diff --git a/README.Rmd b/README.Rmd index f0a94a1..dbe47ae 100644 --- a/README.Rmd +++ b/README.Rmd @@ -37,13 +37,13 @@ write_entry <- function(x) { # dat <- readr::read_csv("data/amyloid_db.csv") %>% # filter(`Current status` == "Active") %>% # select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability", -# "Includes structural information", "Identifies APRs", "Data sources and links to other db", "Current status", "Last updated", "doi", "link") +# "Includes structural information", "Identifies APRs", "Data sources and links to other db", "Current status", "Published or last update", "doi", "link") dat <- read_sheet("https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3QbYioYorrzAqu3zgNUZqDSA/edit?usp=sharing",sheet = "database_list", col_types = "c") %>% select(1:14) %>% filter(`Current status` == "Active") %>% select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability", - "Includes structural information", "Identifies APRs", "Current status", "Last updated", "Data sources and links to other db", "doi", "link") + "Includes structural information", "Identifies APRs", "Current status", "Published or last update", "Data sources and links to other db", "doi", "link") # cat_df <- data.frame(categories = c("Active", "Non-active"), diff --git a/docs/index.Rmd b/docs/index.Rmd index ff1338d..6c59dd2 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -29,7 +29,7 @@ dat <- read_sheet("https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3Q str_remove(., 'https://doi.org/') %>% str_remove(., 'http://dx.doi.org/'),""), Database = paste0("", Database, ""), - `Last updated` = `Last updated` %>% as.Date(., "%d-%m-%Y"), + `Published or last update` = `Published or last update` %>% as.Date(., "%d-%m-%Y"), Focus = Focus %>% as.factor(), `Type of data` = `Type of data` %>% as.factor(), `Includes experimental conditions` = `Includes experimental conditions` %>% as.factor(), @@ -39,8 +39,8 @@ dat <- read_sheet("https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3Q `Current status` = `Current status` %>% as.factor(), `Only amyloids` = `Only amyloids` %>% as.factor()) %>% select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability", - "Includes structural information", "Identifies APRs", "Current status", "Last updated", "Data sources and links to other db", "DOI") %>% - arrange(desc(`Last updated`)) + "Includes structural information", "Identifies APRs", "Current status", "Published or last update", "Data sources and links to other db", "DOI") %>% + arrange(., `Current status`, desc(`Published or last update`)) # dat <- readr::read_csv("../data/amyloid_db.csv", col_select = c(, 1:14), col_types = "fcfffffff?cccf") %>% # # filter(`Current status` == "Active") %>% @@ -48,10 +48,10 @@ dat <- read_sheet("https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3Q # str_remove(., 'https://doi.org/') # %>% str_remove(., 'http://dx.doi.org/'),""), # Database = paste0("", Database, ""), -# `Last updated` = `Last updated` %>% as.Date(., "%d-%m-%Y"),) %>% +# `Published or last update` = `Published or last update` %>% as.Date(., "%d-%m-%Y"),) %>% # select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability", -# "Includes structural information", "Identifies APRs", "Current status", "Last updated", "Data sources and links to other db", "DOI") %>% -# arrange(desc(`Last updated`)) +# "Includes structural information", "Identifies APRs", "Current status", "Published or last update", "Data sources and links to other db", "DOI") %>% +# arrange(desc(`Published or last update`)) hover_text <- c("Name and link to a database", @@ -62,9 +62,9 @@ hover_text <- c("Name and link to a database", "Indicates the database usability", "Indicates if database contains structural information of proteins and peptides", "Indicates if database identifies amyloidogenic regions of proteins", - "The data sources of database and links to other databases", - "The last update", "Current status of database", + "The last update or publication date", + "The data sources of database and links to other databases", "DOI") @@ -117,7 +117,7 @@ datatable(dat, extensions = c('Buttons', 'FixedColumns', 'FixedHeader', 'ColReor backgroundColor = '#d6edff') %>% formatStyle(c("Current status"), backgroundColor = styleEqual(c("Active", "Non-active"), c('#d6edff', '#d3d3d3'), default = '#d6edff'), color = "black") %>% - formatStyle(c("Last updated"), + formatStyle(c("Published or last update"), backgroundColor = styleEqual(c(NA, "NA"), c('#d3d3d3', '#d3d3d3'), default = '#d6edff'), color = "black") ``` @@ -139,7 +139,7 @@ We manually curated all information for databases featured in a **Amyloid-relate - what kind of structural information is gathered (*Includes structural information** column), - do they highlight proteins APRs (**Identifies APRs** column), - current status of database (**Current status**), -- date of last update or publication date (**Last updated** column), +- date of last update or publication date (**Published or last update** column), - external sources of proteins/peptides in database (we didn't mention own discoveries) and links to and other sources that are integrated into the database (**Data sources and links to other db** column), - link to publication (**DOI** column) @@ -150,6 +150,7 @@ The **Updates** tab indicates latest changes in the list. ### Updates +**08/08/2024** - minor name corrections made | No status changes in inactive amyloid databases | Server instability reported for AmyLoad **17/07/2024** - first release diff --git a/docs/index.html b/docs/index.html index c231134..ef007b9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3436,8 +3436,8 @@

Amyloid databases list