Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

[1]  Pierre-Antoine Champin,et al.  JSON-LD 1.1 – A JSON-based Serialization for Linked Data , 2019 .

[2]  John A. Kunze,et al.  The BagIt File Packaging Format (V1.0) , 2018, RFC.

[3]  David C. Paris,et al.  Better , 2017 .

[4]  Bertil Schmidt,et al.  Next-generation sequencing: big data meets high performance computing. , 2017, Drug discovery today.

[5]  Esther Landhuis,et al.  Neuroscience: Big brain, big data , 2017, Nature.

[6]  Lei Xie,et al.  Harnessing Big Data for Systems Pharmacology , 2016, bioRxiv.

[7]  Jeremy Leipzig,et al.  A review of bioinformatic pipeline frameworks , 2016, Briefings Bioinform..

[8]  Marco Cremaschi,et al.  Enriching API Descriptions by Adding API Profiles Through Semantic Annotation , 2016, ICSOC.

[9]  Kathleen M Jagodnik,et al.  Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd , 2016, Nature Communications.

[10]  Mary Goldman,et al.  Rapid and efficient analysis of 20,000 RNA-seq samples with Toil , 2016, bioRxiv.

[11]  Andrew D. Rouillard,et al.  The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins , 2016, Database J. Biol. Databases Curation.

[12]  Jie Li,et al.  Rethinking big data: A review on the data quality and usage issues , 2016 .

[13]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[14]  Zhiyong Lu,et al.  Crowdsourcing in biomedicine: challenges and opportunities , 2016, Briefings Bioinform..

[15]  Arthur W. Toga,et al.  Big biomedical data as the key resource for discovery science , 2015, J. Am. Medical Informatics Assoc..

[16]  Lior Pachter,et al.  The NIH BD2K center for big data in translational genomics , 2015, J. Am. Medical Informatics Assoc..

[17]  Philip E. Bourne,et al.  The NIH Big Data to Knowledge (BD2K) initiative , 2015, J. Am. Medical Informatics Assoc..

[18]  Andrew D. Rouillard,et al.  GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions , 2015, Bioinform..

[19]  Mike Thelwall,et al.  ResearchGate: Disseminating, communicating, and measuring Scholarship? , 2015, J. Assoc. Inf. Sci. Technol..

[20]  Zhiyong Lu,et al.  Scaling drug indication curation through crowdsourcing , 2015, Database J. Biol. Databases Curation.

[21]  Rodrigo Costas,et al.  Do “altmetrics” correlate with citations? Extensive comparison of altmetric indicators with citations from a multidisciplinary perspective , 2014, J. Assoc. Inf. Sci. Technol..

[22]  Areej Al-Wabil,et al.  Human Factors in the Design and Evaluation of Bioinformatics Tools , 2015 .

[23]  M. Ragan-Kelley,et al.  The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication. , 2014 .

[24]  Helen Shen,et al.  Interactive notebooks: Sharing the code , 2014, Nature.

[25]  Alex Rodriguez,et al.  Experiences building Globus Genomics: a next‐generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services , 2014, Concurr. Comput. Pract. Exp..

[26]  Nancy Wilkins-Diehr,et al.  XSEDE: Accelerating Scientific Discovery , 2014, Computing in Science & Engineering.

[27]  David A Chambers,et al.  Big Data and Large Sample Size: A Cautionary Note on the Potential for Bias , 2014, Clinical and Translational Science.

[28]  Chamberlain Ryan,et al.  Using Docker to Support Reproducible Research , 2014 .

[29]  Vincent J. Henry,et al.  OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.

[30]  Michelle Dunn,et al.  The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data , 2014, J. Am. Medical Informatics Assoc..

[31]  F TerrySharon,et al.  The global alliance for genomics & health. , 2014 .

[32]  Olga Baysal,et al.  Mining modern repositories with elasticsearch , 2014, MSR 2014.

