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Open science at EMBL�Introduction and Overview

30 November 2022

Victoria Yan ( 0000-0003-1982-9145)�Bastian Drees ( 0000-0003-3508-602X)

EMBL Office for Scientific Information Management

EMBL Open Science training for new Group Leaders

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What is not Open Science?

Slide adapted from Anna Kreshuk

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Why Open Science?

Problems and Crises:

Reproducibility
Affordability (serials crisis)
Reusability
Transparency
Metrics and assessment
Communication gap (science – society)
...

The Turing Way Community, & Scriberia. (2021). Illustrations from the Turing Way book dashes. Zenodo. https://doi.org/10.5281/zenodo.5706310

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What is Open Science?

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Gallagher, et al. Open Science principles for accelerating trait-based science across the Tree of Life. Nat Ecol Evol 4, 294 (2020). https://doi.org/10.1038/s41559-020-1109-6

UNESCO Recommendations on Open Science (2021)

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EMBL aims to be a

leader and innovator in open science –

in terms of the scientific results it produces as well as in the way research in molecular biology is performed.

Open Science aims to make scientific research

accessible and transparent, and to remove barriers…

EMBL research is open

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Open Science policy at EMBL

Research articles, data, software

Show progress and create spirit

Spirit of the policy: transparent, open, trustworthy, FAIR

Supporting guidelines

Policy in line with funders

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21/10/2022

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Office for Scientific Information Management

Szilárd Library

EMBL Archive

and Records Management

Open Science Support

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Office for Scientific Information Management (OSIM)

https://www.embl.org/internal-information/news/topic/we-are-embl

https://www.embl.org/news/lab-matters/welcome-maria-papanikolaou/

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09/11/2022

https://www.embl.org/jobs/position/HD02318

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EMBL Open Science Policy - Publications

Publish all articles initially as a preprint.

Publish Open Access with a

CC-BY licence.

Link publications to ORCID during submission.

Deposit in EPMC within 6 months of publication.

Standard EMBL affiliation acknowledgment

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Credit and visibility of all research outputs

Register on ORCID, add id to SAP HR system
Using ORCIDs during submissions
Claim past publications on EuropePMC
Claim preprints, datasets, methods, and other research outputs

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Central Article Processing Charge (APC) Budget

Open Access

EMBL lead author
no grant can cover APCs
CC-BY licence (no NC-ND)
APC discounts and publisher agreements
Check Open Science Policy Compliance
(Advise on exceptions)
(Publisher policy and licence agreements)

Invoice

Shopping Cart

(112 Off-prints)

Check OS Compliance

Approval

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Open Access Publishing

OA publishing agreements

Publish and read agreements

Springer DEAL
Wiley DEAL
CoB
Nature P&R (2023)
RSC R&P (2023)
RUP R&P (2023)

Prepayment schemes

IUCr

OA membership

NAR
PLOS
Royal Society

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Projekt DEAL

Access to 1.600 Wiley and 1.900 Springer journals (1997 – present)

Publish OA in 1.420 Wiley and 1.900 Springer journals for free

20% discount in 110 Wiley and 600 Springer fully OA journals

No agreement with Elsevier:

~ 200 German institutions canceled subscriptions
42 scientists resigned from editorial activities

No one complained

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EMBL Open Science Policy – Open Source Software

Analysis

Services

Methods

Education

Open Source by default.

Made available in open community software repositories.

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Research Data Management

Introduce Research Data Management

What is a Data Management Plan (DMP)?

Resources and support at EMBL

EMBL's DMP template
Data Management App
STOCKS

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EMBL Open Science Policy - Data

Accessible

Interoperrable

Reusable

Findable

FAIR Principles – for all projects from the start

Data Mgmt Plan

+

=

Permanent ID

Indexed, Documented

Who, where, retrieval, authorization

Requirements Benefits

Formats,

standards

Metadata,

Licence

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Research Data Management

What is Research Data?

All research data that was USED or PRODUCED

Simulation, observational data
Code, scripts
AV data
Raw and processed

What is Metadata?

Data on data

Administrative, Descriptive, Structural
Who, when, how, why
Resources, reagents
Experimental information, treatment, conditions
Licence, location, Persistent identifiers => reuse

Slide adapted from Jeanne Wilbrandt

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Standards and databases for data, metadata

Administrative: relevant to managing it
Descriptive/citation: assists with discovery/identity
Structural: how the data came about & is structured

Slide adapted from Lisanna Paladin (EMBL BioIT)

FAIRsharing.org

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DMP template

Data management plan template

Data Management guide (Wiki - Ellenberg lab)

A DMP is a formal living document that outlines what you will do with the data during and after the project.

Required at EMBL at the project level.

Who can support you with DMPs?

