some_fixes

BioGenies · Jul 18, 2024 · 8037484 · 8037484
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diff --git a/README.Rmd b/README.Rmd
@@ -24,7 +24,7 @@ library(magrittr)
 library(dplyr)
 
 write_entry <- function(x) {
-  res <- glue("1. {Database}: [publication](https://doi.org/{doi})", .envir = x)
+  res <- glue("1. {Database}: [publication]({doi})", .envir = x)
   
   if(is.character(unlist(x[["link"]])))
     res <- glue(res, "[database]({link})", .sep = "; ", .envir = x)
@@ -35,8 +35,8 @@ write_entry <- function(x) {
 
 dat <- readr::read_csv("data/amyloid_db.csv") %>% 
   # filter(`Current status` == "Active") %>% 
-  select("Database", "doi", "link", "Focus...3", "Tipe of data", "Includes experimental conditions", "Focus...6",
-         "Includes structural information", "Identifies APRs", "sources_and_links", "Current status", "Last updated")
+  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")
 
 
 cat_df <- data.frame(categories = c("Active", "Non-active"),

diff --git a/data/amyloid_db.csv b/data/amyloid_db.csv
@@ -1,27 +1,27 @@
-Described,Database,Focus,Tipe of data,Includes experimental conditions,Focus,Includes structural information,Identifies APRs,Current status,Last updated,doi,link,protein_types,protein_origins,experimental_results,in_silico_results,interactions_crossinteractions,only_amyloid-like,3d_structures,download,sources_and_links,notes
-TRUE,Amyloid Atlas 2024,Amyloids,Experimental,No,General,Structure for the wt protein and the aggregate,No,Active,22-05-2024,https://doi.org/10.1016/j.cell.2021.08.013,https://people.mbi.ucla.edu/sawaya/amyloidatlas/,multiple,yes,yes,no,no,yes,yes,single file,PDB,polarity and energy maps
-TRUE,CARs DB,IDP regions,Prediction,No,General,Sequence-only,APRs,Active,08-09-2023,https://doi.org/10.1007/978-1-0716-3441-7_10,http://carsdb.ppmclab.com/,multiple,yes,no,yes,no,yes,no,easy,"DisProt, UniProt, Waltz",cryptic amyloidogenic regions
-FALSE,AmyloGraph,interactions,Experimental,No,General,Sequence-only,No,Active,08-06-2023,https://doi.org/10.1093/nar/gkac882,http://amylograph.com/,multiple,no,yes,no,yes,yes,no,easy,PubMed,amyloid-amyloid interactions
-FALSE,AL-Base,Amyloids,Experimental,No,Specific,Sequence-only,No,Active,18-05-2024,https://doi.org/10.1080/13506120802676781,https://wwwapp.bumc.bu.edu/BEDAC_ALBase/,light chains,yes,yes,no,no,yes,no,easy,NCBI,
-TRUE,Waltz DB 2.0,Amyloids,both,Yes,General,Structure for the wt protein and the aggregate,APRs,Active,08-01-2020,https://doi.org/10.1093/nar/gkz758,http://waltzdb.switchlab.org/,multiple,no,yes,yes,no,no,yes,easy,"PubMed, Uniprot",
-FALSE,CPAD2,Amyloids,Experimental,Yes,General,Structure for the wt protein,APRs,Active,15-04-2024,https://doi.org/10.1080/13506129.2020.1715363,https://web.iitm.ac.in/bioinfo2/cpad2/index.html,multiple,yes,yes,no,no,no,yes,easy,"CPAD, Waltz, AmyLoad, AmyPro, UniProt, PDB",
-FALSE,StAmP,Amyloids,both,No,General,Sequence-only,APRs,Active,09-03-2022,https://doi.org/10.1093/bioinformatics/btac126,https://stamp.switchlab.org/,multiple,no,yes,yes,no,yes,yes,easy,"PDB, Uniprot",
