[Bioc-devel] OrganismDb package for Drosophila.melanogaster

Tue Nov 15 20:34:17 CET 2016

On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
> Hi Pariksheet,
>
> On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
>> Hi folks,
>>
>> It would be great to have an OrganismDb package for
>> Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and
>> Rattus.norvegicus.
>>
>> While trying to do this on my own using the Homo.sapiens package as a
>> starting point, I found the most similar looking keys to relate
>> org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and
>> "GENEID" though there's a ".1" tacked to the end "GENEID" which makes it
>> harder to supply the graphInfo object to OrganismDbi:::.loadOrganismDbiPkg:
>>
>> !> key_ <- function(db, key) sort(as.character(
>>  +                                select(db, keys(db, key), key,
>> key)[[key]]))
>>  > key_head <- function(db, key) head(key_(db, key))
>>  > key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID")
>>  'select()' returned 1:1 mapping between keys and columns
>>  [1] "FBgn0000003.1" "FBgn0000008.1" "FBgn0000014.1" "FBgn0000015.1"
>>  [5] "FBgn0000017.1" "FBgn0000018.1"
>>  > key_head(org.Dm.eg.db, "ENSEMBL")
>>  [1] "FBgn0000008" "FBgn0000014" "FBgn0000015" "FBgn0000017" "FBgn0000018"
>>  [6] "FBgn0000022"
>>  >
>>
>> In other words, like Rattus.norvegicus, it might be good do add a UCSC
>> "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as good of
>> a candidate (at least without some ugliness)?  I was looking at creating a
>> dm6 UCSC "refGene" TxDb.
> You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The
> man page, ?makeTxDbFromUCSC, also has helper functions that display
> available genomes, tables and tracks.

I'm not completely sure of the result, but

library(OrganismDb)
odb = makeOrganismDbFromUCSC("dm6", tableName="refGene")

might be most of the way there?

Martin

>
> Valerie
>
>> I imagine one would query the UCSC public MySQL
>> server and then do the SQLite conversion.  Although the conversion to
>> SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite
>> and I'm having a hard time finding a well supported tool to do it; I don't
>> want to introduce errors or harm reproducibility.  What do you use for
>> MySQL to SQLite conversion?  Or would it be more sensible for you
>> benevolent dictators to generate the package(s)?
>>
>> Pariksheet
>>
>> ---
>> Pariksheet Nanda
>> PhD Candidate in Genetics and Genomics
>> System Administrator, Storrs HPC Cluster
>> University of Connecticut
>>
>> ---
>>  > sessionInfo()
>>  R Under development (unstable) (2016-11-13 r71655)
>>  Platform: x86_64-pc-linux-gnu (64-bit)
>>  Running under: Ubuntu 16.04.1 LTS
>>
>>  locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>  attached base packages:
>>  [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>  [8] methods   base
>>
>>  other attached packages:
>>   [1] Rattus.norvegicus_1.3.1
>>   [2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0
>>   [3] org.Rn.eg.db_3.4.0
>>   [4] Mus.musculus_1.3.1
>>   [5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
>>   [6] org.Mm.eg.db_3.4.0
>>   [7] Homo.sapiens_1.3.1
>>   [8] GO.db_3.4.0
>>   [9] OrganismDbi_1.17.1
>>  [10] org.Hs.eg.db_3.4.0
>>  [11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
>>  [12] org.Dm.eg.db_3.4.0
>>  [13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0
>>  [14] GenomicFeatures_1.27.2
>>  [15] AnnotationDbi_1.37.0
>>  [16] Biobase_2.35.0
>>  [17] GenomicRanges_1.27.6
>>  [18] GenomeInfoDb_1.11.4
>>  [19] IRanges_2.9.8
>>  [20] S4Vectors_0.13.2
>>  [21] BiocGenerics_0.21.0
>>  [22] BiocInstaller_1.25.2
>>
>>  loaded via a namespace (and not attached):
>>   [1] compiler_3.4.0             XVector_0.15.0
>>   [3] bitops_1.0-6               tools_3.4.0
>>   [5] zlibbioc_1.21.0            biomaRt_2.31.1
>>   [7] RSQLite_1.0.0              lattice_0.20-34
>>   [9] Matrix_1.2-7.1             graph_1.53.0
>>  [11] DBI_0.5-1                  rtracklayer_1.35.1
>>  [13] Biostrings_2.43.0          grid_3.4.0
>>  [15] XML_3.98-1.5               RBGL_1.51.0
>>  [17] BiocParallel_1.9.1         Rsamtools_1.27.2
>>  [19] GenomicAlignments_1.11.1   SummarizedExperiment_1.5.3
>>  [21] RCurl_1.95-4.8
>>  >
>>
>> 	[[alternative HTML version deleted]]
>>
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>
>
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