PubChem as a resource for chemical information education

Presented at the Fall 2020 American Chemical Society (ACS) National Meeting (Virtual) on August 20, 2020.

Sunghwan Kim & Evan Bolton
National Library of Medicine, National Institutes of Health, Rockville, Maryland, United States


==== Abstract ====

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource that contains one of the largest corpus of publicly available chemical information. It is one of the top five most visited chemistry web sites in the world, with more than four million unique users per month (as of April 2020). Considering that many of PubChem users are undergraduate students in academic institutions, PubChem has a great potential as an online resource for chemical education. However, it also has some important issues with data accuracy, data provenance, structure standardization, terminologies and so on, because PubChem is essentially a data aggregator that collects heterogeneous data from 700+ data sources in various domains. This presentation will discuss various aspects of PubChem as a chemical information education resource. Especially, a focus will be given on how to help students develop the ability to critically assess chemical information available in PubChem and other public databases.

1. PubChem as a Resource for Chemical Information Education ACS Fall 2020 Virtual Meeting August 20, 2020 Sunghwan Kim, Ph.D., M.Sc.

2. PubChem ( https://pubchem.ncbi.nlm.nih.gov ) Public chemical database. Developed and maintained by the U.S. National Institutes of Health. Contains various chemical entities: Small molecules siRNAs & miRNAs Carbohydrates Lipids Peptides Chemically modified macromolecules ……

3. PubChem ( https://pubchem.ncbi.nlm.nih.gov ) Collects chemical information from 750+ data sources and disseminates it to the public free of charge. 103 million unique chemical structures. Crosslinks to many other databases. Search, analysis, download and visualization tools. A key resource in many areas: Cheminformatics Chemical biology Medicinal chemistry Drug discovery

4. PubChem Usage Statistics 2016 2017 2018 >4.3 million unique users per month (Apr. 2020) 2019 2020 Source: Google Analytics

5. Top 5 Chemistry Websites acs.org rsc.org sigmaaldrich.com pubchem.ncbi.nlm.nih.gov cas.org Source: https://www.alexa.com/topsites/category/Top/Science/Chemistry PubChem is the only public website among them. PubChem Usage Statistics

6. ~36% of PubChem users are between 18-24 . (likely to be college students) PubChem Usage Statistics

7. PubChem as an online resource for chemical education Popularity: Many young people are already using PubChem. Sustainability: It is sixteen years old and not going away soon. Zero-cost (to students): U.S. taxpayers have already paid for it.

8. Popularity: Many young people are already using PubChem. Sustainability: It is sixteen years old and not going away soon. Zero-cost (to students): U.S. taxpayers have already paid for it. A strong potential as an education resource, especially for small organizations like: primarily undergraduate institutions (PUIs) community colleges (CCs) PubChem as an online resource for chemical education

9. How about R1 universities with large endowments? Likely to have access to proprietary databases. Primarily used for research. Inconvenient off-campus access. Students will lose access when they graduate. Most students will eventually rely on public resources.  Need for training/education opportunities while in school. PubChem as an online resource for chemical education

10. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

11. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

12. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

13. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

14. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

15. Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

16. Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

17. Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

18. Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

19. Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

20. He Ne Ar Kr Xe Rn Li Na K Rb Cs Fr Kim et al., Chem. Teacher International , 2020. doi: 10.1515/cti-2020-0006

21. Exploring Chemical Information in PubChem Search by chemical name Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

22. Why should students learn programmatic access? PubChem users have very diverse backgrounds/interests. PubChem’s web interfaces are optimized to perform commonly requested tasks interactively. Everything you can do with PubChem through the web browser can be automated through PubChem’s programmatic interfaces . Programmatic access enables one to do much more complicated and specialized tasks that cannot be done through the web browser.

23. Why should students learn programmatic access? Programming skills are essential for: automating routine tasks and processing/analyzing a large data set  Important skills for students pursuing STEM careers in the age of big data.

24. Programmatic Access to PubChem Multiple programmatic access routes. Two major programmatic access methods. PUG-REST (primarily for computed properties). Kim et al., Nucleic Acids Res. 2018, 46(W1):W563-570. https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest PUG-View (primarily for text information). Kim et al., J. Cheminform . 2019, 11:56. https://pubchemdocs.ncbi.nlm.nih.gov/pug-view Jupyter Notebooks containing sample codes (in python/R) are freely available at LibreTexts: https://chem.libretexts.org/link?143689

25. Cheminformatics On-Line Chemistry Course (OLCC) Kim et al., J. Chem. Educ. , 2020, submitted.

26. Cheminformatics OLCC Unique challenges to teaching cheminformatics Cheminformatics is not an established chemistry field.  Chemistry + Informatics + Computer Science + Library Science + Pharmaceutical Science + …… Not so many faculty members with Cheminformatics expertise. No textbook suitable for undergraduate chemistry students.

27. The Cheminformatics OLCC addresses these issues ! Cheminformatics OLCC Unique challenges to teaching cheminformatics Cheminformatics is not an established chemistry field.  Chemistry + Informatics + Computer Science + Library Science + Pharmaceutical Science + …… Not so many faculty members with Cheminformatics expertise. No textbook suitable for undergraduate chemistry students.

28. Course website Cheminformatics experts Prepare online reading materials & homework problem sets Cheminformatics OLCC

29. Course website Cheminformatics experts Prepare online reading materials & homework problem sets Course Instructor Students Run the course using the course materials at multiple schools Cheminformatics OLCC

30. Course website Cheminformatics experts Prepare online reading materials & homework problem sets Course Instructor Students Run the course using the course materials at multiple schools Face-to-face meeting Online discussion among experts, instructors, & students through the website Cheminformatics OLCC

31. It was offered three times: Fall 2015: 36 students from 4 schools Spring 2017: 47 students from 9 schools Fall 2019: 23 students from 5 schools All course materials are available at: CCCE website ( http://olcc.ccce.divched.org ) LibreTexts ( https://libretexts.org ) (free online textbook site) Many of the course materials cover PubChem data, tools and services . Cheminformatics OLCC

32. PubChem-related topics in Cheminformatics OLCC Critical assessment of chemical information Chemical representations (e.g., InChI and SMILES) As alternatives to chemical name queries For chemical data exchange/integration/sharing Search by chemical name Search by chemical structure Identity search 2-D/3-D similarity search Substructure/superstructure search Molecular formula search Structure clustering and structure-activity relationship analysis Automation of chemical data retrieval through a computer code Cheminformatics OLCC

33. Many PubChem users are likely to be college students. Summary PubChem has a strong potential as a resource for chemical information training because of its: popularity sustainability low cost

34. Summary PubChem supports various use cases beyond simple chemical name search. Search by chemical structure Search by gene/protein name PubChem Periodic Table and Element pages Programmatic access

35. Summary PubChem works with the chemical education community to provide chemical information training for students. Please reach out to us for collaboration if you are interested.

36. Acknowledgements Evan Bolton Jie Chen Tiejun Cheng Asta Gindulyte Jia He Siqian He Qingliang (Leon) Li Benjamin Shoemaker Thiessen Paul Olga Pujolras Bo Yu Leonid Zaslavsky Jian (Jeff) Zhang Zhi (Leon ) Sun The PubChem Team PubChem users, depositors, and collaborators Funded by the National Library of Medicine

37. Thank you! Questions? Sunghwan Kim, Ph.D., M.Sc. Email: [email protected] SlideShare: https://www.slideshare.net/SunghwanKim95/presentations