title: BIOSPIDA: A Relational Database Translator for NCBI.
abstract: As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.
authors.affiliation: Center for Operations Research in Medicine and HealthCare.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Hagen
authors.forename: Eva K
authors.initials: EK
authors.lastname: Lee
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D015870:Gene Expression; D009317:National Library of Medicine (U.S.); D039781:PubMed; D012984:Software; D014481:United States