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Article written by: Amanda Hunter & Tracey P. Lauriault

The Organisation for Economic Co-operation and Development (OECD) recently published a policy response to COVID-19 in which they suggest that open science, and the policies & standards that support it, can accelerate the health, social, and economic responses to the virus as barriers to information access are eliminated.

As the first in a series of blog posts about Open Science (OS) and FAIR principles in Canada, here we highlight the key role open science plays in communicating and disseminating official COVID-19 research and public health data before assessing if official COVID-19 reporting in Canada adheres to OS principles.

In a next post, we will analyze official COVID-19 reporting in Canada to assess whether or not these follow Open Science, FAIR principles, and the Open Data Charter in the sharing of COVID-19 data.

What is Open Science?

The OECD Open Science program states that the benefits of open science is that it promotes a more accurate verification of scientific results, reduces duplication, increases productivity, and promotes trust in science.

https://www.oecd.org/science/inno/open-science.htm

Open science (OS) is a movement, a practice and a policy toward transparent, accessible, reliable, trusted and reproducible science. This is achieved by sharing how research and data collection are done so as to make research results accessible and standardized, created once and reused by many. This includes techniques, tools, technologies, and platforms should also be open source wherever possible.

In OS the outputs of the scientific process are considered to be a public good, thus wherever possible articles are published in open access (OA) journals, and research data are shared with the public and other scientists who may want to re-purpose those data in new work, or by people who want to verify the veracity of research results. Reporting COVID-19 Cases by normalizing an open by default approaches means that health scientists, population health experts and government officials make this part of their workflow (maintaining individual privacy of course), and by doing so decision makers beyond government, can scrutinize the results, leading to trust the results while also increasing data sharing.

What role does open science play in combating COVID-19?

In the early stages of the pandemic, knowing the genome provided crucial information to help scientists and researchers identify the origin of the outbreak, treat the infection, develop a diagnostic test and work on the vaccine. In other words, the easier—and quicker—researchers can produce, share and access scientific data, the quicker and the more informed is the collaborative response to the virus.

During the 2002-03 SARS outbreak it took five months to publish a full genome of the virus largely due to information blackouts and lack of data sharing. In contrast, the full genome of COVID-19 was published to an open-access platform nearly a month after the first patient was admitted to the hospital in Wuhan. This provided researchers around the world with a head start. Since OS policies have been operationalized during the pandemic, the resulting free flow of ideas in terms of biomedical research has accelerated (OECD).

The implementation of OS standards during COVID-19 has indeed been largely successful. OECD described how collaborative research and  thee global sharing of information reached unprecedented levels, for example:

  • In March 2020, 12 countries (including Canada) launched the Public Health Emergency COVID-19 Initiative at the level of Chief Science advisors, calling for open access to publications and machine-readable access to data related to COVID-19.
  • Open online platform Vivli offers an easy way to request anonymized data from clinical trials.
  • A COVID-19 Open Research Dataset [CORD-19] was developed that hosts 157,000 + scholarly articles about COVID-19 and related coronaviruses; 75,000 of which are full-text machine-readable data that can be used for AI and natural language processing.

These online, open-source platforms have supported rapid scientific COVID-19 research. OS, facilitated by standards, shared infrastructure and techniques, policies and licences, has been instrumental in the global fight against the pandemic.

Yet, despite the numerous successes, many challenges remain. For example, not all COVID-19 related health research and data adhere to the FAIR principles. FAIR principles are a standards approach which support the application of open science by making data Findable, Accessible, Interoperable, and Reusable. Failure to adhere to FAIR principles has led to an overall lack of communication and coordination during the pandemic. In Canada, data should also adhere to CARE principles, which address issues of Indigenous data governance with respect to Indigenous knowledge along with the OCAP Principles of the First Nation Information Governance Centre (FNIGC). More on this in the following section.

The reporting COVID-19 demographic data and reports in Canada to date falls short on standardized classifications in terms of demographics, as we discussed in an earlier blog post, which makes doing a comparative analysis difficult or impossible: for example, many countries define “recoveries” differently, and in Canada, since health is the jurisdictional responsibility of the provinces and territories, each report in their own way. Even though numerous official organizations publish COVID-19 and health related data, as open data databases or in open data portals, there remains an overall lack of interoperability, comparability and standards.

