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==Open Data in Science==
==Open Data in Science==


# scientific data deemed to belong to the commons (e.g. the human genome)
See: [[Open Data in Science]]
# infrastructural data essential for scientific endeavour (e.g. in Geographic information systems)
# data published in scientific articles which are factual and therefore not copyrightable


* '''Open Notebook Science''' refers to the application of the Open Data concept to as much of the scientific process as possible, including failed experiments and raw experimental data.
===Definition===
Peter Murray-Rust of the Unilever Centre for Molecular Sciences Informatics at the University of Cambridge (UK):
“The emerging Open Data movement shares many goals with the Open Access and Open Source movements, but encompasses its own distinct issues that are in need of examination by the scientific community. Many advocates of Open Data believe that, although there are substantial potential benefits from sharing and reusing digital data upon which scientific advances are built, today much of it is being lost or underutilized because of legal, technological and other barriers."
(http://www.arl.org/sparc/announce/102405.html)
===Requirements for Open Data in science===
Quoted from http://www.windley.com/archives/2006/05/free_the_data.shtml
 
* Re-use structures including schemas and ontologies. It’s more important to use well-understood structures than to use any particular idiom.
* Re-use the licenses that have already been developed. Licensing meta-data (ala Creative Commons) is also important.
* Enable re-use of ideas (contrasted with the expression of the idea). We have to find the proper scope of ‘derivative works’ and re-examine the issue of database copyright. Shockingly, copying the bibliographic data from a work (for purposes of citation) can be seen as a violation of some licenses.
* Attach policy information that says how the information can be used. Some experimental data depends critically on personally identifying information. Anonymization is a hard task either not working well or being at odds with the underlying research purpose of the data.
* Use open standards
(Weitzner presentation at http://www.w3.org/2006/Talks/0525-web-data-publishing/#(3); qutoed here [http://www.windley.com/archives/2006/05/free_the_data.shtml])
===Open Data in Science must be machine-readable===
Murray-Rust (cited by Richard Poynder):
" traditional subscription publishers like the American Chemical Society and Wiley explicitly forbid text mining of papers they publish. At the same time these publishers insist that authors not only sign over the copyright in the paper, but also ownership of the supplemental data, despite the fact that factual data are not subject to copyright.
After failing to persuade Open Access advocates to hear his concerns, Murray-Rust began to direct his energies to what he calls the Open Data movement, for which he is now a leading advocate. While he remains an advocate for OA, he explains, he has come to believe that the issue of Open Data needs to be addressed separately. For where the Open Access movement is concerned only with ensuring that scholarly papers are human readable, the Open Data movement requires that they are also machine readable. And since Open Data implies reuse, it is vital that licences are provided that specifically permit this.
Fortunately, Science Commons stepped into the breach, and is proving a valuable ally, not least by developing the Open Data protocol and the recently-announced Public Domain Dedication & Licence (PDDL) — thereby providing the first component of the legal framework that Murray-Rust believes is needed to enable text mining, and helping in the creation of the chemical semantic web."
(http://poynder.blogspot.com/2008/01/open-access-interviews-peter-murray.html)
===Status Report: Access to Research Data in the OECD===
From http://www.firstmonday.org/issues/issue12_6/wunsch/index.html:
"Throughout OECD Member countries, continuously growing quantities of data are collected by publicly funded researchers and research institutions. This rapidly expanding body of research data represents both a massive investment of public funds and a potential source of the knowledge needed to address the myriad challenges facing humanity.
To promote improved scientific and social return on the public investments in research data, OECD member countries have established a variety of laws, policies and practices concerning access to research data at the national level. In this context, it was recognized that international guidelines would be an important contribution to fostering the global exchange and use of research data.
At the outset, the third OECD Global Research Village Conference addressed policy implications of the use of Information and Communication Technologies (ICT) for the global science system in 2000 [7]. In particular, the conference discussed issues of access to publicly financed research related to ICT as for instance access to intellectual property and data resources. In 2001, the OECD’s Committee for Scientific and Technological Policy (CSTP) agreed to the establishment of a Working Group to draw up commonly agreed principles to guide access to publicly financed research. Access to and sharing of research data from public funding was chosen as the most appropriate focus for the activities of the Working Group [8]. Collaborations with similar working groups such as CODATA [9] were sought.
In 2004, OECD Science and Technology Ministers declared that fostering broader, open access to and wide use of research data will enhance the quality and productivity of science systems worldwide. Ministers adopted a Declaration on Access to Research Data from Public Funding, asking the OECD to take further steps towards proposing Principles and Guidelines on Access to Research Data from Public Funding, based on commonly agreed principles to facilitate optimal cost-effective access to digital research data from public funding, and taking into account possible restrictions related to security, property rights and privacy (Annex) [10]. It recognizes “that open access to, and unrestricted use of, data promotes scientific progress and facilitates the training of researchers” and “will maximize the value derived from public investments in data collection efforts”, and entrusted the OECD ’s Committee for Scientific and Technological Policy (CSTP) to work towards the establishment of access regimes for digital research data from public funding. The Ministers asked for the guidelines to be endorsed by the OECD Council at a later stage.
An expert group was formed to support this objective of translating Minister’s goals into an OECD policy instrument. The objective of the Expert Group is to draft useful and relevant guidelines that can be used by national governments and a wide variety of research organizations to facilitate and improve the international sharing of, and access to, digital research data gathered with the assistance of public funding.
The nature of “public funding” of research varies significantly from one country to the next, as do existing data access policies and practices at the national, disciplinary and institutional levels. These differences call for a flexible approach to data access and recognition that one size does not fit all."
(http://www.firstmonday.org/issues/issue12_6/wunsch/index.html)
===More Information===
SPARC Open Data Email Discussion List, at http://www.arl.org/sparc/opendata/index.html
[[2004 OECD Ministerial Declaration on Access to Digital Research Data from Public Funding]]


