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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.  ...  to a specific item of interest, for example published experimental results associated with a particular biological database entry.  ...  Jeff Milton, and Joe Mulvaney for assistance with system administration and installation of the PDB clone. Project funding was provided by National Science Foundation Award # 0544575.  ... 
doi:10.1093/nar/gkn317 pmid:18515836 pmcid:PMC2447735 fatcat:d2utaoxvzzaovelv3e6oqpswx4

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  
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.  ...  To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB).  ...  Background Biological databases and the biological literature have traditionally been distinct resources.  ... 
doi:10.1186/1471-2105-11-220 pmid:20429930 pmcid:PMC2880030 fatcat:3ci26fwsonblnlrcjxoyjz2wzm

Changes in Scholarly Communication and the Potential Impact on Biocuration

Philip Bourne
2009 Nature Precedings  
A composite view of journal and database content results • Biolit integrates biological literature and biological databases and includes: http://www.wwpdb.org http://biolit.ucsd.edu  ...  Copyright remains with the author So change is afoot… Hold that thought… At the same time think about the notion -is a biological database really that different from a biological journal?  ...  Enter PLoS iStructure … • Authoring starts with a PDB file • Annotated molecular views are added -the associated metadata defining those views is stored with the publication • Other data types can be validated  ... 
doi:10.1038/npre.2009.3229 fatcat:msh6kzk55fc6phgvntlbue4xxu

Changes in Scholarly Communication and the Potential Impact on Biocuration

Philip Bourne
2009 Nature Precedings  
A composite view of journal and database content results • Biolit integrates biological literature and biological databases and includes: http://www.wwpdb.org http://biolit.ucsd.edu  ...  Copyright remains with the author So change is afoot… Hold that thought… At the same time think about the notion -is a biological database really that different from a biological journal?  ...  Enter PLoS iStructure … • Authoring starts with a PDB file • Annotated molecular views are added -the associated metadata defining those views is stored with the publication • Other data types can be validated  ... 
doi:10.1038/npre.2009.3229.1 fatcat:dlgevrecljcbxpp6s46iylrpla

Other Structure-Based Databases [chapter]

Helge Weissig, Philip E. Bourne
2005 Methods of biochemical analysis  
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.  ...  Crossreferences to biological databases will also be detected and added to the metadata, allowing the manuscript content to be more easily integrated with the database.  ... 
doi:10.1002/0471721204.ch11 fatcat:wxuduryxofep7fpbp7zwlwesp4

Database Citation in Full Text Biomedical Articles

Şenay Kafkas, Jee-Hyub Kim, Johanna R. McEntyre, Vincent Larivière
2013 PLoS ONE  
Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records.  ...  Molecular biology and literature databases represent essential infrastructure for life science research.  ...  Acknowledgments We would like to thank the Rebholz research group at the EBI (2003-2012) for developing the Whatizit service, the EBI Literature Services Group for the development of many of the core data  ... 
doi:10.1371/journal.pone.0063184 pmid:23734176 pmcid:PMC3667078 fatcat:cix3dhrmw5f3ppwk5s5yrojwr4

Calling International Rescue: knowledge lost in literature and data landslide!

Teresa K. Attwood, Douglas B. Kell, Philip McDermott, James Marsh, Steve R. Pettifer, David Thorne
2009 Biochemical Journal  
PubMed Central and BioLit BioLit is a suite of open-source tools designed to integrate open literature with biological databases [55] .  ...  Unfortunately, however, we have no way of knowing what the error rates in the literature or in biological databases actually are, or indeed what are the rates of propagation of those errors between databases  ... 
doi:10.1042/bj20091474 pmid:19929850 pmcid:PMC2805925 fatcat:7it5axfto5dbnlisys73ejhixy

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  
Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task.  ...  Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central.  ...  It provided an enhanced version of full-text articles by integrating clickable links to PDB and Gene Ontology within the full-text of articles accessible from the BioLit portal (26) .  ... 
doi:10.1093/database/bas026 pmid:22685160 pmcid:PMC3371192 fatcat:tahqnxaktbg4di25weof2a57ea

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  
of structural 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.  ...  tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration  ...  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

BioTextQuest + : a knowledge integration platform for literature mining and concept discovery

Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos
2014 Computer applications in the biosciences : CABIOS  
growth of scientific corpora and the plethora of tools designed to mine PubMed V R and related biological databases.  ...  , functional annotation, document clustering and data integration towards literature mining and concept discovery.  ...  analysis as well as integration with a rich collection of biological databases and automated bioinformatics analysis.  ... 
doi:10.1093/bioinformatics/btu524 pmid:25100685 fatcat:gyf7y7qvxfbb5maq4ofsrrh25a

Semantic Web meets Integrative Biology: a survey

H. Chen, T. Yu, J. Y. Chen
2012 Briefings in Bioinformatics  
Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels.  ...  We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration  ...  For example, BioLit is a Web server that integrates biological literature with databases, by generating semantic annotations for the open access documents [76] .  ... 
doi:10.1093/bib/bbs014 pmid:22492191 fatcat:n5xm5kbc75ethlnfwfmgwdtnhq

Utopia documents: linking scholarly literature with research data

T. K. Attwood, D. B. Kell, P. McDermott, J. Marsh, S. R. Pettifer, D. Thorne
2010 Bioinformatics  
A different approach was taken with BioLit (Fink et al., 2008) , an open-source system that integrates a subset of papers from PubMed Central with structural data from the Protein Data Bank (PDB) (Kouranov  ...  Utopia Documents brings us a step closer to integrated scholarly literature and research data.  ... 
doi:10.1093/bioinformatics/btq383 pmid:20823323 pmcid:PMC2935404 fatcat:6g5dto5pqfetbordnwmukpyymi

Dpaper: An Authoring Tool for Extractable Digital Papers

Xiaoqiu Le, Xiaoqiu Le, Chenyu Mao, Yuanbiao He, Changlei Fu & Liyuan Xu, Chenyu Mao, Yuanbiao He, Changlei Fu & Liyuan Xu
2016 Journal of Data and Information Science  
The PhD papers are represented as Web pages and structured XML files, which are marked with semantic tags.  ...  Purpose: To develop a structured, rich media digital paper authoring tool with an objectbased model that enables interactive, playable, and convertible functions.  ...  The tool is supposed to facilitate the integration of the open literature and biological data (Fink & Bourne, 2007) .  ... 
doi:10.20309/jdis.201607 fatcat:mn2iwxxthbebnj34us5i5wfe3e

Citing a Data Repository: A Case Study of the Protein Data Bank

Yi-Hung Huang, Peter W. Rose, Chun-Nan Hsu, Tingting Li
2015 PLoS ONE  
Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations.  ...  A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text.  ...  BioLit [20] provided a comprehensive view on the literature data that links to biomedical databases by integrating the content of PubMed Central (PMC) with that of the PDB repository, based on the text-mining  ... 
doi:10.1371/journal.pone.0136631 pmid:26317409 pmcid:PMC4552849 fatcat:6ld5uhbpznfvtibmvdlbssw43m

Using open access literature to guide full-text query formulation

Heather Piwowar, Heather Piwowar, Wendy Chapman
2010 Nature Precedings  
We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched.  ...  Much scientific knowledge is contained in the details of the full-text biomedical literature.  ...  Domain-specific biomedical NLP and data integration systems, such as Textpresso , Pharmspresso , BioText , and BioLit , illustrate the potential value of accessing, exploring, and analyzing full-text,  ... 
doi:10.1038/npre.2010.4267.1 fatcat:p7cgyhz7arbwfibfhmwklsgs74
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