Open science data

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Open science data is a type of open data focused on publishing observations and results of scientific activities available for anyone to analyze and reuse. A major purpose of the drive for open data is to allow the verification of scientific claims, by allowing others to look at the reproducibility of results,[1] and to allow data from many sources to be integrated to give new knowledge.[2] While the idea of open science data has been actively promoted since the 1950s, the rise of the Internet has significantly lowered the cost and time required to publish or obtain data.

History[edit]

The concept of open access to scientific data was institutionally established with the formation of the World Data Center system (now the World Data System), in preparation for the International Geophysical Year of 1957–1958.[3] The International Council of Scientific Unions (now the International Council for Science) established several World Data Centers to minimize the risk of data loss and to maximize data accessibility, further recommending in 1955 that data be made available in machine-readable form.[4]

The first initiative to create a database of electronic bibliography of open access data was the Educational Resources Information Center (ERIC) in 1966. In the same year, MEDLINE was created – a free access online database managed by the National Library of Medicine and the National Institute of Health (USA) with bibliographical citations from journals in the biomedical area, which later would be called PubMed, currently with over 14 million complete articles.[5]

In 1995 GCDIS (US) put its position clearly in On the Full and Open Exchange of Scientific Data (A publication of the Committee on Geophysical and Environmental Data - National Research Council):

"The Earth's atmosphere, oceans, and biosphere form an integrated system that transcends national boundaries. To understand the elements of the system, the way they interact, and how they have changed with time, it is necessary to collect and analyze environmental data from all parts of the world. Studies of the global environment require international collaboration for many reasons:

  • to address global issues, it is essential to have global data sets and products derived from these data sets;
  • it is more efficient and cost-effective for each nation to share its data and information than to collect everything it needs independently; and
  • the implementation of effective policies addressing issues of the global environment requires the involvement from the outset of nearly all nations of the world.

International programs for global change research and environmental monitoring crucially depend on the principle of full and open data exchange (i.e., data and information are made available without restriction, on a non-discriminatory basis, for no more than the cost of reproduction and distribution)."

[6]

The last phrase highlights the traditional cost of disseminating information by print and post. It is the removal of this cost through the Internet which has made data vastly easier to disseminate technically. It is correspondingly cheaper to create, sell and control many data resources and this has led to the current concerns over non-open data.

More recent uses of the term include:

  • SAFARI 2000 (South Africa, 2001) used a license informed by ICSU and NASA policies[7]
  • The human genome[8] (Kent, 2002)
  • An Open Data Consortium on geospatial data[9] (2003)
  • Manifesto for Open Chemistry[10] (Murray-Rust and Rzepa, 2004) (2004)
  • Presentations to JISC and OAI under the title "open data"[11] (Murray-Rust, 2005)
  • Science Commons launch[12] (2004)
  • First Open Knowledge Forums (London, UK) run by the Open Knowledge Foundation (London UK) on open data in relation to civic information and geodata[13] (February and April 2005)
  • The Blue Obelisk group in chemistry (mantra: Open Data, Open Source, Open Standards) (2005) doi:10.1021/ci050400b
  • The Petition for Open Data in Crystallography is launched by the Crystallography Open Database Advisory Board.[14](2005)
  • XML Conference & Exposition 2005[15] (Connolly 2005)
  • SPARC Open Data mailing list[16] (2005)
  • First draft of the Open Knowledge Definition explicitly references "Open Data"[17] (2005)
  • XTech[18] (Dumbill, 2005),[19] (Bray and O'Reilly 2006)

In 2004, the Science Ministers of all nations of the OECD (Organisation for Economic Co-operation and Development), which includes most developed countries of the world, signed a declaration which essentially states that all publicly funded archive data should be made publicly available.[20] Following a request and an intense discussion with data-producing institutions in member states, the OECD published in 2007 the OECD Principles and Guidelines for Access to Research Data from Public Funding as a soft-law recommendation.[21]

In 2005 Edd Dumbill introduced an “Open Data” theme in XTech, including:

In 2006 Science Commons[22] ran a 2-day conference in Washington where the primary topic could be described as Open Data. It was reported that the amount of micro-protection of data (e.g. by license) in areas such as biotechnology was creating a Tragedy of the anticommons. In this the costs of obtaining licenses from a large number of owners made it uneconomic to do research in the area.

