Dataset Information

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

ABSTRACT: The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics.The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/.andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Prlic A

PROVIDER: S-EPMC5167066 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

Prlic Andreas A Kalro Tara T Bhattacharya Roshni R Christie Cole C Burley Stephen K SK Rose Peter W PW

Bioinformatics (Oxford, England) 20160822 24

The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while ...[more]

PMID: 27551105

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Project description:BACKGROUND: Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB). RESULTS: BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC) and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java). CONCLUSIONS: The integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our knowledge this is the first time that database and literature have been integrated in this way and it speaks to the opportunities afforded by open and free access to both database and literature content.

Dataset Information

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

Publications

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

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