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Open Science and FAIR Data

26 September 2023

Victoria Yan ( 0000-0003-1982-9145)

Open Science Research Information Specialist

EMBL EIPOD Data Management Workshop 2023

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What is not Open Science?

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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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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 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

Standard EMBL affiliation acknowledgment

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Green OA: self-archiving and manuscript versions

  • Preprint server
    • arXiv, bioRxiv, medRxiv

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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

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  • As a reader
    • Unpaywall
    • Openaccessbutton

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Partner in PubMed Central International archive network

Repository of choice for international science funders

Innovative search

  • articles and preprints
  • full text and abstracts
  • article sections (e.g. in results)

Enriched article

  • peer reviews
  • protocols and reagents
  • funding, citations & more...

Accessible data

  • links to over 40 databases
  • search by experimental data

Free open database of life sciences literature from trusted sources

What is Europe PMC?

Why use Europe PMC?

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Creative Commons License: How open is it?

Open

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Closed Access is increasing: a double dipping world

Barbers, I., & Pollack, P. (2021). Open Access in Deutschland.

Seinfeld (TV Series), The Implant (1993)

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Subscription and publication costs

Subscriptions:

  • +5-6% per year
  • Elsevier, Nature, Wiley: 60% of all subscription costs
  • Cell: +40% since 2016
  • Nature: +110% since 2006

Publication costs (APC):

  • +65-100 % since 2011*
  • If all EMBL articles were gold OA: ~ 3.500.000 €
  • Cell: 8.500 € & Nature: 9.500 €; average: ~4.000€ per article

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*https://treemaps.openapc.net/apcdata/openapc

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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)

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Acceptance

Ticket System

OSIM@EMBL.org

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)
  • Prepayment schemes
    • IUCr
  • OA membership
    • NAR
    • PLOS
    • Royal Society

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ORCID (Open Researcher and Contributer ID)

  • Register on ORCID
  • Using ORCIDs during submissions
  • Claim past publications on EuropePMC
  • Claim preprints, datasets, methods, and other research outputs

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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.

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EMBL Open Science Policy - Data

Accessible

Interoperrable

Reusable

Findable

FAIR Principles – for all projects from the start

Data Mgmt Plan

+

+

=

Persistent 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

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What is Metadata?

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

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Slide adapted from Jeanne Wilbrandt

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Resources and Support at EMBL

OS policy guidelines:

Data Management Checklist

Data Management Template

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Contact:

OSIM@embl.org

Jean-Karim Heriche: heriche@embl.de

Bio-IT: bio-it@embl.org

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

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Contact:

STOCKS team: gbcs@embl.de

STOCKS Training: bio-it@embl.org

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.

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More Info: DMA intranet page

Contact DMA team: dma@embl.de

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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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www.embl.org/osim

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

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Thank you!