For each term, get its ancestor at a given level
and add the ID and name of the ancestor to the ontology metadata.
By default, lower numbers are higher in the ontology
(e.g. level 0 includes the most broad ontology term).
When a terms does not have an ancestor at a given level
(e.g. lvl=3 but the term itself is at level 1) the term is assigned
to itself as its own ancestor.
When a term has multiple ancestors at a given level,
the first ancestor is arbitrarily chosen.
add_ancestors(
ont,
lvl = 2,
include_self = TRUE,
prefix = "ancestor",
fill_na = TRUE,
i = 1,
force_new = FALSE
)An ontology of class ontology_DAG.
Depth of the ancestor terms to add. Will get the closest ancestor to this level if none have this exact level.
For dag_offspring() and dag_ancestors(), this controls whether to also include the query term itself.
A prefix for the ancestor column names.
If TRUE, fill ancestor columns with
NA values using the term ID and name.
Index of ancestor to use when more than one is available.
Add the data again even if the associated column already exists.
ont <- get_ontology("hp")
#> ⠙ iterating 8 done (3.9/s) | 2.1s
#> ⠹ iterating 14 done (4.9/s) | 2.8s
#> Importing ontology via GitHub.
#> Loading required namespace: piggyback
#> Identifying latest release for: obophenotype/human-phenotype-ontology
#> Preparing ontology_index object from: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-05-06/hp.obo
#> Parsing [Typedef] sections in the obo file [3/3]
#> Parsing [Term] sections in the obo file [1000/19650]
#> Parsing [Term] sections in the obo file [2000/19650]
#> Parsing [Term] sections in the obo file [3000/19650]
#> Parsing [Term] sections in the obo file [4000/19650]
#> Parsing [Term] sections in the obo file [5000/19650]
#> Parsing [Term] sections in the obo file [6000/19650]
#> Parsing [Term] sections in the obo file [7000/19650]
#> Parsing [Term] sections in the obo file [8000/19650]
#> Parsing [Term] sections in the obo file [9000/19650]
#> Parsing [Term] sections in the obo file [10000/19650]
#> Parsing [Term] sections in the obo file [11000/19650]
#> Parsing [Term] sections in the obo file [12000/19650]
#> Parsing [Term] sections in the obo file [13000/19650]
#> Parsing [Term] sections in the obo file [14000/19650]
#> Parsing [Term] sections in the obo file [15000/19650]
#> Parsing [Term] sections in the obo file [16000/19650]
#> Parsing [Term] sections in the obo file [17000/19650]
#> Parsing [Term] sections in the obo file [18000/19650]
#> Parsing [Term] sections in the obo file [19000/19650]
#> Parsing [Term] sections in the obo file [19650/19650]
#> remove 473 obsolete terms
#> Adding term metadata.
#> IC_method: IC_offspring
#> Adding ancestor metadata.
#> Getting absolute ontology level for 19,177 IDs.
#> 82 ancestors found at level 2
#> Translating ontology terms to names.
#> Translating ontology terms to ids.
#> Converted ontology to: adjacency
#> Getting absolute ontology level for 19,177 IDs.
#> Caching file --> /github/home/.cache/R/KGExplorer/ontologies/github/hp_v2025-05-06.rds
ont2 <- add_ancestors(ont, lvl=4)
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.