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SBML Level 3: an extensible format for the exchange and reuse of biological models

Keating, Sarah M ; Waltemath, Dagmar ; König, Matthias ; [et al.]

EMBO ; 2020

In: Molecular Systems Biology Vol. 16, No. 8 ( 2020-08)

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In: Molecular Systems Biology, EMBO, Vol. 16, No. 8 ( 2020-08)

Type of Medium: Online Resource

ISSN: 1744-4292 , 1744-4292

URL: Article

DOI: 10.15252/msb.20199110

Language: English

Publisher: EMBO

Publication Date: 2020

detail.hit.zdb_id: 2193510-5

SSG: 12

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FAIR Principles: Interpretations and Implementation Considerations

Jacobsen, Annika ; de Miranda Azevedo, Ricardo ; Juty, Nick ; [et al.]

MIT Press ; 2020

In: Data Intelligence Vol. 2, No. 1-2 ( 2020-01), p. 10-29

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In: Data Intelligence, MIT Press, Vol. 2, No. 1-2 ( 2020-01), p. 10-29

Abstract: The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.

Type of Medium: Online Resource

ISSN: 2641-435X

URL: Article

DOI: 10.1162/dint_r_00024

Language: English

Publisher: MIT Press

Publication Date: 2020

detail.hit.zdb_id: 2973844-1

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Erratum: The Systems Biology Graphical Notation

Le Novère, Nicolas ; Hucka, Michael ; Mi, Huaiyu ; [et al.]

Springer Science and Business Media LLC ; 2009

In: Nature Biotechnology Vol. 27, No. 9 ( 2009-9), p. 864-864

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 27, No. 9 ( 2009-9), p. 864-864

Type of Medium: Online Resource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/nbt0909-864d

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2009

detail.hit.zdb_id: 1494943-X

detail.hit.zdb_id: 1311932-1

SSG: 12

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The Data Use Ontology to streamline responsible access to human biomedical datasets

Lawson, Jonathan ; Cabili, Moran N. ; Kerry, Giselle ; [et al.]

Elsevier BV ; 2021

In: Cell Genomics Vol. 1, No. 2 ( 2021-11), p. 100028-

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In: Cell Genomics, Elsevier BV, Vol. 1, No. 2 ( 2021-11), p. 100028-

Type of Medium: Online Resource

ISSN: 2666-979X

URL: Article

DOI: 10.1016/j.xgen.2021.100028

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 3110160-4

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GA4GH: International policies and standards for data sharing across genomic research and healthcare

Rehm, Heidi L. ; Page, Angela J.H. ; Smith, Lindsay ; [et al.]

Elsevier BV ; 2021

In: Cell Genomics Vol. 1, No. 2 ( 2021-11), p. 100029-

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In: Cell Genomics, Elsevier BV, Vol. 1, No. 2 ( 2021-11), p. 100029-

Type of Medium: Online Resource

ISSN: 2666-979X

URL: Article

DOI: 10.1016/j.xgen.2021.100029

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 3110160-4

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Empirical validation of an automated approach to data use oversight

Cabili, Moran N. ; Lawson, Jonathan ; Saltzman, Andrea ; [et al.]

Elsevier BV ; 2021

In: Cell Genomics Vol. 1, No. 2 ( 2021-11), p. 100031-

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In: Cell Genomics, Elsevier BV, Vol. 1, No. 2 ( 2021-11), p. 100031-

Type of Medium: Online Resource

ISSN: 2666-979X

URL: Article

DOI: 10.1016/j.xgen.2021.100031

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 3110160-4

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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry, Julie A. ; Juty, Nick ; Blomberg, Niklas ; [et al.]

Public Library of Science (PLoS) ; 2017

In: PLOS Biology Vol. 15, No. 6 ( 2017-6-29), p. e2001414-

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In: PLOS Biology, Public Library of Science (PLoS), Vol. 15, No. 6 ( 2017-6-29), p. e2001414-

Type of Medium: Online Resource

ISSN: 1545-7885

URL: Article

DOI: 10.1371/journal.pbio.2001414

DOI: 10.1371/journal.pbio.2001414.g001

DOI: 10.1371/journal.pbio.2001414.g002

DOI: 10.1371/journal.pbio.2001414.g003

DOI: 10.1371/journal.pbio.2001414.g004

DOI: 10.1371/journal.pbio.2001414.g005

DOI: 10.1371/journal.pbio.2001414.g006

DOI: 10.1371/journal.pbio.2001414.t001

DOI: 10.1371/journal.pbio.2001414.t002

DOI: 10.1371/journal.pbio.2001414.t003

DOI: 10.1371/journal.pbio.2001414.s001

DOI: 10.1371/journal.pbio.2001414.s002

DOI: 10.1371/journal.pbio.2001414.s003

DOI: 10.1371/journal.pbio.2001414.s004

DOI: 10.1371/journal.pbio.2001414.s005

DOI: 10.1371/journal.pbio.2001414.s006

DOI: 10.1371/journal.pbio.2001414.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2017

detail.hit.zdb_id: 2126773-X

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Dead simple OWL design patterns

Osumi-Sutherland, David ; Courtot, Melanie ; Balhoff, James P. ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Journal of Biomedical Semantics Vol. 8, No. 1 ( 2017-12)

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In: Journal of Biomedical Semantics, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2017-12)

Type of Medium: Online Resource

ISSN: 2041-1480

URL: Article

DOI: 10.1186/s13326-017-0126-0

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2548651-2

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VO: Vaccine Ontology

He, Yongqun ; Cowell, Lindsay ; Diehl, Alexander ; [et al.]

Springer Science and Business Media LLC ; 2009

In: Nature Precedings ( 2009-8-5)

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In: Nature Precedings, Springer Science and Business Media LLC, ( 2009-8-5)

Type of Medium: Online Resource

ISSN: 1756-0357

URL: Article

DOI: 10.1038/npre.2009.3553

Language: Unknown

Publisher: Springer Science and Business Media LLC

Publication Date: 2009

detail.hit.zdb_id: 2637018-9

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Author Guide for Addressing Animal Methods Bias in Publishing

Krebs, Catharine E. ; Camp, Celean ; Constantino, Helder ; [et al.]

Wiley ; 2023

In: Advanced Science

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In: Advanced Science, Wiley

Abstract: There is growing recognition that animal methods bias, a preference for animal‐based methods where they are not necessary or where nonanimal‐based methods may already be suitable, can impact the likelihood or timeliness of a manuscript being accepted for publication. Following April 2022 workshop about animal methods bias in scientific publishing, a coalition of scientists and advocates formed a Coalition to Illuminate and Address Animal Methods Bias (COLAAB). The COLAAB has developed this guide to be used by authors who use nonanimal methods to avoid and respond to animal methods bias from manuscript reviewers. It contains information that researchers may use during 1) study design, including how to find and select appropriate nonanimal methods and preregister a research plan, 2) manuscript preparation and submission, including tips for discussing methods and choosing journals and reviewers that may be more receptive to nonanimal methods, and 3) the peer review process, providing suggested language and literature to aid authors in responding to biased reviews. The author's guide for addressing animal methods bias in publishing is a living resource also available online at animalmethodsbias.org, which aims to help ensure fair dissemination of research that uses nonanimal methods and prevent unnecessary experiments on animals.

Type of Medium: Online Resource

ISSN: 2198-3844 , 2198-3844

URL: Article

DOI: 10.1002/advs.202303226

Language: English

Publisher: Wiley

Publication Date: 2023

detail.hit.zdb_id: 2808093-2

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