{"id":15111485,"url":"https://github.com/biogenies/amyloid-database-list","last_synced_at":"2026-02-17T23:02:45.619Z","repository":{"id":248883163,"uuid":"829964863","full_name":"BioGenies/amyloid-database-list","owner":"BioGenies","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-14T15:43:47.000Z","size":3996,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-11T14:26:21.036Z","etag":null,"topics":["aggregation","amyloid-fibrils","amyloidosis","aprs","database","databases","fibrils","idps","interaction","prion","prions"],"latest_commit_sha":null,"homepage":"http://biogenies.info/amyloid-database-list/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioGenies.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-07-17T10:44:21.000Z","updated_at":"2024-11-14T15:43:50.000Z","dependencies_parsed_at":"2024-07-22T09:30:32.684Z","dependency_job_id":"2eedd7b7-216a-4f80-9b5f-5b07e3cab56b","html_url":"https://github.com/BioGenies/amyloid-database-list","commit_stats":{"total_commits":24,"total_committers":2,"mean_commits":12.0,"dds":0.04166666666666663,"last_synced_commit":"c1c05f35f4f1ec482c1d4203f91d86c76f5faac3"},"previous_names":["biogenies/amyloid-database-list"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Famyloid-database-list","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Famyloid-database-list/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Famyloid-database-list/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Famyloid-database-list/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/amyloid-database-list/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247371304,"owners_count":20928179,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["aggregation","amyloid-fibrils","amyloidosis","aprs","database","databases","fibrils","idps","interaction","prion","prions"],"created_at":"2024-09-26T00:20:27.694Z","updated_at":"2026-02-17T23:02:45.575Z","avatar_url":"https://github.com/BioGenies.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/\",\n  out.width = \"100%\"\n)\n```\n\n# The dynamic landscape of amyloid-related databases\n\n\u003c!-- This curated list collects peer-reviewed machine learning models dedicated to predicting specific properties of peptides.  --\u003e\nFor an interactive and browse-able list, please visit: https://biogenies.info/amyloid-database-list/.\n\n```{r, echo=FALSE,message=FALSE,results='asis'}\nlibrary(glue)\nlibrary(magrittr)\nlibrary(dplyr)\nlibrary(googlesheets4)\n\nwrite_entry \u003c- function(x) {\n  res \u003c- glue(\"1. {Database}: [publication]({doi})\", .envir = x)\n  \n  if(is.character(unlist(x[[\"link\"]])))\n    res \u003c- glue(res, \"[database]({link})\", .sep = \"; \", .envir = x)\n  \n  paste0(res, \".\")\n}\n\n\n# dat \u003c- readr::read_csv(\"data/amyloid_db.csv\") %\u003e% \n#   filter(`Current status` == \"Active\") %\u003e%\n#   select(\"Database\", \"Focus\", \"Type of data\", \"Only amyloids\", \"Includes experimental conditions\", \"Usability\",\n#          \"Includes structural information\", \"Identifies APRs\", \"Data sources and links to other db\", \"Current status\", \"Published or last update\", \"doi\", \"link\")\n\ndat \u003c- read_sheet(\"https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3QbYioYorrzAqu3zgNUZqDSA/edit?usp=sharing\",sheet = \"database_list\", col_types = \"c\") %\u003e% \n  select(1:14) %\u003e% \n  filter(`Current status` == \"Active\") %\u003e%\n  select(\"Database\", \"Focus\", \"Type of data\", \"Only amyloids\", \"Includes experimental conditions\", \"Usability\",\n         \"Includes structural information\", \"Identifies APRs\", \"Current status\", \"Published or last update\", \"Data sources and links to other db\", \"doi\", \"link\")\n\n\n# cat_df \u003c- data.frame(categories = c(\"Active\", \"Non-active\"),\n                     # nice_names = c(\"Active\", \"Non-active\"))\n\ncat_df \u003c- data.frame(categories = c(\"Experimental\", \"Prediction\", \"Experimental and prediction\"),\n                     nice_names = c(\"Only experimental data\", \"Predictions\", \"Experimental data and predictions\"))\n\nall_tools \u003c- sapply(1L:nrow(cat_df), function(ith_category_id) {\n  part_dat \u003c- dat %\u003e% filter(`Type of data` == cat_df[ith_category_id, \"categories\"])\n  row_order \u003c- order(part_dat[[\"Database\"]])\n  paste0(paste0(\"## \", cat_df[ith_category_id, \"nice_names\"], \"\\n\\n\"),\n         paste0(sapply(row_order, function(ith_row)\n           write_entry(part_dat[ith_row, ])), \n           collapse = \"\\n\"), \"\\n\\n\\n\")\n})\n\nlinks \u003c- gsub(pattern = \" \", replacement = \"-\", x = cat_df[[\"nice_names\"]]) %\u003e% \n  gsub(pattern = \"[()]\", replacement = \"\", x = .) %\u003e% \n  tolower() %\u003e% \n  paste0(\"(#\", ., \")\")\n\ncat(paste0(\"- [\", cat_df[[\"nice_names\"]], \"]\", links), \"\\n\\n\", sep = \"\\n\")\n\ncat(all_tools, sep = \"\\n\")\n```\n\n### About and citation\n\nThe database was developed by **BioGenies** team. If you want to get to know us and our projects visit our webpage [BioGenies](https://biogenies.info/).\n\n```{r, echo=FALSE,results='asis'}\ncat(readLines(\"./data/citation.md\"), sep = \"\\n\")\n```\n\nThis project was supported by the **National Science Centre Poland**, SONATA 19 grant [**2023/51/D/NZ7/02847**]. \n\n[![National Science Centre Poland](docs/ncn_logo.png){width=600}](https://ncn.gov.pl/en)   \n\nOpen access was funded by **Medical University of Białystok**, [**B.SUB.24.592**].\n\n[![Medical University of Bialystok](docs/mub_logo.png){width=100}](https://www.umb.edu.pl/en/index.php)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Famyloid-database-list","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Famyloid-database-list","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Famyloid-database-list/lists"}