SALON ontology for the formal description of sequence alignments

BMC Bioinformatics

Research

José F. Aldana-Montes¹  Antonio Benítez-Hidalgo¹  María del Mar Roldán-García¹  Ismael Navas-Delgado¹ 

[1] Departamento de Lenguajes y Ciencias de la Computación, University of Málaga, Málaga, Spain;University of Málaga, ITIS Software, Ada Byron Research Building, Málaga, Spain;Instituto de Investigación Biomédica de Málaga – IBIMA, Málaga, Spain;

关键词: Sequence alignment;    Ontology;    Linked data;    Data integration;    Semantic web;   

DOI  :  10.1186/s12859-023-05190-7

 received in 2021-03-16, accepted in 2023-02-15,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundInformation provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identifying regions of similarity in DNA, RNA, or protein sequences. However, there is no consensus about the specific common terminology and representation for sequence alignments. Thus, automatically linking the wide existing knowledge about the sequences with the alignments is challenging.ResultsThe Sequence Alignment Ontology (SALON) defines a helpful vocabulary for representing and semantically annotating pairwise and multiple sequence alignments. SALON is an OWL 2 ontology that supports automated reasoning for alignments validation and retrieving complementary information from public databases under the Open Linked Data approach. This will reduce the effort needed by scientists to interpret the sequence alignment results.ConclusionsSALON defines a full range of controlled terminology in the domain of sequence alignments. It can be used as a mediated schema to integrate data from different sources and validate acquired knowledge.

【 授权许可】

CC BY   
© The Author(s) 2023

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