Where does Canada stand on Open Science?

Canada was implementing an open science framework before the pandemic as follows.

National Action Plan on Open Government

The Government of Canada recently published Canada’s 2018-2020 National Action Plan on Open Government, listing ten commitments to furthering the open government initiative. The plan asserts five commitments to implementing OS in Canada by the end of 2020, as seen below:

A screenshot showing a portion of Canada's 2018-2020 National Action Plan on  Open Government. The main issue addressed here is the difficulty for Canadians to access scientific research outputs: thus the commitments focus on making federal science, scientific data, and scientists themselves more accessible.

The OS portion of Canada’s 2018-2020 National Action Plan on Open Government. It aims to address the difficulty for Canadians to access scientific research: thus the commitments on making federal science, scientific data, and scientists themselves more accessible (Government of Canada, 2018).

The Action Plan addresses issues of accessibility and transparency of scientific research and outlines 5 commitments to amending these issues. These commitments include:

  1. Development of an OS roadmap,
  2. Providing an open access platform for publications,
  3. Raising awareness of federal scientists’ work,
  4. Promoting OS and soliciting feedback on stakeholder needs, and
  5. Measuring progress & benefits of the OS implementation.

Despite the comprehensiveness of the Roadmap (see below), Canada has not yet moved past the Action Plan’s second commitment—to provide a platform for Canadians to find and access open access (OA) publications from federal scientists—despite the projected March 2020 deadline. Also, at the time of writing, there is no federal open science platform or portal for users to access open science data in Canada even though there is an open data portal. The New Digital Research Infrastructure Organization (NDRIO) does show promise.

There are however some open data initiatives, such as the Federal Open Government and COVID-19 section on the Open Government Canada Portal.  Here Epidemiological and economic research data, with mathematical modeling reports, a map of cases and deaths by province, daily and weekly detailed epidemiological reports, and an ongoing dataset of COVID-19 cases, deaths, recoveries, and testing rates in Canada’s provinces and territories are made available. This is a significant improvement from the early days of reporting, as data journalist Kenyon Wallace discovered that on a daily basis, the Province of Ontario published new data but each time they did they overrode the previous day’s reports. His article and some work by Lauriault with the Ontario Open Government team resulted in changing that practice and raw data are now updated daily and reported. Open data is but one part of the OS process as we will see when we look at the FAIR principles.

Open Science Roadmap

The plan’s first commitment, to “develop a Canada Open Science Roadmap…” was completed and published in February 2020. The document provides ten recommendations made by Chief Science Advisor, Dr. Mona Nemer, to advance Canada’s OS initiatives. Like the policy brief by OECD, the roadmap is driven by the importance of trust among collaborators, inclusiveness of varying perspectives, and transparent processes throughout.

A screenshot of the cover of Canada’s Roadmap for Open Science (Government of Canada, 2020)

Canada’s Roadmap for Open Science (Government of Canada, 2020)

Most importantly, the Roadmap describes a commitment to developing an OS framework, including adopting the FAIR principles and “open by design and by default” specifications. The roadmap asserts Canada’s commitment to upholding these standards and policies via 10 recommendations:

10 recommendations made in the Roadmap for Open Science. Key points include the adoption of an OS framework in Canada, making federal scientific research outputs ‘open by default’, and implementing FAIR principles. (Government of Canada, 2020).

10 recommendations in the Roadmap for Open Science. Key points include the adoption of an OS framework, making federal scientific research outputs ‘open by default’, and implementing FAIR principles (Government of Canada, 2020).

Model Science Integrity Policy

Canada also has a Model Science Integrity Policy (MSIP) for the public service. The MSIP represents an internal commitment to integrity and accountability in science. Various mandates in the MSIP state that their purpose is to increase public trust in the credibility and reliability of government research and scientific activities, and ensure that research and scientific information are made available in keeping with the Government of Canada’s Directive on Open Government. The MSIP echoes Canada’s commitment to OS.