=Open Data Organizations=
=Open Data Organizations=

Revision as of 13:24, 4 March 2009

Definition

From the Wikipedia at http://en.wikipedia.org/wiki/Open_Data

"Open Data is a philosophy and practice requiring that certain data are freely available to everyone, without restrictions from copyright, patents or other mechanisms of control. It has a similar ethos to a number of other "Open" movements and communities such as Open Source and Open access.

Open Data is often focussed on non-textual material such as maps, genomes, chemical compounds, mathematical and scientific formulae, medical data and practice, bioscience and biodiversity. Problems often arise because these are commercially valuable or can be aggregated into works of value. Access to, or re-use of, the data are controlled by organisations, both public and private. Control may be through access restrictions, licenses, copyright, patents and charges for access or re-use. Advocates of Open Data argue that these restrictions are against the communal good and that these data should be made available without restriction or fee. In addition, it is important that the data are re-usable without requiring further permission, though the types of re-use (such as the creation of derivative works) may be controlled by license."


Characteristics

Fundamental Open Data Rights:

"Arguments made on behalf of Open Data include:


  • "Data belong to the human race". Typical examples are genomes, data on organisms, medical science, environmental data.
  • Public money was used to fund the work and so it should be universally available.
  • It was created by or at a government institution (this is common in US National Laboratories and government agencies)
  • Facts cannot legally be copyrighted.
  • Sponsors of research do not get full value unless the resulting data are freely available
  • Restrictions on data re-use create an anticommons
  • Data are required for the smooth process of running communal human activities (map data, public institutions)
  • In scientific research, the rate of discovery is accelerated by better access to data."

(http://en.wikipedia.org/wiki/Open_Data)


Relation to other open activities:

"There are a number of other "Open" philosophies which are similar to, but not synonymous with Open Data but which may overlap, be supersets, or subsets. Here they are briefly listed and compared.


