{"id":14959384,"url":"https://github.com/tomasonjo/clinical-agent","last_synced_at":"2025-05-02T12:31:45.203Z","repository":{"id":243451081,"uuid":"811496923","full_name":"tomasonjo/clinical-agent","owner":"tomasonjo","description":"This project is designed for a simple LLM agent with tools on a clinical knowledge graph in Neo4j.","archived":false,"fork":false,"pushed_at":"2024-08-17T18:03:44.000Z","size":454,"stargazers_count":19,"open_issues_count":1,"forks_count":6,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-07T02:06:13.053Z","etag":null,"topics":["agent","chatgpt","graph","graphrag","langchain","llm","neo4j","openai"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tomasonjo.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":"2024-06-06T17:55:42.000Z","updated_at":"2025-03-19T16:17:47.000Z","dependencies_parsed_at":"2024-06-09T02:40:04.226Z","dependency_job_id":"a1048098-c2ca-40ca-b13c-e30f5207100c","html_url":"https://github.com/tomasonjo/clinical-agent","commit_stats":{"total_commits":4,"total_committers":2,"mean_commits":2.0,"dds":0.25,"last_synced_commit":"74d3a9c92bc909b62f719fa57cd79c759634a40a"},"previous_names":["tomasonjo/clinical-agent"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomasonjo%2Fclinical-agent","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomasonjo%2Fclinical-agent/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomasonjo%2Fclinical-agent/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomasonjo%2Fclinical-agent/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tomasonjo","download_url":"https://codeload.github.com/tomasonjo/clinical-agent/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252038191,"owners_count":21684645,"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":["agent","chatgpt","graph","graphrag","langchain","llm","neo4j","openai"],"created_at":"2024-09-24T13:19:35.538Z","updated_at":"2025-05-02T12:31:42.433Z","avatar_url":"https://github.com/tomasonjo.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# clinical-agent\n\nThis project is designed for a simple LLM agent with tools on a clinical knowledge graph in Neo4j.\n\n![Workflow diagram](https://raw.githubusercontent.com/tomasonjo/clinical-agent/main/static/clinical.png)\n\n## Setup\n\n1. Download and restore the [Clinical database dump](https://drive.google.com/file/d/1r5mHYuDjl-ilB8_vqgCqMUnziqGbOete/view?usp=drive_link).\n\n2. Set environment variables in `.env`.\n\n3. Run the following command:\n\n```\ndocker compose up \n```\n\n## Example questions\n\n*  What are associated foods with cancer?\n*  What are known clinically relevant gene variants for gene CLN3?\n*  In which tissues are expressed proteins associated with prostate carcinoma?\n\n## Todo\n\n* Better entity mapping from input to database (Using a combination of keyword search and/or biomedical text embeddings)\n* More tools\n\n## Contributions\n\nContributions are welcomed","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomasonjo%2Fclinical-agent","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftomasonjo%2Fclinical-agent","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomasonjo%2Fclinical-agent/lists"}