PubChem is a public chemical database maintained by the U.S. National Institutes of Health containing information on small molecules, lipids, nucleic acids, and other chemical substances. It receives over 5 million unique users per month, many of whom are students. PubChem has potential as an educational resource given its popularity, sustainability, and zero cost to students. PubChem collaborates with academic partners to develop resources like an online cheminformatics course and chemical safety summaries.

1. PubChem and Its Application for
Cheminformatics Education
Sunghwan Kim, Ph.D., M.Sc.

2. ▪ 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
• ……
PubChem is a Public Chemical Information Resource

3. PubChem is a Data Aggregator
PubChem Sources: https://pubchem.ncbi.nlm.nih.gov/sources
Gov’t
agencies
Academic
institutions
Publishers
Pharma
companies
Chemical
vendors
Scientific
databases
790+ Data sources Users
o Biomedical Researchers
• Chemical biology
• Medicinal chemistry
• Drug design & discovery
• Cheminformatics
o Data scientists
o Patent agents/examiners
o Chemical safety officers
o Educators/librarians
o Students

4. Structures & properties Spectra Chemical
Health & Safety
Bioactivity Chemical vendors & synthesis
PubChem Has a Wide Range of Chemical Information
Drugs
Patents & Literature

5. 0
1
2
3
4
5
6
Unique
Monthly
Users
(millions)
Time
Monthly Usage Statistics
(interactive users only)
▪ >5 million unique interactive users per month at peak (Oct. 2021)
▪ Programmatic requests are not included.
▪ These statistics are lower-bound.
Source: Google Analytics

6. User Demographics
(June 2020 through May 2021)
36.5%
27.4%
13.5%
10.4%
6.7% 5.4%
0
1
2
3
4
5
6
18-24 25-34 35-44 45-54 55-64 65+
Number
of
Users
(millions)
Age
34.64% of total users
~40% of PubChem users are aged between 18 and 24.
(likely to be college students)

7. 75% of PubChem Users Come through Search Engines

8. ▪ Popularity: many young people are already using PubChem.
▪ Sustainability: it is 17 years old and not going away soon.
▪ Zero-cost (to students): U.S. taxpayers have already paid for it.

9. PubChem presents a strong potential as an education resource
especially for small organizations like:
• primarily undergraduate institutions (PUIs)
• community colleges (CCs)
▪ Popularity: many young people are already using PubChem.
▪ Sustainability: it is 17 years old and not going away soon.
▪ Zero-cost (to students): U.S. taxpayers have already paid for it.

10. 10
➢ 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.

11. PubChem’s Application for Education

12. ▪ Cheminformatics OnLine Chemistry Course (OLCC)
(with the Chemical Education community)
▪ PubChem Laboratory Chemical Safety Summary (LCSS)
(with the Chemical Health and Safety community)
PubChem’s Application for Education

13. Kim et al., J. Chem. Educ., 2021, 98 (2), 416-425

14. Cheminformatics OLCC
Collaborative Teaching
Instructors at
multiple schools
Open Education
Resource (OER)
Development
Cheminformatics
experts from
outside

15. Cheminformatics
experts
Prepare online reading materials &
homework problem sets
Instructional Approach
Course website

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

17. 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
Instructional Approach

18. Enrollment Statistics
Semester # Schools # Students Participating schoolsa
Fall 2015 4 36
UALR (6), Centre (4), WVU (5), UNF
(21)
Spring 2017 9 47
UALR (12), Centre (0b), UHSP (3),
IQS (6c), SDSU (4), Potsdam (3),
UIS (6), Campbell (12), Rutgers (1)
Fall 2019 5 23
UALR (2), Centre (3), UHSP (4),
IQS (9c), Otterbein (5),
a Numbers in parentheses are the numbers of enrolled students at individual schools.
b The course was taken by three faculty and staff members who participated in a faculty learning circle.
No students enrolled.
c Not formally enrolled as the course was offered as a non-credit seminar.

19. OLCC Course websites
2015 • http://olcc.ccce.divched.org/Fall2015OLCC
• https://chem.libretexts.org/link?50598
2017 • http://olcc.ccce.divched.org/Spring2017OLCC
• https://chem.libretexts.org/link?83678
2019 • https://chem.libretexts.org/link?143689
Course Websites
➢ All course materials are freely available for reuse at:
▪ Committee on Computers in Chemical Education (CCCE) website
(http://olcc.ccce.divched.org)
▪ LibreTexts (https://libretexts.org)

20. Topics Covered in Cheminformatics OLCC

21. ▪ Critical assessment of chemical information
▪ Chemical representations (e.g., InChI and SMILES)
▪ Search by chemical name
▪ Search by chemical structure
o Identity search
o 2-D/3-D similarity search
o Substructure/superstructure search
▪ Structure clustering
▪ Structure-activity relationship analysis
▪ Automation of chemical data retrieval
PubChem-Related Topics

22. ▪ Python Jupyter Notebooks
(with sample codes and assignments)
o Programmatic access to PubChem data
o Cheminformatics tasks using open-source
software packages
(e.g., RDKit, scikit-learn, and Mordred).
o Bioactivity prediction using machine learning
and PubChem data.
Python/R Programming (Fall 2019)

