Search for annotation tags
The search query. Queries can include plain text or ontology terms They also support conjunctions ("alpha AND beta"), disjunctions ("alpha OR beta") grouping ("(alpha OR beta) AND gamma"), prefixing ("alpha*"), wildcard characters ("BRCA?") and fuzzy matches ("alpha~").
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
search_annotations("traumatic")
#> 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>
#> 22: <NA> <NA>
#> 23: <NA> <NA>
#> 24: <NA> <NA>
#> 25: <NA> <NA>
#> 26: <NA> <NA>
#> 27: <NA> <NA>
#> 28: <NA> <NA>
#> 29: <NA> <NA>
#> 30: <NA> <NA>
#> 31: <NA> <NA>
#> 32: <NA> <NA>
#> category.name category.URI
#> value.name
#> <char>
#> 1: traumatic acid
#> 2: traumatic diaphragmatic hernia
#> 3: traumatic glaucoma
#> 4: traumatic brain injury
#> 5: traumatic avascular necrosis
#> 6: traumatic myositis ossificans
#> 7: traumatic encephalopathy
#> 8: avoidance of stimuli associated with traumatic event
#> 9: post-traumatic stress disorder
#> 10: post-traumatic stress disorder symptom measurement
#> 11: brain stem hemorrhage, traumatic
#> 12: secondary non-traumatic avascular necrosis
#> 13: post-traumatic epilepsy
#> 14: iatrogenic or traumatic pituitary deficiency
#> 15: post-traumatic stress disorder
#> 16: injury
#> 17: concussion
#> 18: crush syndrome
#> 19: kluver-bucy syndrome
#> 20: spinal cord injury
#> 21: acute stress reaction
#> 22: osteoporosis
#> 23: response to trauma exposure
#> 24: cerebrospinal fluid rhinorrhea
#> 25: spinal cord injury
#> 26: injury
#> 27: kluver-bucy syndrome
#> 28: wound myiasis
#> 29: dementia pugilistica
#> 30: acute stress disorder
#> 31: cerebrospinal fluid leak
#> 32: kummell disease
#> value.name
#> value.URI
#> <char>
#> 1: http://purl.obolibrary.org/obo/CHEBI_545687
#> 2: http://www.ebi.ac.uk/efo/EFO_1001861
#> 3: http://purl.obolibrary.org/obo/MONDO_0001626
#> 4: http://purl.obolibrary.org/obo/MONDO_0858950
#> 5: http://purl.obolibrary.org/obo/MONDO_0018375
#> 6: http://purl.obolibrary.org/obo/MONDO_0021929
#> 7: http://purl.obolibrary.org/obo/MONDO_0043512
#> 8: http://purl.obolibrary.org/obo/HP_0032942
#> 9: http://www.ebi.ac.uk/efo/EFO_0001358
#> 10: http://www.ebi.ac.uk/efo/EFO_0008535
#> 11: http://www.ebi.ac.uk/efo/EFO_1001276
#> 12: http://purl.obolibrary.org/obo/MONDO_0018376
#> 13: http://purl.obolibrary.org/obo/MONDO_0043264
#> 14: http://purl.obolibrary.org/obo/MONDO_0019845
#> 15: http://purl.obolibrary.org/obo/MONDO_0005146
#> 16: http://www.ebi.ac.uk/efo/EFO_0000546
#> 17: http://www.ebi.ac.uk/efo/EFO_0011023
#> 18: http://www.ebi.ac.uk/efo/EFO_1001299
#> 19: http://www.ebi.ac.uk/efo/EFO_0007335
#> 20: http://www.ebi.ac.uk/efo/EFO_1001919
#> 21: http://www.ebi.ac.uk/efo/EFO_0005223
#> 22: http://www.ebi.ac.uk/efo/EFO_0003882
#> 23: http://www.ebi.ac.uk/efo/EFO_0008483
#> 24: http://purl.obolibrary.org/obo/MONDO_0020773
#> 25: http://purl.obolibrary.org/obo/MONDO_0043797
#> 26: http://purl.obolibrary.org/obo/MONDO_0021178
#> 27: http://purl.obolibrary.org/obo/MONDO_0005817
#> 28: http://purl.obolibrary.org/obo/MONDO_0015622
#> 29: http://purl.obolibrary.org/obo/MONDO_0019976
#> 30: http://purl.obolibrary.org/obo/MONDO_0003763
#> 31: http://purl.obolibrary.org/obo/MONDO_0043327
#> 32: http://purl.obolibrary.org/obo/MONDO_0003940
#> value.URI