{"id":25926922,"url":"https://github.com/astrabert/pubmed-md","last_synced_at":"2026-04-11T15:38:34.726Z","repository":{"id":279551166,"uuid":"938195138","full_name":"AstraBert/pubmed-md","owner":"AstraBert","description":"Get PubMed titles and abstracts in a LLM-friendly way🤖","archived":false,"fork":false,"pushed_at":"2025-02-24T15:15:12.000Z","size":15,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-26T06:32:39.831Z","etag":null,"topics":["flask","markdown","pubmed","rest-api","streamlit"],"latest_commit_sha":null,"homepage":"https://pubmed-md.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AstraBert.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","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":"2025-02-24T15:14:44.000Z","updated_at":"2025-02-24T18:03:55.000Z","dependencies_parsed_at":"2025-02-26T06:32:44.237Z","dependency_job_id":"58c5092a-a869-44cf-9d0a-a0b074cd90d8","html_url":"https://github.com/AstraBert/pubmed-md","commit_stats":null,"previous_names":["astrabert/pubmed-md"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraBert%2Fpubmed-md","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraBert%2Fpubmed-md/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraBert%2Fpubmed-md/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraBert%2Fpubmed-md/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AstraBert","download_url":"https://codeload.github.com/AstraBert/pubmed-md/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241731744,"owners_count":20010781,"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":["flask","markdown","pubmed","rest-api","streamlit"],"created_at":"2025-03-03T20:04:06.151Z","updated_at":"2025-12-31T01:04:39.603Z","avatar_url":"https://github.com/AstraBert.png","language":"Python","funding_links":["https://github.com/sponsors/AstraBert"],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003epubmed.md\u003c/h1\u003e\r\n\r\n\u003ch2 align=\"center\"\u003eGet PubMed titles and abstracts in a LLM-friendly way🤖\u003c/h2\u003e\r\n\r\n\u003ch3 align=\"center\"\u003eIf you find pubmed.md useful, please consider to support us through donation:\u003c/h3\u003e\r\n\u003cdiv align=\"center\"\u003e\r\n    \u003ca href=\"https://github.com/sponsors/AstraBert\"\u003e\u003cimg src=\"https://img.shields.io/badge/sponsor-30363D?style=for-the-badge\u0026logo=GitHub-Sponsors\u0026logoColor=#EA4AAA\" alt=\"GitHub Sponsors Badge\"\u003e\u003c/a\u003e\r\n\u003c/div\u003e\r\n\u003cbr\u003e\r\n\u003cdiv align=\"center\"\u003e\r\n    \u003cimg src=\"logo.png\" alt=\"NewsReport AI Logo\" width=300 height=300\u003e\r\n\u003c/div\u003e\r\n\r\n**pubmed.md** is a simple [Streamlit]() application that scrapes the titles and abstracts of PubMed articles and returns them in a LLM-friendly way. The backend is a REST API built with [Flask]().\r\n\r\n# Install and launch🚀\r\n\r\nThe first step, common to both the Docker and the source code setup approaches, is to clone the repository and access it:\r\n\r\n```bash\r\ngit clone https://github.com/AstraBert/pubmed-md.git\r\ncd pubmed-md/\r\n```\r\n\r\nOnce there, you can choose one of the two following approaches:\r\n\r\n### Docker (recommended)🐋\r\n\r\n\u003e _Required: [Docker](https://docs.docker.com/desktop/) and [docker compose](https://docs.docker.com/compose/)_\r\n\r\n- Launch the Docker application:\r\n\r\n```bash\r\ndocker compose up backend -d\r\ndocker compose up frontend -d\r\n```\r\n\r\n- Or\r\n\r\n```bash\r\n# On Linux/MacOS\r\nbash start_services.sh\r\n# On Windows\r\n.\\start_services.ps1\r\n```\r\n\r\nYou will see the application running on http://localhost:8501 and you will be able to use it. Depending on your connection and on your hardware, the set up might take some time (up to 30 mins to set up) - but this is only for the first time your run it!\r\n\r\n### Source code🗎\r\n\r\n\u003e _Required: [python](https://www.python.org/)_\r\n\r\n- Create and activate a virtual environment:\r\n\r\n```bash\r\npython3 -m venv .venv\r\n# Linux/macOS\r\nsource .venv/bin/activate\r\n# Windows PS\r\n.venv\\Scripts\\Activate.ps1\r\n# Windows CMD\r\n.venv\\Scripts\\activate.bat\r\n```\r\n\r\n- Install all necessary dependencies:\r\n\r\n```bash\r\npython3 -m pip install -r requirements.txt\r\n```\r\n\r\n- Launch the REST API:\r\n\r\n```bash\r\ncd scripts/\r\ngunicorn api:app -b 0.0.0.0:5000\r\n```\r\n\r\n- Launch the Streamlit app:\r\n\r\n```bash\r\nstreamlit run app.py\r\n```\r\n\r\nYou will see the application running on http://localhost:8501 and you will be able to use it.\r\n\r\n## How it works\r\n\r\nThe backend is a REST API with one endpoint - `pubmed`: this endpoint receives a request from the frontend that carries the ID of the article whose title and abstract are to scrape, and sends a request to NCBI through the `Entrez` protocol available in BioPython. The request is processed and returned as XML text: the XML text is then converted to markdown.\r\n\r\n## Contributing\r\n\r\nContributions are always welcome! Follow the contributions guidelines reported [here](CONTRIBUTING.md).\r\n\r\n## License and rights of usage\r\n\r\nThe software is provided under MIT [license](./LICENSE).\r\n\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrabert%2Fpubmed-md","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fastrabert%2Fpubmed-md","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrabert%2Fpubmed-md/lists"}