23. ▪ Python Jupyter Notebooks
(with sample codes and assignments)
o Programmatic access to PubChem data
o Cheminformatics tasks using open-source
software packages
(e.g., RDKit, scikit-learn, and Mordred).
o Bioactivity prediction using machine learning
and PubChem data.
▪ Similar materials for the R language
(using JupyterLab and R-Studio)
Python/R Programming (Fall 2019)

24. ▪ Students had two options to run the notebooks:
o Download and run them on their own computers.
o Run the notebooks on JupyterHub available through LibreTexts.
Python/R Programming (Fall 2019)

25. ▪ Students had two options to run the notebooks:
o Download and run them on their own computers.
o Run the notebooks on JupyterHub available through LibreTexts.
Python/R Programming (Fall 2019)
▪ After the 2019 OLCC, the Jupyter notebooks were converted
into Mathematica scripts.
(thanks to Joshua Schrier, Fordham University)

26. ▪ Small projects for the last 2-4 weeks of the semester
(in 2015 & 2017 OLCCs).
▪ Various projects were done, ranging from the development of
an Android app to the creation of educational video tutorials.
o Select students had opportunities to give oral presentations about their
projects at a special symposium at the Spring 2016 ACS National
Meeting in San Diego.
o Some student projects were evolved into more formal, long-term projects
o One student's project eventually became the basis of a master's thesis.
Student Projects

27. ▪ Setting aside four weeks out of one semester for student
projects made it difficult to cover a broad area of
cheminformatics with the remaining time.
→ Inclusion of student projects in the 2019 OLCC was up to the discretion
of the instructor at each participating school.
Student Projects

28. ▪ Cheminformatics OnLine Chemistry Course (OLCC)
(with the Chemical Education community)
▪ PubChem Laboratory Chemical Safety Summary (LCSS)
(with the Chemical Health and Safety community)
PubChem’s Application for Education

29. ▪ https://pubchem.ncbi.nlm.nih.gov/lcss
▪ A concise view of health and safety data for a
given compound.
▪ Supports chemical risk assessment in
laboratories at academic institutions.
PubChem Laboratory Chemical Safety Summary (LCSS)

30. Data Content
• GHS Classification
• Synonyms
• Identifiers
• Physical Properties
• Toxicity Data
• Exposure Limits
• Health and Symptoms
• First Aid
• Flammability & Explosivity
• Stability and Reactivity
• Storage and Handling
• Cleanup and Disposal
• Additional Considerations
Data Sources
• CDC ATSDR Toxic
Substance Portal
• NOAA CAMEO Chemicals
• Regulation(EC)No121272/2008
• DrugBank
• EPA Air Toxics
• EPA Chemical Data Report
• HSDB
• ILO ICSC
• NCI Investigational Drugs
• NIOSH Pocket Guide
• OSHA Occupational
Chemical DB
PubChem Laboratory Chemical Safety Summary (LCSS)

31. ▪ LCSS data are organized based on the
format described by
the National Research Council in
“Prudent Practices in the Laboratory:
Handling and Management of
Chemical Hazards” (2011)
Free PDF available from http://www.nap.edu/catalog/12654/prudent-
practices-in-the-laboratory-handling-and-management-of-chemical.
PubChem Laboratory Chemical Safety Summary (LCSS)

32. ❑ Access to PubChem LCSS
▪ From the Compound Summary
(ex: https://pubchem.ncbi.nlm.nih.gov/
compound/tetrahydrofuran)
▪ From the LCSS project page
(https://pubchemdocs.ncbi.nlm.nih.gov/lcss)
▪ From the Classification Browser
(https://pubchem.ncbi.nlm.nih.gov/classification)
PubChem Laboratory Chemical Safety Summary (LCSS)

33. ❑ Downloading PubChem LCSS data
▪ PubChem LCSS data are downloadable in XML, JSON, ASN.1
▪ Bulk download via FTP
(ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-LCSS.xml.gz)
▪ Additional PubChem data are available
(through programmatic access routes: PUG-REST & PUG-View)
PubChem Laboratory Chemical Safety Summary (LCSS)
Customization of LCSS
for specific procedures at individual institutions

34. ▪ Encodes the link to the LCSS
page for a chemical.
❑ LCSS & Chemical QR code
https://pubchem.ncbi.nlm.nih.gov/
rest/pug_view/qr/long/compound/
8028/LCSS/SVG
▪ Easy and quick access from mobile
devices to chemical health and safety
information.
PubChem Laboratory Chemical Safety Summary (LCSS)

35. Summary
➢ PubChem is a public database containing a wide range of chemical information.
➢ It is used by millions of users every month and many of them are young students.
➢ PubChem has a great potential as an education resource because of its
popularity, sustainability, and zero cost.
➢ PubChem is actively collaborating with people in academia.
▪ Cheminformatics OLCC
▪ PubChem LCSS
➢ Please reach out to us if you are interested in collaborating with us.

36. Acknowledgements
➢ The PubChem Team
➢ ACS CHED Committee on Computers in Chemical Education (CCCE)
➢ ACS CHAS
➢ LibreTexts / UC Davis
➢ Cheminformatics OLCC participants
➢ Funding
▪ NLM/NIH

37. Thank you!
Questions?
Sunghwan Kim, Ph.D., M.Sc.
Email: kimsungh@ncbi.nlm.nih.gov
SlideShare: https://www.slideshare.net/SunghwanKim95/presentations