-TRUE,AmyLoad,Amyloids,both,Yes,General,Sequence-only,No,Active,17-06-2015,https://doi.org/10.1093/bioinformatics/btv375,http://comprec-lin.iiar.pwr.edu.pl/amyload/,multiple,no,yes,yes,no,no,no,easy,"TANGO, Waltz, AmylFrag, Aggrescan, AmylHex, ",
-TRUE,AmyPro,Amyloids,Experimental,No,General,Structure for the wt protein,APRs,Active,25-08-2023,https://doi.org/10.1093/nar/gkx950,http://amypro.net,multiple,yes,yes,no,no,no,yes,easy,"PDB, Uniprot, PubMed",
-TRUE,A3D-MODB,Amyloids,Prediction,No,General,Structure for the wt protein and the aggregate,STAPs,Active,28-10-2023,https://doi.org/10.1093/nar/gkad942,https://biocomp.chem.uw.edu.pl/A3D2/MODB,,,,,,,,,,
-FALSE,Cross-Beta DB,Amyloids,both,Yes,General,Structure for the wt protein,APRs,Active,01-05-2024,https://doi.org/10.1101/2024.02.12.579644,https://crossbetadb.crbm.cnrs.fr/,multiple,yes,yes,yes,no,yes,yes,easy,"PDB, AmyPro, Uniprot, PubMed",
-TRUE,SAPdb,other,Experimental,Yes,Specific,Structure for the wt protein,STAPs,Active,10-04-2021,https://doi.org/10.1016/j.compbiomed.2021.104391,https://webs.iiitd.edu.in/raghava/sapdb/,multiple,no,yes,yes,no,no,yes,no,,
-FALSE,Fibrilizer,Amyloids,Prediction,No,Specific,Structure for the wt protein,No,Active,05-02-2013,http://dx.doi.org/10.1016/j.bpj.2012.12.037,https://amyloid.cs.mcgill.ca/database/index.html,multiple,no,no,yes,no,yes,yes,easy,,
-,ZipperDB,Amyloids,Prediction,No,General,Structure for the wt protein and the aggregate,APRs,Non-active,,https://doi.org/10.1073/pnas.0915166107,https://services.mbi.ucla.edu/zipperdb/intro,,,,,,,,,,
-TRUE,PrionScan,Prion,Prediction,No,General,Sequence-only,APRs,Active,03-07-2019,https://doi.org/10.1186/1471-2164-15-102,http://webapps.bifi.es/prionscan,multiple,yes,no,yes,no,yes,no,easy,,
-,pE-DB,,,,,,,Non-active,dead,https://doi.org/10.1093/nar/gkt960,https://pedb.vib.be/,,,,,,,,,,
-,AmyPDB,,,,,,,Non-active,dead,https://doi.org/10.1186/1471-2105-9-273,http://amypdb.genouest.org/; https://amypdb.univ-rennes1.fr/,,,,,,,,,,
-,ProADD,,,,,,,Non-active,dead,https://doi.org/10.6026%2F97320630010390,http://bicmku.in/ProADD,,,,,,,,,,
-,AmyCo,,,,,,,Non-active,dead,https://doi.org/10.1080/13506129.2019.1603143,http://bioinformatics.biol.uoa.gr/amyco,,,,,,,,,,
-,fibril_one,,,,,,,Non-active,dead,https://doi.org/10.1110%2Fps.0204302,http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one,,,,,,,,,,
-TRUE,AmyloBase,Amyloids,Experimental,Yes,General,Sequence-only,No,Active,12-07-2024,https://doi.org/10.1038%2Fembor.2011.116,http://bioserver2.sbsc.unifi.it/AmyloBase.html,multiple,yes,yes,no,no,no,no,easy-medium,Pubmed,
-,Amyloïdose gezamenlijk,,,,,,,Non-active,dead,https://doi.org/10.3109/13506129.2014.964858,http://www.amyloidosis.nl/,,,,,,,,,,
-,amyloid interactome,,,,,,,Non-active,dead,https://doi.org/10.1371/journal.pone.0173163,http://83.212.109.111/amyloid_interactome,,,,,,,,,,
-TRUE,PrionHome,Prion,both,Yes,General,Structure for the wt protein,No,Non-active,dead,https://doi.org/10.1371/journal.pone.0031785,https://libaio.biol.mcgill.ca/prion,,,,,,,,,,
-,THERPA v2,,,,,,,Non-active,dead,http://dx.doi.org/10.1080/19336896.2019.1689789,http://www.nih.go.kr/therpa ; https://therpa.pythonanywhere.com/,,,,,,,,,,
