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add UniProt 2025 paper to the citations
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moosa-r committed Jan 1, 2025
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30 changes: 15 additions & 15 deletions R/uniprot_coordinates.R
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#' protein's coordinates information.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -169,9 +169,9 @@ rba_uniprot_coordinates_search <- function(accession = NULL,
#' @return Genome coordinates of your supplied proteins.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -270,9 +270,9 @@ rba_uniprot_coordinates_location_protein <- function(accession,
#' @return A list with genome coordinates of your supplied protein.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -371,9 +371,9 @@ rba_uniprot_coordinates <- function(accession = NULL,
#' location and taxonomy ID.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -473,9 +473,9 @@ rba_uniprot_coordinates_location <- function(taxid,
#' @return Genome coordinates of your supplied proteins.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
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72 changes: 36 additions & 36 deletions R/uniprot_proteins.R
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Expand Up @@ -90,9 +90,9 @@
#' information that UniProt has about that entity.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -283,9 +283,9 @@ rba_uniprot_proteins_search <- function(accession = NULL,
#' supplied accession.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -385,9 +385,9 @@ rba_uniprot_proteins <- function(accession,
#' your supplied cross-reference database name and ID.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -518,9 +518,9 @@ rba_uniprot_proteins_crossref <- function(db_id,
#' information that UniProt has about that entity.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -716,9 +716,9 @@ rba_uniprot_features_search <- function(accession = NULL,
# #' @return
# #'
# #' @references \itemize{
# #' \item The UniProt Consortium, UniProt: the universal protein
# #' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
# #' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
# #' \item The UniProt Consortium , UniProt: the Universal Protein
# #' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
# #' https://doi.org/10.1093/nar/gkae1010
# #' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
# #' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
# #' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -861,9 +861,9 @@ rba_uniprot_features_search <- function(accession = NULL,
#' annotations in a sub-list named "features".
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1053,9 +1053,9 @@ rba_uniprot_features <- function(accession,
#' information that UniProt has about that Variation.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1263,9 +1263,9 @@ rba_uniprot_variation_search <- function(accession = NULL,
#' protein entry.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1422,9 +1422,9 @@ rba_uniprot_variation <- function(id,
#' hit) and Antigenic features are organized under the "features" sub-list.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1524,9 +1524,9 @@ rba_uniprot_antigens_search <- function(accession = NULL,
#' UniProt protein's sequence.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1741,9 +1741,9 @@ rba_uniprot_epitope <- function(accession, ...) {
#' "features" sub-list.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -1836,9 +1836,9 @@ rba_uniprot_mutagenesis_search <- function(accession = NULL,
#' UniProt protein's sequence.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down
24 changes: 12 additions & 12 deletions R/uniprot_proteomes.R
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Expand Up @@ -42,9 +42,9 @@
#' proteome (search hit) and contains informations pertinent to that proteome.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -194,9 +194,9 @@ rba_uniprot_proteomes_search <- function(name = NULL,
#' get_proteins argument.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -313,9 +313,9 @@ rba_uniprot_proteomes <- function(upid,
#' @return a list containing gene-centric proteins search hits.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down Expand Up @@ -407,9 +407,9 @@ rba_uniprot_genecentric_search <- function(upid = NULL,
#' @return A list containing information of Gene-Centric proteins.
#'
#' @references \itemize{
#' \item The UniProt Consortium, UniProt: the universal protein
#' knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1,
#' 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
#' \item The UniProt Consortium , UniProt: the Universal Protein
#' Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
#' https://doi.org/10.1093/nar/gkae1010
#' \item Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas
#' Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd
#' Turner, Maria Martin, The Proteins API: accessing key integrated protein
Expand Down
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