So I'm going to turn this over to Sunghwan Kim
and he is going to take you through teaching PubChem
Hello everyone thank you very much for joining us today.
For the next 20 minutes or so I will talk about how to use PubChem in the chemistry
classroom.
So what is PubChem?
PubChem is a public chemical information resource at NIH.
Basically what it does is collect chemical information from hundreds of data sources
in the public domain and disseminated back to the public free of charge.
PubChem is a very popular chemistry website.
For example, last March we had more than 2.9 million unique users.
Then who are our users?
Generally speaking, about a half of our users are between age 18 and 24.
And those in this age group are likely to be college students.
Many of them are required to take some chemistry courses like general chemistry, organic chemistry.
Then you may wonder how they use PubChem?
The most common use case of PubChem is a search through Google.
If you use Google to search for chemical by name, usually it gives a PubChem record at
the top of the search result.
Then click it to go to PubChem and get the information.
Basically, students are using PubChem as a reference material like CRC handbook or Merck
index.
Essentially, this has been a traditional activity in the chemistry classroom for decades, or
perhaps centuries.
Let's suppose that you want to find some property of a chemical.
Let's say the boiling point of ethanol.
You can find it from PubChem much quicker than from any hardcopy references . But at
the end of the day, what you learn from this activity is still the boiling point of ethanol,
regardless of where you find it.
And the educational value of this activity is not very different, regardless of what
reference you views.
What additional educational values can PubChem provide compared to the 19th century Merck
index?
To answer this question, we have to look at PubChem in a different way.
Most people view PubChem as a single information resource.
But you can also view PubChem as a gateway to many information resources.
In other words, PubChem provides access to all sorts of chemical information scheduled
across hundreds of data sources.
With that said, the students are now exposed to an extremely large amount of data.
So it is necessary for us to help them to get the most out of this big chemical information.
It means more emphasis of chemical education should be given to chemical education.
What can you teach using PubChem ? Here are some examples.
And we are going to review them briefly during this webinar.
First, PubChem can be used to help students to build the ability to critically assess
chemical data.
Today I will show you two examples.
The first one is about finding the boiling point of benzene from PubChem.
This is a screenshot for the PubChem compound summary page for benzene.
The compound summary page provides an aggregated view of all information available in PubChem
for a given compound.
If you scroll down this page, you will find the boiling point section for benzene.
Currently PubChem has six boiling point data from five different sources.
Some sources used Fahrenheit and others used Celsius with various precisions.
And once source explicitly specify the atmosphere pressure at which the boiling point was measured.
Which is a good practice.
And importantly, some gave a single value as a boiling point while others gave a range
of values.
Actually, one source gave two boiling points.
One as a value and the other as a range of values.
What is going on?
If you click these source names, the hidden part it is a expanded and now you can see
one is for benzene and the other is for coal tar.
And you can see that the links to the webpage where the data was collected from.
So what is happening here is that 176 is the boiling point of benzene.
But the other is for coal tar.
Coal tar is a mixture of various hydrocarbons including benzene.
So you can get benzene from coal tar through distillation.
Basically, coal tar is the natural source of benzene.
So, some sources used benzene and coal tar interchangeably.
And that is also reflected in PubChem through data integration.
So from this example, the students can learn that there are multiple contexts of a chemical.
And understand why they are integrated in a single record.
And realize that care should be taken when searching for chemical data.
The next example is about finding CAS numbers for SIO two from PubChem.
In PubChem SIO two has 22 CAS numbers.
Each of these CAS numbers represent a different context of SIO two.
Depending on whether it means SIO 2 in general or a specific form.
Or solid SIO 2, can be amorphous or crystalline.
The crystalline SIO 2 can be classified into different polymorphs.
And the property of SIO 2 depends on how it is processed and whether it is pure or it
contains some contaminants.
In PubChem, all of these are aggregated into a single record because they have the same
chemical formula.
SIO 2.
So again, from this example, students can learn the importance of the context of chemical
data.
Now the second one is about how to search PubChem by chemical structure.
You can type a chemical name into the Google search box but what would you do if you don't
know the name of the compound but it's a structure?
In PubChem, you have two options.
First, you can draw the structure using molecular drawing software called PubChem sketcher,
or use a line notation for the structure.
Several line notations for chemical structures have been developed but the most commonly
used ones are SMILES, InChI, and InChiKey and all of these are supported in PubChem.
Currently, PubChem has two structure search interfaces.
Chemical structure search is older but the stable interface.
