Read an Open Biological and Biomedical Ontologies (OBO) formatted file
References
The format is described here
Examples
oboFile <- system.file(
package = "BaseSet", "extdata",
"go-basic_subset.obo"
)
gs <- getOBO(oboFile)
head(gs)
#> elements sets name namespace
#> 1 GO:0000001 GO:0048308 mitochondrion inheritance biological_process
#> 2 GO:0000001 GO:0048311 mitochondrion inheritance biological_process
#> 3 GO:0000002 GO:0007005 mitochondrial genome maintenance biological_process
#> 4 GO:0000003 GO:0008150 reproduction biological_process
#> 5 GO:0000003 GO:0008150 reproduction biological_process
#> 6 GO:0000003 GO:0008150 reproduction biological_process
#> def
#> 1 "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
#> 2 "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
#> 3 "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome." [GOC:ai, GOC:vw]
#> 4 "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
#> 5 "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
#> 6 "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
#> synonym alt_id subset comment
#> 1 "mitochondrial inheritance" EXACT [] <NA> <NA> <NA>
#> 2 "mitochondrial inheritance" EXACT [] <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA>
#> 4 "reproductive physiological process" EXACT [] GO:0019952 goslim_agr <NA>
#> 5 "reproductive physiological process" EXACT [] GO:0019952 goslim_agr <NA>
#> 6 "reproductive physiological process" EXACT [] GO:0019952 goslim_agr <NA>
#> consider relationship set_name ref_origin ref_code
#> 1 <NA> <NA> organelle inheritance <NA> <NA>
#> 2 <NA> <NA> mitochondrion distribution <NA> <NA>
#> 3 <NA> <NA> mitochondrion organization <NA> <NA>
#> 4 <NA> <NA> biological_process Wikipedia Reproduction
#> 5 <NA> <NA> biological_process Wikipedia Reproduction
#> 6 <NA> <NA> biological_process Wikipedia Reproduction
#> fuzzy
#> 1 1
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1