Indigenous Data Governance 

Finally, Canada has some commitment to supporting Indigenous rights to self-determination and data governance, but does not incorporate standards such as CARE principles which support OS  nor the OCAP Principles when it comes to Indigenous data governance. These extend the FAIR principles.

The Global Indigenous Data Alliance (GIDA) introduced the CARE principles to complement the FAIR principles in 2019. The CARE principles for Indigenous data governance were developed to address a lack of engagement between the open science movement and Indigenous rights and interests (GIDA, 2019).

The FAIR principles focus on data accessibility of data and sharing but fail to address power differences and the impact of colonialism experienced by Indigenous peoples and their right to exercise control and ownership of data about them and local and traditional knowledge. The CARE principles are crucial for the recognition and advancement of these rights as they encourage open science (and other ‘open’ movements) to “consider both people and purpose in their advocacy and pursuits” (GIDA, 2019). The CARE principles are contrasted with the FAIR principles in the below image from the GIDA website:

The CARE principles, which are “collective benefit, authority to control, responsibility, and ethics”, contrasted with the FAIR principles, which are “findable, accessible, interoperable, and reusable” (GIDA, 2019)

The CARE principles are “collective benefit, authority to control, responsibility, and ethics”, contrasted with the FAIR principles, which are “findable, accessible, interoperable, and reusable” (GIDA, 2019)

The OCAP Principles of Ownership, Control, Access and Possession are another set of important principles, that are a better fit in the Canadian Context.  Members of our project currently taking the Fundamentals of OCAP course and we hope to better incorporate these approaches in our work and in how we assess official reporting. Though Indigenous data governance and handling of Indigenous knowledge are not addressed in the Open Science Roadmap, the Data Strategy Roadmap for the Federal Public Service does demonstrate a federal approach to supporting Indigenous data strategies (see below):

Recommendation #8 from the Data Strategy Roadmap for the Federal Public Service which states Canada’s recognition of the Indigenous right to self-determination and data governance (Government of Canada, 2019)

Recommendation #8 from the Data Strategy Roadmap for the Federal Public Service which states Canada’s recognition of the Indigenous right to self-determination and data governance (Government of Canada, 2019)

Next Steps

Much progress has been made in terms of publishing, reporting and communicating data in the short time since COVID-19 began (though not without pressure from the media!). Open access to scientific research and public health reports have been helpful to facilitate the rapid response to the virus and keeping the public informed on how science informs governments actions. There is, however, much left to be done.

  1. Open Science should consider bias in data as well as invisibilities for example interdisciplinary work that helps paint the fuller picture of the impact of the virus. For example, interdisciplinary and intersectional approaches to data categories, including research based in critical race theory (CRT), Indigenous perspectives, socio-demographics and gig labour groups for example.
  2. Second, as suggested by the OECD, making COVID-19 data Findable, Accessible, Interoperable and Reusable is critical for a more effective rapid response. Lack of adherence to FAIR principles currently presents challenges to open science research.
  3. Finally, a meaningful Canadian OS framework should also incorporate standards for Indigenous Data Governance such as CARE Principles and OCAP Principles ensure respectful data practices are followed.

The Tracing COVID-19 Data team is in the process of developing a framework to assess official COVID-19 reporting in Canada to see if they comply with OS, FAIR, CARE, OCAP, and open-by-default at all levels of government. We will draw on Canada’s commitments OS and FAIR in – Canada’s 2018-2020 National Action Plan on Open Government, Open Science Roadmap, the Model Science Integrity Policy and the Open Data Charter.

Is Canada FAIR?

Stay tuned!

Recommendation

All official Federal, Provincial/Territorial and City public COVID-19 data reporting should be open data, open by design and by default, research should be published in open access (OA) Journals and should adhere to open science (OS) such as the FAIR principles , CARE Principles, OCAP Principles and the Open Data Charter.

