Searching the Ontology Lookup Service is done first by creating an object `OlsSearch` using the `OlsSearch()` constructor. Query responses are then retrieved with the `olsSearch()` function.
OlsSearch(
q,
ontology = "",
type = "",
slim = "",
fieldList = "",
queryFields = "",
exact = FALSE,
groupField = FALSE,
obsoletes = FALSE,
local = TRUE,
childrenOf = "",
rows = 20L,
start = 0L
)
olsSearch(object, all = FALSE)
# S4 method for class 'OlsSearch'
show(object)
olsRows(object)
olsRows(object) <- value
allRows(object)`characher(1)` containing the search query.
`character()` defining the ontology to be queried. Default is the empty character, to search all ontologies.
`character()` restricting the search to an entity type, one of `"class"`, `"property"`, `"individual"` or `"ontology"`.
`character()` restricts the search to an particular set of slims by name.
`character()` specifcies the fields to return. The defaults are iri, label, short_form, obo_id, ontology_name, ontology_prefix, description and type. Default is `""` for all fields.
`character()` specifcies the fields to query, the defaults are label, synonym, description, short_form, obo_id, annotations, logical_description, iri. Default is `""` for all fields.
`logical(1)` defining if exact matches should be returned. Default is `FALSE`.
`logical(1)`, set to `TRUE` to group results by unique id (IRI).
`logical(1)` defining whether obsolete terms should be queried. Default is `FALSE`.
`character(1)`, default is `FALSE`. Set to `TRUE` to only return terms that are in a defining ontology e.g. only return matches to gene ontology terms in the gene ontology, and exclude ontologies where those terms are also referenced.
`character()` to restrict a search to children of a given term. Supply a list of IRI for the terms that you want to search under.
`integer(1)` defining the number of query returns. Default is 20L. Maximum number of values returned by the server is 1000. To retrieve the next results, set `start` 1000. See examle below.
`integer(1)` defining the results page. number. Default is 0L.
`OlsSeach` result object.
`logical(1)` Should all rows be retrieved. Default is `FALSE`. Can also be set in the queary object directly with `allRows()`.
replacement value
- OLS3 API (the OLS4 API should function identically to the OLS3): <http://www.ebi.ac.uk/ols4/ols3help>
- REST API for OLS: <https://www.ebi.ac.uk/ols4/swagger-ui/index.html>
## Many results across all ontologies
OlsSearch(q = "trans-golgi")
#> Object of class 'OlsSearch':
#> query: trans-golgi
#> requested: 20 (out of 13264)
#> response(s): 0
## Exact matches
OlsSearch(q = "trans-golgi", exact = TRUE)
#> Object of class 'OlsSearch':
#> query: trans-golgi
#> requested: 20 (out of 258)
#> response(s): 0
## Exact match in the gene ontology (go or GO) only
OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "go")
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: trans-golgi
#> requested: 20 (out of 35)
#> response(s): 0
OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "GO")
#> Object of class 'OlsSearch':
#> ontolgy: GO
#> query: trans-golgi
#> requested: 20 (out of 35)
#> response(s): 0
## Exact match in the GO and Uberon
OlsSearch(q = "trans-golgi", exact = TRUE,
ontology = c("GO", "Uberon"))
#> Object of class 'OlsSearch':
#> ontolgies: GO, Uberon
#> query: trans-golgi
#> requested: 20 (out of 39)
#> response(s): 0
## Testing different ESI queries
OlsSearch(q = "electrospray", ontology = "MS")
#> Object of class 'OlsSearch':
#> ontolgy: MS
#> query: electrospray
#> requested: 20 (out of 0)
#> response(s): 0
OlsSearch(q = "ionization", ontology = "MS")
#> Object of class 'OlsSearch':
#> ontolgy: MS
#> query: ionization
#> requested: 20 (out of 0)
#> response(s): 0
OlsSearch(q = "electrospray ionization", ontology = "MS")
#> Object of class 'OlsSearch':
#> ontolgy: MS
#> query: electrospray ionization
#> requested: 20 (out of 0)
#> response(s): 0
OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)
#> Object of class 'OlsSearch':
#> ontolgy: MS
#> query: electrospray ionization
#> requested: 20 (out of 0)
#> response(s): 0
## Request 5 results instead of 20 (default)
OlsSearch(q = "plasma,membrane", ontology = "go", rows = 5)
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: plasma,membrane
#> requested: 5 (out of 4199)
#> response(s): 0
## Same as above
OlsSearch(q = "plasma membrane", ontology = "go", rows = 5)
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: plasma membrane
#> requested: 5 (out of 4199)
#> response(s): 0
## or, once the object was created
(res <- OlsSearch(q = "plasma,membrane", ontology = "go"))
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: plasma,membrane
#> requested: 20 (out of 4199)
#> response(s): 0
olsRows(res) <- 5
res
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: plasma,membrane
#> requested: 5 (out of 4199)
#> response(s): 0
## all results
res <- allRows(res)
res
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: plasma,membrane
#> requested: 4199 (out of 4199)
#> response(s): 0
res <- OlsSearch(q = "trans-golgi", ontology = "go", rows = 5)
res
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: trans-golgi
#> requested: 5 (out of 926)
#> response(s): 0
res <- olsSearch(res)
res
#> Object of class 'OlsSearch':
#> ontolgy: go
#> query: trans-golgi
#> requested: 5 (out of 926)
#> response(s): 5
as(res, "data.frame")
#> iri ontology_name ontology_prefix
#> 1 http://purl.obolibrary.org/obo/GO_0000138 go GO
#> 2 http://purl.obolibrary.org/obo/GO_0005802 go GO
#> 3 http://purl.obolibrary.org/obo/GO_1990676 go GO
#> 4 http://purl.obolibrary.org/obo/GO_0032588 go GO
#> 5 http://purl.obolibrary.org/obo/GO_0098629 go GO
#> short_form description label obo_id
#> 1 GO_0000138 The Golg.... Golgi trans cisterna GO:0000138
#> 2 GO_0005802 The netw.... trans-Golgi network GO:0005802
#> 3 GO_1990676 The lipi.... Golgi trans cisterna membrane GO:1990676
#> 4 GO_0032588 The lipi.... trans-Golgi network membrane GO:0032588
#> 5 GO_0098629 A proces.... trans-Golgi network membrane organization GO:0098629
#> type
#> 1 class
#> 2 class
#> 3 class
#> 4 class
#> 5 class
trms <- as(res, "olsTerms")
trms
#> Object of class 'olsTerms' with 5 entries
#> From the GO ontology
#> GO:0000138, GO:0005802 ... GO:0032588, GO:0098629
termPrefix(trms)
#> GO:0000138 GO:0005802 GO:1990676 GO:0032588 GO:0098629
#> "GO" "GO" "GO" "GO" "GO"
termId(trms)
#> GO:0000138 GO:0005802 GO:1990676 GO:0032588 GO:0098629
#> "GO:0000138" "GO:0005802" "GO:1990676" "GO:0032588" "GO:0098629"
## Setting rows and start parameters
tg1 <- OlsSearch(q = "trans-golgi", rows = 5, start = 0) |>
olsSearch() |>
as("data.frame")
tg2 <- OlsSearch(q = "trans-golgi", rows = 5, start = 5) |>
olsSearch() |>
as("data.frame")
tg3 <- OlsSearch(q = "trans-golgi", rows = 10, start = 0) |>
olsSearch() |>
as("data.frame")
## The two consecutive small results are identical
## to the larger on.
identical(rbind(tg1, tg2), tg3)
#> [1] TRUE