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PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data.  ...  This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability.  ...  ACKNOWLEDGEMENTS We would like to thank all collaborators and partners at the EMBL-EBI, EMBL, wwPDB, EMDB, CCP4, SASBDB, CCPN, CCDC, CEITEC, MRC-LMB and other collaborative efforts, as well as the structural  ... 
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
wwPDB Format Protein Data Bank in Europe The Protein Data Bank in Europe (PDBe) is an integrated structural data resource that aims to evolve with the science of structural biology and with the needs  ...  Biopolymers 101:659-668 Gutmanas A, Alhroub Y, Battle GM, et al. (2014) PDBe: Protein Data Bank in Europe.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Identifying ELIXIR Core Data Resources

Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger (+2 others)
2016 F1000Research  
The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe.  ...  At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data.  ...  Acknowledgements We thank all the colleagues who have contributed over many years to arriving at this position and state of clarity since the ELIXIR Preparatory Phase.  ... 
doi:10.12688/f1000research.9656.1 pmid:27803796 pmcid:PMC5070591 fatcat:6nxebcvvfjcibowlvx3vo7357m

Identifying ELIXIR Core Data Resources

Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger (+2 others)
2017 F1000Research  
The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe.  ...  At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data.  ...  Acknowledgements We thank all the colleagues who have contributed over many years to arriving at this position and state of clarity since the ELIXIR Preparatory Phase.  ... 
doi:10.12688/f1000research.9656.2 pmid:27803796 pmcid:PMC5070591 fatcat:irmr4gvvtna2dpsa7ncssff7au

EOSC-Life Report on the work of the initial demonstrators

Frauke Leitner, Jose Maria Carazo, Johanna Bischof, Natalie Haley, Pauline Audergon, Carlos Oscar Sorzano, Laura del Cano, Pablo Conesa, Cymon J. Cox, Gianluca De Moro, Corre Erwan, Katrina Exter (+32 others)
2021 Zenodo  
deliverable 3.2 is a report on the demonstrator projects, the eight scientific and technical pilot projects that were selected to provide concrete scientific use-cases and guide and structure the work done in  ...  We report in this deliverable the process of integration of the demonstrators within EOSC-Life, the achievement of the demonstrators who developed and made available to the scientific community several  ...  Demonstrator 1 work was also presented at the OECD/Science Europe workshop "Research Infrastructures mobilisation in response to COVID-19: lessons learned" satellite event to the International Conference  ... 
doi:10.5281/zenodo.4817722 fatcat:r4rso6bxcrdfdon7iaznxaql6i

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
repositories and biological knowledge bases agreed and implemented in the field with WP6 to 9 (Use Cases), and WP3 (Data)", as well has ensuring that resources were registered in appropriate ELIXIR registries  ...  The main aim of this deliverable is to present our progress for the implementation of our interoperability framework for EXCELERATE Use Cases WP6-9 and the ELIXIR Data Platform (WP3).  ...  Human Protein Atlas, MINT, PDBe) and three Deposition Databases (BioSamples, PDBe, EGA) are marked-up so far in their Live deploys.  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

The Role of Community-Driven Data Curation for Enterprises [chapter]

Edward Curry, Andre Freitas, Sean O'Riáin
2010 Linking Enterprise Data  
The chapter is supported by case studies from Wikipedia, The New York Times, Thomson Reuters, Protein Data Bank and ChemSpider upon which best practices for both social and technical aspects of community-driven  ...  In response, curation teams have turned to community crowd-sourcing and semi-automated metadata tools for assistance.  ...  Acknowledgements In writing this chapter we were fortunate to be have access to a number of thought leaders in the area willing to share their time, insights and experiences.  ... 
doi:10.1007/978-1-4419-7665-9_2 fatcat:jbwv772pbrhyddyz7guxp4kkvi

Measuring the Value and Impact of the Europe PMC Repository [article]

