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