-TRUE,The Prion Disease Database,Prion,Experimental,Yes,Specific,Sequence-only,No,Non-active,dead,https://doi.org/10.1093/database/bap011,http://prion.systemsbiology.net,,,,,,,,,,
+Described,Database,Focus,Type of data,Includes experimental conditions,Usability,Includes structural information,Identifies APRs,Current status,Last updated,doi,link,Data sources and links to other db,Only amyloids,,,,,,,,notes,protein_types,protein_origins,experimental_results,in_silico_results,interactions_crossinteractions,,3d_structures,download
+TRUE,Amyloid Atlas 2024,Amyloids,Experimental,No,General,Structure for the wt protein and the aggregate,No,Active,22-05-2024,https://doi.org/10.1016/j.cell.2021.08.013,https://people.mbi.ucla.edu/sawaya/amyloidatlas/,PDB; PubMed,Yes,,,,,,,,polarity and energy maps,multiple,yes,yes,no,no,,yes,single file
+TRUE,CARs DB,IDP regions,Prediction,No,General,Sequence-only,APRs,Active,08-09-2023,https://doi.org/10.3389/fmolb.2022.882160,http://carsdb.ppmclab.com/,DisProt; UniProt,Yes,,,,,,,,cryptic amyloidogenic regions,multiple,yes,no,yes,no,,no,easy
+TRUE,AmyloGraph,Interactions,Experimental,No,General,Sequence-only,No,Active,08-06-2023,https://doi.org/10.1093/nar/gkac882,http://amylograph.com/,PubMed; UniProt,Yes,,,,,,,,amyloid-amyloid interactions,multiple,no,yes,no,yes,,no,easy
+FALSE,AL-Base,Amyloids,Experimental,No,Specific,Sequence-only,No,Active,18-05-2024,https://doi.org/10.1080/13506120802676781,https://wwwapp.bumc.bu.edu/BEDAC_ALBase/,Nucleotide; Protein; PubMed; UniProt; PDB,Yes,,,,,,,,,light chains,yes,yes,no,no,,no,easy
+TRUE,Waltz DB 2.0,Amyloids,Both,Yes,General,Structure for the wt protein and the aggregate,APRs,Active,08-01-2020,https://doi.org/10.1093/nar/gkz758,http://waltzdb.switchlab.org/,PubMed; UniProt; PDB,No,,,,,,,,,multiple,no,yes,yes,no,,yes,easy
+TRUE,CPAD2,Amyloids,Experimental,Yes,General,Structure for the wt protein,APRs,Active,15-04-2024,https://doi.org/10.1080/13506129.2020.1715363,https://web.iitm.ac.in/bioinfo2/cpad2/index.html,CPAD; Waltz-DB 2.0; AmyLoad; AmyPro; UniProt; PDB; PubMed,No,,,,,,,,,multiple,yes,yes,no,no,,yes,easy
+FALSE,StAmP,Amyloids,Both,No,Specific,Sequence-only,APRs,Active,09-03-2022,https://doi.org/10.1093/bioinformatics/btac126,https://stamp.switchlab.org/,PDB; UniProt,Yes,,,,,,,,,multiple,no,yes,yes,no,,yes,easy
+TRUE,AmyLoad,Amyloids,Both,Yes,General,Sequence-only,No,Active,17-06-2015,https://doi.org/10.1093/bioinformatics/btv375,http://comprec-lin.iiar.pwr.edu.pl/amyload/,TANGO; WALTZ AmylFrag; AGGRESCAN; AmylHex; PubMed,No,,,,,,,,,multiple,no,yes,yes,no,,no,easy
+TRUE,AmyPro,Amyloids,Experimental,No,General,Structure for the wt protein,APRs,Active,25-08-2023,https://doi.org/10.1093/nar/gkx950,http://amypro.net,PDB; UniProt; PubMed,No,,,,,,,,,multiple,yes,yes,no,no,,yes,easy
+TRUE,A3D-MODB,Amyloids,Prediction,No,General,Structure for the wt protein and the aggregate,STAPs,Active,28-10-2023,https://doi.org/10.1093/nar/gkad942,https://biocomp.chem.uw.edu.pl/A3D2/MODB,UniProt; The Human Protein Atlas; RGD; MGI; ZFIN; WormBase; FlyBase; TAIR; SGD; PomBase; EchoBase; WholeCellKB,,,,,,,,,,,,,,,,,
