Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
TLDR
The FAIR Data Principles as discussed by the authors are a set of data reuse principles that focus on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.Abstract:
There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.read more
Citations
More filters
Journal ArticleDOI
Deep learning-based electroencephalography analysis: a systematic review.
Yannick Roy,Hubert Banville,Isabela Albuquerque,Alexandre Gramfort,Tiago H. Falk,Jocelyn Faubert +5 more
TL;DR: In this paper, the authors present a review of 154 studies that apply deep learning to EEG, published between 2010 and 2018, and spanning different application domains such as epilepsy, sleep, brain-computer interfacing, and cognitive and affective monitoring.
Journal ArticleDOI
Evaluation and accurate diagnoses of pediatric diseases using artificial intelligence
Huiying Liang,Brian Tsui,Hao Ni,Carolina C. S. Valentim,Sally L. Baxter,Guangjian Liu,Wenjia Cai,Daniel S. Kermany,Daniel S. Kermany,Xin Sun,Jiancong Chen,Liya He,Jie Zhu,Pin Tian,Hua Shao,Lianghong Zheng,Rui Hou,Sierra Hewett,Sierra Hewett,Gen Li,Gen Li,Ping Liang,Xuan Zang,Zhiqi Zhang,Liyan Pan,Huimin Cai,Rujuan Ling,Shuhua Li,Yongwang Cui,Shusheng Tang,Hong Ye,Xiaoyan Huang,Waner He,Wenqing Liang,Qing Zhang,Jianmin Jiang,Wei Yu,Jianqun Gao,Wanxing Ou,Yingmin Deng,Qiaozhen Hou,Bei Wang,Cuichan Yao,Yan Liang,Shu Zhang,Yaou Duan,Runze Zhang,Sarah Gibson,Charlotte Zhang,Oulan Li,Edward Zhang,Gabriel Karin,Nathan Nguyen,Xiaokang Wu,Xiaokang Wu,Cindy Wen,Jie Xu,Wenqin Xu,Bochu Wang,Winston Wang,Jing Li,Jing Li,Bianca Pizzato,Caroline Bao,Daoman Xiang,Wanting He,Wanting He,Suiqin He,Yugui Zhou,Yugui Zhou,Weldon W Haw,Weldon W Haw,Michael H. Goldbaum,Adriana H. Tremoulet,Chun-Nan Hsu,Hannah Carter,Long Zhu,Kang Zhang,Kang Zhang,Kang Zhang,Huimin Xia +80 more
TL;DR: This study shows that MLCs can query EHRs in a manner similar to the hypothetico-deductive reasoning used by physicians and unearth associations that previous statistical methods have not found, and provides a proof of concept for implementing an AI-based system to aid physicians in tackling large amounts of data, augmenting diagnostic evaluations, and to provide clinical decision support in cases of diagnostic uncertainty or complexity.
Journal ArticleDOI
Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives.
Wanneng Yang,Hui Feng,Xuehai Zhang,Jian Zhang,John H. Doonan,William D. Batchelor,Lizhong Xiong,Jianbing Yan +7 more
TL;DR: Main developments on high-throughput phenotyping in the controlled environments and field conditions as well as for post-harvest yield and quality assessment in past decades are reviewed and the latest multiomics works combining high- throughput phenotypesing and genetic studies are described.
Journal ArticleDOI
Artificial Intelligence in Dentistry: Chances and Challenges.
TL;DR: This succinct narrative review describes the application, limitations and possible future of AI-based dental diagnostics, treatment planning, and conduct, for example, image analysis, prediction making, record keeping, as well as dental research and discovery.
Journal ArticleDOI
Crop Phenomics: Current Status and Perspectives.
Chunjiang Zhao,Ying Zhang,Jianjun Du,Guo Xinyu,Weiliang Wen,Shenghao Gu,Jinglu Wang,Fan Jiangchuan +7 more
TL;DR: The challenges and prospective of crop phenomics are discussed in order to provide suggestions to develop new methods of mining genes associated with important agronomic traits, and propose new intelligent solutions for precision breeding.
