Exploring Databases

Concepts

Possible IA topics

[TODO]

Non-IA topics

[TODO]

Database vs modelling

A guided tour of chemical databases

This walkthrough showcases some of the specialized databases containing data that may be difficult to find in PubChem, ChemSpider, or NIST Webbook. These include SDBS for organic spectra, PDB for macromolecules, and CCDB for X-ray structures. You will need some organic chemistry, biochemistry, or knowledge of X-ray structures to understand this guided tour.

SDBS PubChem ChemSpider NIST Webbook PDB CCDB Wikipedia Handbooks - CRC, aq sol

Calculated vs experimental data

[TODO]

Database tools

http://www.cheminfo.org/

Tutorial projects

Tutorial 1: Planning searches & using Chemistry Databases

In this tutorial you will learn to solve a scientific problem using databases. I teach you how to plan for a database project, including how to prepare a spreadsheet for data collection. You will then, as a group, curate data from three public chemistry databases (PubChem, NIST Webbook, ChemSpider) and merge them with data from molecular modelling; this is then visualized using a "bubble chart" --- which then resolves the research question.

Tutorial 2: Structural searches

Searching by name is only one of the ways to find chemical information. Most of the time the molecules would have too many isomers for a formula search to be practical, and you won't know how to name them either. In this tutorial you will learn how to search through the above three databases using structural searches where you draw a structure in order to find it in the database. You will, additionally, be asked to make meaning out of this data.

Tutorial 3: Four ways of accessing PubChem

Manual access 3rd party tools

• http://www.cheminfo.org/
• chemMine tools http://chemminetools.ucr.edu/ Access through spreadsheet Programmatic access: JS / python

Data analysis and visualization

See data analysis.