Journal of Cheminformatics ( IF 7.1 ) Pub Date : 2020-01-20 , DOI: 10.1186/s13321-019-0406-z Rajarshi Guha 1 , Egon Willighagen 2
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
自创刊以来， 《化学信息学杂志》就重点关注化学信息学领域的新颖方法和最佳实践。然而，我们尚未讨论的一个领域是有关化学信息学教育方面的文章。
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.
特别是，我们制定了一套针对教育类别的手稿指南，可以在https://jcheminf.biomedcentral.com/submission-guidelines/preparing-your-manuscript/educational上查看。我们对说明式和教程式的文章都感兴趣。前者可以包括呈现现有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。其他主题可以集中在课堂上化学信息学教学的各个方面。特别是对化学信息课程教学实验的描述将引起人们的兴趣。
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.
教育文章的一个关键要求是它们使用可免费访问的工具和数据，以确保读者可以在最小的限制下理解材料。这与其他文章类型的要求一致，但对于教育文章，我们计划要求使用开源工具和具有开放许可证的可重用数据。
总之，我们认为需要教育文章类型，并且此类文章将提高期刊对其读者以及更广泛的化学信息学界的价值。
- 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) R. J Stat Softw 中的化学信息学功能 18(6):1–6
隶属关系
Vertex 制药公司，50 Northern Ave，Boston，MA，02210，美国拉贾什·古哈
马斯特里赫特大学，Universiteitssingel 50, 6229 ER , 马斯特里赫特, 荷兰埃贡·维利哈根
贡献
两位作者都对教育文章类型的发展以及这篇社论的写作做出了贡献。两位作者阅读并批准了最终手稿。
通讯作者
Correspondence to Rajarshi Guha.
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引用这篇文章
Guha, R.，Willigagen, E. 学习化学信息学。 《化学信息》杂志12, 4 (2020)。 https://doi.org/10.1186/s13321-019-0406-z
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