[BioC] GO terms for E. coli micro arrays (ecoliK12.db generation)

[Marc Carlson]

Hi Gaspard,

Thank you for your input.  The number of map-able GO terms in a chip
package will almost always be a subset of the number of GO terms in the
source database.  This is just a a consequence of the fact that most
chips don't measure all of the genes.  I would love to improve this
situation with the number of GO mappings, but the source I have for GO
to entrez gene mappings (NCBI) has only provided the mappings you see
here.  This is also why there is no evidence code.  I only have what
NCBI gave me.  I could consider using blast2GO mappings instead, but
then the nature of the data changes.  And so far we have only used
blast2GO for those organisms where it was the only option.  If you have
another good primary source for such mappings, I would love to know
about it.  As you have discovered, not many people are using any of the
E coli stuff yet for chip packages (in fact, you might be the 1st). 
Most people only use the organism packages org.EcK12.eg.db
<http://www.bioconductor.org/packages/release/data/annotation/html/org.EcK12.eg.db.html>
or org.EcSakai.eg.db
<http://www.bioconductor.org/packages/release/data/annotation/html/org.EcSakai.eg.db.html>. 
But, since these are based on the same sources, the data representation
will be similar.  Finally, I would encourage you not to comment out the
VACUUM an ANALYZE statements in AnnotationDbi when you make chip
packages.  Instead, I would recommend that you use more liberal write
permissions so that your code can perform writes on your newly created
DBs. 


  Marc



Gaspard Lequeux wrote:
>
> Hej,
>
> Has anybody succeeded in constructing an ecoliK12.db database with
> usable Gene Ontology annotations? topGO is an nice R package that
> works very well with the yeast genome, and I would like to use it with
> E. coli but almost no GO terms are apparently available for E. coli
> when using the tools provided by AnnotationDbi.
>
>
> No ecoliK12.db database exists in the repositories, but according to
> the documentation in the AnnotationDbi package, this should be very
> easy with the makeECOLICHIP_DB command from that package.
>
> However, code didn't run. First some modifications had to be done to
> the AnnotationDbi package. I downloaded the sourcecode
> (AnnotationDbi_1.6.0.tar.gz). I also made sure that ecoliK12.db0 was
> installed (version ecoliK12.db0_2.2.11.tar.gz was used).
>
> In the directory AnnotationDbi/R, the 2 following files were modified.
>
>
> sqlForge_baseMapBuilder.R:
>
> Comment out line 234:
>
> sql <- "INSERT INTO probe2gene SELECT DISTINCT m.probe_id, u.gene_id \
> FROM min_other_rank as m INNER JOIN src.unigene as u WHERE \
> m.gene_id=u.unigene_id;"
>
> and line 235:
>
> sqliteQuickSQL(db, sql)
>
> Otherwise one gets the error:
>
> RS-DBI driver: (error in statement: no such table: src.unigene)
>
>
>
> sqlForge_tableBuilder.R
>
> Comment out line 181:
>
> sqliteQuickSQL(db, "ANALYZE;")
>
> and lines 3179 and 3180:
>
> sqliteQuickSQL(db, "VACUUM probe_map;")
> sqliteQuickSQL(db, "ANALYZE;")
>
> Otherwise one gets the error:
>
> RS-DBI driver: (RS_SQLite_exec: could not execute1: attempt to write a
> readonly database)
>
>
> The package was retarred and installed with:
>
> R CMD INSTALL AnnotationDbi_1.6.0.tar.gz
>
>
> I also downloaded the annotation file for the ecoli2 array from
> affymetrix (E_coli_2.na28.annot.csv).
>
> R was started and the following commands were given (make sure the
> directory 'ecoliK12.db' exist, also the path to the site-library may
> vary):
>
> library(AnnotationDbi);library(ecoliK12.db0)
>
> makeECOLICHIP_DB(affy=TRUE,prefix='ecoliK12',fileName="E_coli_2.na28.annot.csv",
>
> baseMapType='eg',chipSrc='/usr/local/lib/R/site-library/ecoliK12.db0/extdata/chipsrc_ecoliK12.sqlite',
>
> chipMapSrc='/usr/local/lib/R/site-library/ecoliK12.db0/extdata/chipmapsrc_ecoliK12.sqlite',
>
> chipName='E_coli_2',outputDir='ecoliK12.db',version='2.2.11')
>
> In the ecoliK12.db directory, another ecoliK12.db directory was
> created by those R commands. This directory was tarred (tar -czf
> ecoliK12.db_2.2.11.tar.gz ecoliK12.db/) resulting in an installable
> package that technically works with topGO.
>
> But not many GO terms are associated with the probes; much less than
> the number of GO terms that can be found for each probe in the probe
> annotation file provided by affymetrix.
>
> The table below lists the number of GO terms found in the different
> tables for the three ontologies:
>
> MG1655: the number of GO terms annotated to the probes of MG1655, as
> found in the affymetrix probe annotation file (that array contains
> also probes for other E. coli; they are filtered out for this table).
>
> ecoliK12.db: the number of GO terms that are found in the database
> generated by the makeECOLICHIP_DB command from above.
>
> ecoliK12.db0: the number of GO terms that are found in the original
> database that makeECOLICHIP_DB uses for generating the ecoliK12.db
> database. It should be noted that also in that database, no evidence
> codes occur (the evidence column has everywhere the value '-').
>
>                     GO_BP_all  GO_CC_all  GO_MF_all
> MG1655              9899       7023       17925
> ecoliK12.db         6394       2999       211
> ecoliK12.db0        33526      17367      1266
>
> (the comparison was done with the _all tables from the database, to be
> able to compare with the affymetrix file)
>
> Why are there not more GO terms found in the ecoliK12.db? Using other
> baseMapType than 'eg' does not help. Only 'refseq' doesn't crash, but
> even less GO terms are obtained than with 'eg'. Furthermore, for
> refseq, I think some modification has to be done to the cleanRefSeqs
> function in sqlForge_baseMapBuilder.R (the line with baseMap[,2] =
> sub("\\.\\d+?$", "", baseMap[,2], perl=TRUE) should be changed to
> baseMap[,2] = sub("^[^_]*_([^_]*)_.*", "\\1", baseMap[,2], perl=TRUE)).
>
> Trying to add the GO terms of the affymetrix file afterwards to the
> database, doesn't work (no better results in topGO: still only few
> (less than 10) significant nodes when comparing aerobic with anaerobic
> grown cells giving more than 2000 differently expressed genes).
>
> A possible problem might be that affymetrix provides also the
> redundant GO terms to the probes and that I added all those to the
> GO_XX and GO_XX_all tables. The GO_XX tables should normally only
> contain the most specific GO terms.
>
> Is this a known problem? Should I give up doing GO analysis with topGO
> for E. coli? Or is there a workaround?
>
> The R version used is R version 2.7.1 (2008-06-23) on Debian (however
> for AnnotationDbi and ecoliK12.db0 the most recent versions were
> downloaded from the bioC website, together with their dependencies) .
>
> Thank you very much for any suggestions,
>
> Gaspard
>
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