{"id":51644520,"url":"https://github.com/scienceverse/papers","last_synced_at":"2026-07-13T21:30:50.801Z","repository":{"id":365268030,"uuid":"1270995619","full_name":"scienceverse/papers","owner":"scienceverse","description":"a repository of open access papers converted to metacheck paperlist objects in .rds format","archived":false,"fork":false,"pushed_at":"2026-06-28T06:03:51.000Z","size":1163,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-06-28T08:06:07.792Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/scienceverse.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-06-16T08:32:20.000Z","updated_at":"2026-06-28T06:03:54.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/scienceverse/papers","commit_stats":null,"previous_names":["scienceverse/papers"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/scienceverse/papers","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scienceverse%2Fpapers","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scienceverse%2Fpapers/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scienceverse%2Fpapers/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scienceverse%2Fpapers/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scienceverse","download_url":"https://codeload.github.com/scienceverse/papers/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scienceverse%2Fpapers/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35437763,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-13T02:00:06.543Z","response_time":119,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2026-07-13T21:30:50.235Z","updated_at":"2026-07-13T21:30:50.795Z","avatar_url":"https://github.com/scienceverse.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# papers\n\nA shared repository of open-access scientific manuscripts for validating tools\nthat automatically check scientific papers. The goal is to provide a common,\ncitable benchmark corpus that developers of tools such as\n[Statcheck](https://github.com/MicheleNuijten/statcheck),\n[Regcheck](https://github.com/JamieCummins/regcheck),\n[Metacheck](https://github.com/scienceverse/metacheck), and\n[ESCIcheck](https://github.com/giladfeldman/escicheck)\ncan use to systematically test and validate their tools on real published\nliterature.\n\nAll papers in this repository are open-access and are shared in accordance\nwith their original licenses (typically CC-BY 4.0).\n\n**18 corpora, 15,179 papers, as of 2026-06-21.**\n\nIf you are building a new corpus for this repository, read\n[downloading_articles.md](downloading_articles.md) first -- it documents\ndozens of lessons learned (publisher-specific access patterns, GROBID\nconversion pitfalls, common bugs in DOI/sampling logic, and the release\nchecklist) from building the corpora below. Skipping it means re-discovering\nthe same problems from scratch.\n\n---\n\n## Repository organisation\n\nEach journal corpus lives in its own subfolder and contains:\n\n```\n\u003ccorpus\u003e/\n  README.md         description, coverage, and known gaps\n  manifest.csv      one row per paper: DOI, title, year, filenames, provenance\n  metadata.json     Dublin Core metadata describing the corpus as a dataset\n  build.R           fully reproducible script to regenerate the corpus from scratch\n  pdf/              original PDF files, named \u003ccorpus\u003e.\u003carticle_id\u003e.pdf\n```\n\nIn addition, compiled **paperlist** objects (`.rds` files) are distributed as\nGitHub Release assets and can be downloaded directly from R using metacheck\n(see below). These are the primary format used by Metacheck, Regcheck, and\nrelated tools.\n\n### File formats\n\n| Format | Location | Description |\n|--------|----------|-------------|\n| PDF | `\u003ccorpus\u003e/pdf/` | Original publisher PDFs |\n| Paperlist (`.rds`) | GitHub Release asset | Structured R objects extracted from PDFs via GROBID; the main format for tool validation |\n| TEI-XML | not stored | Intermediate GROBID output used to generate paperlists |\n\nOther formats (plain text, JSON) can be added to a corpus subfolder if needed.