PubChem for Newbies

PubChem is arguably the most important free repository of information about small molecules on the planet. Although its size is staggering (over 10 million unique compounds), what makes PubChem important is its completely open approach to chemical information. Never before in the history of chemistry has so much information been made available, free to anyone who cares to use it.

Despite PubChem's pioneering approach, many factors make the service difficult to learn and navigate. Most notably, its practical yet bewildering integration into NIH's other far-flung database activities serve as highly effective camouflage for the treasures that lie beneath.

With this in mind, I thought it would be useful to collect all Depth-First articles on PubChem into one place. They have been broken down into categories, although many articles contain elements useful to anyone interested in PubChem.

For Chemists

• Five Ways to Use PubChem Right Now Food for thought and grounds for further research.
• Simple CAS Number Lookup with PubChem Could this be PubChem's killer app?
• How to Find Chemical Information on the Internet: Why Open Source, Open Access, and Open Data Matter PubChem is also part of the process.

For Hackers

• Hacking PubChem: Visually Inspect Results for CAS Number and Keyword Searches Radically change the look of PubChem.
• Hacking PubChem: Convert CAS Numbers into PubChem CIDs with Ruby Could this be PubChem's killer app?
• Hacking PubChem: Learning to Speak PUG I hope you like angle brackets.
• Java Interface to PubChem's Power User Gateway Taming those angle brackets with Java.
• The Best API May Be No API at All: PubChem and PDB Designing the obvious.
• Hacking PubChem: Power User Gateway The preferred method to program PubChem.
• Open Source and Open Data: Why We Should Eat Our Own Dogfood Open Source software and open databases should go hand-in-hand, but not in this case.
• The Problem With Ferrocene Big trouble ahead.
• Hacking PubChem: Direct Access With FTP Cheminformatics' most radical idea in the last 25 years - download all of PubChem onto your hard drive.
• Hacking PubChem: Entrez Programming Utilities One of the preferred methods to access PubChem programatically.
• Hacking PubChem: Query By Smiles Don't try this at home.
• Hacking PubChem with Ruby One of my first attempts to use Ruby for cheminformatics.

For Everyone

• PubChem is a Platform Just like the Apple ][ - hardly perfect, but good enough and infinitely hackable.
• Thirty-Two Free Chemistry Databases PubChem in its context.
• Hacking PubChem: Why the Open Access Fight is Just the Beginning Just getting an open database is not the end of the story.
• Hacking PubChem: Free Speech or Free Beer? It depends on what the meaning of the word 'is' is.
• Toward and Open Worldwide Chemical Information Network Back in 1965, Walter M. Carlson was way ahead of his time.
• Changes My first blog post - inspired, in part, by the launch of PubChem.

If you've got a favorite PubChem resource you'd like to share, please feel free to leave a comment.