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Impact of the Protein Data Bank Across Scientific Disciplines

Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki
2020 Data Science Journal  
The Protein Data Bank archive (PDB) was established in 1971 as the 1st open access digital data resource for biology and medicine.  ...  Our analysis highlights frequently-cited structures and identifies milestone structures that have demonstrated impact across scientific fields.  ...  RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
doi:10.5334/dsj-2020-025 fatcat:2ahclmqdmbaddmvhr6sj4nonma

Effect of Impact Factor and Discipline on Journal Data Sharing Policies

David B Resnik, Melissa Morales, Rachel Landrum, Min Shi, Jessica Minnier, Nicole A. Vasilevsky, Robin E. Champieux
2019 Accountability in Research  
Both Impact Factors and discipline are associated with the presence of a data sharing policy.  ...  In this study, we extended previous work to analyze the data sharing policies of 447 journals across several scientific disciplines, including biology, clinical sciences, mathematics, physics, and social  ...  It does not represent the views of the NIEHS, NIH, or U.S. government.  ... 
doi:10.1080/08989621.2019.1591277 pmid:30841755 pmcid:PMC6533124 fatcat:symxmucypvdybdtm7wtpo7qvua

Analysis of impact metrics for the Protein Data Bank

Christopher Markosian, Luigi Di Costanzo, Monica Sekharan, Chenghua Shao, Stephen K. Burley, Christine Zardecki
2018 Scientific Data  
PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics.  ...  Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules.  ...  We gratefully acknowledge contributions from all members of the Research Collaboratory for Structural Bioinformatics PDB, our Worldwide Protein Data Bank partners, and the Rutgers Office of Research Analytics  ... 
doi:10.1038/sdata.2018.212 pmid:30325351 pmcid:PMC6190746 fatcat:6o4xdmnaenadzbbsvgzekefwye

Data publishing and archival

Nene Djenaba Barry
2021 Zenodo  
Slides used for the Data publishing and archival session of training on "Best practices and Data Management and Stewardship" held by ELIXIR Luxembourg on 17 June 2021.  ...  X-ray Imaging Data Bank (CXIDB) •Biological Magnetic Resonance Data Bank (BMRB) •Electron Microscopy Data Bank (EMDB) •Worldwide Protein Data Bank (wwPDB) •Structural Biology Data Grid Other Omics  ...  impact; While considering diversity of outputs and research cultures Use of qualitative and quantitative metrics Rewarding individual competing scientists -gaining scientific prestige Rewarding  ... 
doi:10.5281/zenodo.5524794 fatcat:vhns7ttd7bf5lgxitcvnrmmhne

Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank"

Jodi Basner
2017 RCSB Protein Data Bank  
Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community Discipline Factors Appendix F Citation rates vary between disciplines and fields.  ...  Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community The PDB has  ...  Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community What is the Threshold for "Highly Cited"?  ... 
doi:10.2210/rcsb_pdb/pdb-cit-anal-2017 fatcat:odfaoxnry5bglb7eij5vhtcnwy

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Stephen K. Burley, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Christine Zardecki
2017 Protein Science  
The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International  ...  It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org).  ...  (wwPDB; wwpdb.org), 8 consisting of the RCSB Protein Data Bank, 9, 10 Protein Data Bank Japan (PDBj), 11 the Protein Data Bank in Europe (PDBe), 12 and BioMa-gResBank (BMRB). 13 The wwPDB organization  ... 
doi:10.1002/pro.3331 pmid:29067736 pmcid:PMC5734314 fatcat:7jdrdkkw6ffffeu2xpsqp3le4i

Openaire2020 D7.5 – Data Citation Standards And Index Requirements

Florian Graef, Jo McEntyre
2016 Zenodo  
This deliverable report gives an overview of data citation practices across earth-, life-, social sciences and humanities.  ...  It furthermore introduces a tool developed to ease standard compliant data citation and discusses data citation indexes and metrics.  ...  The following is a summary of the mini-workshop we held to understand the challenges of data citation across disciplines. The full write up of the workshop can be found here 5 .  ... 
doi:10.5281/zenodo.1257268 fatcat:yov25ukfxze63ml3t2s47vyici

Journal research data sharing policies: a study of highly-cited journals in neuroscience, physics, and operations research

Antti M. Rousi, Mikael Laakso
2020 Scientometrics  
The findings revealed that one of the most important factors influencing the dimensions of what, where and when of research data policies was whether the journal's scope included specific data types related  ...  This study provides an analysis of the research data sharing policies of highly-cited journals in the fields of neuroscience, physics, and operations research as of May 2019.  ...  To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/.  ... 
doi:10.1007/s11192-020-03467-9 fatcat:loxpzrz24zgd7prc5xtuzlxrwm

