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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  GO.db_3.6.0 AnnotationDbi_1.42.1 IRanges_2.14.10 S4Vectors_0.18.3 Biobase_2.40.0  BiocGenerics_0.26.0 loaded via a namespace (and not attached):  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  bit_1.1-14 compiler_3.5.1 pkgconfig_2.0.1 memoise_1.1.0