References

Canadian Internet Policy and Public Interest Clinic. Open Data, Open Citizens? https://cippic.ca/en/open_governance/open_data_and_privacy

Centres for Disease Control and Prevention. (n.d.). SARS- Associated Coronavirus (SARS-CoV) Sequencing. https://www.cdc.gov/sars/lab/sequence.html

CTVNews. (2020). Project Pandemic: Reporting on COVID-19 in Canada. 
https://www.ctvnews.ca/health/coronavirus/project-pandemic

Federated Research Data Repository. (2018). FAIR Principles. 
https://www.frdr-dfdr.ca/docs/en/fair_principles/

Global Indigenous Data Alliance. (2019). CARE Principles for Indigenous Data Governance. 
https://www.gida-global.org/care

Government of Canada. (2014). Directive on open government. 
https://www.tbs-sct.gc.ca/pol/doc-eng.aspx?id=28108

Government of Canada. (May, 2016). Open by default and modern, easy to use formats. 
https://open.canada.ca/en/content/open-default-and-modern-easy-use-formats

Government of Canada. (2017). Model policy on scientific integrity.
https://www.ic.gc.ca/eic/site/063.nsf/eng/h_97643.html

Government of Canada. (2018). Canada’s 2018-2020 National Action Plan on Open Government. https://open.canada.ca/en/content/canadas-2018-2020-national-action-plan-open-government#toc8

Government of Canada. (2018). Report to the Clerk of the Privy Council: A Data Strategy Roadmap for the Federal Public Service. https://www.canada.ca/content/dam/pco-bcp/documents/clk/Data_Strategy_Roadmap_ENG.pdf

Government of Canada. (2020). Coronavirus disease (COVID-19): Outbreak update.
https://www.canada.ca/en/public-health/services/diseases/coronavirus-disease-covid-19.html?utm_campaign=not-applicable&utm_medium=vanity-url&utm_source=canada-ca_coronavirus

Government of Canada. (2020). Office of the Chief Science Advisorhttps://www.ic.gc.ca/eic/site/063.nsf/eng/h_97646.html

Government of Canada. (2020). Open Government Portal.
https://open.canada.ca/data/en/dataset

Lauriault, T. (2020, April 17). Tracing COVID-19 Data: COVID-19 Demographic Reporting. Datalibre.
http://datalibre.ca/2020/04/17/covid-19-demographic-reporting/

National Centre for Biotechnology Information. (2020). Public Health Emergency COVID-19 Initiative.
https://www.ncbi.nlm.nih.gov/pmc/about/covid-19/?cmp=1

Open Data Charter. (n.d.). The International Open Data Charter.
https://opendatacharter.net

Organisation for Economic Co-operation and Development. (2020, May 12). OECD Policy Responses to Coronavirus (COVID-19): Why open science is critical to combatting COVID-19.
http://www.oecd.org/coronavirus/policy-responses/why-open-science-is-critical-to-combatting-covid-19-cd6ab2f9/

Ford & Airhihenbuwa. (2010). The public health critical race methodology: Praxis for antiracism research. Science Direct.
https://www.sciencedirect.com/science/article/abs/pii/S0277953610005800#!

Semantic Scholar. (2020). CORD-19: COVID-19 Open Research Dataset.
shorturl.at/wETZ5 

The Lancet. (January, 2020). Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

The National Academies of Science, Engineering, Medicine. (2018). Open Science by Design: Realizing a Vision for 21st Century Research. Chapter 1, Front Matter. 
https://www.nap.edu/read/25116/chapter/1

The Star. (2020). Coronavirus & COVID-19 Data. https://www.thestar.com/coronavirus/data.html

Vivli. (2020).
https://vivli.org/about/overview-2/

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I was taking snack break and while doing so perused the #census in twitter and found this little gem. It is a bit long, but I like the idea nonetheless.  This is simply animating a power point with images if how many’s in a 100 in Ottawa.  We can do so much with data, and why not this type of reporting of the findings, and some engaging visualizations like they do in the NY Times while we are at it!  Looks like the Peel Region did something similar with their data!

Ottawa as a 100 person village

This, I love:

The Open Dinosaur Project was founded to involve scientists and the public alike in developing a comprehensive database of dinosaur limb bone measurements, to investigate questions of dinosaur function and evolution. We have three major goals:1) do good science; 2) do this science in the most open way possible; and 3) allow anyone who is interested to participate. And by anyone, we mean anyone! We do not care about your education, geographic location, age, or previous background with paleontology. The only requirement for joining us is that you share the goals of our project and are willing to help out in the efforts.