In 2007 SPARC and Science Commons announced a consolidation and enhancement of their author addenda.[23]

In 2007 the OECD (Organisation for Economic Co-operation and Development) published the Principles and Guidelines for Access to Research Data from Public Funding.[24] The Principles state that:

Access to research data increases the returns from public investment in this area; reinforces open scientific inquiry; encourages diversity of studies and opinion; promotes new areas of work and enables the exploration of topics not envisioned by the initial investigators.

In 2010 the Panton Principles launched,[25] advocating Open Data in science and setting out for principles to which providers must comply to have their data Open.

In 2011 LinkedScience.org was launched to realize the approach of the Linked Open Science[26] to openly share and interconnect scientific assets like datasets, methods, tools and vocabularies.

In 2012, the Royal Society published a major report, "Science as an Open Enterprise",[27] advocating open scientific data and considering its benefits and requirements.

In 2013 the G8 Science Ministers released a Statement[28] supporting a set of principles for open scientific research data

In 2015 the World Data System of the International Council for Science adopted a new set of Data Sharing Principles[29][30] to embody the spirit of 'open science'. These Principles are in line with data policies of national and international initiatives and they express core ethical commitments operationalized in the WDS Certification of trusted data repositories and service.

Relation to open access[edit]

Much data is made available through scholarly publication, which now attracts intense debate under "Open Access" and semantically open formats – like to offer the scientific articles in JATS format. The Budapest Open Access Initiative (2001) coined this term:

By "open access" to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

The logic of the declaration permits re-use of the data although the term "literature" has connotations of human-readable text and can imply a scholarly publication process. In Open Access discourse the term "full-text" is often used which does not emphasize the data contained within or accompanying the publication.

Some Open Access publishers do not require the authors to assign copyright and the data associated with these publications can normally be regarded as Open Data. Some publishers have Open Access strategies where the publisher requires assignment of the copyright and where it is unclear that the data in publications can be truly regarded as Open Data.

The ALPSP and STM publishers have issued a statement about the desirability of making data freely available:[31]

Publishers recognise that in many disciplines data itself, in various forms, is now a key output of research. Data searching and mining tools permit increasingly sophisticated use of raw data. Of course, journal articles provide one ‘view’ of the significance and interpretation of that data – and conference presentations and informal exchanges may provide other ‘views’ – but data itself is an increasingly important community resource. Science is best advanced by allowing as many scientists as possible to have access to as much prior data as possible; this avoids costly repetition of work, and allows creative new integration and reworking of existing data.

and

We believe that, as a general principle, data sets, the raw data outputs of research, and sets or sub-sets of that data which are submitted with a paper to a journal, should wherever possible be made freely accessible to other scholars. We believe that the best practice for scholarly journal publishers is to separate supporting data from the article itself, and not to require any transfer of or ownership in such data or data sets as a condition of publication of the article in question.

Even though this statement was without any effect on the open availability of primary data related to publications in journals of the ALPSP and STM members. Data tables provided by the authors as supplement with a paper are still available to subscribers only.

Relation to peer review[edit]

In an effort to address issues with the reproducibility of research results, some scholars are asking that authors agree to share their raw data as part of the scholarly peer review process.[32] As far back as 1962, for example, a number of psychologists have attempted to obtain raw data sets from other researchers, with mixed results, in order to reanalyze them. A recent attempt resulted in only seven data sets out of fifty requests. The notion of obtaining, let alone requiring, open data as a condition of peer review remains controversial.[33]

Open research computation[edit]

Main article: Open research computation

To make sense of scientific data they must be analysed. In all but the simplest cases, this is done by software. The extensive use of software poses problems for the reproducibility of research. To keep research reproducible, it is necessary to publish not only all data, but also the source code of all software used, and all the parametrization used in running this software. Presently, these requests are rarely ever met. Ways to come closer to reproducible scientific computation are discussed under the catchword "open research computation".

