Open Science by Design Realizing a Vision for 21st Century Research (2018) / Chapter Skim
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3 The State of Open Science
3 The State of Open Science
Pages 59-106
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From page 59... ...
issued its declaration, there have been numerous efforts to promote and realize open science. A growing number of public and private research sponsors around the world are mandating open publication, open data, or both, on the part of grantees, with some variety in the specifics of their policies, including the National Institutes of Health, the National Science Foundation, the Bill & Melinda Gates Foundation, 59
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Most of these efforts focus on open publication. For example, Science-Metrix, a Canadian science data analytics company, found that as of 2013 over half the articles published during the period 2007–2012 were available for free download (Science-Metrix, 2014)
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FIGURE 3-1 Open science policies adopted by research funders and research organizations around the world. SOURCE: ROARMap, University of Southampton.
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Examples of disciplinary approaches are described in the boxes throughout this chapter, including biological sciences such as genomic research and precision medicine; astronomy and astrophysics; earth sciences; and economics. Regarding funders, the proportion of open publications that are based on research supported by NIH and the Wellcome Trust is high and increasing, which is understandable given their mandates requiring deposit in PubMed Central or Europe PubMed Central (PMC)
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Part of the committee's task was to provide illustrations from several scientific disciplines within the biological sciences, social sciences, physical sciences, and earth sciences. The section includes examples drawn from biomedical sciences, economics, astronomy and astrophysics, and earth sciences, along with other examples from outside of those disciplines.
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. 1 Although the majority of open access journals do not require APCs, these journals account for a minority of the open access articles published worldwide, and only 18 percent of the open access articles published in the United States (Crawford, 2018)
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Accessed December 4, 2017. Several entities provide guidelines for assessing the quality of open access journals.
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To improve the visibility and impact of research, the majority of open access policies and laws require or request authors to deposit their articles into an open access repository, which has become a key infrastructure component to support these policies. Networked open access repositories enable funders and institutions to track funded research output across repositories, deliver data usage, host collections of academic journals, and link related content across the network (COAR, 2015a)
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From page 67... ...
. Since April of that year, authors of NIH-funded research have been required to deposit, or have deposited for them, their final accepted peer-reviewed manuscripts in PMC, with an allowa ble embargo period of up to 12 months (NIH Public Access Policy, 2016; Var mus, 2008)
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From page 68... ...
Scholarly articles provided by Harvard faculty and researchers are stored, preserved, and made available in the Digital Access to Scholarship at Harvard (DASH) , a free open access repository available to anyone with internet access.
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. While an effective open access policy can build support for open access, institutions considering adopting their own open access policies are able to refer to the current Harvard model policy (see Box 3-3)
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specified by the Provost's Office. The Provost's Office may make the article available to the public in an open-access repository.
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. This preprint server will join the existing EarthArXiv as preprint servers for the earth and space science community (Voosen, 2017)
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. The American Economic Review and other American Economic Association journals required data archiving starting in 2004.
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SocArXiv Social sciences 2016 Open Science Framework (OSF) 633 PsyArXiv Psychology 2016 OSF 191 engrXiv Engineering 2016 OSF 35 ChemRxiv Chemistry 2017 ACS N/A AgriXiv Agriculture 2017 OSF N/A EarthArXiv Earth Sciences 2017 OSF N/A LawArXiv Law 2017 OSF N/A NutriXiv Nutritional Sciences 2017 OSF N/A Sport RXiv Sport science 2017 OSF N/A Services with preprint functions Social Science Research Network (SSRN)
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From page 74... ...
Building on the best practices of other funders, such as the Bill & Melinda Gates Foundation and the Wellcome Trust, the commission hopes that the platform will contribute to a more diversified and competitive open access publishing market. One contractor or a consortium led by one contractor will be selected to run the platform with a 4-year initial contract.
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The study discovered that the average APC for partner institution publications in full open access journals is $1,892 (Figure 3-4)
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Private Foundation Initiatives Open access publishing has increasingly become part of the business process among the philanthropic community. For example, the Bill & Melinda Gates Foundation has one of the most stringent open-access policies.
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. During recent infectious diseases outbreaks in 2016, the publishing community largely agreed, at the prompting of WHO and funders such as the Bill & Melinda Gates Foundation and the Wellcome Trust, to adopt open science practices, including early publication of data and preprints and open access publication (PLOS, 2016)
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From page 78... ...
Big Science Data Open data is largely the norm in fields such as high-energy physics and astronomy, as funding for these projects is significant, and as such data distribution is well thought out and closely monitored by the respective federal agencies. Good examples include the Large Hadron Collider, and some of the large scale astrophysical archives (Hubble Legacy Archive, Sloan Digital Sky Survey, etc.)
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With the size and complexity of datasets continually increasing, yesterday's "big data" appears less big today, today's "big data" will appear small in five or ten years, and so forth. BOX 3-5 Astronomy and Astrophysics The Sloan Digital Sky Survey (SDSS)
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2017. Sloan Digital Sky Survey.
