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Integration of open access literature into the RCSB Protein Data Bank using BioLit

Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne, J Lynn Fink
2010 BMC Bioinformatics  
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.  ...  Acknowledgements We gratefully acknowledge all scientists who openly share their data in public  ... 
doi:10.1186/1471-2105-11-220 pmid:20429930 pmcid:PMC2880030 fatcat:3ci26fwsonblnlrcjxoyjz2wzm

BioLit: integrating biological literature with databases

J. L. Fink, S. Kushch, P. R. Williams, P. E. Bourne
2008 Nucleic Acids Research  
As an example of a possible use of BioLit, we also present an instance of the Protein Data Bank fully integrated with BioLit data.  ...  BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed  ...  Funding to pay the Open Access publication charges for this article was provided by National Science Foundation Award #0544575. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn317 pmid:18515836 pmcid:PMC2447735 fatcat:d2utaoxvzzaovelv3e6oqpswx4

The RCSB Protein Data Bank: redesigned web site and web services

P. W. Rose, B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich (+3 others)
2010 Nucleic Acids Research  
data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources.  ...  The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base.  ...  Michael Gilson and Tiquing Liu at UCSD worked with us on the integration with BindingDB.  ... 
doi:10.1093/nar/gkq1021 pmid:21036868 pmcid:PMC3013649 fatcat:aciwaivaenfubmhs2r3tc37qiu

Open Access: Taking Full Advantage of the Content

Philip E. Bourne, J. Lynn Fink, Mark Gerstein
2008 PLoS Computational Biology  
This opens up the possibility of integrating database and literature content, which is one goal of BioLit, using the PLoS corpus and the RCSB Protein Data Bank (PDB; http://www.pdb.org) as a test bed.  ...  The key idea is manipulation of article text as ''data'' and integration of articles with other bioinformatics information resources.  ... 
doi:10.1371/journal.pcbi.1000037 pmid:18369428 pmcid:PMC2275780 fatcat:2ld3gmedyvfvrm7pn6romemfji

Other Structure-Based Databases [chapter]

Helge Weissig, Philip E. Bourne
2005 Methods of biochemical analysis  
PDB validation server Validate the format and content of a PDB entry using the same software procedures as used by the PDB.  ...  Part of the Whatif package. http://www.cmbi.kun.nl/gv/whatcheck/ SFCheck Validate the experimental structure factors associated with an X-ray diffraction experiment (Vaguine et al., 1999).  ...  A new effort, the BioLit project, aims to obviate the need for this human curation step by integrating the open access literature and biological data.  ... 
doi:10.1002/0471721204.ch11 fatcat:wxuduryxofep7fpbp7zwlwesp4

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2012 Database: The Journal of Biological Databases and Curation  
Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates.  ...  High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze  ...  Acknowledgements The authors thank the GEO and MEDLINE curators for helpful discussions on curation practices and data processing.  ... 
doi:10.1093/database/bas026 pmid:22685160 pmcid:PMC3371192 fatcat:tahqnxaktbg4di25weof2a57ea