\nIf you need a format that is not yet available, please\n[open an issue](https://github.com/scienceverse/papers/issues).\n\n---\n\n## Available corpora\n\n18 corpora, 15,179 papers in total.\n\n| Corpus | Journal | Papers | Years | License |\n|--------|---------|--------|-------|---------|\n| [bmcmed](bmcmed/) | BMC Medicine | 1000 | 2016-2025 | CC-BY 4.0 |\n| [bmcoral](bmcoral/) | BMC Oral Health | 1000 | 2016-2025 | Mostly CC-BY 4.0 |\n| [collabra](collabra/) | Collabra: Psychology | 748 | 2017-2026 | CC-BY 4.0 |\n| [ece3](ece3/) | Ecology and Evolution | 1543 | 2011-2026 | Mixed CC-BY 4.0/3.0, CC-BY-NC 3.0 |\n| [elife](elife/) | eLife | 1000 | 2017-2026 | CC-BY 4.0 |\n| [frontiers](frontiers/) | Frontiers in Psychology | 1000 | 2017-2026 | CC-BY 4.0 |\n| [ijos](ijos/) | International Journal of Oral Science | 724 | 2009-2026 | Mostly CC-BY 4.0 |\n| [iperc](iperc/) | i-Perception | 496 | 2017-2026 | CC-BY 4.0 |\n| [jdm](jdm/) | Judgment and Decision Making | 855 | 2006-2022 | CC-BY 4.0 |\n| [joc](joc/) | Journal of Cognition | 447 | 2017-2026 | CC-BY 4.0 |\n| [jssm](jssm/) | Journal of Sports Science and Medicine | 1000 | 2014-2026 | CC-BY 4.0 or CC-BY-NC-ND 4.0 |\n| [natcomm](natcomm/) | Nature Communications | 1000 | 2017-2026 | Mostly CC-BY 4.0 |\n| [openmind](openmind/) | Open Mind | 293 | 2017-2026 | CC-BY 4.0 |\n| [plosbio](plosbio/) | PLOS Biology | 1000 | 2016-2025 | CC-BY 4.0 or CC0 |\n| [plosmed](plosmed/) | PLOS Medicine | 1000 | 2016-2025 | CC-BY 4.0 or CC0 |\n| [plosone](plosone/) | PLOS ONE | 1000 | 2016-2025 | CC-BY 4.0 or CC0 |\n| [psychsci_oa](psychsci_oa/) | Psychological Science (OA subset) | 270 | 2014-2026 | CC-BY 4.0 or CC-BY-NC |\n| [scan](scan/) | Social Cognitive and Affective Neuroscience | 803 | 2017-2026 | Mixed CC-BY variants |\n\nEach corpus's `README.md` documents its specific coverage, sampling method\n(complete corpus vs. stratified random sample), and known gaps/exclusions.\n\n---\n\n## Loading papers in R with metacheck\n\nInstall metacheck from GitHub if you have not already:\n\n```r\n# install.packages(\"pak\")\npak::pkg_install(\"scienceverse/metacheck\")\n```\n\nThen download and load a corpus:\n\n```r\n# See what corpora are available and whether they are cached locally\nmetacheck::papers_available()\n\n# Download a corpus to your local cache (~18 MB for collabra)\nmetacheck::papers_download(\"collabra\")\n\n# Load the corpus into R as a paperlist object\npapers \u003c- metacheck::papers_load(\"collabra\")\n\n# Run a check module on all papers\nresults \u003c- metacheck::module_run(papers, \"ethics_check\")\n\n# Remove the cached corpus to free disk space\nmetacheck::papers_remove(\"collabra\")\n```\n\nThe paperlist format is a named list of paper objects, each containing full\ntext, section structure, references, figures, tables, equations, and\nbibliographic metadata. It is the native input format for all metacheck\nmodules.\n\n---\n\n## FAIR principles\n\nThis repository is designed to be a FAIR (Findable, Accessible, Interoperable,\nReusable) data resource:\n\n- **Findable**: every paper is identified by its DOI in `manifest.csv`; each\n  corpus has a `metadata.json` file with Dublin Core metadata\n- **Accessible**: all PDFs are open-access; paperlist files are freely\n  downloadable via `metacheck::papers_download()`\n- **Interoperable**: paperlist objects follow the\n  [scienceverse](https://github.com/scienceverse) schema; metadata uses the\n  Dublin Core standard\n- **Reusable**: all corpora use open licenses; each `build.R` script fully\n  reproduces the dataset from original sources\n\n---\n\n## Contributing\n\nTo add a new corpus, follow the structure above and open a pull request.\nThe `build.R` script should be fully self-contained and reproducible, and\n`manifest.csv` should list every paper with its DOI and provenance. See\n[collabra/build.R](collabra/build.R) for a worked example.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscienceverse%2Fpapers","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscienceverse%2Fpapers","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscienceverse%2Fpapers/lists"}