Import ontology file to an ontology_DAG object

import_obo(
  file,
  relation_type = character(0),
  inherit_relations = TRUE,
  verbose = simona_opt$verbose,
  ...
)

import_owl(
  file,
  relation_type = character(0),
  inherit_relations = TRUE,
  verbose = simona_opt$verbose,
  ...
)

import_ontology(
  file,
  robot_jar = simona_opt$robot_jar,
  JAVA_ARGS = "",
  verbose = simona_opt$verbose,
  ...
)

import_ttl(file, relation_type = "part_of", verbose = simona_opt$verbose, ...)

Arguments

file: Path of the ontology file or an URL.
relation_type: Semantic relation types to include. Note is_a relation is always included.
inherit_relations: Relations may also be structured as a DAG. It controls whether to merge with a relations's offspring relations.
verbose: Whether to print messages.
...: Pass to create_ontology_DAG().
robot_jar: The path of the robot.jar file. It can be downloaded from https://github.com/ontodev/robot/releases. Internally, the file is converted to the obo format and parsed by import_obo(). The value of robot_jar can be set as a global option simona_opt$robot_jar = ....
JAVA_ARGS: Options for java. For example you can set -Xmx20G if you want to increase the memory to 20G for java.

Value

An ontology_DAG object.

Details

Public bio-ontologies can be obtained from Ontology Foundry or BioPortal.

The import_obo() function parses the ontology file in .obo format. To parse other formats, external tool robot.jar is required.

import_owl() only recognizes <owl:Class> and <owl:ObjectProperty>. If the .owl file does not contain these tags, please use import_ontology() directly.

robot.jar can automatically recognize the following formats:

json: OBO Graphs JSON
obo: OBO Format
ofn: OWL Functional
omn: Manchester
owl: RDF/XML
owx: OWL/XML
ttl: Turtle

The description of the ROBOT tool is at http://robot.obolibrary.org/convert.

import_ttl() is a simple parser for the .ttl format files. It only recognizes terms that have the owl:Class object. The "is_a" relation is recognized by the predicate rdfs:subClassOf or an ontology-specific predicate that contains .*/isa. Other relation types are defined with the predicate owl:ObjectProperty. The format is parsed by a Perl script system.file("scripts", "parse_ttl.pl", package = "simona").

Examples

# \donttest{
# The plant ontology: http://obofoundry.org/ontology/po.html 
import_obo("https://raw.githubusercontent.com/Planteome/plant-ontology/master/po.obo")
#> Parsing [Typedef] sections in the obo file [13/13]
#> Parsing [Term] sections in the obo file [1000/1791]
#> Parsing [Term] sections in the obo file [1791/1791]
#> remove 134 obsolete terms
#> There are more than one root:
#>   PO:0009012, PO:0025131
#>   A super root (~~all~~) is added.
#> An ontology_DAG object:
#>   Source: po, releases/2024-04-17 
#>   1658 terms / 1778 relations
#>   Root: ~~all~~ 
#>   Terms: PO:0000001, PO:0000002, PO:0000003, PO:0000004, ...
#>   Max depth: 11 
#>   Avg number of parents: 1.07
#>   Avg number of children: 1.06
#>   Aspect ratio: 39:1 (based on the longest distance from root)
#>                 38.2:1 (based on the shortest distance from root)
#>   Relations: is_a
#> 
#> With the following columns in the metadata data frame:
#>   id, short_id, name, namespace, definition
# }
# \donttest{
import_owl("http://purl.obolibrary.org/obo/po.owl") 
#> Parsing 13 <owl:ObjectProperty> ...
#> Parsing 1996 <owl:Class> ...
#> Parsing 81 <rdf:Description> ...
#> remove 337 obsolete terms
#> There are more than one root:
#>   PO:0009012, PO:0025131
#>   A super root (~~all~~) is added.
#> An ontology_DAG object:
#>   Source: Plant Ontology, http://purl.obolibrary.org/obo/po/releases/2024-04-17/po.owl 
#>   1658 terms / 1778 relations
#>   Root: ~~all~~ 
#>   Terms: PO:0000001, PO:0000002, PO:0000003, PO:0000004, ...
#>   Max depth: 11 
#>   Avg number of parents: 1.07
#>   Avg number of children: 1.06
#>   Aspect ratio: 39:1 (based on the longest distance from root)
#>                 38.2:1 (based on the shortest distance from root)
#>   Relations: is_a
#> 
#> With the following columns in the metadata data frame:
#>   id, short_id, name, namespace, definition
# }
# \dontrun{
# The plant ontology: http://obofoundry.org/ontology/po.html 
dag = import_ontology("http://purl.obolibrary.org/obo/po.owl", robot_jar = ...)
#> Error in eval(expr, envir, enclos): '...' used in an incorrect context
# }
# \donttest{
# file is from https://bioportal.bioontology.org/ontologies/MSTDE
import_ttl("https://jokergoo.github.io/simona/MSTDE.ttl")
#> Downloading https://jokergoo.github.io/simona/MSTDE.ttl...
#> Parsing .ttl file...
#> Constructing the DAG_ontology object...
#> There are more than one root:
#>   http://purl.bioontology.org/ontology/MSTDE/MT010001,
#>   http://purl.bioontology.org/ontology/MSTDE/MT020001,
#>   http://purl.bioontology.org/ontology/MSTDE/MT030001,
#>   http://purl.bioontology.org/ontology/MSTDE/MT050008,
#>   http://purl.bioontology.org/ontology/MSTDE/MT050027,
#>     and other 272 terms ...
#>   A super root (~~all~~) is added.
#> An ontology_DAG object:
#>   Source: file183a02fffee32_MSTDE.ttl 
#>   1411 terms / 1415 relations
#>   Root: ~~all~~ 
#>   Terms: http://purl.bioontology.org/ontology/MSTDE/MT010001,
#>          http://purl.bioontology.org/ontology/MSTDE/MT010002,
#>          http://purl.bioontology.org/ontology/MSTDE/MT010003,
#>          http://purl.bioontology.org/ontology/MSTDE/MT010004, ...
#>   Max depth: 6 
#>   Avg number of parents: 1.00
#>   Avg number of children: 1.00
#>   Aspect ratio: 161.4:1 (based on the longest distance from root)
#>                 162:1 (based on the shortest distance from root)
#>   Relations: is_a, part_of
#> 
#> With the following columns in the metadata data frame:
#>   id, name, short_id, definition
# }