Want to sign up? Email project head Andy Farke (andrew.farke@gmail.com), and welcome aboard!

[via datalibre]

Jon Udell’s latest innovators podcast, Open Data Access with Steven Willmott:

There’s growing awareness of the need to publish data online, and to support programmatic access to that data. In this conversation, host Jon Udell talks with Steven Willmott about how his company, 3Scale, helps businesses create and manage application programming interfaces to their data.

Says Jon on his blog:

In the latest installment of my Innovators podcast, which ran while I was away on vacation, I spoke with Steven Willmott of 3scale, one of several companies in the emerging business of third-party API management. As more organizations get into the game of providing APIs to their online data, there’s a growing need for help in the design and management of those APIs.

By way of demonstration, 3scale is providing an unofficial API to some of the datasets offered by the United Nations. The UN data at http://data.un.org, while browseable and downloadable, is not programmatically accessible. If you visit 3scale’s demo at www.undata-api.org/ you can sign up for an access key, ask for available datasets — mostly, so far, from the World Health Organization (see below) — and then query them. [more…]

beers for canadaFor the price of a beer (or a pitcher, or a round), you can support VisibleGovernment.ca … the non-profit that promotes online tools for government transparency, openness and accessibility around government and civic data (yay!).

They’ve got a little fundraiser going, in celebration of Canada Day: Beers for Canada

How we’ll spend your money

We work on several aspects of transparency:

  • Creating new tools: We work with developers and designers to build websites that encourage citizens and governments to communicate openly.
  • Encouraging government openness: We show elected officials the benefits of open, two-way discourse, highlighting places where information is lacking and celebrating the efforts of those who want to be more transparent.
  • Public awareness: We emphasize the civic importance of transparency and open government.
  • Working with other organizations: We share and collaborate with organizations like the Sunlight Foundation, MySociety and Changecamp.

We’re also organizing Code For Canada, an application design competition that awards prizes to people who build web, facebook, and iPhone apps that provide visualization, analysis, and access to federal government data sets.

So, go support a worthy cause.

ibelieveinopenVisiblegovernment.ca has launched a new site, ibelieveinopen, asking candidates (and citizens) to take a pledge for openness:

I believe candidates should:

  • Support reforms that increase government transparency and accountability.
  • Make campaign promises specific and measurable, and report progress on promises and their metrics at least semi-annually.
  • Publish the content of his or her daily schedule, including meetings with lobbyists and special interest groups.
  • Support reforms allowing free access to scientific and survey data gathered by government institutions.
  • Support reforms that make it easier for Canadians to obtain government information they have a right to know.

As of today, there are 51 candidate pledges (29 Greens, 21 NDP, and 1 Libera)l.

You might consider sending your candidates an email asking them if they intend to take the pledge. This is what I sent to my candidates:

Hello,

Will [Candidate Name] be signing this pledge?
http://ibelieveinopen.ca/

51 candidates have done so already.

Hugh McGuire

Remember hearing about SETI@home? Check out, and download, Gridrepublic.org:

GridRepublic members run a screensaver that allows their computers to work on public-interest research projects when the machines are not otherwise in use. This screensaver does not affect performance of the host computer any more than an ordinary screensaver does.

By aggregating idle resources from users around the world, we create a massive supercomputer.

Gridrepublic is built on the system that started as SETI@home, which was turned into a general distributed computing platform BOINC. Gridrepublic is a central place for all projects using this distributed platform, where you can dowload & install the system and even better, choose which projects your computer’s idle time will be supporting, including:

Einstein@home: you can contribute your computer’s idle time to a search for spinning neutron stars (also called pulsars) using data from the LIGO and GEO gravitational wave detectors.

BBC Climate Change: The same model that the Met Office uses to make daily weather forecasts has been adapted to run on home PCs. The model incorporates many variable parameters, allowing thousands of sets of conditions. Your computer will run one individual set of conditions– in effect your individual version of how the world’s climate works– and then report back to the research team what it calculates. This experiment was described on the BBC television documentary Meltdown (BBC-4, February 20th, 2006). Note: workunits require several months of screensaver time; faster computers recommended.

