PANTHER.db update to the last version of PANTHERdb database?
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@alfonsosaera-19747
Last seen 2.7 years ago

Hi,

This is my first post here, hopefully it is in the right place and form :-)

According to the PANTHER.db information

PANTHER.db object:
| ORGANISMS: ...
| PANTHERVERSION: 12.0
| PANTHERSOURCEURL: ftp.pantherdb.org
| PANTHERSOURCEDATE: 2017-Sep15
| package: AnnotationDbi
| Db type: PANTHER.db
| DBSCHEMA: PANTHER_DB
| DBSCHEMAVERSION: 2.1
| UNIPROT to ENTREZ mapping: 2017-Sep15

The current Bioconductor PANTHER.db package version 1.0.4 (as by February 2019) contains PANTHER database version 12.0 (released on 2017-Sep15).

However, according to PANTHERdb website, the latest PANTHERdb is Version 14.0, released on 2018-12-03, generated from the 2018_04 release of ReferenceProteome dataset.

Is there any plans to update the Bioconductor PANTHER.db package?

Or, alternatively, how could I download the latest version of the PANTHERdb database?

Thank you very much for your help!

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

>Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

>locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

>attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

>other attached packages:
[1] PANTHER.db_1.0.4     RSQLite_2.1.1        AnnotationDbi_1.44.0 IRanges_2.16.0       S4Vectors_0.20.1     Biobase_2.42.0       BiocGenerics_0.28.0 

>loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         digest_0.6.18      DBI_1.0.0          blob_1.1.1         tools_3.5.2        bit64_0.9-7        bit_1.1-14         xfun_0.4          
 [9] compiler_3.5.2     pkgconfig_2.0.2    BiocManager_1.30.4 memoise_1.1.0      knitr_1.21
PANTHER.db update annotation go • 457 views
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@juliusmuller-11789
Last seen 24 months ago
Germany/Heidelberg

Yes, I can update PANTHER.db to the latest version in the coming weeks.

If you need the update faster, you could adapt the helper script in:

file.path(find.package("PANTHER.db"),"script","build_sqlite_denorm.R")

and replace the database file:

 file.path(find.package("PANTHER.db"),"extdata","PANTHER.db.sqlite")

If you want to give it a try, feel free to ask me about further details.

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