Accelerating Scientists' Knowledge Turns

A “knowledge turn” is a cycle of a process by a professional, including the learning generated by the experience, deriving more good and leading to advance. The majority of scientific advances in the public domain result from collective efforts that depend on rapid exchange and effective reuse of results. We have powerful computational instruments, such as scientific workflows, coupled with widespread online information dissemination to accelerate knowledge cycles. However, turns between researchers continue to lag. In particular method obfuscation obstructs reproducibility. The exchange of “Research Objects” rather than articles proposes a technical solution; however the obstacles are mainly social ones that require the scientific community to rethink its current value systems for scholarship, data, methods and software.

[1]  Mitch Waldrop,et al.  Big data: Wikiomics , 2008, Nature.

[2]  Steve Pettifer,et al.  Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web , 2008, PLoS Comput. Biol..

[3]  Tom Heath,et al.  Linked Data: Evolving the Web into a Global Data Space , 2011, Linked Data.

[4]  Carole A. Goble,et al.  Scientific Social Objects: The Social Objects and Multidimensional Network of the myExperiment Website , 2011, 2011 IEEE Third Int'l Conference on Privacy, Security, Risk and Trust and 2011 IEEE Third Int'l Conference on Social Computing.

[5]  Sumithra Velupillai,et al.  De-identifying Swedish clinical text - refinement of a gold standard and experiments with Conditional random fields , 2010, J. Biomed. Semant..

[6]  Monya Baker,et al.  Next-generation sequencing: adjusting to data overload , 2010, Nature Methods.

[7]  Jane Yakowitz,et al.  Tragedy of the Data Commons , 2011 .

[8]  Ralph Schroeder,et al.  e‐Research Infrastructures and Open Science: Towards a New System of Knowledge Production? 1 , 2007 .

[9]  Vincent Larivière,et al.  Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research , 2010, PloS one.

[10]  Steffen Mazanek,et al.  SHARE: a web portal for creating and sharing executable research papers , 2011, ICCS.

[11]  Bin Chen,et al.  Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data , 2010, BMC Bioinformatics.

[12]  James D. Herbsleb,et al.  Scientific software production: incentives and collaboration , 2011, CSCW.

[13]  J. Mclaughlin,et al.  Colonic transcriptional profiling in resistance and susceptibility to trichuriasis: Phenotyping a chronic colitis and lessons for iatrogenic helminthosis , 2010, Inflammatory bowel diseases.

[14]  Anne E. Trefethen,et al.  Toward interoperable bioscience data , 2012, Nature Genetics.

[15]  Paul R. Fisher,et al.  A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices , 2009 .

[16]  Christine L. Borgman,et al.  The conundrum of sharing research data , 2012, J. Assoc. Inf. Sci. Technol..

[17]  Tim Clark,et al.  Alzforum and SWAN: the present and future of scientific web communities , 2007, Briefings Bioinform..

[18]  Hang Nguyen,et al.  Cross-generational knowledge flows in edge organizations , 2007, Ind. Manag. Data Syst..

[19]  Carole A. Goble,et al.  Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..

[20]  Carole A. Goble,et al.  Recycling workflows and services through discovery and reuse , 2007, Concurr. Comput. Pract. Exp..

[21]  David M. Shotton,et al.  Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article , 2009, PLoS Comput. Biol..

[22]  Jill P Mesirov,et al.  Accessible Reproducible Research , 2010, Science.

[23]  Benjamin F. Jones,et al.  Supporting Online Material Materials and Methods Figs. S1 to S3 References the Increasing Dominance of Teams in Production of Knowledge , 2022 .

[24]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[25]  J. Tate,et al.  The RNA WikiProject: community annotation of RNA families. , 2008, RNA.

[26]  Gunther Eysenbach,et al.  Can Tweets Predict Citations? Metrics of Social Impact Based on Twitter and Correlation with Traditional Metrics of Scientific Impact , 2011, Journal of medical Internet research.

[27]  A. Brass,et al.  A systematic, data-driven approach to the combined analysis of microarray and QTL data. , 2008, Developments in biologicals.

[28]  C. Lintott,et al.  Galaxy Zoo: morphologies derived from visual inspection of galaxies from the Sloan Digital Sky Survey , 2008, 0804.4483.

[29]  Piotr Nowakowski,et al.  The Collage Authoring Environment , 2011, ICCS.

[30]  John Whitfield,et al.  Collaboration: Group theory , 2008, Nature.

[31]  David L. Donoho,et al.  A Universal Identifier for Computational Results , 2011, ICCS.

[32]  Steve Pettifer,et al.  Ceci n'est pas un hamburger: modelling and representing the scholarly article , 2011, Learn. Publ..

[33]  S. Shapin Pump and Circumstance: Robert Boyle's Literary Technology , 1984 .

[34]  David M. Shotton,et al.  The Five Stars of Online Journal Articles - a Framework for Article Evaluation , 2012, D Lib Mag..

[35]  Carole A. Goble,et al.  Towards the Preservation of Scientific Workflows , 2011, iPRES.

[36]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[37]  J. Ioannidis,et al.  Public Availability of Published Research Data in High-Impact Journals , 2011, PloS one.

[38]  Fausto Giunchiglia,et al.  Scientific Knowledge Objects v.1 , 2009 .

[39]  Herbert Van de Sompel,et al.  An HTTP-Based Versioning Mechanism for Linked Data , 2010, LDOW.

[40]  Carole A. Goble,et al.  RightField: embedding ontology annotation in spreadsheets , 2011, Bioinform..

[41]  Carole A. Goble,et al.  Why Linked Data is Not Enough for Scientists , 2010, 2010 IEEE Sixth International Conference on e-Science.

[42]  M. Mcluhan Understanding Media: The Extensions of Man , 1964 .

[43]  Jane Hunter,et al.  Scientific Publication Packages - A Selective Approach to the Communication and Archival of Scientific Output , 2008, Int. J. Digit. Curation.

[44]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[45]  Alan Ruttenberg,et al.  The SWAN biomedical discourse ontology , 2008, J. Biomed. Informatics.

[46]  Victoria Stodden,et al.  The Scientific Method in Practice: Reproducibility in the Computational Sciences , 2010 .

[47]  Robert Stevens,et al.  A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis , 2007, Nucleic acids research.

[48]  D. Kell,et al.  Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[49]  David M. Shotton,et al.  CiTO, the Citation Typing Ontology , 2010, J. Biomed. Semant..

[50]  Andy Brass,et al.  Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection , 2011, Proceedings of the National Academy of Sciences.

[51]  Michael A. Nielsen,et al.  Reinventing Discovery: The New Era of Networked Science , 2011 .

[52]  Carole A. Goble,et al.  The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows , 2009, Future Gener. Comput. Syst..