Reply to “FAIR chemical structure in the Journal of Cheminformatics”,Journal of Cheminformatics

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Reply to “FAIR chemical structure in the Journal of Cheminformatics”
Journal of Cheminformatics ( IF 8.6 ) Pub Date : 2021-07-07 , DOI: 10.1186/s13321-021-00521-3
Rajarshi Guha ₁ , Nina Jeliazkova ₂ , Egon Willighagen ₃ , Barbara Zdrazil ₄

Affiliation

Schymanski and Bolton [1] requests the adoption of a FAIR approach to improve the FAIRness (findability, accessibility, interoperability, reusability) of chemical structures in the Journal of Cheminformatics. Currently, our journal encourages open science practices, but at the same time does not provide much guidance on how to implement these practices. Because FAIR chemical data is important [2], we welcome the open standard proposal and intend to adopt it as recommendation to authors.

Specifically, we will update the author guidelines that authors can improve the FAIRness by opting-in to provide chemical structures in open data associated with our journal articles in this format. For submissions where data is already provided in a FAIR format, an index file in this format can be provided. Second, we will make reviewers aware of this new, optional open standard.

While we agree with the importance of FAIR data, we also foresee practical complications when making this obligatory for all articles. Particularly, for the Database article type, the proposal may be both redundant to existing editorial standards as well as problematic for really large datasets as used in, for example, Probst and Reymond [3].

As a result, rather than require, we strongly recommend that authors include structure data in open, machine readable formats and identifiers, and point towards Schymanski and Bolton [1] as a means of doing so.

1.
Schymanski E, Bolton E (2021) FAIR Chemical structure in the Journal of Cheminformatics. J Cheminform. https://doi.org/10.1186/s13321-021-00520-4[cito:agreesWith] [cito:obtainsBackgroundFrom] [cito:repliesTo]
Article PubMed PubMed Central Google Scholar
2.
Coles SJ, Frey JG, Willighagen EL, Chalk Stuart J (2020) Taking FAIR on the ChIN: the chemistry implementation network. Data Intell 2:131–8. https://doi.org/10.1162/DINT_A_00035[cito:citesAsAuthority] [cito:obtainsBackgroundFrom]
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3.
Probst D, Reymond J-L (2020) Visualization of very large high-dimensional data sets as minimum spanning trees. J Cheminform 12(1):12. https://doi.org/10.1186/s13321-020-0416-x[cito:citesAsDataSource]
Article PubMed PubMed Central Google Scholar

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Affiliations

Vertex Pharmaceuticals, Boston, MA, 02129, USA
Rajarshi Guha
Ideaconsult Ltd, Sofia, Bulgaria
Nina Jeliazkova
Department of Bioinformatics-BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
Egon Willighagen
Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
Barbara Zdrazil

Authors

Rajarshi GuhaView author publications
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Nina JeliazkovaView author publications
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Egon WillighagenView author publications
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Barbara ZdrazilView author publications
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Contributions

All authors were involved in designing and writing this reply and all read and approved the final manuscript.

Corresponding author

Correspondence to Egon Willighagen.

Competing interests

All authors are editors for the Journal of Cheminformatics and have a contract with SpringerNature. Adoption of this new standard is expected to result in more data reuse, which has a positive impact on the number of citations that articles that provide the data get, which in turn benefits the journal and the publisher.

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Guha, R., Jeliazkova, N., Willighagen, E. et al. Reply to “FAIR chemical structure in the Journal of Cheminformatics”. J Cheminform 13, 49 (2021). https://doi.org/10.1186/s13321-021-00521-3

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Received: 25 May 2021
Accepted: 25 May 2021
Published: 07 July 2021
DOI: https://doi.org/10.1186/s13321-021-00521-3

中文翻译：

回复“化学信息学杂志FAIR化学结构”

Schymanski 和 Bolton [1] 要求在 Journal of Cheminformatics 中采用 FAIR 方法来提高化学结构的 FAIRness（可查找性、可访问性、互操作性、可重用性）。目前，我们的期刊鼓励开放的科学实践，但同时并没有就如何实施这些实践提供太多指导。由于 FAIR 化学数据很重要 [2]，我们欢迎开放标准提案并打算采用它作为对作者的建议。

具体来说，我们将更新作者指南，作者可以通过选择在与我们的期刊文章相关的开放数据中以这种格式提供化学结构来提高公平性。对于已经以 FAIR 格式提供数据的提交，可以提供这种格式的索引文件。其次，我们会让审阅者了解这个新的、可选的开放标准。

虽然我们同意 FAIR 数据的重要性，但在对所有文章强制执行时，我们也预见到实际的复杂性。特别是，对于数据库文章类型，提案可能对现有的编辑标准来说是多余的，而且对于 Probst 和 Reymond [3] 中使用的真正大的数据集也有问题。

因此，我们强烈建议作者以开放的、机器可读的格式和标识符包含结构数据，而不是要求，并指出 Schymanski 和 Bolton [1] 作为这样做的一种手段。

1.
Schymanski E、Bolton E (2021) 化学信息学杂志中的 FAIR 化学结构。J化学形式。https://doi.org/10.1186/s13321-021-00520-4 [cito:agreesWith] [cito:obtainsBackgroundFrom] [cito:repliesTo]
文章 PubMed PubMed Central Google Scholar
2.
Coles SJ、Frey JG、Willighagen EL、Chalk Stuart J (2020) 在 ChIN 上公平对待：化学实施网络。数据智能 2：131-8。https://doi.org/10.1162/DINT_A_00035 [cito:citesAsAuthority] [cito:obtainsBackgroundFrom]
文章谷歌学术
3.
Probst D, Reymond JL (2020) 将非常大的高维数据集可视化为最小生成树。J Cheminform 12(1):12。https://doi.org/10.1186/s13321-020-0416-x [cito:citesAsDataSource]
文章 PubMed PubMed Central Google Scholar

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隶属关系

Vertex Pharmaceuticals，波士顿，马萨诸塞州，02129，美国
拉贾希·古哈
Ideaconsult Ltd, 索非亚, 保加利亚
尼娜·耶利亚兹科娃
荷兰马斯特里赫特马斯特里赫特大学 NUTRIM 营养与代谢转化研究学院生物信息学系-BiGCaT
埃贡·威利格根
奥地利维也纳大学药物科学系药物化学部
芭芭拉·兹德拉齐尔

作者

Rajarshi Guha查看作者出版物
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Nina Jeliazkova查看作者出版物
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Egon Willighagen查看作者出版物
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Barbara Zdrazil查看作者出版物
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贡献

所有作者都参与了此回复的设计和撰写，并且都阅读并批准了最终手稿。

通讯作者

与 Egon Willighagen 的通信。

利益争夺

所有作者都是 Journal of Cheminformatics 的编辑，并与 SpringerNature 签订了合同。采用这一新标准预计将导致更多的数据重用，这对提供数据的文章获得的引用次数产生积极影响，从而使期刊和出版商受益。

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