{"id":30188674,"url":"https://github.com/cod3licious/pubvis","last_synced_at":"2025-08-12T17:45:48.795Z","repository":{"id":22286929,"uuid":"82224582","full_name":"cod3licious/pubvis","owner":"cod3licious","description":"PubVis - Web Application for the Interactive Exploration and Discovery of Scientific Publications","archived":false,"fork":false,"pushed_at":"2025-03-23T14:07:58.000Z","size":82192,"stargazers_count":7,"open_issues_count":6,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-03-23T15:20:02.212Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/cod3licious.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":"2017-02-16T20:47:39.000Z","updated_at":"2025-03-23T14:08:01.000Z","dependencies_parsed_at":"2022-09-03T13:23:46.314Z","dependency_job_id":"fcaea605-046f-4d4a-b3c9-c63aa80fc4bf","html_url":"https://github.com/cod3licious/pubvis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cod3licious/pubvis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cod3licious%2Fpubvis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cod3licious%2Fpubvis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cod3licious%2Fpubvis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cod3licious%2Fpubvis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cod3licious","download_url":"https://codeload.github.com/cod3licious/pubvis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cod3licious%2Fpubvis/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270108902,"owners_count":24528772,"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","status":"online","status_checked_at":"2025-08-12T02:00:09.011Z","response_time":80,"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":"2025-08-12T17:45:47.388Z","updated_at":"2025-08-12T17:45:48.726Z","avatar_url":"https://github.com/cod3licious.png","language":"Python","readme":"# READ ME\n\nThis is a short introduction to the PubVis web application. For more details please see the accompanying [paper](http://arxiv.org/abs/1706.08094). A demo of the app is running [here](https://pubvis.onrender.com) (with PubMed articles about different cancer types) and [here](https://arxvis.onrender.com) (with arXiv articles about machine learning).\n\nIf any of this code was helpful for your research, please consider citing it:\n\n    @article{horn2017pubvis,\n      title   = {Interactive Exploration and Discovery of Scientific Publications with PubVis},\n      author  = {Horn, Franziska},\n      journal = {arXiv preprint arXiv:1706.08094},\n      year    = {2017}\n    }\n\nIf you have any questions please don't hesitate to send me an [email](mailto:cod3licious@gmail.com) and of course if you should find any bugs or want to contribute other improvements, pull requests are very welcome!\n\n\n## Quick start\n\n1.) Open a terminal in the pubvis repo folder.\n\n2.) Install all required packages (assumes an existing uv installation):\n```\nuv sync\n```\n\n3.) Optional: By default we're working with PubMed articles; if you want to work with arXiv articles instead, set `SOURCE = \"arxiv\"` in `src/__init__.py`.\n\n4.) Download the articles (either from pubmed or arxiv):\n```\nuv run python src/utils/download_articles.py\n```\nThis will create a folder `raw_texts/pubmed` inside the pubvis folder in which the downloaded articles are saved as json files (this will take a while).\n\n5.) Create the database and trained models (in `src/static/assets`), and two json files (in `src/static/json`) for the frontend from the downloaded articles:\n```\nuv run python src/utils/setup.py\n```\n\n6.) Install frontend dependencies and build (create dist folder; requires node.js and npm installation):\n```\ncd fronted\nnpm i\nnpm run build\n```\n\n7.) Optional: Run tests (requires `frontend/dist/` exists):\n```\nuv run poe test\n```\n\n8.) Run the FastAPI app locally (from the root folder):\n```\nuv run uvicorn src.main:app --reload\n```\nOpen your browser at http://127.0.0.1:8000/ to see the results.\n\n\n### Acknowledgements\n\nThis project was initially a collaboration with [Dmitry Monin](https://www.linkedin.com/in/dmitry-monin-72624176/), who designed and implemented the original frontend. The frontend of the current version was implemented with the help of [Marcel Lengert](https://www.linkedin.com/in/marcel-lengert/).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcod3licious%2Fpubvis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcod3licious%2Fpubvis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcod3licious%2Fpubvis/lists"}