See also[edit]

References[edit]

  1. ^ Spiegelhalter, D. Open data and trust in the literature. The Scholarly Kitchen. Retrieved 7 September 2018.
  2. ^ Wilkinson, M.D.; Dumontier, M.; Aalbersberg, I.J.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J.-W.; da Silva Santos, L.B.; Bourne, P.E.; Bouwman, J.; Brookes, A.J.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, Scott; Evelo, C. T.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A.J.G.; Groth, P.; Goble, C.; Grethe, J. S.; Heringa, J.; ’t Hoen, P.A.C; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S. J.; Martone, M.E.; Mons, A.; Packer, A.L.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M. A.; Thompson, M.; van der Lei, J.; van Mulligen, E.; Velterop, J.; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; Mons, B. (2016). "The FAIR Guiding Principles for scientific data management and stewardship". Scientific Data. 3: 160018. Bibcode:2016NatSD...360018W. doi:10.1038/sdata.2016.18. ISSN 2052-4463. PMC 4792175. PMID 26978244.
  3. ^ Committee on Scientific Accomplishments of Earth Observations from Space, National Research Council (2008). Earth Observations from Space: The First 50 Years of Scientific Achievements. The National Academies Press. p. 6. ISBN 978-0-309-11095-2. Retrieved 2010-11-24.
  4. ^ World Data Center System (2009-09-18). "About the World Data Center System". NOAA, National Geophysical Data Center. Retrieved 2010-11-24.
  5. ^ Machado, Jorge. "Open data and open science". In Albagli, Maciel, Abdo. "Open Science, Open Questions", 2015
  6. ^ National Research Council (1995). On the Full and Open Exchange of Scientific Data. Washington, DC: The National Academies Press. doi:10.17226/18769. ISBN 978-0-309-30427-6.
  7. ^ "Safari 2000 Data Policy" (PDF). Archived from the original (PDF) on September 29, 2006. Retrieved May 28, 2011.
  8. ^ Bruce Stewart (2002). "Keeping Genome Data Open;An Interview with Jim Kent".
  9. ^ "Open Data Consortium ca. 2003". Archived from the original on 2011-07-27. Retrieved 2011-05-28.
  10. ^ Peter Murray-Rust, Henry Rzepa 2004
  11. ^ "Open Data" at CERN Workshop on Innovations in Scholarly Communication (OAI4) Peter Murray-Rust, 2005
  12. ^ Report on Science Commons Dec 2004
  13. ^ Open Knowledge Forums
  14. ^ http://www.crystallography.net/
  15. ^ Semantic Web Data Integration with hCalendar and GRDDL; Dan Connolly | From Syntax to Semantics (XML 2005) Atlanta, GA, USA
  16. ^ "SPARC Open Data Mailing list". Archived from the original on 2011-06-02. Retrieved 2011-05-28.
  17. ^ [1]
  18. ^ XTech 2005
  19. ^ Tim Bray and Tim O'Reilly
  20. ^ OECD Declaration on Open Access to publicly funded data Archived 20 April 2010 at the Wayback Machine
  21. ^ OECD Principles and Guidelines for Access to Research Data from Public Funding
  22. ^ "Science Commons in Washington 2006". Archived from the original on 2011-05-23. Retrieved 2011-05-28.
  23. ^ SPARC-OAF forum
  24. ^ "OECD Principles and Guidelines for Access to Research Data from Public Funding". OECD.
  25. ^ Launch of the Panton Principles for Open Data in Science and 'Is It Open Data?' Web Service
  26. ^ Kauppinen, T.; Espindola, G. M. D. (2011). "Linked Open Science-Communicating, Sharing and Evaluating Data, Methods and Results for Executable Papers". Procedia Computer Science. 4: 726–731. doi:10.1016/j.procs.2011.04.076.
  27. ^ "Final report - Science as an open enterprise". royalsociety.org. Retrieved 2017-09-29.
  28. ^ "G8 Science Ministers Statement". Foreign & Commonwealth Office.
  29. ^ "Global Data Organization Adopts Open Data Sharing Principles". AlphaGalileo. Retrieved 8 January 2016.
  30. ^ Emerson, Claudia; Faustman, Elaine M.; Mokrane, Mustapha; Harrison, Sandy (2015). "World Data System (WDS) Data Sharing Principles". doi:10.5281/zenodo.34354. Cite journal requires |journal= (help)
  31. ^ A statement by the Association of Learned and Professional Society Publishers (ALPSP) and the International Association of Scientific, Technical and Medical Publishers (STM) Archived 2014-02-08 at the Wayback Machine, Association of Learned and Professional Society Publishers
  32. ^ "The PRO Initiative for Open Science". Peer Reviewers' Openness Initiative. Retrieved 15 September 2018.
  33. ^ Witkowski, Tomasz (2017). "A Scientist Pushes Psychology Journals toward Open Data". Skeptical Inquirer. 41 (4): 6–7. Archived from the original on 2018-09-15.

External links[edit]


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