playing with ontologies

ontologyPlay.R

# ontologyPlot package requires bioconductor package Rgraphvis
# source("https://bioconductor.org/biocLite.R")
# biocLite("Rgraphvis")
# install.packages('ontologyIndex')
# install.packages('ontologyPlot')

library(ontologyIndex)
library(ontologyPlot)

download.file(url = 'http://purl.obolibrary.org/obo/uberon.obo',destfile = 'uberon.obo')


# get is_a connections. I'm doing this to understand which relationships to take
forRelationships = get_ontology('uberon.obo',propagate_relationships = c('is_a'))

# here I am taking all relationships that "is_a" "part_of" relationship
relationships  = get_descendants(forRelationships,'part_of')

# Now I re-read the ontology to get all connections I am interested in
uberon = ontologyIndex::get_ontology('uberon.obo',propagate_relationships = c(relationships,'contributes_to_morphology_of','is_a'),
                                     extract_tags = 'everything')


# here I get all children of the term "brain"
uberonBrain = get_descendants(uberon,'UBERON:0000955') %>% unique

relatedTerms = uberon$xref[uberonBrain] %>% unlist %>% unique

uberonOrgans = get_descendants(uberon,'UBERON:0000062') %>% unique # organ
uberonOrgans = uberonOrgans[!uberonOrgans %in% uberonBrain] # remove all brain regions from organs



# this is a list of brain regions
baseRegionTerms =
    list(All = 'UBERON:0000955',
         Cerebrum = c('UBERON:0001869', # cerebral hemisphere
                      'UBERON:0005401', # cerebral hemisphere gray matter
                      'UBERON:0016526', # lobe of cerebral hemisphere
                      'UBERON:0001890', # forebrain
                      'birnlex_1042', # cerebrum
                      'birnlex_1173'), # regional part of cerebrum,
         Cortex = c('UBERON:0001870', # frontal cortex
                    'UBERON:0000956'), # cerebral cortex
         BasalForebrain = 'UBERON:0002743', # basal forebrain
         Striatum = 'UBERON:0002435',
         Amygdala = 'UBERON:0001876',
         Hippocampus = 'UBERON:0002421',
         Subependymal = c('UBERON:0005357', # brain ependyma
                          'UBERON:0005380'), # olfactory bulb subependymal zone
         Thalamus = c('UBERON:0010225', # thalamic complex, kinda contraversial used to be UBERON:0001903 "thalamic reticular nucleus"
                      'birnlex_954', # thalamus
                      'birnlex_1517'), # regional part of thalamus
         Brainstem = 'UBERON:0002298',
         Midbrain = 'UBERON:0001891',
         # SubstantiaNigra = 'UBERON:0002038',
         LocusCoeruleus = 'UBERON:0002148',
         Cerebellum = 'UBERON:0002037',
         SpinalCord = 'UBERON:0002240')

# see how they stand in the ontology
onto_plot(uberon,baseRegionTerms %>% unlist)

# look at all descendants of cortex. sometimes plots additonal terms to connect things to each other. not sure why
onto_plot(uberon,get_descendants(uberon,'UBERON:0001870'),fontsize = 70)

# look at all ancestors of brain
onto_plot(uberon,get_ancestors(uberon,'UBERON:0000955'))