NDLI: Automatic biosystems comparison using semantic and name similarity

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Automatic biosystems comparison using semantic and name similarity

Content Provider	ACM Digital Library
Author	Lushbough, Carol M. Thavappiragasam, Mathialakan Gnimpieba, Etienne Z.
Abstract	With the growth of bio-systems model development, automatic approaches are needed to support systems biologists in model similarity evaluation. Several algorithms have been proposed, but they lack efficiency. We have developed an efficient, intuitive approach using name and semantic similarity checking. Individual components in two given SBML models are compared by their names using ParaABioS (a heuristic Parallelizable Algorithm for Similarity Based Biosystems Comparison) and by their meaning using annotated URI (Unified Resource Identifier). We developed a tool SMBLcompare, an implementation of this approach for automatic bio-systems model comparison in SBML format. This implementation has been embedded into a web portal for small biosystems comparison and also integrated into the Bioextract Server (bioextract.org) in order to be able to use within workflows designed to address escience challenges. SBMLcompare has been successfully used on FOCM (Folate One Carbon Metabolite) models and two genome-scale yeast metabolic models iND750, iFF708. The similarity result showed a significant improvement compared to existing related work (over 10%).
Starting Page	790
Ending Page	796
Page Count	7
File Format	PDF
ISBN	9781450328944
DOI	10.1145/2649387.2660850
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Bio systems Similar models Annotated bio element Workflow Hpc Escience Metabolite naming
Content Type	Text
Resource Type	Article

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