[Genome] Gene ontology and the genome browser

[Ann Zweig]

> Hello again Avi,
> 
>     We do try to keep our go builds up-to-date.  Both the hg18 and mm8 
> assemblies point to the most recent go build that we have.  We 
> downloaded the go data from their website on Feb 11 2006.  They have 
> called that particular go database go_200601.  We call it go060211.
> 
> wget --timestamping 
> http://www.godatabase.org/dev/database/archive/latest/go_200601-assocdb-data.gz 
> 
> 
>     So, assuming your proteinIDs are not from a more recent or earlier 
> go release, they should be in sync with our go060211 database.
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> fungazid fungazid wrote:
>>  
>> Hello Ann,
>>  
>> you said:
>> "go.goaPart.dbObjectSymbol (via hg18.knownGene.proteinID)"
>>  
>> Unlike hg18.knownGene.name, the proteinID of any gene-accession can be 
>> changed from one swissprot build to another. Are the Go-builds in the 
>> link you sent suited to the proteinIds ? Is there a way to make sure 
>> about it ?
>>  
>> Many thanks,
>> Avi
>>
>>
>> */Ann Zweig <ann at soe.ucsc.edu>/* wrote:
>>
>>     Hello Avi,
>>
>>     There is not a ready-made table that includes hg18 (and mm8) known
>>     gene names
>>     and go annotations. But there is a 'go' database which has a
>>     relationship with
>>     the hg18 (and mm8) database. Since you are working with large
>>     tables, I would
>>     suggest that you download the 'go' tables that you will need and
>>     then write some
>>     SQL joins to get the information you want.
>>
>>     You can download tables from the 'go' database at our ftp server:
>>     ftp://hgdownload.cse.ucsc.edu/goldenPath/go/database/
>>
>>     In this directory, the files are structured like so:
>>
>>     - *.sql files: the MySQL commands used to create the tables.
>>     - *.txt.gz files: the database tables in a tab-delimited format
>>     compressed with gzip.
>>
>>     Tables of particular interest to you might be the goaPart table and
>>     the term
>>     table. The tables in the go database are related to the knownGene
>>     table like so:
>>
>>     go.goaPart.dbObjectSymbol (via hg18.knownGene.proteinID)
>>
>>     go.term.acc (via go.goaPart.goId)
>>
>>     go.goaPart.goId (via go.term.acc)
>>     go.graph_path.term1_id (via go.term.id)
>>     go.graph_path.term2_id (via go.term.id)
>>     go.term2term.term1_id (via go.term.id)
>>     go.term2term.term2_id (via go.term.id)
>>     go.term_dbxref.term_id (via go.term.id)
>>     go.term_definition.term_id (via go.term.id)
>>     go.term_synonym.term_id (via go.term.id)
>>
>>     If you are interested in the table structure and other table
>>     relationships,
>>     please visit our table browser (press the "Tables" link in the blue
>>     navigation
>>     bar across the top of the browser).
>>
>>     This should get you started in your quest. If you need more detailed
>>     help,
>>     please feel free to write back.
>>
>>
>>     Regards,
>>
>>     ----------
>>     Ann Zweig
>>     UCSC Genome Bioinformatics Group
>>     http://genome.ucsc.edu
>>
>>
>>
>>     fungazid fungazid wrote:
>>      > Dear all,
>>      >
>>      > Hello to you,
>>      >
>>      > I downloaded knownGene mysql-tables of mm8 and hg18, and I want
>>     to attach each gene name (‘name’ column) to its gene ontology
>>     annotations (Go). I would like to know it there is any simple way to
>>     achieve this task either in the UCSC site or in other sites. If
>>     there is a ready-made table somewhere, it is also a good idea. If
>>     you think it is better to use othe gene table than knownGene, I can
>>     listen.
>>      >
>>      > The table should be something like
>>      >
>>      >
>>     
>> ----------------------------------------------------------------------------------- 
>>
>>      > fields:
>>      > Identifier ,Symbol ,Gene name,Category of term , GO ID, GO Term,
>>     Source Evidence, PubMed
>>      >
>>      > example - content of a record:
>>      >
>>      > NM_001005484
>>      > OR4F5
>>      > Olfactory receptor, family 4, subfamily F, member 5
>>      > molecular_function
>>      > GO:0004872
>>      > receptor activity
>>      > IEA
>>      > -
>>      >
>>      > ------------------------------------------------------------------
>>      >
>>      >
>>      > I tried genetools software
>>     (http://www.genetools.microarray.ntnu.no/egon/index.php), which is
>>     designed to do exactly that, but I believe I need to verify what I 
>> got.
>>      >
>>      >
>>      > Thanks
>>      > Avi
>>      >
>>      >
>>      >
>>      >
>>      >
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