Biological information specialists for biological informatics

P Bryan Heidorn, Carole L Palmer, Dan Wright
2007 Journal of Biomedical Discovery and Collaboration  
We call for a broadening of the definition of bioinformatics and bioinformatics training to span biological disciplines and biological scales.  ...  Data management and integration are complicated and ongoing problems that will require commitment of resources and expertise from the various biological science communities.  ...  Acknowledgements This material is based upon work supported by the National Science Foundation under Grant No. IIS-0534567.  ... 
doi:10.1186/1747-5333-2-1 pmid:17295920 pmcid:PMC1802079 fatcat:oqp6uxj4hjbwxop2imqpimlhlq

Accelerating Science: A Computing Research Agenda [article]

Vasant G. Honavar, Mark D. Hill, Katherine Yelick
2016 arXiv   pre-print
The emergence of "big data" offers unprecedented opportunities for not only accelerating scientific advances but also enabling new modes of discovery.  ...  Despite successful automation of routine aspects of data management and analytics, most elements of the scientific process currently require considerable human expertise and effort.  ...  The article has benefited from discussions with and feedback from the broader scientific community, and current and former members of the Computing Community Consortium Council, especially Greg Hager,  ... 
arXiv:1604.02006v1 fatcat:trlbanyknnb6ro4pxrvnm6fc7y

Developing data literacy competencies to enhance faculty collaborations

Don MacMillan
2015 Liber Quarterly: The Journal of European Research Libraries  
This paper will describe the development of two IL workshops designed to scaffold student learning in the biological sciences across two second-year courses, detailing the long-term collaboration between  ...  In each workshop, students are guided through the discovery and analysis of life sciences data from multiple sites, encouraged to integrate text and data sources, and supported in completing research assignments  ...  , but foster the integration of that content across disciplines.  ... 
doi:10.18352/lq.9868 fatcat:gwgrht3ygza4vo2fb4tlybukyq

Protein Data Bank: the single global archive for 3D macromolecular structure data

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell (+70 others)
2018 Nucleic Acids Research  
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules.  ...  Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data  ...  ; rcsb. org) (3), the Protein Data Bank in Europe (PDBe; pdbe. org) (4), Protein Data Bank Japan (PDBj; pdbj.org) (5) and BioMagResBank (BMRB; www.bmrb.wisc.edu) (6) .  ... 
doi:10.1093/nar/gky949 pmid:30357364 pmcid:PMC6324056 fatcat:ca3xenxsdzgvnb7vcwi2gtomoa

The scientific impact of the Cambridge Structural Database: a citation-based study

Ruth Wong, Frank H. Allen, Peter Willett
2010 Journal of Applied Crystallography  
Four groups of the most highly cited scientific articles (46 in total), which either describe the Cambridge Structural Database (CSD) System or report scientific research applications of the CSD, have  ...  The effect of citations from new journals, particularlyActa Crystallographica Section E: Structure Reports Online,Crystal Growth and DesignandCrystEngCommis clearly reflected in the data.  ...  2002) and the Protein Data Bank (PDB; Berman et al., 2000) ] that were established in the 1960s and early 1970s.  ... 
doi:10.1107/s0021889810019680 fatcat:aoxjjhunzng7bidcb7utdij4qq

3475 A TL1 Team Approach to CNS-Localized Delivery of Neurotrophic Factors for Treatment of Parkinson's Disease

Adithya Gopinath, Shaheen Farhadi
2019 Journal of Clinical and Translational Science  
GDNF-G3 fusion proteins will circumvent major therapeutic shortcomings of early GDNF human trials by anchoring GDNF to the midbrain in a preclinical animal model of PD over a therapeutically-relevant timescale  ...  post-mortem brain tissue from the same animals to examine degree of degeneration.  ...  will impact all levels of HIV policy across Europe.  ... 
doi:10.1017/cts.2019.295 fatcat:5bqhsxvwirh6ho3gf6bemrqgrm

Digital Curation for Science, Digital Libraries, and Individuals

Neil Beagrie
2008 International Journal of Digital Curation  
, sharing, and re-using data.  ...  The creation, management and use of digital materials are of increasing importance for a wide range of activities.  ...  Acknowledgements I would like to thank Maggie Jones, Philip Lord, and Helen Hockx-yu for reading and commenting on an earlier version of this paper.  ... 
doi:10.2218/ijdc.v1i1.2 fatcat:lnm6pw2a2vb7zbymujkbmwu2pm
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