Anoushka Davé, Vivek Seth, Emma Pottinger, Cristina Rosenberg, Xavier Potau, Peter Varnai
2019 Figshare  
The authors conducted surveys and interviews to compile quantitative and qualitative data for calculating a variety of economic values.  ...  This is the final report from the study which measures the value and impact of Europe PMC.  ...  , Protein Data Bank in Europe (PDBe) and BioStudies 8 • Allowing bulk download via FTP (File Transfer Protocol) of full text open access content and other datasets • An API is a set of functions  ... 
doi:10.6084/m9.figshare.8326559.v1 fatcat:h3amqlslgbhcrfnepqhvztkkqa

Measuring the Value and Impact of the Europe PMC Repository [article]

Anoushka Davé, Vivek Seth, Emma Pottinger, Cristina Rosenberg, Xavier Potau, Peter Varnai
2019 Figshare  
The authors conducted surveys and interviews to compile quantitative and qualitative data for calculating a variety of economic values.  ...  This is the final report from the study which measures the value and impact of Europe PMC.  ...  , Protein Data Bank in Europe (PDBe) and BioStudies 8 • Allowing bulk download via FTP (File Transfer Protocol) of full text open access content and other datasets • An API is a set of functions  ... 
doi:10.6084/m9.figshare.8326559 fatcat:vu7nkpfvdvfmze6uyvqfg3y5dq

Referee report. For: A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 2 approved with reservations]

Roland L. Dunbrack
2020
.: PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res. 2018; 46(D1): D486-D492.  ...  Seibel PN, Krüger J, Hartmeier S, et al.: XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics. 2006; 7: 490.  ...  I suppose it is necessary for European funding bodies to hear it, and in the United States we often find ourselves doing the same thing while trying to secure funding for bioinformatics infrastructure  ... 
doi:10.5256/f1000research.22602.r63141 fatcat:65v2v46cgbggzlbxfrq2gagjae

Report of the Executive Committee for 2019

A. T. Ashcroft
2020 Acta Crystallographica Section A: Foundations and Advances  
Out of 133 structures deposited in the Protein Data Bank (PDB), only ten complete data sets have been deposited in a public repository.  ...  Hackert, IUCr Representative Worldwide Protein Data Bank (wwPDB) The Protein Data Bank (PDB) has been a key resource for macromolecular crystallographers for almost 50 years, and its policies and development  ...  The Panel on Capacity Building (PCB) Fellowship programme is open to young scientists who participated at one of the COSPAR CBWs, enabling them to build on skills gained at the workshop.  ... 
doi:10.1107/s2053273320009705 pmid:33125357 fatcat:3k3oz64sanfffngbfoex4anz4u

Report of the Executive Committee for 2016

M. Dacombe, A. T. Ashcroft
2018 Acta Crystallographica Section A: Foundations and Advances  
The first such meeting was held in December 2015 in Pretoria, South Africa, with a focus on Big Data and Open Data.  ...  Full details of CODATA activities are available from its web site at http://www.codata.org.  ...  Whitfield, IUCr Representative Worldwide Protein Data Bank (wwPDB) The Protein Data Bank has been an essential resource for macromolecular crystallographers for more than 40 years, and its policies and  ... 
doi:10.1107/s2053273317009780 pmid:29724970 fatcat:pchaqu3bjvaejmnp5wh2f6crv4

Heterogeneous Data Processing for Information and Knowledge Management in Glycomics and Glycoproteomics

Julien Mariethoz, Frédérique Lisacek
2022
Sriram Neelamegham (State University of New York at Buffalo, Buffalo, USA) for supporting our contribution to the SNFG nomenclature and turning our suggestion into a fruitful discussion in the SNFG group  ...  ■ ACKNOWLEDGMENTS We thank our UniCarbKB collaborators Nicki Packer for fruitful discussions and Matthew Campbell for his help on using the data.  ...  Dataset of GAG-protein complexes extracted from the Protein Data Bank A dataset of protein-GAG complexes was automatically retrieved from the Protein Data Bank (https://www.rcsb.org/, March 2017) using  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4