[33]  Dirk Merkel,et al.  Docker: lightweight Linux containers for consistent development and deployment , 2014 .

[34]  Sharon F Terry,et al.  The global alliance for genomics & health. , 2014, Genetic testing and molecular biomarkers.

[35]  Raghunath Nambiar,et al.  A look at challenges and opportunities of Big Data analytics in healthcare , 2013, 2013 IEEE International Conference on Big Data.

[36]  Benjamin M. Good,et al.  Dizeez: An Online Game for Human Gene-Disease Annotation , 2013, PloS one.

[37]  Benjamin M. Good,et al.  Crowdsourcing for bioinformatics , 2013, Bioinform..

[38]  Euan A. Adie,et al.  Altmetric: enriching scholarly content with article‐level discussion and metrics , 2013, Learn. Publ..

[39]  James C Hu,et al.  Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. , 2012, Virology.

[40]  Christoph Steinbeck,et al.  Bioinformatics Meets User-Centred Design: A Perspective , 2012, PLoS Comput. Biol..

[41]  Vassilios Ioannidis,et al.  ExPASy: SIB bioinformatics resource portal , 2012, Nucleic Acids Res..

[42]  Janet M Thornton,et al.  ELIXIR: a distributed infrastructure for European biological data. , 2012, Trends in biotechnology.

[43]  Jihoon Kim,et al.  iDASH: integrating data for analysis, anonymization, and sharing , 2012, J. Am. Medical Informatics Assoc..

[44]  Benjamin V. Hanrahan,et al.  Modeling problem difficulty and expertise in stackoverflow , 2012, CSCW.

[45]  Brent S. Pedersen,et al.  BioStar: An Online Question & Answer Resource for the Bioinformatics Community , 2011, PLoS Comput. Biol..

[46]  Julio Saez-Rodriguez,et al.  Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge , 2011, Science Signaling.

[47]  Janet Atkinson-Grosjean,et al.  Socio-Cultural characteristics of usability of bioinformatics databases and tools , 2011 .

[48]  L. Hood,et al.  Predictive, personalized, preventive, participatory (P4) cancer medicine , 2011, Nature Reviews Clinical Oncology.

[49]  Joan C. Bartlett,et al.  Why Choose This One? Factors in scientists' selection of bioinformatics tools , 2011, Inf. Res..

[50]  J. Carpenter.  May the best analyst win. , 2011, Science.

[51]  Susanna-Assunta Sansone.  Omics Data Sharing – BioSharing: on Data Policies’s Plans and Reporting Standards , 2010 .

[52]  Vito Perrone,et al.  Better bioinformatics through usability analysis , 2009, Bioinform..

[53]  Peter Gregor,et al.  Usability and User-Centered Design in Scientific Software Development , 2009, IEEE Software.

[54]  Daniel Gautheret,et al.  Metagenome Annotation Using a Distributed Grid of Undergraduate Students , 2008, PLoS biology.

[55]  Brian Clifton,et al.  Advanced Web Metrics with Google Analytics , 2008 .

[56]  A. Califano,et al.  Dialogue on Reverse‐Engineering Assessment and Methods , 2007, Annals of the New York Academy of Sciences.

[57]  Cynthia S. Gadd,et al.  The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System—a one-stop gateway to online bioinformatics databases and software tools , 2006, Nucleic Acids Res..

[58]  Personalizing PageRank Based on Domain Profiles , 2004 .

[59]  Taher H. Haveliwala.  Topic-sensitive PageRank , 2002, IEEE Trans. Knowl. Data Eng..

[60]  Rajeev Motwani,et al.  The PageRank Citation Ranking : Bringing Order to the Web , 1999, WWW 1999.

[61]  Timothy W. Finin,et al.  Yahoo! as an ontology: using Yahoo! categories to describe documents , 1999, CIKM '99.

[62]  Gerard Salton,et al.  A vector space model for automatic indexing , 1975, CACM.