+TRUE,Cross-Beta DB,Amyloids,Both,Yes,General,Structure for the wt protein,APRs,Active,01-05-2024,https://doi.org/10.1101/2024.02.12.579644,https://crossbetadb.crbm.cnrs.fr/,PDB; AmyPro; UniProt; PubMed,Yes,,,,,,,,,multiple,yes,yes,yes,no,,yes,easy
+TRUE,SAPdb,Peptides,Experimental,Yes,Specific,Structure for the wt protein,STAPs,Active,10-04-2021,https://doi.org/10.1016/j.compbiomed.2021.104391,https://webs.iiitd.edu.in/raghava/sapdb/,PubMed,No,,,,,,,,,multiple,no,yes,yes,no,,yes,no
+TRUE,Fibrilizer,Amyloids,Prediction,No,Specific,Structure for the wt protein,No,Active,05-02-2013,http://dx.doi.org/10.1016/j.bpj.2012.12.037,https://amyloid.cs.mcgill.ca/database/index.html,,Yes,,,,,,,,,multiple,no,no,yes,no,,yes,easy
+,ZipperDB,Amyloids,Prediction,No,General,Structure for the wt protein and the aggregate,APRs,Non-active,NA,https://doi.org/10.1073/pnas.0915166107,https://services.mbi.ucla.edu/zipperdb/intro,,,,,,,,,,,,,,,,,,
+TRUE,PrionScan,Prion,Prediction,No,General,Sequence-only,APRs,Active,03-07-2019,https://doi.org/10.1186/1471-2164-15-102,http://webapps.bifi.es/prionscan,UniProt; ENA; Protein; KEGG; Pfam; QuickGO,Yes,,,,,,,,,multiple,yes,no,yes,no,,no,easy
+,pE-DB,,,,,,,Non-active,NA,https://doi.org/10.1093/nar/gkt960,https://pedb.vib.be/,,,,,,,,,,,,,,,,,,
+,AmyPDB,,,,,,,Non-active,NA,https://doi.org/10.1186/1471-2105-9-273,http://amypdb.genouest.org/; https://amypdb.univ-rennes1.fr/,,,,,,,,,,,,,,,,,,
+,ProADD,,,,,,,Non-active,NA,https://doi.org/10.6026%2F97320630010390,http://bicmku.in/ProADD,,,,,,,,,,,,,,,,,,
+,AmyCo,,,,,,,Non-active,NA,https://doi.org/10.1080/13506129.2019.1603143,http://bioinformatics.biol.uoa.gr/amyco,,,,,,,,,,,,,,,,,,
+,fibril_one,,,,,,,Non-active,NA,https://doi.org/10.1110%2Fps.0204302,http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one,,,,,,,,,,,,,,,,,,
+TRUE,AmyloBase,Amyloids,Experimental,Yes,General,Sequence-only,No,Active,12-07-2024,https://doi.org/10.1038%2Fembor.2011.116,http://bioserver2.sbsc.unifi.it/AmyloBase.html,PubMed; UniProt,Yes,,,,,,,,,multiple,yes,yes,no,no,,no,easy-medium
+,Amyloïdose gezamenlijk,,,,,,,Non-active,NA,https://doi.org/10.3109/13506129.2014.964858,http://www.amyloidosis.nl/,,,,,,,,,,,,,,,,,,
+,amyloid interactome,,,,,,,Non-active,NA,https://doi.org/10.1371/journal.pone.0173163,http://83.212.109.111/amyloid_interactome,,,,,,,,,,,,,,,,,,
+TRUE,PrionHome,Prion,Both,Yes,General,Structure for the wt protein,No,Non-active,NA,https://doi.org/10.1371/journal.pone.0031785,https://libaio.biol.mcgill.ca/prion,,,,,,,,,,,,,,,,,,
+,THERPA v2,,,,,,,Non-active,NA,http://dx.doi.org/10.1080/19336896.2019.1689789,http://www.nih.go.kr/therpa ; https://therpa.pythonanywhere.com/,,,,,,,,,,,,,,,,,,
+TRUE,The Prion Disease Database,Prion,Experimental,Yes,Specific,Sequence-only,No,Non-active,NA,https://doi.org/10.1093/database/bap011,http://prion.systemsbiology.net,,,,,,,,,,,,,,,,,,
diff --git a/docs/index.Rmd b/docs/index.Rmd
@@ -21,26 +21,28 @@ knitr::opts_chunk$set(echo = FALSE)
 library(DT)
 library(dplyr)
 