Rosetta@home: needs your help to determine the 3-dimensional shape of proteins as part of research that may ultimately contribute to cures for major human diseases such as AIDS / HIV, Malaria, Cancer, and Alzheimer’s.
Proteins@Home: investigating the “Inverse Protein Folding Problem”: Whereas “Protein Folding” seeks to determine a protein’s shape from its amino acid sequence, “Inverse Protein Folding” begins with a protein of known shape and seeks to “work backwards” to determine the amino acid sequence from which it is generated.

Quantum Monte Carlo: Reactions between molecules are important for virtually all parts of our lives. The structure and reactivity of molecules can be predicted by Quantum Chemistry, but the solution of the vastly complex equations of Quantum Theory often require huge amounts of computing power. This project seeks to raise the necessary computing time in order to further develop the very promising Quantum Monte Carlo (QMC) method for general use in Quantum Chemistry.

Donate here.

Create Change Canada

is an educational initiative that examines new opportunities in scholarly communication, advocates changes that recognize the potential of the networked digital environment, and encourages active participation by scholars and researchers to guide the course of change.

Create Change was developed by the Association of Research Libraries (ARL) and SPARC (Scholarly Publishing and Academic Resources Coalition) and is supported by the Association of College and Research Libraries (ACRL). The website was adapted for the Canadian environment by SPARC and the Canadian Association of Research Libraries (CARL). The US version of Create Change is available here.

Create Change has a small section (relative to the others) on data. It refers to the 2005 National Consultation on Access to Scientific Research Data (NCASRD) report. But alas, there remains no national strategy or resources for infrastructures and policies on the issue of open access, dissemination and preservation of scientific data in Canada since that report. The NCASRD report was also only briefly mentioned in the October 2007 Canadian Digital Information Strategy (CDIS). I am glad Create Change mentions the NCASRD report as it is one of the few consultations that included data specialists and scientists, making its recommendations relevant, grounded in practice and includes clear recommendations and strategies overlooked by the CDIS.

The Harnessing Data Section also refers to the Research Data Centre Program which is a closed shop when it comes to citizens as it is a Statistics Canada initiative only open to researchers, a great US National Institute of Health (NIH) genetic sequence database GenBank® and a Canadian Astronomy Data Centre. Odd that the Science Commons and the work of government departments that disseminate scientific data such as NRCan’s Data Discovery Portal is not mentioned! Both of these were groundbreaking. Most notably the very progressive Geobase Unrestricted Use Licence Agreement, open and free access to some (not all) of Canada’s national framework data and GeoGratis which disseminates free data. Canadian’s still do not have access to basic national, provincial and municipal geomatics data sets (let alone a most socio demographic data), nonetheless, the work of GeoConnections is surely to grow and their dissemination, accord signing, technological approaches, standards and partnership practices can most certainly be emulated elsewhere.

I hope Create Change will help open up natural and social science data to Canadians. At the moment their site provides much more on open access journals, new forms to disseminate and discover scholarly works, methods to create those works, and the scholarly merit system. There is less on scientific data, perhaps as is normally the case in Canada, scientific organizations like CODATA, or science producing organizations are not at these tables. I fully support the direction Create Change is going, however, journals, scholarship and the merit system evolve around access to data – data is what informs scholarly works and I would love to see more input from the data people!

I was very excited to see which journals are accessible in their Expanding Access Section and I look forward to seeing scientific organizations contribute to their Harnessing Data Section.  They most certainly have the right cultural institutions, publishing, and library people at the table but they are missing scientific data associations and archivists.

mapping london

I’m in an Advanced GIS class for which I need to produce a final cartographic project. The project must begin in ArcGIS but from there I’m free to use anything else (Illustrator, Flash, Google Earth, etc). In the spirit of John Snow, I’d like to make my upcoming trip to London a force for academic good.

Any ideas, to help out?

us political blogmap It seems that there is an explosion of data visualization work being done on the political process and the Presidential election in the US of A. I just landed on PresidentialWatch08 a site for all you political junkie/blogospheria/dataviz fans. They’ve got a lovely map of influential political blogs and news sites. The project seems to be run by a web analytics company, linkfluence.

Anyone planning anything similar in Canada?

[via infosthetics]

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