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Accessed November 16, 2017. SDSS (Sloan Digital Sky Survey)
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The Long Tail of Science The long tail of science is increasingly gaining attention in the open science community. While big data tend to comprise homogeneous, standardized, and regulated data, long-tail data can be relatively small and heterogeneous individually but very large in the number of datasets (Heidorn, 2008; Borgman, 2015; eIRG, 2016; see Table 3-2)
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was founded in 2005 and is dedi cated "to creating public resources that everyone can access" and to a "highly participatory approach to research-participant communication and interaction" (Church, 2005; Harvard Personal Genome Project, 2014; Ball et al., 2014)
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2015. NIH's genomic data sharing policy: timing and tradeoffs.
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and the National Data Service (NDS) are leading the way in the path towards establishing a universal, easy-to-use data publishing and management framework, but this is an area that will require consistent long-term attention before it can be said that the problem has been solved (See Box 3-7)
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NDS (National Data Service)
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2017b. A vision for accelerating discovery through data sharing, Online.
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. The Green Report contained several recommendations, including the need for the development of budgeting information for collections and assessing and projecting costs; the identification and dissemination of policies and best practices on organization, management, physical and online access, and long-term preservation; and issues related to data and metadata accessibility, especially the need to document physical objects and make collection information available online, and develop an online clearinghouse for information on contents and access to federal scientific collections.
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The National Science Foundation's data sharing policy states "Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing" (NSF, 2018a)
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A few examples of such university repositories are the International Ocean Discovery Program, the Oregon State University Marine and Geology repository, the Scripps Institution of Oceanography Collections, and the University of California, Berkeley Museum of Paleontology. Many university repositories have maintained funding through difficult times, but an alarming number are facing budget cuts that have led to closure and loss of valuable scientific collections.
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, many other high-value research collections remain at risk. BOX 3-8 Earth Sciences Perhaps the best developed model for open data in the earth sciences is in support of the scientific ocean drilling effort whose current incarnation is the International Ocean Discovery Program (IODP; http://iodp.org/about-iodp/his tory)
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The Magnetics Information Consortium (MagIC; http://earthref.org/MagIC) provides a data archive that al lows the discovery and reuse of such data for the broader earth sciences com munity.
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Participants in the program must be willing to share their health data, provide a biospecimen, and be recontacted for future research. The PMI data is envisioned as a public resource that will be accessible not only to researchers, but also to interested members of the public, e.g., "citizen scientists." The specifics of data sharing and access are under development and are expected to adhere to a set of privacy and trust principles (The White House, 2015b)
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2015. The Precision Medicine Initiative cohort program – Building a research foundation for 21st century medicine.
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at the Federal Reserve Bank of Kansas City began working to doc ument data inputs and methods for various fields in economics with an em phasis on widely used microeconomic datasets such as the Current Popula tion Survey and the Survey of Income and Program Participation (Federal Reserve Bank of Kansas City, 2018)
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Federal Reserve Bank of Kansas City.
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http://www.cancerimagingarchive.net Influenza Research Database http://www.fludb.org National Addiction & HIV Data Archive Program (NAHDAP) http://www.icpsr.umich.edu/icpsrweb/NAHDAP/index.jsp National Database for Autism Research (NDAR)
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http://www.peptideatlas.org http://www.proteomexchange.org http://www.ebi.ac.uk/pride/archive Physical Sciences Australian Antarctic Data Centre (AADC) http://www1.data.antarctica.gov.au Cold and Arid Regions Science Data Center (CARD)
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Qualitative Data Repository https://www.icpsr.umich.edu/icpsrweb/landing.jsp https://qdr.syr.edu Structural Databases Biological Magnetic Resonance Data Bank (BMRB) http://www.bmrb.wisc.edu Cambridge Crystallographic Data Centre (CCDC)
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http://www.itis.gov Knowledge Network for Biocomplexity (KNB) https://knb.ecoinformatics.org NCBI Taxonomy http://www.ncbi.nlm.nih.gov/taxonomy Unstructured and/or BioStudies https://www.ebi.ac.uk/biostudies Large Data CSIRO Data Access Portal https://data.csiro.au GigaDB http://gigadb.org SimTK https://simtk.org Swedish National Data Service https://snd.gu.se/en SOURCE: http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.
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From page 101... ...
. Additionally, publication of laboratory protocols via electronic research notebooks or open access repository for science methods such as protocols.io, which allows forking and amendments to existing protocols, is a helpful feature to accelerate methodological development toward an open science enterprise (PLOS, 2017b; Goodman, 2018)
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From page 102... ...
that is developed and deployed to support specific challenges in data sharing and data-driven research. For example, the RDA Data Publishing Services Working Group developed a model for "an open, universal literature-data cross-linking service that improves visibility, discoverability, reuse, and reproducibility by bringing existing article/data links together, normalizes them using a common schema, and exposes the full set as an open service" (RDA, 2017b)
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From page 103... ...
A landmark publication of Science International (composed of ICSU, the InterAcademy Partnership, The World Academy of Sciences, and the International Social Science Council) entitled Open Data in a Big Data World highlights critical issues related to open data and open science while laying out a framework for how the vision of Open Data in a Big Data World can be achieved (Science International, 2015)
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The Australian National Data Service (ANDS) , established in 2008, is a joint collaboration between Monash University and the Australian National University and the Commonwealth Scientific and Industrial Research Organisation (CSIRO)
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. In South Africa, the African Data Intensive Research Cloud "aims to establish resources to support data intensive radio astronomy research among collaborating partners in South Africa and African Square Kilometer Array telescope partner countries" (Simmonds et al., 2016, p.
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