Class "OlsSearch"

Searching the OLS is done using the OlsSearch data structure.

Objects from the Class

Objects can be created with the constructor function OlsSearch.

Slots

q:

Object of class "character" ~~

ontology:

Object of class "character" ~~

type:

Object of class "character" ~~

slim:

Object of class "character" ~~

fieldList:

Object of class "character" ~~

queryFields:

Object of class "character" ~~

exact:

Object of class "logical" ~~

groupField:

Object of class "logical" ~~

obsoletes:

Object of class "logical" ~~

local:

Object of class "character" ~~

childrenOf:

Object of class "character" ~~

rows:

Object of class "integer" ~~

start:

Object of class "integer" ~~

url:

Object of class "character" ~~

numFound:

Object of class "integer" ~~

response:

Object of class "data.frame" ~~

Methods and functions

coerce

signature(from = "OlsSearch", to = "data.frame"): ...

coerce

signature(from = "OlsSearch", to = "Terms"): ...

show

signature(object = "OlsSearch"): ...

olsRows

signature(object = "OlsSearch"): ... The value can be updated with the olsRows replacement method. To request all responses, use allRows.

Author

Laurent Gatto <lg390@cam.ac.uk>

Examples

OlsSearch(q = "trans-golgi")
#> Object of class 'OlsSearch':
#>   query: trans-golgi 
#>   requested: 20 (out of 13983)
#>   response(s): 0 
OlsSearch(q = "cell")
#> Object of class 'OlsSearch':
#>   query: cell 
#>   requested: 20 (out of 241622)
#>   response(s): 0 
OlsSearch(q = "cell", exact = TRUE)
#> Object of class 'OlsSearch':
#>   query: cell 
#>   requested: 20 (out of 7221)
#>   response(s): 0 
OlsSearch(q = "cell", exact = TRUE, ontology = "go")
#> Object of class 'OlsSearch':
#>   ontolgy: go 
#>   query: cell 
#>   requested: 20 (out of 0)
#>   response(s): 0 
OlsSearch(q = "cell", exact = TRUE, ontology = "GO")
#> Object of class 'OlsSearch':
#>   ontolgy: GO 
#>   query: cell 
#>   requested: 20 (out of 0)
#>   response(s): 0 

OlsSearch(q = "electrospray", ontology = "MS")
#> Object of class 'OlsSearch':
#>   ontolgy: MS 
#>   query: electrospray 
#>   requested: 20 (out of 8)
#>   response(s): 0 
OlsSearch(q = "ionization", ontology = "MS")
#> Object of class 'OlsSearch':
#>   ontolgy: MS 
#>   query: ionization 
#>   requested: 20 (out of 56)
#>   response(s): 0 
OlsSearch(q = "electrospray ionization", ontology = "MS")
#> Object of class 'OlsSearch':
#>   ontolgy: MS 
#>   query: electrospray ionization 
#>   requested: 20 (out of 59)
#>   response(s): 0 
OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)
#> Object of class 'OlsSearch':
#>   ontolgy: MS 
#>   query: electrospray ionization 
#>   requested: 20 (out of 1)
#>   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 1551)
#>   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 1551)
#>   response(s): 0 
olsRows(res) <- 5
res
#> Object of class 'OlsSearch':
#>   ontolgy: go 
#>   query: plasma,membrane 
#>   requested: 5 (out of 1551)
#>   response(s): 0 
## all results
res <- allRows(res)
res
#> Object of class 'OlsSearch':
#>   ontolgy: go 
#>   query: plasma,membrane 
#>   requested: 1551 (out of 1551)
#>   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 329)
#>   response(s): 0 
res <- olsSearch(res)
res
#> Object of class 'OlsSearch':
#>   ontolgy: go 
#>   query: trans-golgi 
#>   requested: 5 (out of 329)
#>   response(s): 5 
as(res, "data.frame")
#>                                                   id
#> 1 go:class:http://purl.obolibrary.org/obo/GO_0000138
#> 2 go:class:http://purl.obolibrary.org/obo/GO_1990676
#> 3 go:class:http://purl.obolibrary.org/obo/GO_0032588
#> 4 go:class:http://purl.obolibrary.org/obo/GO_0005802
#> 5 go:class:http://purl.obolibrary.org/obo/GO_0030140
#>                                         iri short_form     obo_id
#> 1 http://purl.obolibrary.org/obo/GO_0000138 GO_0000138 GO:0000138
#> 2 http://purl.obolibrary.org/obo/GO_1990676 GO_1990676 GO:1990676
#> 3 http://purl.obolibrary.org/obo/GO_0032588 GO_0032588 GO:0032588
#> 4 http://purl.obolibrary.org/obo/GO_0005802 GO_0005802 GO:0005802
#> 5 http://purl.obolibrary.org/obo/GO_0030140 GO_0030140 GO:0030140
#>                                   label ontology_name ontology_prefix  type
#> 1                  Golgi trans cisterna            go              GO class
#> 2         Golgi trans cisterna membrane            go              GO class
#> 3          trans-Golgi network membrane            go              GO class
#> 4                   trans-Golgi network            go              GO class
#> 5 trans-Golgi network transport vesicle            go              GO class
#>   is_defining_ontology
#> 1                 TRUE
#> 2                 TRUE
#> 3                 TRUE
#> 4                 TRUE
#> 5                 TRUE
res <- as(res, "Terms")
res
#> Object of class 'Terms' with 5 entries
#>  From the GO ontology
#>   GO:0000138, GO:1990676 ... GO:0005802, GO:0030140 
termPrefix(res)
#> GO:0000138 GO:1990676 GO:0032588 GO:0005802 GO:0030140 
#>       "GO"       "GO"       "GO"       "GO"       "GO" 
termId(res)
#>   GO:0000138   GO:1990676   GO:0032588   GO:0005802   GO:0030140 
#> "GO:0000138" "GO:1990676" "GO:0032588" "GO:0005802" "GO:0030140"