CL-GODB: A Common Lisp GO Database Manipulation Library

The Gene Ontology (GO), is a controlled vocabulary used to aid the description of gene and gene product attributes in a variety of organisms. There are three different ontologies that describe molecular functions, biological processes, and cellular components.

The Gene Ontology Database (GODB) stores the known information about these genes and gene products.

Example Use

Use of the CL-GODB begins with creation of a handle in order to index search results and the creation of a database connection.

cl-prompt:(godb:make-godb-handle)
#<CL-GODB:GO-HANDLE 205F1D04>

cl-prompt: (godb:connect mygohandle "data source name/user/password")
#<GODB:GO-HANDLE 2061155C> connecting as "data source name/user"
#<SQL::ODBC-DATABASE "data source name/user" 205F450C>

From there the full library of functions can be accessed. For example, staring with one go accession we can find out information on the term that describes it plus the gene products to which it is associatied. Note that the lower four slots are not filled until that data is requested.

cl-prompt: (godb:get-term-by-acc mygohandle "GO:0000121")
#<GODB:TERM 205ED59C >

cl-prompt: (describe *)
#< GODB:TERM 205ED59C > is a CL-GODB:TERM
TERM-ID          118
NAME             "glycerol-1-phosphatase activity"
ACCESSION        CL-GODB::GO\:000012
TERM-TYPE        "molecular_function"
DEFINITION       #<unbound slot>
IS-OBSOLETE      0
IS-ROOT          0
IS-A             NIL
PART-OF          NIL
CHILDREN         NIL
COMPONENTS       NIL

cl-prompt: (godb:go-accession-gene-products mygohandle "GO:0000121")
(#<CL-GODB:GENE-PRODUCT 2153362C> #<CL-GODB:GENE-PRODUCT 2153365C> #<CL-GODB:GENE-PRODUCT 2153368C> 
#<CL-GODB:GENE-PRODUCT 215336BC>)

cl-prompt: describe (first *)
#<CL-GODB:GENE-PRODUCT 205F88B4> is a CL-GODB:GENE-PRODUCT
ID                       1739416
GENE-SYMBOL              "TIGR_TGI:S.cerevisiae_TC15486"
DBXREF-ID                1882451
SPECIES-ID               141031
FULL-NAME                "(DL)-glycerol-3-phosphatase 1"
SPECIES-COMMON-NAME      NIL

Features

CL-GODB provides a new way to access and interact with the GO Database. As queries are made, the results are indexed locally. This indexing makes successive queries faster, requiring fewer database accesses. In addition to the library of functions, there is a graphical interface that allows the user to browse the database in tree form.

Applications

One application that uses the CL-GODB is GOALIE.

Another application is the CL-GODB GUI,which allows quick browsing of the ontology. It provides information on terms and their associated gene symbols.

Requirements

CL-GODB uses LispWorks with Common SQL and requires a local copy of the GO Database.

The CL-GODB Dictionary

The CL-GODB dictionary contains all the definitions comprising the library.

Acknowledgments

This project was sponsored by the Google Summer of Code program. The Lisp NYC group provided moral guidance and support. The NYU Courant Bioinformatics Group provided all the rest.

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2005-08-10
Page updated.
2005-06-14
Started the site.