GO.db source obo file?
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brismiller • 0
@brismiller-16664
Last seen 3.2 years ago

Hey everybody,

I am wondering if it is possible to get an .obo file from the GO.db package? From my understanding, GO.db uses SQL queries to retrieve the ontology information and I am wondering if this information could be organized into and obo file so I can use other programs such as BiNGO (for network visualization in Cytoscape). 

When I use BiNGO with the geneontology.org's core obo file (http://purl.obolibrary.org/obo/go.obo) I get slightly different results than if I use GOstats (which relies on GO.db for ontology information). I just want a way to access (or generate) an obo file from GO.db so that my visualization results are consistent with my GOstats results.

Many thanks in advance, session info below if interested.

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GO.db_3.6.0          AnnotationDbi_1.42.1 IRanges_2.14.10      S4Vectors_0.18.3     Biobase_2.40.0      
[6] BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18    digest_0.6.15   DBI_1.0.0       RSQLite_2.1.1   blob_1.1.1      tools_3.5.1     bit64_0.9-7    
 [8] bit_1.1-14      compiler_3.5.1  pkgconfig_2.0.1 memoise_1.1.0  
gene ontology gostats go.db ontologies • 474 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 10 hours ago
United States

You should be able to do this directly. The GSEABase package has a function called getOBOCollection that you should be able to use, and then the GOstats package will do the right thing with it. See ?hyperGTest,OBOHyperGParams-method

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@martin-morgan-1513
Last seen 10 weeks ago
United States

Likely the reason for differences is because the version of GO you use for visualization is different from the version used by GO.db. For me with version 3.6.0 of GO.db (same as you), loading the library and printing GO.db gives

> GO.db
GODb object:
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2018-Mar28
| Db type: GODb
| package: AnnotationDbi
| DBSCHEMA: GO_DB
| GOEGSOURCEDATE: 2018-Apr4
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| DBSCHEMAVERSION: 2.1

looking around at the GOSOURCEURL a bit and navigating to the 'latest' as of GOSOURCEDATE lead me to ftp://ftp.geneontology.org/pub/go/godatabase/archive/lite/2018-03-24/ where I see an obo-xml file. Maybe this is close enough to what you need?

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