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
usageCount: Number of times the annotation is used in Gemma.
Results are sorted by this field in decreasing order.
search_annotations("traumatic")
#> category.name category.URI
#> <char> <char>
#> 1: disease model http://gemma.msl.ubc.ca/ont/TGEMO_00101
#> 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>
#> category.name category.URI
#> <char> <char>
#> value.name
#> <char>
#> 1: traumatic brain injury
#> 2: traumatic encephalopathy
#> 3: traumatic acid
#> 4: traumatic glaucoma
#> 5: traumatic avascular necrosis
#> 6: traumatic myositis ossificans
#> 7: traumatic neuropathy
#> 8: traumatic brain injury, non-human animal
#> 9: traumatic ear canal avulsion, non-human animal
#> 10: traumatic hemoperitoneum, non-human animal
#> 11: traumatic pericardial effusion, non-human animal
#> 12: traumatic pericarditis, non-human animal
#> 13: traumatic dental fracture, non-human animal
#> 14: traumatic pharyngitis, non-human animal
#> 15: traumatic rectovaginal fistula, non-human animal
#> 16: traumatic splenic rupture, non-human animal
#> 17: traumatic diaphragmatic rupture, non-human animal
#> 18: traumatic myositis, non-human animal
#> 19: traumatic keratitis, non-human animal
#> 20: traumatic nasolacrimal duct injury, non-human animal
#> value.name
#> <char>
#> value.URI usageCount
#> <char> <int>
#> 1: http://purl.obolibrary.org/obo/MONDO_0858950 39
#> 2: http://purl.obolibrary.org/obo/MONDO_0043512 2
#> 3: http://purl.obolibrary.org/obo/CHEBI_545687 0
#> 4: http://purl.obolibrary.org/obo/MONDO_0001626 0
#> 5: http://purl.obolibrary.org/obo/MONDO_0018375 0
#> 6: http://purl.obolibrary.org/obo/MONDO_0021929 0
#> 7: http://purl.obolibrary.org/obo/MONDO_0100634 0
#> 8: http://purl.obolibrary.org/obo/MONDO_1013018 0
#> 9: http://purl.obolibrary.org/obo/MONDO_1013810 0
#> 10: http://purl.obolibrary.org/obo/MONDO_1013844 0
#> 11: http://purl.obolibrary.org/obo/MONDO_1013869 0
#> 12: http://purl.obolibrary.org/obo/MONDO_1013962 0
#> 13: http://purl.obolibrary.org/obo/MONDO_1014296 0
#> 14: http://purl.obolibrary.org/obo/MONDO_1014363 0
#> 15: http://purl.obolibrary.org/obo/MONDO_1014372 0
#> 16: http://purl.obolibrary.org/obo/MONDO_1014698 0
#> 17: http://purl.obolibrary.org/obo/MONDO_1015354 0
#> 18: http://purl.obolibrary.org/obo/MONDO_1015837 0
#> 19: http://purl.obolibrary.org/obo/MONDO_1016429 0
#> 20: http://purl.obolibrary.org/obo/MONDO_1016444 0
#> value.URI usageCount
#> <char> <int>