information occurred much more frequently in the literature than the public database. CONCLUSIONS: By identifying and resolving the conflicts, we expect that pathway databases can be cleaned and used for better secondary analyses such as gene/protein annotation, network dynamics and qualitative/quantitative simulation.
Files in This Item:
T201501680.pdf Download
DOI
10.1186/1472-6947-15-S1-S3
Appears in Collections:
1. College of Medicine (의과대학) > BioMedical Science Institute (의생명과학부) > 1. Journal Papers
Yonsei Authors
Kim, Sangwoo(김상우) ORCID logo https://orcid.org/0000-0001-5356-0827
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/140247
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