OlsSearch: Querying OLS

In lgatto/rols: An R interface to the Ontology Lookup Service

Querying OLS

Description

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.

Usage

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 signature 'OlsSearch'
show(object)

olsRows(object)

olsRows(object) <- value

allRows(object)

Arguments

q	'characher(1)' containing the search query.
ontology	'character()' defining the ontology to be queried. Default is the empty character, to search all ontologies.
type	'character()' restricting the search to an entity type, one of '"class"', '"property"', '"individual"' or '"ontology"'.
slim	'character()' restricts the search to an particular set of slims by name.
fieldList	'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.
queryFields	'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.
exact	'logical(1)' defining if exact matches should be returned. Default is 'FALSE'.
groupField	'logical(1)', set to 'TRUE' to group results by unique id (IRI).
obsoletes	'logical(1)' defining whether obsolete terms should be queried. Default is 'FALSE'.
local	'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.
childrenOf	'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.
rows	'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.
start	'integer(1)' defining the results page. number. Default is 0L.
object	'OlsSeach' result object.
all	'logical(1)' Should all rows be retrieved. Default is 'FALSE'. Can also be set in the queary object directly with 'allRows()'.
value	replacement value

Author(s)

Laurent Gatto

References

- 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>

Examples

## Many results across all ontologies
OlsSearch(q = "trans-golgi")

## Exact matches
OlsSearch(q = "trans-golgi", exact = TRUE)

## Exact match in the gene ontology (go or GO) only
OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "go")
OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "GO")

## Exact match in the GO and Uberon
OlsSearch(q = "trans-golgi", exact = TRUE,
          ontology = c("GO", "Uberon"))

## Testing different ESI queries
OlsSearch(q = "electrospray", ontology = "MS")
OlsSearch(q = "ionization", ontology = "MS")
OlsSearch(q = "electrospray ionization", ontology = "MS")
OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)

## Request 5 results instead of 20 (default)
OlsSearch(q = "plasma,membrane", ontology = "go", rows = 5)
## Same as above
OlsSearch(q = "plasma membrane", ontology = "go", rows = 5)

## or, once the object was created
(res <- OlsSearch(q = "plasma,membrane", ontology = "go"))
olsRows(res) <- 5
res

## all results
res <- allRows(res)
res

res <- OlsSearch(q = "trans-golgi", ontology = "go", rows = 5)
res
res <- olsSearch(res)
res
as(res, "data.frame")
trms <- as(res, "olsTerms")
trms
termPrefix(trms)
termId(trms)

## 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)

lgatto/rols documentation built on April 29, 2024, 12:20 p.m.