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Design and Use of Relational Databases in Chemistry, by TJ O'Donnell
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Optimize Your Chemical Database
Design and Use of Relational Databases in Chemistry helps programmers and users improve their ability to search and manipulate chemical structures and information, especially when using chemical database "cartridges". It illustrates how the organizational, data integrity, and extensibility properties of relational databases are best utilized when working with chemical information.
The author facilitates an understanding of existing relational database schemas and shows how to design new schemas that contain tables of data and chemical structures. By using database extension cartridges, he provides methods to properly store and search chemical structures. He explains how to download and install a fully functioning database using free, open-source chemical extension cartridges within PostgreSQL. The author also discusses how to access a database on a computer network using both new and existing applications.
Through examples of good database design, this book shows you that relational databases are the best way to store, search, and operate on chemical information.
- Sales Rank: #1069349 in Books
- Published on: 2008-12-05
- Original language: English
- Number of items: 1
- Dimensions: 9.10" h x .90" w x 6.20" l, 1.30 pounds
- Binding: Hardcover
- 224 pages
About the Author
President, gNova Inc., San Diego, California, USA
Most helpful customer reviews
3 of 3 people found the following review helpful.
Very helpful in creating a cheminformatic relational database
By Matt Ketterer
I would say the title of this book is quite accurate. It does not cover all the details of implementation, some is left up to the user, but it guides you in the "Design and Use" aspect quite well. It even contains free code along with authors own CHORD package (Based on a commercial product) that he can sell you or you can just use the code from the book which is quite extensive and written in Perl, Python, and C(based on the very useful open-source package Open Babel)that you can use in your postgresql database. While I had to also get a book on postgresql for the technical set up aspects, this book deals with relational database design and how to search and store chemical information in a meaningful way. I would say that it is expertly written, with every chapter useful, and not some books where there is a lot of junk chapters not needed.
One wish I would have liked to see is more on client side setup, and the ability to automatically interact more with the database, but these are things that could possibly come out in the second edition?
4 of 4 people found the following review helpful.
Convincing
By Thompson N. Doman
Relational databases and the relational model are far from new concepts, having first appeared 40 years ago. When we think of where data lives, we usually think of it residing in a relational database of some sort. However, there are domains like chemical informatics where the uptake of these databases is uneven - there are still many cheminformatics scientists who have never written a line of SQL, and still rely on antiquated models of large dataset handling and storage - like flat files in a unix system.
This book aims to change that. From the first sentence of chapter 1: "The goal of this book is to convince you that relational databases are the best way to store, search, and even operate on chemical information." By the time I had finished reading this book, I was indeed convinced. From the fundamentals of relational databases, to SQL, to IT considerations like client/web applications and how to store, search, and manipulate data, O'Donnell moves on to cover how chemistry is actually represented in such databases and what you can do with it. To make this practical he discusses how to implement an actual chemistry Relational Database Management System (RDBMS) in PostgreSQL, a popular open-source RDBMS.
The book is a manageable size - 229 pages - which seems about right, of which 35 or so comprise 9 very helpful Appendices including lots of code snippets, which for me are the best way to learn. This is the kind of book I still keep out on my desk for reference to things like Table A.4 in the back. While this may seem too esoteric to some readers, it is to me an invaluable resource describing the SMARTS (a chemistry substructure specification language) implementation of one of the most popular sets of chemistry "keys" used in cheminformatics practice. Someone so inclined could learn much of the SMARTS language just by studying how these 166 keys are encoded by SMARTS strings. Readers will probably find numerous other things of this nature in the book that can be applied to their own work.
O'Donnell has made a valuable contribution to the domain of chemical informatics, and I hope he convinces others of the power of relational databases in chemistry.
5 of 14 people found the following review helpful.
much improvement needed
By A.Reader1
This is a book on storing and searching chemical structures in relational databases. It has two audiences: 1) scientists such as chemists/biologists/biochemists etc who need to work with modern IT tools like RDBMSs. These people probably do not have formal computer science training and 2) IT professionals like application developers, DB admins, DB programmers who need to provide support to, or develop for, laboratory scientists working with chemical structure data.
All in all, this is a strange book. And not in a good way. Let me explain why.
First, the book has a very "Open Source" feel with the author employing languages like Perl, Python, PHP, Java throughout and an open source DB I've never heard of - PostgreSQL. When you visit the author's website you can see why - he's obviously running his consulting company on this DB and has developed his own data cartridge (CHORD) for storing chemical structures. I've got no problem with anyone running their commercial venture as they see fit but when you write a book on chemical databases you should focus on the technologies the average user is likely to encounter. And that is not open source. This would be tools like Windows, Oracle and MS Visual Studio - VB, C#, C++ and a host of proprietary chemical software.
Second, the first six chapters on database design and related topics are unsuitable for both target audiences. Database design is a very large and important topic. It's difficult to convey all the required information in just 6 chapters covering 70 pages. This text is written at too a high a level for the scientific audience. They would need many other books and lots of hands-on experience to become proficient at design. Then these chapters would make sense. For experienced IT and DB professionals this material is trivial.
Third, there's no discussion at all of desktop chemical databases like ISIS/Base or ChemFinder. This is a significant omission IMHO.
Fourth, with a title like "Design and Use of Relational Databases in Chemistry" I was expecting a major discussion and critical comparison of the various commercial Oracle chemical database cartridges. After all, Oracle dominates the marketplace at places like Big Pharma and large chemical companies. How do these cartridges work? What are the features to look for when buying? What are pros and cons to using these products? How much do they cost (approx.)? How to develop software program using them, what do their code samples look like etc etc. None of that stuff is here.
Fifth, starting around chapter 8 or 9 this book goes off the deep end. It becomes far too technical. The only people interested in this material would be a select group of hardcore database programmers with a very good understanding of chemistry using a relatively uncommon DB called PostgreSQL. This book quickly turns into a work for the author to document the technical aspects of his database(s). Too narrow in scope.
Chapter 13 has useful info on how to construct a schema for chemicals and related experimental data. Chapters 5 and 12 may also be of some use to application developers. However, the coverage of client-side applications is kinda skimpy.
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