References
More filters
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
UniProt: A hub for protein information
Alex Bateman,Maria Jesus Martin,Claire O'Donovan,Michele Magrane,Rolf Apweiler,Emanuele Alpi,Ricardo Antunes,Joanna Arganiska,Benoit Bely,Mark Bingley,Carlos Bonilla,Ramona Britto,Borisas Bursteinas,Gayatri Chavali,Elena Cibrian-Uhalte,Alan Wilter Sousa da Silva,Maurizio De Giorgi,Tunca Doğan,Francesco Fazzini,Paul Gane,Leyla Jael Garcia Castro,Penelope Garmiri,Emma Hatton-Ellis,Reija Hieta,Rachael P. Huntley,Duncan Legge,W Liu,Jie Luo,Alistair MacDougall,Prudence Mutowo,Andrew Nightingale,Sandra Orchard,Klemens Pichler,Diego Poggioli,Sangya Pundir,Luis Pureza,Guoying Qi,Steven Rosanoff,Rabie Saidi,Tony Sawford,Aleksandra Shypitsyna,Edward Turner,Vladimir Volynkin,Tony Wardell,Xavier Watkins,Hermann Zellner,Andrew Peter Cowley,Luis Figueira,Weizhong Li,Hamish McWilliam,Rodrigo Lopez,Ioannis Xenarios,Lydie Bougueleret,Alan Bridge,Sylvain Poux,Nicole Redaschi,Lucila Aimo,Ghislaine Argoud-Puy,Andrea H. Auchincloss,Kristian B. Axelsen,Parit Bansal,Delphine Baratin,Marie Claude Blatter,Brigitte Boeckmann,Jerven Bolleman,Emmanuel Boutet,Lionel Breuza,Cristina Casal-Casas,Edouard de Castro,Elisabeth Coudert,Béatrice A. Cuche,M Doche,Dolnide Dornevil,Séverine Duvaud,Anne Estreicher,L Famiglietti,Marc Feuermann,Elisabeth Gasteiger,Sebastien Gehant,Vivienne Baillie Gerritsen,Arnaud Gos,Nadine Gruaz-Gumowski,Ursula Hinz,Chantal Hulo,Florence Jungo,Guillaume Keller,Vicente Lara,P Lemercier,Damien Lieberherr,Thierry Lombardot,Xavier D. Martin,Patrick Masson,Anne Morgat,Teresa Batista Neto,Nevila Nouspikel,Salvo Paesano,Ivo Pedruzzi,Sandrine Pilbout,Monica Pozzato,Manuela Pruess,Catherine Rivoire,Bernd Roechert,Michel Schneider,Christian J. A. Sigrist,K Sonesson,S Staehli,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Laure Verbregue,Anne Lise Veuthey,Cathy H. Wu,Cecilia N. Arighi,Leslie Arminski,Chuming Chen,Yongxing Chen,John S. Garavelli,Hongzhan Huang,Kati Laiho,Peter B. McGarvey,Darren A. Natale,Baris E. Suzek,C. R. Vinayaka,Qinghua Wang,Yuqi Wang,Lai-Su L. Yeh,Meher Shruti Yerramalla,Jian Zhang +127 more
TL;DR: An annotation score for all entries in UniProt is introduced to represent the relative amount of knowledge known about each protein to help identify which proteins are the best characterized and most informative for comparative analysis.
Journal ArticleDOI
The simbad astronomical database
Marc Wenger,François Ochsenbein,Daniel Egret,Pascal Dubois,François Bonnarel,S. Borde,Françoise Genova,G. Jasniewicz,S. Laloë,Soizick Lesteven,R. Monier +10 more
TL;DR: SIMBAD as discussed by the authors is the astronomical data base produced and maintained by the Centre de Donnees astronomiques de Strasbourg (CDS) at the Observatoire of Strasbourg, France.
Journal ArticleDOI
Ten simple rules for reproducible computational research.
TL;DR: It is emphasized that reproducibility is not only a moral responsibility with respect to the scientific field, but that a lack of reproducible can also be a burden for you as an individual researcher.
Journal ArticleDOI
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
Peter W. Rose,Andreas Prlić,Chunxiao Bi,Wolfgang F. Bluhm,Cole H. Christie,Shuchismita Dutta,Rachel Kramer Green,David S. Goodsell,John D. Westbrook,Jesse Woo,Jasmine Young,Christine Zardecki,Helen M. Berman,Philip E. Bourne,Stephen K. Burley +14 more
TL;DR: Recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web are described.
Related Papers (5)
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
SciPy 1.0: fundamental algorithms for scientific computing in Python.
Pauli Virtanen,Ralf Gommers,Travis E. Oliphant,Matt Haberland,Matt Haberland,Tyler Reddy,David Cournapeau,Evgeni Burovski,Pearu Peterson,Warren Weckesser,Jonathan Bright,Stefan van der Walt,Matthew Brett,Joshua Wilson,K. Jarrod Millman,Nikolay Mayorov,Andrew Nelson,Eric Jones,Robert Kern,Eric B. Larson,CJ Carey,Ilhan Polat,Yu Feng,Eric Moore,Jake Vanderplas,Denis Laxalde,Josef Perktold,Robert Cimrman,Ian Henriksen,Ian Henriksen,E. A. Quintero,Charles R. Harris,Anne M. Archibald,Antônio H. Ribeiro,Fabian Pedregosa,Paul van Mulbregt,SciPy . Contributors +36 more