Acquires parent terms of a given URI based on ontologies loaded into Gemma. Propagated relations are subClassOf and has_part
Term URI
TRUE to receive results as-is from Gemma, or FALSE to enable
parsing. Raw results usually contain additional fields and flags that are
omitted in the parsed results.
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
The name of a file to save the results to, or NULL to not write
results to a file. If raw == TRUE, the output will be the raw endpoint from the
API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
Whether or not to overwrite if a file exists at the specified filename.
A data table with annotations (annotation search result value objects)
matching the given identifiers. A list if raw = TRUE. A 400 error if required parameters are missing.
The fields of the output data.table are:
category.name: Category that the annotation belongs to
category.URI: URI for the category.name
value.name: Annotation term
value.URI: URI for the value.name
usageCount: Number of times the annotation is used in Gemma.
Results are sorted by this field in decreasing order.
get_annotation_parents("http://purl.obolibrary.org/obo/MONDO_0000408")
#> category.name category.URI
#> <char> <char>
#> 1: <NA> <NA>
#> 2: <NA> <NA>
#> 3: <NA> <NA>
#> 4: <NA> <NA>
#> 5: <NA> <NA>
#> 6: <NA> <NA>
#> 7: <NA> <NA>
#> 8: <NA> <NA>
#> 9: <NA> <NA>
#> 10: <NA> <NA>
#> 11: <NA> <NA>
#> 12: <NA> <NA>
#> 13: <NA> <NA>
#> 14: <NA> <NA>
#> 15: <NA> <NA>
#> 16: <NA> <NA>
#> 17: <NA> <NA>
#> 18: <NA> <NA>
#> 19: <NA> <NA>
#> 20: <NA> <NA>
#> 21: <NA> <NA>
#> category.name category.URI
#> <char> <char>
#> value.name
#> <char>
#> 1: psychiatric disorder
#> 2: brain disorder
#> 3: central nervous system disorder
#> 4: disease
#> 5: alcohol-related disorders
#> 6: mental disorder
#> 7: human disease
#> 8: alcohol-induced mental disorder
#> 9: characteristic
#> 10: nervous system disorder
#> 11: entity
#> 12: continuant
#> 13: specifically dependent continuant
#> 14: disposition
#> 15: realizable entity
#> 16: alcohol-induced disorders
#> 17: developmental disorder of mental health
#> 18: substance-related disorder
#> 19: specific developmental disorder
#> 20: disease by developmental or physiological process
#> 21: disease by body system or component
#> value.name
#> <char>
#> value.URI usageCount
#> <char> <int>
#> 1: http://purl.obolibrary.org/obo/MONDO_0002025 3
#> 2: http://purl.obolibrary.org/obo/MONDO_0005560 2
#> 3: http://purl.obolibrary.org/obo/MONDO_0002602 1
#> 4: http://purl.obolibrary.org/obo/MONDO_0000001 1
#> 5: http://purl.obolibrary.org/obo/MONDO_0021698 1
#> 6: http://purl.obolibrary.org/obo/MONDO_0005084 1
#> 7: http://purl.obolibrary.org/obo/MONDO_0700096 0
#> 8: http://purl.obolibrary.org/obo/MONDO_0002326 0
#> 9: http://purl.obolibrary.org/obo/COB_0000502 0
#> 10: http://purl.obolibrary.org/obo/MONDO_0005071 0
#> 11: http://purl.obolibrary.org/obo/BFO_0000001 0
#> 12: http://purl.obolibrary.org/obo/BFO_0000002 0
#> 13: http://purl.obolibrary.org/obo/BFO_0000020 0
#> 14: http://purl.obolibrary.org/obo/BFO_0000016 0
#> 15: http://purl.obolibrary.org/obo/BFO_0000017 0
#> 16: http://purl.obolibrary.org/obo/MONDO_0021699 0
#> 17: http://purl.obolibrary.org/obo/MONDO_0005503 0
#> 18: http://purl.obolibrary.org/obo/MONDO_0002494 0
#> 19: http://purl.obolibrary.org/obo/MONDO_0000592 0
#> 20: http://purl.obolibrary.org/obo/MONDO_7770007 0
#> 21: http://purl.obolibrary.org/obo/MONDO_7770006 0
#> value.URI usageCount
#> <char> <int>