{"id":30687643,"url":"https://github.com/zakariaaithssain/medgraphetl","last_synced_at":"2026-05-16T18:03:49.098Z","repository":{"id":306455824,"uuid":"1025764874","full_name":"zakariaaithssain/MedGraphETL","owner":"zakariaaithssain","description":"ETL Pipeline Applying NER and RE to PubMed Cancer Articles, Normalizing Entities via UMLS API, and Representing the Extracted Data as A Graph Database.","archived":false,"fork":false,"pushed_at":"2025-08-24T22:35:06.000Z","size":35176,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-08-24T22:54:47.099Z","etag":null,"topics":["cancer","graphdb","mongodb-atlas","neo4j-aura","ner","pubmed-api","re","scispacy","spacy","umls-api"],"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/zakariaaithssain.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,"zenodo":null}},"created_at":"2025-07-24T19:04:23.000Z","updated_at":"2025-08-22T13:35:55.000Z","dependencies_parsed_at":"2025-07-25T22:22:43.450Z","dependency_job_id":"e6df0b03-116b-48fc-991a-fd2f1b21fdc6","html_url":"https://github.com/zakariaaithssain/MedGraphETL","commit_stats":null,"previous_names":["zakariaaithssain/adaptive-cancer-graph","zakariaaithssain/medgraphetl"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/zakariaaithssain/MedGraphETL","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zakariaaithssain%2FMedGraphETL","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zakariaaithssain%2FMedGraphETL/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zakariaaithssain%2FMedGraphETL/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zakariaaithssain%2FMedGraphETL/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zakariaaithssain","download_url":"https://codeload.github.com/zakariaaithssain/MedGraphETL/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zakariaaithssain%2FMedGraphETL/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273208777,"owners_count":25064204,"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":"2025-09-01T02:00:09.058Z","response_time":120,"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":["cancer","graphdb","mongodb-atlas","neo4j-aura","ner","pubmed-api","re","scispacy","spacy","umls-api"],"created_at":"2025-09-02T00:03:47.610Z","updated_at":"2026-05-16T18:03:49.091Z","avatar_url":"https://github.com/zakariaaithssain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MedGraphETL:\n\n\n_“This product uses publicly available data from the U.S. National Library of Medicine (NLM), National Institutes of Health, Department of Health and Human Services; NLM is not responsible for the product and does not endorse or recommend this or any other product.”_\n\n## Project Overview  \n\nMedGraphETL is an end-to-end ETL pipeline that builds a biomedical knowledge graph from biomedical articles. The extracted data is transformed into a graph structure and loaded into a Neo4j instance, where it can be explored and queried. The frontend only provides a high-level exploration of the graph.\n\n\n**Note:**  \nThis project uses **SciSpacy** for Named Entity Recognition (NER) and **spaCy matchers** for Relation Extraction (RE).  \nThe extracted data is **not reviewed or validated by medical professionals**.\n\n\n## Architecture Overview\n\nThe system is composed of three containerized services:\n\n- **ETL Service**: Extracts biomedical articles data from APIs and stores it in MongoDB, Transforms data via Natural Language Processing (NLP), and finally Preprocesses and Loads structured data into Neo4j.\n- **API Service**: Exposes graph data through a REST API backed by Neo4j.\n- **Frontend Service**: Provides a lightweight UI for high-level exploration of the graph.\n\n**NOTE:** More technical details about each service are available in the `README` files inside each service's folder.\n\n\n## Running the Project\n### ETL Execution Model\n\nThe ETL service is **not started automatically** with Docker Compose.\n\nThis is a deliberate design choice:  \n- The focus of the project is on the ETL pipeline and graph construction rather than the API or the frontend.\n- Once built, graph exploration does not require ETL to be running\n- Prevents accidental reprocessing of data\n\nThe ETL pipeline is executed independently when data ingestion or updates are required.\nSee `etl/README.md` for instructions on running the ETL service.\n\n### API and Frontend Execution Model\n- Run the ETL service to build the graph\n- Create the `.env` file inside `src/medgraphetl/api/` (See `.env.example` file inside `src/medgraphetl/api/`)\n- Make sure Docker and Docker Compose are installed, then run:\n\n```bash\ndocker compose up --build \n```\n\n\n## Detailed Main Files Structure \n\n```text\n.\n├── src/\n│   └── medgraphetl/\n│       ├── api/\n│       │   ├── .env.example\n│       │   ├── Dockerfile\n│       │   ├── main.py\n│       │   ├── requirements.txt\n│       │   ├── README.md\n│       │   ├── .dockerignore\n│       │   └── routers/\n│       │       ├── graph_info.py\n│       │       ├── helpers.py\n│       │       ├── nodes.py\n│       │       └── relations.py\n│       │\n│       ├── etl/\n│       │   ├── .env.example\n│       │   ├── Dockerfile\n│       │   ├── main.py\n│       │   ├── requirements.txt\n│       │   ├── README.md\n│       │   ├── .dockerignore\n│       │   ├── data/\n│       │   │   ├──ready_for_neo4j/\n│       │   ├── config/\n│       │   │   ├── apis_config.py\n│       │   │   ├── log_config.py\n│       │   │   ├── mongodb_config.py\n│       │   │   ├── neo4jdb_config.py\n│       │   │   ├── nlp_config.py\n│       │   │   └── settings.py\n│       │   ├── modules/\n│       │   │   ├── mongo.py\n│       │   │   ├── neo4j.py\n│       │   │   ├── nlp.py\n│       │   │   ├── pubmed_api.py\n│       │   │   ├── pubmedcentral_api.py\n│       │   │   └── umls_api.py\n│       │   └── scripts/\n│       │       ├── extract.py\n│       │       ├── load.py\n│       │       └── transform/\n│       │           ├── annotate.py\n│       │           └── clean.py\n│       │\n│       └── frontend/\n│           ├── .env.local.example\n│           ├── Dockerfile\n│           ├── .dockerignore\n│   ├── README.md\n│   ├── package.json\n│   ├── package-lock.json\n│   ├── public/\n│   └── src/\n│\n├── docker-compose.yml\n├── .gitignore\n├── LICENSE\n└── README.md \n```\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"imgs/medgraph.png\" width=\"700\"/\u003e\n\u003cimg src=\"imgs/front.png\" width=\"700\"/\u003e\n\u003cimg src=\"imgs/nodes_page.png\" width=\"700\"/\u003e\n\u003cimg src=\"imgs/relations.png\" width=\"700\"/\u003e\n\n\n\u003c/p\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzakariaaithssain%2Fmedgraphetl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzakariaaithssain%2Fmedgraphetl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzakariaaithssain%2Fmedgraphetl/lists"}