  • Open Source Software is concerned with the licenses under which computer programs can be distributed and is not normally concerned primarily with data.
  • Open Content has similarities to Open Data and may be seen as a superset but differs in that it emphasizes creative works while Open Data is more oriented towards factual data and the output of the scientific research process.
  • Open Knowledge. The Open Knowledge Foundation argues for Openness in a range of issues including, but not limited to, those of Open Data. It covers (a) scientific, historical, geographic or otherwise (b) Content such as music, films, books (c) Government and other administrative information

(http://en.wikipedia.org/wiki/Open_Data)


Open Data are opposed by Closed Data:

"Several intentional or unintentional mechanisms exist for restricting access to or re-use of data. They include:


  • compilation in databases or websites to which only registered members or customers can have access.
  • use of a proprietary or closed technology or encryption which creates a barrier for access.
  • copyright forbidding (or obfuscating) re-use of the data.
  • license forbidding (or obfuscating) re-use of the data
  • patent forbidding re-use of the data (for example the 3-dimensional coordinates of some experimental protein structures have been patented)
  • restriction of robots to websites, with preference to certain search engines
  • aggregating factual data into "databases" which may be covered by "database rights" or "database directives" (e.g. Directive on the legal protection of databases)
  • time-limited access to resources such as e-journals (which on traditional print were available to the purchaser indefinitely)
  • political, commercial or legal pressure on the activity of organisations providing Open Data (for example the American Chemical Society lobbied the US Congress to limit funding to the National Institutes of Health for its Open Pubchem data."

(http://en.wikipedia.org/wiki/Open_Data)


Open Data Policies

RECOMMENDATIONS from the U.S. Public Policy Committee of the ACM (USACM):


  • Data published by the government should be in formats and approaches that promote analysis and reuse of that data.


  • Data republished by the government that has been received or stored in a machine-readable format (such as online regulatory filings) should preserve the machine-readability of that data.


  • Information should be posted so as to also be accessible to citizens with limitations and disabilities.


  • Citizens should be able to download complete datasets of regulatory, legislative or other information, or appropriately chosen subsets of that information, when it is published by government.


  • Citizens should be able to directly access government-published datasets using standard methods such as queries via an API (Application Programming Interface).


  • Government bodies publishing data online should always seek to publish using data formats that do not include executable content.


  • Published content should be digitally signed or include attestation of publication/creation date, authenticity, and integrity.

(http://www.acm.org/public-policy/open-government)


Open Data Domains

The concept of Open Data is used in different contexts, i.e. mostlhy as either the availability of scientific raw data and as open access to publicly funded, 'government' information.

(There is of course an obvious overlap when the scientific data are produced by public funding or government institutions.)


Open Access to Government Information

See Open Access to Government Information, as well as Open Government Data and Open Public Data


Open Data in Science

See: Open Data in Science


Open Data Organizations

Open Data Companies

"“Open data is to media what open source is to technology. Open data is an approach to content creation that explicitly recognizes the value of implicit user data. The internet is the first medium to give a voice to the attention that people pay to it. Successful open data companies listen for and amplify the rich data that their audiences produce.” (http://www.attentiontrust.org/node/430)

  • Adaptive Blue- Extended browsing
  • Aggregate Knowledge- Outsourced recommendations
  • Atten.TV- Attention media
  • Buzzlogic- Tracking influence
  • ClearForest – Text analytics
  • Daylife- Hi-touch algorithmic news
  • Feedburner- RSS content management
  • Lijit Networks- Ranking people
  • Majestic Research- Online behavior for investors
  • Meetup- America offline
  • MyBlogLog- Reader communities
  • Omnidrive- Open data storage
  • Right Media- Transparent ad network
  • Stumbleupon- The "forward" button

(http://www.attentiontrust.org/node/428)

Open Data Repositories

open data sets availiable on the Web.

Examples include Wikipedia, Geonames, MusicBrainz

See also: PubChem


Status Report 2007

Peter Suber:

"With or without mandates, more governments committed themselves to OA for publicly funded data. Norway adopted an OA mandate for public geodata. Canada, Ireland, and Australia began providing OA to publicly funded digital mapping data, without a mandate. After long resistance, the UK Ordnance Survey began to do the same, at least experimentally. (Earlier in the year, a legal analysis by Charlotte Waelde, an expert on intellectual property at the University of Edinburgh, concluded that the data are not protected by copyright but at most, only by the database right; a JISC report recommended a general UK policy of OA for research data; and the new UK Prime Minister Gordon Brown endorsed the principle of public access to public data.) The Committee of Ministers of the Council of Europe recommended "wide public access to research results to which no copyright restrictions apply" (i.e. data). Publishing consultant Eve Gray reported that the South African government was moving toward a policy of OA for publicly funded research data. The Australian government proposed an Australian National Data Service to promote OA and re-use of publicly funded research data. The Organisation for Economic Co-operation and Development (OECD) issued principles and guidelines to implement its 2004 Declaration on Access to Research Data from Public Funding. California is about to adopt the strongest and broadest OA mandate for greenhouse gas data in the US, and Pennsylvania is about to join the other 49 states in mandating OA for state statutes. And the UN Convention on Long-range Transboundary Air Pollution (LRTAP) adopted an OA mandate for most kinds of data covered by the convention.

