Channels ▼

Google's Summer of Code: Part I

December, 2005: Google's Summer of Code

CL-GODB: A Common Lisp GO Database Manipulation Library

Name: Samantha Kleinberg
School: New York University
Major: Physics and Computer Science
Project: CL-GODB
Project Page:
Mentor: Marco Antoniotti
Mentoring Organization: LispNYC (

CL-GODB is a new interface to the GO Database ( written in Common Lisp. The Gene Ontology (GO) is a collection of terms organized in a taxonomy representing a controlled vocabulary used to describe genes, gene products, their functions, and the processes they are involved in for a variety of organisms. The GO Database (GODB) represents the ontological information and gene product annotations in a convenient relational database format (the GO database uses MySQL).

Until now, there have been no interfaces to the database that use Common Lisp. This is inconvenient as there are Bioinformatics and Systems Biology tools that employ the language (BioLingua, GOALIE, and the BioCYC suite, for instance).

GOALIE, developed by Marco Antoniotti and Bud Mishra in NYU's Bioinformatics Group ( analyzes time course data from micro-array clustering experiments. The CL-GODB library will be integrated into GOALIE, improving the tool's functionality and efficiency.

The library works by building an incremental, as-needed, internal image of the GO database contents in core. This improves the speed of queries and facilitates the construction of more complex predicates that may be needed in an application such as GOALIE.

Users start by creating a handle that identifies their session and is linked to several hash indexes used in the in-core caching. Once they have connected to their copy of the GO database, they have access to a variety of built-in SQL queries, which take advantage of the indexing and add to the stored data. The queries range from getting basic information about a term, to finding a term's lineage using a choice of hierarchies.

As a testbed for the CL-GODB library, we built a GUI application that is available as a standalone executable. The CL-GODB Viewer lets users browse the hierarchy with a graphical tree view and provides information about each term and its associated genes, in a manner similar to that of several other GO viewer applications available online.

Creating the CL-GODB was challenging at times, as it was my first project in Common Lisp. The biggest hurdle was making sure that case-sensitivity vagaries were taken care of, as Common Lisp and MySQL behave differently under Windows and UNIX. In the end, it did work and I learned more about the intricacies of SQL syntax than I ever wanted to know.

Figure 1


Related Reading

More Insights

Currently we allow the following HTML tags in comments:

Single tags

These tags can be used alone and don't need an ending tag.

<br> Defines a single line break

<hr> Defines a horizontal line

Matching tags

These require an ending tag - e.g. <i>italic text</i>

<a> Defines an anchor

<b> Defines bold text

<big> Defines big text

<blockquote> Defines a long quotation

<caption> Defines a table caption

<cite> Defines a citation

<code> Defines computer code text

<em> Defines emphasized text

<fieldset> Defines a border around elements in a form

<h1> This is heading 1

<h2> This is heading 2

<h3> This is heading 3

<h4> This is heading 4

<h5> This is heading 5

<h6> This is heading 6

<i> Defines italic text

<p> Defines a paragraph

<pre> Defines preformatted text

<q> Defines a short quotation

<samp> Defines sample computer code text

<small> Defines small text

<span> Defines a section in a document

<s> Defines strikethrough text

<strike> Defines strikethrough text

<strong> Defines strong text

<sub> Defines subscripted text

<sup> Defines superscripted text

<u> Defines underlined text

Dr. Dobb's encourages readers to engage in spirited, healthy debate, including taking us to task. However, Dr. Dobb's moderates all comments posted to our site, and reserves the right to modify or remove any content that it determines to be derogatory, offensive, inflammatory, vulgar, irrelevant/off-topic, racist or obvious marketing or spam. Dr. Dobb's further reserves the right to disable the profile of any commenter participating in said activities.

Disqus Tips To upload an avatar photo, first complete your Disqus profile. | View the list of supported HTML tags you can use to style comments. | Please read our commenting policy.