And PubChem search beta uses newer technologies but it was released as a test version.
You can access the two structures search interfaces from the PubChem homepage.
And both interfaces support various types of search including identity search, substructure,
superstructure search, similarity search, and molecular formulas search.
And you can provide the infrastructure using PubChem compound ID, or line notations like
smiles, InChI, and InChiKey.
You can also draw the infrastructure using the PubChem sketcher or upload a file that
contains the inpu structure.
And PubChem is actively working on a new interface that will replace the two existing interfaces.
So please stay tuned.
Another important topic to cover is structure clustering and structure activity analysis.
Or SAR analysis.
Structure clustering is about grouping compounds into small clusters according to their structural
similarities.
It is helpful in classifying molecules is according to their structural characteristics.
As an example, these are some anti-allergic agents from PubChem.
They can be grouped into three major clusters.
Like dipeptides, glucocorticoids, and antihistamines.
Based on these clustering results, you can expect that the anti-allergic activities of
these compounds may come from three different mechanisms of action.
And SAR analysis is about clustering compounds and bioassay data simultaneously.
It is useful for identifying structural characteristics responsible for the bio activity of molecules.
Unfortunately the structure clustering and SAR analysis tools will be retired by the
end of this year but the same tasks can be done using third-party software after downloading
necessary data from PubChem.
The last one is automated data retrieval using a computer code.
PubChem provides multiple programmatic aspects routes.
Among them PUG-REST is the simplest and easiest to learn.
It can be used with popular programming languages like Python, so students can learn to automate
data retrieval from PubChem by writing a short script.
Let me briefly talk about Cheminformatics OLCC.
It was an NSF funded project led by Professor Belford at the University of Arkansas, Little
Rock.
And PubChem was actively involved in this project as part of our outreach effort for
the chemical education community.
Teaching chemical cam informatics to undergraduate chemistry majors has many unique challenges.
First cheminformatics is not a field of chemistry but a mix of many different fields.
Because of that not so many faculty members have the expertise to keep teach the course.
In addition to that, there is no textbook suitable for undergraduate chemistry majors.
There are some cheminformatics textbooks.
But most of them are written for computer science majors or graduate students.
Or cover narrow topics that focuses on medicinal chemistry and drug discovery.
Cheminformatics OLCC aimed to address these issues, at least partially.
In Cheminformatics OLCC, experts were recruited from various places including industry, government
and academia.
And they prepared reading materials and homework problems sets.
And they were made available online through the OLCC website.
And the instructors at multiple participating schools used these online materials to deliver
the Cheminformatics course at their schools.
Concurrently the instructors had face to face meetings with the students in the classroom
at the same time the Cheminformatics experts got engaged in online discussions with students
through OLCC website.
We ran this course twice.
In fall, 2015.
We had about 30 students from four schools.
And in spring, 2017, there were about 50 students from 10 schools.
All the course materials developed during this course are available at the OLCC website,
olcc.ccce.divched.org, and Libre Texts, chem.libretexts.org.
So if anybody wants to use these materials for his own course, he can use them for free.
And many of the course materials covered PubChem data, tools, and services.
Here, is a quick summary of PubChem related topics covered in the Cheminformatics OLCC.
Basically it includes everything I mentioned today and more.
In summary, a majority of PubChem users are likely to be college students.
And they use PubChem as a reference material.
But, there are many other things that students can do beyond this use case.
PubChem can also be used as a free online Cheminformatics education resource.
And Cheminformatics OLCC is a good example.
And finally, we are very interested in working together with the chemical education community.
So if you're interested, please reach out to us for collaboration.
Thank you and I am more than happy to answer your questions.
[Peter Cooper] Thank you Sunghwan.
We will leave it open for a couple of minutes to see if there are any questions.
We do have a couple of questions.
Let me get to those.
So there are two questions that relate to the same thing.
One, what third-party tools can be used to replicate the SAR functions that will be discontinued?
[Sunghwan] We are not allowed to endorse any commercial software or third-party software
so we cannot answer that question.
But if you send me an email, I can tell you about that.
In person.
[Peter] I think it is okay if you want to.
To mention something.
We don't endorse it.
An example would be fine.
[Sunghwan] In my opinion, R is the best one, it is free.
It runs on PC and Mac and Linux.
And in the case of R there are many tutorials out there.
So you can start from there.
[Peter] Thank you.
I don't see any additional questions right now.
So thanks everybody for coming.
And we are having another webinar next week on BLAST.
Please check that out.
Thank you very much for coming.