{"id":49832544,"url":"https://github.com/forrtproject/flora-extractor","last_synced_at":"2026-05-13T21:37:37.008Z","repository":{"id":355377193,"uuid":"1224903724","full_name":"forrtproject/flora-extractor","owner":"forrtproject","description":"FloRA extractor","archived":false,"fork":false,"pushed_at":"2026-05-11T18:58:25.000Z","size":620,"stargazers_count":2,"open_issues_count":16,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-05-11T20:38:48.205Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/forrtproject.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":"AGENTS.md","dco":null,"cla":null}},"created_at":"2026-04-29T18:44:33.000Z","updated_at":"2026-05-03T09:16:25.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/forrtproject/flora-extractor","commit_stats":null,"previous_names":["forrtproject/flora-extractor"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/forrtproject/flora-extractor","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/forrtproject%2Fflora-extractor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/forrtproject%2Fflora-extractor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/forrtproject%2Fflora-extractor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/forrtproject%2Fflora-extractor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/forrtproject","download_url":"https://codeload.github.com/forrtproject/flora-extractor/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/forrtproject%2Fflora-extractor/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33001371,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-13T13:14:54.681Z","status":"ssl_error","status_checked_at":"2026-05-13T13:14:51.610Z","response_time":115,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2026-05-13T21:37:34.445Z","updated_at":"2026-05-13T21:37:37.002Z","avatar_url":"https://github.com/forrtproject.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FLoRA Extractor\n\nA Python tool that discovers, extracts, and validates replication and reproduction studies for the [FLoRA database](https://forrt.org/replication-hub/flora/).\n\n**Part of the [FORRT](https://forrt.org) project.**\n\n---\n\n## What It Does\n\nStarting from keyword searches of academic databases, FLoRA Extractor:\n1. **Discovers** candidate replication/reproduction papers from OpenAlex and curated lists\n2. **Filters** false positives using rule-based and LLM classification\n3. **Extracts** the target study and replication outcome from each paper\n4. **Validates** results through a crowdsourced voting web interface\n\n---\n\n## Architecture\n\n```\nStage 1: search/      → data/candidates.csv   (discover candidates)\nStage 2: filter/      → data/filtered.csv     (remove false positives)\nStage 3: extract/     → data/extracted.csv    (link original + code outcome)\nStage 4: validate/    → Flask web app         (human voting, export)\n```\n\nEach stage is independently runnable. See [CLAUDE.md](CLAUDE.md) for full technical details.\n\n---\n\n## Quick Start\n\n\u003e **Note:** The commands below are the target state once all stages are implemented.\n\u003e Currently, `flora_selected.csv` can be used to seed Stage 4 directly.\n\n```bash\n# 1. Clone and setup\ngit clone https://github.com/forrtproject/flora-extractor.git\ncd flora-extractor\npip install -r requirements.txt\ncp .env.example .env   # fill in your API keys\n\n# 2. Run the pipeline\npython search/run_search.py        # → data/candidates.csv\npython filter/run_filter.py        # → data/filtered.csv\npython extract/run_extract.py      # → data/extracted.csv\n\n# 3. Start the validation web app\npython -m validate.import_csv      # load into SQLite\npython -m validate.app             # → http://localhost:5001\n```\n\n---\n\n## API Keys Required\n\nAdd to your `.env` file (copy from `.env.example`):\n\n```\nRESEARCHER_EMAIL=you@example.com      # for OpenAlex/Crossref API politeness\nGEMINI_API_KEY=...                    # primary LLM\nGEMINI_API_KEY_2=...                  # optional: rotate for higher quota\nOPENAI_API_KEY=...                    # fallback LLM (optional)\nGROBID_URL=http://localhost:8070      # local GROBID server (optional, for full-text extraction)\n```\n\nGet a free Gemini API key at [aistudio.google.com](https://aistudio.google.com).\n\n---\n\n## Data Sources\n\n**Bibliographic databases (primary):**\n\n| Source                                             | Coverage                                         |\n| -------------------------------------------------- | ------------------------------------------------ |\n| [OpenAlex](https://openalex.org)                   | Broad academic literature, free API              |\n| [Semantic Scholar](https://www.semanticscholar.org)| Supplementary coverage                           |\n| [Crossref](https://www.crossref.org)               | DOI resolution and reference lists               |\n| [OpenCitations](https://opencitations.net)         | Reference lists (where OpenAlex coverage is thin)|\n\n**Curated lists (secondary, pluggable):**\n\n| Source                                                                                | Coverage                            |\n| ------------------------------------------------------------------------------------- | ----------------------------------- |\n| [Bob Reed's Replication Network](https://replicationnetwork.com/replication-studies/) | Economics                           |\n| [I4R](https://i4replication.org/reports/)                                             | Institute for Replication reports   |\n\nFull-text acquisition (for Stage 3): [Unpaywall](https://unpaywall.org), [CORE](https://core.ac.uk), arXiv, OSF.\n\n---\n\n## Output Schema\n\nEach extracted record contains:\n\n| Field | Description |\n|-------|-------------|\n| `doi_r` | Replication paper DOI |\n| `doi_o` | Original target study DOI |\n| `title_o` | Original target study title |\n| `outcome` | success / failure / mixed / uninformative / descriptive |\n| `outcome_phrase` | Supporting quote from the paper |\n| `link_evidence` | Evidence used to identify the original |\n| `validation_status` | confirmed / rejected / pending / needs_review |\n\nFull schema: [shared/schema.py](shared/schema.py)\n\n---\n\n## Team Guide\n\n| Team | Stage | Branch | Docs |\n|------|-------|--------|------|\n| Team Search | Stage 1 | `feature/search` | [docs/STAGE1_SEARCH.md](docs/STAGE1_SEARCH.md) |\n| Team Filter | Stage 2 | `feature/filter` | [docs/STAGE2_FILTER.md](docs/STAGE2_FILTER.md) |\n| Team Extract | Stage 3 | `feature/extract` | [docs/STAGE3_EXTRACT.md](docs/STAGE3_EXTRACT.md) |\n| Team Validate | Stage 4 | `feature/validate` | [docs/STAGE4_VALIDATE.md](docs/STAGE4_VALIDATE.md) |\n\n**New team member?** Read [CLAUDE.md](CLAUDE.md) first — it contains architecture, schema, and coding rules.  \n**AI coding agent?** Read [CLAUDE.md](CLAUDE.md) (Claude Code) or [AGENTS.md](AGENTS.md) (all others).  \n**Working in R?** See the R note in [CLAUDE.md](CLAUDE.md#r-support).\n\n---\n\n## Contributing\n\n1. Branch from `dev` using your team's branch name (`feature/search`, etc.)\n2. Use sample data in `misc/` to develop and test independently\n3. Open a PR to `dev` when a feature is stable — don't wait until the end\n4. `main` and `dev` are branch-protected; all merges require a PR review\n\n---\n\n## Related Projects\n\n- [flora_search_approaches](https://github.com/forrtproject/flora_search_approaches) — original R-based pathway pipeline (reference implementation)\n- [FLoRA database](https://forrt.org/replication-hub/flora/) — the database this tool feeds into\n\n---\n\n## License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fforrtproject%2Fflora-extractor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fforrtproject%2Fflora-extractor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fforrtproject%2Fflora-extractor/lists"}