Journal of Cheminformatics ( IF 8.6 ) Pub Date : 2020-01-20 , DOI: 10.1186/s13321-019-0406-z Rajarshi Guha , Egon Willighagen
Since its inception, the Journal of Cheminformatics has made it a point to highlight novel approaches and best practices in cheminformatics. However, one area that we have not addressed are articles on educational aspects of cheminformatics.
Given the increasing importance of chemical information throughout the practice of chemistry, biology and related fields, we realize that articles that focus on introductory aspects of chemical information and cheminformatics would be beneficial to newcomers to the field, which can range from undergraduate students to experienced chemists coming from experimental subfields of chemistry. But we need not restrict ourselves to “introductory” articles. For example, tutorial style articles that describe a common workflow, using a set of open source tools could be generally useful and would be considered within the scope educational article type. We note that the ACS Journal of Chemical Education (ISSN:0021-9584) provides a venue for educational articles in chemistry, and while some cheminformatics related articles have been published (e.g. [1, 2]), we feel that the Journal of Cheminformatics provides a more focused context for cheminformatics specific educational material.
In particular, we have developed a set of guidelines for manuscripts that are intented for the educational category which can be viewed at https://jcheminf.biomedcentral.com/submission-guidelines/preparing-your-manuscript/educational. We are interested in both expository style and tutorial style articles. The former can include articles that present a a pedagogical view of a pre-existing topic, such as chemical similarity or SMILES & SMARTS for pattern matching. Other topics could focus on aspects of teaching cheminformatics in a classroom. In particular descriptions of pedagogical experiments with chemical information curricula will be of interest.
Tutorial style articles are also of interest and are meant to be step by step descriptions of specific types of calculations—for example, the article by Voicu et al. [3], describe the use of the rcdk R package [4] to compute a clustering of a compound collection. While this task is a standard operation, it is useful for novices to see the whole process described explicitly from start to end.
A key requirement for educational articles is that they employ freely accessible tools and data, to ensure that the material can be followed by readers with minimal limitations. This is in line with requirements for other article types, but for educational articles we plan on requiring the use of open source tools and reusable data with an open license.
In summary, we believe that there is a need for the educational article type and that such articles will enhance the value of the journal to its readership and more broadly within the cheminformatics community.
- 1.
Pence HE, Williams A (2010) Chemspider: an online chemical information resource. J Chem Educ 87(11):1123–1124. https://doi.org/10.1021/ed100697w
- 2.
Price GW, Gould PS, Marsh A (2014) Use of freely available and open source tools for in silico screening in chemical biology. J Chem Educ 91(4):602–604. https://doi.org/10.1021/ed400302u
- 3.
Voicu A, Duteanu N, Voicu M, Vlad D, Dumitrascu V (2020) The rcdk and cluster R packages applied to drug candidate selection. J Cheminform. https://doi.org/10.1186/s13321-019-0405-0
- 4.
Guha R (2007) Chemical informatics functionality in R. J Stat Softw 18(6):1–6
Affiliations
Vertex Pharmaceuticals, 50 Northern Ave, Boston, MA, 02210, USA
Rajarshi Guha
Maastricht University, Universiteitssingel 50, 6229 ER , Maastricht, The Netherlands
Egon Willighagen
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Contributions
Both authors contributed to the development of the educational article type, and writing of this editorial. Both authors read and approved the final manuscript.
Corresponding author
Correspondence to Rajarshi Guha.
Competing interests
The authors declare that they have no competing interests.
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Cite this article
Guha, R., Willighagen, E. Learning cheminformatics. J Cheminform 12, 4 (2020). https://doi.org/10.1186/s13321-019-0406-z
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中文翻译：
学习化学信息学
自成立以来，《化学信息学杂志》就着重强调了化学信息学的新方法和最佳实践。但是，我们尚未解决的一个领域是有关化学信息学教育方面的文章。
鉴于化学信息在整个化学，生物学和相关领域的实践中日益重要，我们意识到，侧重于化学信息和化学信息学入门方面的文章将对该领域的新手有所帮助，从本科生到有经验的化学家不等来自化学实验领域。但是，我们不必局限于“介绍性”文章。例如，使用一组开放源代码工具描述通用工作流程的教程风格文章通常可能会很有用，并且将在范围教育文章类型中考虑。我们注意到ACS化学教育杂志（ISSN：0021-9584）提供了在化学教育论文的场所，而一些化学信息学相关的文章已经发表（例如，[ 1，2 ]），我们觉得杂志化学信息学的提供了具体的教育化学信息更集中的背景下材料。
特别是，我们针对教育类别制定了一套手稿指南，可以在https://jcheminf.biomedcentral.com/submission-guidelines/preparing-your-manuscript/educational上查看。我们对说明性样式和教程样式文章都感兴趣。前者可以包括提供先前存在的主题的教学观点的文章，例如化学相似性或用于模式匹配的SMILES＆SMARTS。其他主题可能集中在课堂上教授化学信息学的方面。特别是对带有化学信息课程的教学实验的描述将会引起人们的兴趣。
教程风格的文章也很有趣，旨在逐步描述特定类型的计算，例如Voicu等人的文章。[ 3 ]描述使用rcdk R包[ 4 ]计算化合物集合的聚类。尽管此任务是标准操作，但对于新手来说，从头到尾清楚地描述整个过程非常有用。
教育文章的关键要求是它们使用可自由访问的工具和数据，以确保读者可以以最少的限制阅读该材料。这符合其他文章类型的要求，但是对于教育性文章，我们计划要求使用具有开放许可的开源工具和可重用数据。
总而言之，我们认为教育文章类型是必要的，这类文章将提高期刊对读者的价值，并在化学信息学界更广泛地发挥作用。
- 1。
Pence HE，Williams A（2010）Chemspider：在线化学信息资源。J Chem Educ 87（11）：1123-1124。https://doi.org/10.1021/ed100697w
- 2。
Price GW，Gould PS，Marsh A（2014）使用免费提供的开源工具在化学生物学中进行计算机筛选。J Chem Educ 91（4）：602–604。https://doi.org/10.1021/ed400302u
- 3。
Voicu A，Duteanu N，Voicu M，Vlad D，Dumitrascu V（2020）rcdk和cluster R软件包应用于候选药物的选择。J化学文摘。https://doi.org/10.1186/s13321-019-0405-0
- 4。
Guha R（2007）R. J Stat Softw 18（6）：1-6中的化学信息学功能
隶属关系
Vertex Pharmaceuticals，50 Northern Ave，波士顿，MA，02210，美国
拉贾西·古哈（Rajarshi Guha）
马斯特里赫特大学，Universiteitssingel 50，6229 ER，马斯特里赫特，荷兰
埃贡·威利哈根（Egon Willighagen）
会费
两位作者都为教育文章类型的发展以及本社论的撰写做出了贡献。两位作者均阅读并批准了最终稿。
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引用本文
Guha，R.，Willighagen，E.学习化学信息学。ĴCheminform 12， 4（2020）。https://doi.org/10.1186/s13321-019-0406-z
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