Presentation on a project run in my Chemical Information Science course. Valuable referenced chemical data from 'reliable' static webpages was 'scraped', cleaned, and added to a database for search.

1. <chemical_informatics_project>
<inspires>
<chemistry_majors>
Stuart J. Chalk
Department of Chemistry
University of North Florida
schalk@unf.edu
2014 Fall ACS Meeting

2.  Motivation
 Chemical Information Science: The Course
 Syllabus
 Final Project Outline
 Expected Student Activities
 Submitted Data Sets
 Example Data
 Data Modeling
 Compound Data
 Website
 Future Plans
 Conclusion
Outline
From http://www.embl.de/chemcore/chemcore_services/computational_chemistry/

3. Motivation
 Students are not exposed to informatics in the
regular chemistry curriculum
 There is so much information for the chemist to
access/use they need to know how to deal with it
 Giving students this exposure makes them more
competitive in graduate/professional school
 We need professionals at the interface of chemistry
and information science

4. Chemical Information Science:
A UNF Elective Class
 First taught as a Freshmen Honors course in 2003
“Chemical Informatics”
 Five iterations over the last 10 years
 Now an upper-level three credit elective class
 Fall 2013 cohort – 21 students (three credit lecture)
“Chemical Information Science”

5. Syllabus
 What is information? What is data?
What is metadata? What types of data are there?
 How and where does informatics fit in chemistry?
 How is information organized, stored, related,
formatted, typed?
 The objected oriented view of information
(objects, classes, methods)
 The Semantic Web – What is it why is it important?
 Defining relationships between data, Concept maps
 Controlled vocabularies, Thesauri, Ontologies

6. Syllabus
 The eXtensible Markup Language (XML) and
Scientific Markup Languages
 Understanding and using Web 2.0 technologies
for information retrieval
 Generating Information and Metadata
 Finding Chemical Information
 Tools for Finding, Organizing and Using Chemical Information
 Searching databases
 Internet/browser software for Chemistry
 Using Excel for searching and organizing scientific information

7. Final Project Outline
 The ChemData Database
 For your project you will gather chemical data from sources on
the Internet, organize/filter the data, added it too the Excel
spreadsheet provided, and then send your completed Excel
spreadsheet to Dr. Chalk by the deadline.
 Requirements
 600 pieces of metadata at minimum must be submitted
(excluding reference data)
 The data must be correctly entered in the spreadsheet
(no extra spaces, loss of accuracy, etc.)
 It must be referenced to its origin, and those reference
included in the spreadsheet
 For chemicals, the InChI must be part of the submitted
metadata for each chemical species
 A minimum of six hours of time for this activity is expected
 The Excel Spreadsheet to use is available on the course website.

8.  Find suitable data source (hand coded web page) on
‘reputable’ site with original reference
 Download webpage content to computer
 ‘Scrape’ data out of webpage
 Perform any data normalization (e.g. scientific notation)
 Get metadata about chemicals referenced
 Get metadata about original reference (DOI)
 Import data into Excel and organize
 Assign unique ids and add ids to link data
 Add units and other metadata
Expected Student Activities

9. Submitted Data Sets
 Students used an Excel spreadsheet to organize their data

10. Submitted Data Sets
 They choose to submit data about
 Organic compound properties
 Organic compound reactions
 Solvent properties
 Types of analytical instrumentation
 Analytical instrument operating conditions
 Mathematical equations used in PChem
 Physical constants
 Unit conversion factors

11. Example
Data

12. Data
Modeling

13. Compound Data Table

14. Website

15.  Very positive 
 “Course was an informative and enjoyable overview of the emerging field of
informatics as it relates to the sciences and Chemistry in particular.”
 “What I am taking away from this class is something that can be applied to
other courses and my career. Interesting peek behind the curtains of how
the sharing of scientific knowledge and discovery are evolving.”
 “Dr. Chalk was very enthusiastic about the subject of chemical informatics.
He exposed us to some very helpful chemistry resources that I plan on using
in the future.”
 “Very interesting class with a lot of hands on computer use and learning
experience. The homework was relative to the course information and
helped to prepare for exams. Would retake this class and recommend to a
friend interested in data or computer science.”
Feedback

16. Future Plans
 Finish curating, cleaning up data
 Make site publically available
 For students: provide detailed instructions on how to
find, curate, and submit their own data
 For faculty: provide detailed description of the project
and Excel spreadsheet
 Write up a paper about this for J. Chem. Ed.
 Use site as the basis for a question bank for online
study questions

17. Conclusion
 This was a fun project to run at the end of the class
 Bringing together all that we had talked about in an
activity made it much more tangible for students
 Students liked the idea that the Chem Data website
would be used by other students in chemistry
 I can’t wait to teach this again…

18.  schalk@unf.edu
 Phone: 904-620-5311
 Skype: stuartchalk
 LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
 ResearcherID: http://www.researcherid.com/rid/D-8577-2013
Questions?