title: Standardized representations of the literature: combining diverse sources of ribosomal data.
abstract: We are building a knowledge base (KB) of published structural data on the 30s ribosomal subunit in prokaryotes. Our KB is distinguished by a standardized representation of biological experiments and their results, in a reusable format. It can be accessed by computer programs that exploit the rich interconnections within the data. The KB is designed to support the construction of 3D models of the 30S subunit, as well as the analysis and extension of relevant functional and phylogenetic information. Most published information about the structure of the ubiquitous ribosome focuses on E. coli as a model system. At the same time, thousands of RNA sequences for the ribosome have been gathered and cataloged. The volume and complexity of these data can complicate attempts to separate structural data peculiar to E. coli from data of universal relevance. We have written an application that dynamically queries the KB and the Ribosome Database Project, a repository of ribosomal RNA sequences from other organisms, in order to assess the relevance of structural data to particular organisms. The application uses the RDP alignment to determine whether a set of data refer primarily to conserved, mismatched, or gapped positions. For a set of 16 representative articles evaluated over 211 sequences, 73% of observations have unambiguous translations from E. coli to the other organisms, 21% have somewhat ambiguous translations, and 6% have no translations. There is a wide variation in these numbers over different articles and organisms, confirming that some articles report structural information specific to E. coli while others report information that is quite general.
authors.affiliation: Stanford Section on Medical Informatics, SUMC, CA 94305-5479, USA. rba@smi.stanford.edu
authors.forename: R B
authors.initials: RB
authors.lastname: Altman
authors.forename: N F
authors.initials: NF
authors.lastname: Abernethy
authors.forename: R O
authors.initials: RO
authors.lastname: Chen
mesh_terms: D001185:Artificial Intelligence; D001483:Base Sequence; D003195:Computer Communication Networks; D003196:Computer Graphics; D016208:Databases, Factual; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011387:Prokaryotic Cells; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S