Open Science and Open Access

Introduction and Overview

Dr. Bastian Drees

0000-0003-3508-602X

Dr. Victoria Yan

0000-0003-1982-9145

What is not Open Science?

Slide adapted from Anna Kreshuk

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04/07/2022

Why Open Science?

Problems and Crises of Science:

• Reproducibility
• Affordability (serials crisis)
• Functionality
• Transparency
• Metrics and assessment
• Communication gap and delay (science – society, science - policy)
• ...

https://www.openaire.eu/what-is-open-science

Open Science – A global movement

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“Recognizing the urgency of addressing complex and interconnected environmental, social and economic challenges for the people and the planet, [...]

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Considering that more open, transparent, collaborative and inclusive scientific practices, coupled with more accessible and verifiable scientific knowledge [...] improves the quality, reproducibility and

impact of science, and thereby the reliability of the evidence needed for robust decision making and policy and increased trust in science,...”

An urgent need for Open Science

https://en.unesco.org/science-sustainable-future/open-science/recommendation

Growing shift towards Open Data and Open Source

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• New national, funder and institutional policies.

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• Policies broader in scope including data, software.

2022

Distinction: Open Science, Open Access, Free Access

UNESCO Recommendation on Open Science, https://en.unesco.org/science-sustainable-future/open-science/recommendation

What is Open Access?

BBB Definition of Open Access

Budapest Open Access Initiative (2002)

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Bethesda Statement on OAP (2003)

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Berlin Declaration on OA (2003)

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“1. …right holder (…) grants to all users a free, irrevocable, worldwide, right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship (…)”

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2. Work is deposited in a repository “that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving.”

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Creative Commons License: How open is it?

Road to Open Access?

Green and Gold OA: manuscript versions

• Preprint server
• arXiv, bioRxiv, medRxiv
• Preprints.org, osf.org

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• Repositories
• Europe PMC or Pubmed Central
• ROAR or OpenDOAR

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• Submitting a paper
• Sherpa Romeo, Sherpa Juliet
• Shareyourpaper.org
• Transpose database

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• As a reader
• Unpaywall
• Open Access Button

Gold and Green Open Access: pro & con

Eisen, MB, The inevitable failure of parasitic green open access, 2015, http://www.michaeleisen.org/blog/?p=1710

The hybrid Open Access World

• +40% subscription costs since 2016

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• 8.500 € APC

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• +110% subscription costs since 2006

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• 9.500 € APC

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cOAlition S and Plan S

“With effect from 2021, all scholarly publications (…) funded by public or private grants provided (…), must be published in Open Access Journals, on Open Access Platforms, or made immediately available through Open Access Repositories without embargo.”

https://www.coalition-s.org/

Projekt DEAL

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• Negotiations 2016/17
• No agreement
• ~ 200 German institutions canceled subscriptions
• 42 scientists resigned from editorial activities

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• 2019-2021 (opt. +1yr)
• Access to 1.600 journals (1997 – present)
• Publish OA in 1.420 journals
• 20% discount in 110 fully OA journals

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• 2020-2022 (opt. +1yr)
• Access to 1.900 journals (1997 – present)
• Publish OA in 1.900 journals
• 20% discount in 600 fully OA journals

Alliance of German Science Organizations negotiated nationwide transformative “publish and read” agreements on behalf of all German academic institutions.

Future of OA publishing

Open Access in practice follows market forces

• Gold OA is now the primary way of publishing
• Estimated to be just under 1 billion dollars – Delta Think

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• Unsustainable growth, 3x inflation in APCs, no sign of consumer price sensitivity
• Overall increase in publication volume, introducing new significant cost for OA in addition to journal subscription fee.

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Khoo 2019

Preprints and the future of publishing

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• Cost free, formal peer review organized by the community or journal, integrated with publishing.
• Peer review published alongside preprints increasing transparency, trust, and reduce rounds of review.
• Refereed preprints recognized by funders – EMBO Postdoc Fellowship.
• Preprints in applications and internal reviews

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Publish

Review

Curate

Open Access - Diamond on the horizon

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Publish

Cur-ate

Take-Home: What can (should) you do?

Tennant, J., et al. Ten Hot Topics around Scholarly Publishing. Publications 2019, 7, 34. https://doi.org/10.3390/publications7020034

Ask OSIM

Open Science at EMBL

EMBL Open Science Policy - Publications

EMBL Open Science Policy - Data

Data Mgmt Plan

for all projects

Accessible

Interoperrable

Reusable

Findable

EMBL DMA

EMBL STOCKS

FAIR data ≠ Open Data

FAIR data > Open Data

Think reuse, not publication

EMBL Open Science Policy – Open Source Software

Analysis

Services

Methods

Education

Open Source by default.

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Made available in open community software repositories.

Open Science Policy in Research Institutes and Funders

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04/07/2022

• Promotion of OS Practices
• Open Access and data sharing

• DMP
• Data preservation sharing
• Open Source software
• RCUK and funders

• Publications, OA
• Data, DMP
• Software
• Researcher ID
• Implementation

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Narrower

i.e. Open Access

Broader

i.e. Data, Education

Software

Support and Commitment

Implementation

Policy

• Open Access Policy
• Research data management

Guidelines

Progress

Scope

Intellectual property and patent

Slide modified from Ed-Dash FAIR in (biological) Practice

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04/07/2022

http://www.digitalembryo.org/

Mitotic Cell Atlas

- Jan Ellenberg Group

https://www.mitocheck.org/

You can use a patent to protect your (technical) invention. �You can control copying, making, using, selling or importing

Discoveries, mathematical methods, computer programs are not regarded as inventions but can be Copyrighted. Therapeutic procedures, diagnostic methods and new plant or animal varieties are completely excluded from patentability.

Data cannot be patented and in general, it cannot be copyrighted. It is not possible to copyright facts.

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Choose the appropriate licence for your copyrighted work.

Know in advance which technologies and works you plan to share openly or patent.

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Patents are granted for inventions not known to the public.

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Plan in advance when funded by external grants.

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Consult EMBLEM

grants@embl.org

Open Data amplifies research impact

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Deep learning in Microscopy – Examples given by Anna Kreshuk (EMBL Group Leader)

Data by Robert Cardona

ISBI Neuro segmentation Challenge

Kaggle 2018 Data Science Bowl

– Nuclear Segmentation

Celebrating sharing and reuse of data

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https://researchparasite.com/

https://researchsymbionts.org/

Share data in creative ways to add value and interactivity

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http://www.digitalembryo.org/

Gene Expression Atlas of the

Phallusia mammillata embryo

- Pierre Neveu Group

Mitotic Cell Atlas

- Jan Ellenberg Group

https://www.mitocheck.org/

Thank you for your attention!

Victoria Tianjing Yan

Bastian Drees

Contact: OSIM@EMBL.org

Open Science Support at EMBL