add references

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rols
 Type: Package
 Title: An R interface to the Ontology Lookup Service
-Version: 2.99.3
+Version: 2.99.4
 Authors@R: c(person(given = "Laurent", family = "Gatto",
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0002-1520-2268"),
@@ -28,4 +28,4 @@ Collate: AllClasses.R AllGenerics.R utils.R
          Ontologies.R Terms.R
          cvparam.R OlsSearch.R
          Properties.R zzz.R
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1

NEWS.md

@@ -1,5 +1,9 @@
 # rols 2.99
 
+## CHANGES IN VERSION 2.99.4
+
+- Typo and references in manual pages.
+
 ## CHANGES IN VERSION 2.99.3
 
 - Add orcid.

R/OlsSearch.R

@@ -9,6 +9,14 @@
 ##' object `OlsSearch` using the `OlsSearch()` constructor. Query
 ##' responses are then retrieved with the `olsSearch()` function.
 ##'
+##' @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>
+##'
+##'
 ##' @author Laurent Gatto
 ##'
 ##' @name OlsSearch
@@ -126,16 +134,16 @@
 ##' @param exact `logical(1)` defining if exact matches should be
 ##'     returned. Default is `FALSE`.
 ##'
-##' @param groupField `logical(1)`, set to `TRUE`rue to group results
-##'     by unique id (IRI).
+##' @param groupField `logical(1)`, set to `TRUE` to group results by
+##'     unique id (IRI).
 ##'
 ##' @param obsoletes `logical(1)` defining whether obsolete terms
 ##'     should be queried. Default is `FALSE`.
 ##'
 ##' @param 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
+##'     and exclude ontologies where those terms are also referenced.
 ##'
 ##' @param childrenOf `character()` to restrict a search to children
 ##'     of a given term. Supply a list of IRI for the terms that you

R/Ontologies.R

@@ -111,6 +111,13 @@
 ##' its terms can be requested using the `Terms()` constructor. See
 ##' [Terms()] for details.
 ##'
+##' @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>
+##'
 ##' @author Laurent Gatto
 ##'
 ##' @name Ontologies

R/Properties.R

@@ -5,7 +5,6 @@
 ##' @aliases Properties,Term Properties,Terms
 ##' @aliases Properties,length
 ##'
-##'
 ##' @name Properties
 ##'
 ##' @description
@@ -15,6 +14,13 @@
 ##' and the results are stored as objects of class `Property` or
 ##' `Properties`.
 ##'
+##' @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
 ##'
 ##' ## Term properties

R/Terms.R

@@ -92,6 +92,13 @@
 ##'   synonym only, their iri and whether they are defining the
 ##'   ontology. Any missing value will be reported as `NA`.
 ##'
+##' @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>
+##'
 ##' @name Terms
 ##'
 ##' @author Laurent Gatto