-dat <- readr::read_csv("../data/amyloid_db.csv") %>% 
+dat <- readr::read_csv("../data/amyloid_db.csv", col_select = c(, 1:14), col_types = "fcfffffff?cccf") %>% 
   # filter(`Current status` == "Active") %>% 
-  mutate(DOI = paste0("<a href='", doi,"' >", doi,"</a>"),
-         Link = paste0("<a href='", link,"' > link </a>")) %>% 
-  select("Database", "DOI", "Link", "Focus...3", "Tipe of data", "Includes experimental conditions", "Focus...6",
-         "Includes structural information", "Identifies APRs", "sources_and_links", "Current status", "Last updated")
+  mutate(DOI = paste0("<a href='", doi,"' >", str_remove(doi, 'https://doi.org/'),"</a>"),
+         Database = paste0("<a href='", link,"' >", Database, "</a>"),
+         `Last updated` = `Last updated` %>% as.Date(., "%d-%m-%Y"),) %>% 
+  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") %>% 
+  arrange(desc(`Last updated`))
 
 
-hover_text <- c("Name of a database",
-                "DOI for publications",
-                "Link to the database",
-                "Protein focus of database",
+hover_text <- c("Name and link to a database",
+                "Focus of database",
                 "Type of data database provides",
+                "Indicates if database includes only amyloid proteins and peptides",
                 "Indicates if database includes experimental conditions",
-                "Indicates if database is ",
+                "Indicates the database usability",
                 "Indicates if database contains structural information of proteins and peptides",
                 "Indicates if database identifies amyloidogenic regions of proteins",
-                "The sources and links to other databases",
+                "The data sources of database and links to other databases",
                 "Current status of database",
-                "The last update")
+                "The last update",
+                "DOI")
 
 
 headerCallback <- c(
@@ -73,16 +75,16 @@ datatable(dat, extensions = c('Buttons', 'FixedColumns', 'FixedHeader'),
                          # scrollY = 700,
                          # scrollX = TRUE,
                          scrollCollapse = FALSE,
-                         fixedHeader = TRUE,
+                         # fixedHeader = TRUE,
                          # columnDefs = list(list(width = '200px', targets = c(0))),
-                         fixedColumns = list(leftColumns = 1),
+                         # fixedColumns = list(leftColumns = 1),
                          filter = list(clear = FALSE, plain = TRUE),
                         # lengthMenu = list(25, 50, 75, 100, 125, 150),
                          headerCallback = JS(headerCallback))) %>%  
-  formatStyle(c("Database", "DOI", "Link", "Focus...3", "Tipe of data", "Includes experimental conditions"),
+  formatStyle(c("Database", "Focus", "Type of data", "Includes experimental conditions"),
               backgroundColor = styleEqual(c(FALSE, TRUE), c('#ededed', '#d6edff')))  %>%
-  formatStyle(c("Focus...6",
-         "Includes structural information", "Identifies APRs", "sources_and_links", "Current status", "Last updated"),
+  formatStyle(c("Usability",
+         "Includes structural information", "Identifies APRs", "Data sources and links to other db", "Current status", "Last updated", "DOI"),
               backgroundColor = styleEqual("false", '#ededed', default = '#d6edff'))
 ```