OSIM@embl.org
Jean-Karim Heriche

heriche@embl.de

EMBL Bio-IT

bio-it@embl.org

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STOCKS

STOCKS is a web platform for fundamental research data-management, featuring an inventory system coupled to an Electronic Lab Notebook (ELN).

A relational database to connect reagents to equipment, to protocol, to experiment, to data.

Who can support you with STOCKS?

STOCKS team

gbcs@embl.de

Bio-IT STOCKS Training bio-it@embl.org

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Data Management App

(DMA)

The Data Management Application (DMA) is a flexible and customizable tool to assist you as an EMBL researcher in managing your data and documenting your data lifecycle from production to archiving.

Makes your DMP creation easier - delegate the documentation and description of how you will track your data on the file system level to the DMA docs.

Out of the box tracking for File System operations - sharing, archival, deletion etc.

Who can support you with EMBL's DMA?

DMA team

dma@embl.de

Slide adapted from DMA team presentation and documentation

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Add value and interactivity to Open Data

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21/10/2022

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/

EMBL's Computational Support for Web Apps

https://shiny-portal.embl.de

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Research Assessment in Academia

Impact factors have been shown to:

Be unreliable to measure citations
Promote adverse behaviours in the research community
Do not apply to research outputs other than publications

Academics often rely on journal impact factors and H-indexes to evaluate the quality of research

Research Assessment Reform is an active initiative by researchers, research-performing institutes and funders

The aim is to improve the ways in which researchers and the outputs of scholarly research are evaluated

Notes for presenters:

Existing approaches to research assessment may use simplistic numerical proxies which favour scientists who secure large grants, are affiliated to well known institutions and publish in exclusive journals with high-impact factors, such as Cell, Nature and Science. This method of assessment creates skewed incentives and puts pressure on the research community to succeed in a small number of performance metrics, rather than the full range of valuable scientific contributions.
There is a growing consensus amongst scientists, science funders and policy makers that a new system is needed which appropriately values the full breadth of scientific research outputs and their intrinsic merits.

Some useful resources:

https://www.nature.com/nature-index/news-blog/whats-wrong-with-the-jif-in-five-graphs

https://www.nature.com/articles/d41586-018-02398-z

With more detail: https://arxiv.org/ftp/arxiv/papers/1801/1801.08992.pdf

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What is DORA?

Declaration On Research Assessment

Consider the value and impact of all research outputs (including datasets and software)

Consider a broad range of impact measures

Be explicit about the criteria used to reach hiring, tenure, and promotion decisions

https://sfdora.org

Notes for presenters:

The idea to write the declaration was developed in 2012 during at the Annual Meeting of the American Society for Cell Biology in San Francisco. It has become a worldwide initiative covering all scholarly disciplines and all key stakeholders including funders, publishers, professional societies, institutions, and researchers. It says:

General

Do not use journal-based metrics, such as Journal Impact Factors, as a surrogate measure of the quality of individual research articles, to assess an individual scientist’s contributions, or in hiring, promotion, or funding decisions.

For research institutions:

Be explicit about the criteria used to reach hiring, tenure, and promotion decisions
Consider the value and impact of all research outputs (including datasets and software) in addition to research publications, and consider a broad range of impact measures including qualitative indicators of research impact, such as influence on policy and practice.

For researchers

When involved in committees making decisions about funding, hiring, tenure, or promotion, make assessments based on scientific content rather than publication metrics.
Use a range of article metrics and indicators on personal/supporting statements, as evidence of the impact of individual published articles and other research outputs.
Challenge research assessment practices that rely inappropriately on Journal Impact Factors and promote and teach best practice that focuses on the value and influence of specific research outputs.
Wherever appropriate, cite primary literature in which observations are first reported rather than reviews in order to give credit where credit is due.

All individuals and organizations who are interested in developing and promoting best practice in the assessment of researchers and scholarly research are encouraged to sign DORA.

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Four recommendations on Research Assessment implementation

Clearly state EMBL’s commitment to the principles of DORA. We will include the following text on all job advertisements:

"EMBL supports fair and responsible research assessment, which includes its recruitment and performance assessment processes. We recognise a range of research outputs, discourage inappropriate use of proxies such as journal impact factors, and value research outputs based on their intrinsic merit. EMBL is a signatory of the San Francisco Declaration on Research Assessment (DORA)”

Update the type of research outputs requested of applicants

candidates will be asked to include different research outputs (publications, datasets, software and patents etc.) in their CV and a narrative describing the significance of key research outputs.

Provide guidance to internal and external decision-making committees and evaluators (about funding, hiring, assessment, tenure, or promotion).

Change to SAC explicit instructions and efactoring of Unit review dossier form to include alternative research outputs such as software and data

Communicate of EMBL’s Research Assessment practices

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Contact: www.embl.org/osim | osim@embl.org | library@embl.org | archive@embl.org

Thank you!