The US Government Accountability Office called on four major federal funding agencies (DOE, NASA, NOAA, and NSF) to enforce their existing policies on data sharing. Twenty-two US federal government agencies formed an Interagency Working Group on Digital Data (IWGDD), plan to deposit the data generated by their research grantees in a network of OA repositories, and are considering an OA mandate. The US National Archives joined the OA web portal Geospatial One Stop. The NSF Office of Cyberinfrastructure launched a data interoperability project (INTEROP). Google created a Public Sector Initiative to improve its crawling of OA databases hosted by federal, state, and local government agencies in the US. A group of open government activists convened by O'Reilly Media and Public.Resource.Org drafted principles for open government data. For the first time the US made progress toward OA for its three most notorious non-OA government resources: PACER (Public Access to Court Electronic Records), the database of federal court docket information; NTIS (National Technical Information Service), the online databases of research and business data; and CRS Reports, the highly regarded reports from the Congressional Research Service. The first two began offering OA to selected portions of their content, previously TA, and the third is the subject of a new bill in the Senate to mandate OA.

Nature editorialized in favor of e-notebook science and data sharing, and Nature Biotech recommended "that raw data from proteomics and molecular-interaction experiments be deposited in a public [OA] database before manuscript submission." Maxine Clarke, Publishing Executive Editor at Nature, said that the journal would consider requiring and not merely recommending OA for multimedia data if there were a suitable OA repository supporting annotation and long-term preservation. Wiley threatened legal action when Shelley Batts, a graduate student at the University of Michigan, posted a chart from a Wiley article from the Journal of the Science of Food and Agriculture on her blog; when she replaced it with her own chart of the same data and blogged Wiley's threat, the blogosphere exploded and Wiley said it was all a misunderstanding.

Data-sharing policies were adopted by the UK Medical Research Council, the Ethics Committee of France's Centre National de la Recherche Scientifique (CNRS), the Audiovisual Communications Laboratory at Switzerland's Ecole Polytechnique Fédérale de Lausanne, and the International Telecommunications Union. The NIH launched a new data-sharing program for its neuroscience research. There are too many new OA databases to name separately, but since I've mentioned the NIH, I should add that it launched the Database of Genotype and Phenotype (dbGaP) and SHARe (SNP Health Association Resource). It described SHARe as "one of the most extensive collections of genetic and clinical data ever made freely available to researchers worldwide."

Google began helping researchers exchange datasets up to 120 terabytes in size, too large for ordinary online uploads and downloads. At no charge to the researchers, it will ship a brick-sized box of hard drives from one research team to another, provided that the data have no copyright or licensing restrictions and the bricks stop first at Google headquarters for copying and offline storage. In time, Google hopes to make the datasets OA. The company also began sharing files of its own data with researchers on the condition that they make the results of their research OA.

The year 2007 saw a wave of general OA data repositories spring up, many with built-in features for graphics and analysis: for example, Dabble, Data360, Freebase, Many Eyes, Open Economics, StatCrunch, Swivel, and WikiProteins. At the same time, several projects worked to facilitate the deposit of data in OA repositories, such as EDINA's DataShare and JISC's SPECTRa (Submission, Preservation and Exposure of Chemistry Teaching and Research Data), or to enhance the interface between data repositories and literature repositories, such as JISC's StORe (Source-to-Output Repositories).

By my informal estimate, the fields with the largest advances in OA data during 2007 were archaeology, astronomy, chemistry, the environment (including climate change), geography (including mapping), and medicine (especially, genomics and clinical drug trials)." (http://quod.lib.umich.edu/cgi/t/text/text-idx?c=jep;view=text;rgn=main;idno=3336451.0011.110)

More Information

  1. Open Science
  2. Open Notebook Science
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