{"id":45076969,"url":"https://github.com/ccb-hms/ontology-mapper","last_synced_at":"2026-02-19T13:37:27.667Z","repository":{"id":43487390,"uuid":"393476471","full_name":"ccb-hms/ontology-mapper","owner":"ccb-hms","description":"a tool for mapping free-text descriptions of entities to ontology terms","archived":false,"fork":false,"pushed_at":"2024-07-30T15:10:32.000Z","size":345,"stargazers_count":14,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"main","last_synced_at":"2024-10-01T14:39:24.420Z","etag":null,"topics":["data-cleaning","fair-data","fair-principles","metadata-cleaning","ontology","ontology-mapping","ontology-search","ontology-services","owl","owlready2"],"latest_commit_sha":null,"homepage":"https://ccb-hms.github.io/ontology-mapper","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/ccb-hms.png","metadata":{"files":{"readme":"README-UI.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":"2021-08-06T19:06:34.000Z","updated_at":"2024-08-21T09:44:24.000Z","dependencies_parsed_at":"2023-10-30T20:25:08.634Z","dependency_job_id":"bede0aef-70ce-486c-9ff7-51dc3920e6e9","html_url":"https://github.com/ccb-hms/ontology-mapper","commit_stats":{"total_commits":183,"total_committers":4,"mean_commits":45.75,"dds":0.2568306010928961,"last_synced_commit":"ea7b970d04eb8e2652be1aed2ef541242aecf10f"},"previous_names":[],"tags_count":22,"template":false,"template_full_name":null,"purl":"pkg:github/ccb-hms/ontology-mapper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccb-hms%2Fontology-mapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccb-hms%2Fontology-mapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccb-hms%2Fontology-mapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccb-hms%2Fontology-mapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ccb-hms","download_url":"https://codeload.github.com/ccb-hms/ontology-mapper/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccb-hms%2Fontology-mapper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29615107,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-19T13:04:20.082Z","status":"ssl_error","status_checked_at":"2026-02-19T13:03:33.775Z","response_time":117,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["data-cleaning","fair-data","fair-principles","metadata-cleaning","ontology","ontology-mapping","ontology-search","ontology-services","owl","owlready2"],"created_at":"2026-02-19T13:37:25.828Z","updated_at":"2026-02-19T13:37:27.641Z","avatar_url":"https://github.com/ccb-hms.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ontology-mapper-ui\nThe following information pertains to the text2term UI, which is written [here](https://github.com/ccb-hms/ontology-mapper-ui) and runs online [here](https://text2term.hms.harvard.edu/). It supports fewer features than the base package does, but provides a user interface for non-programmers.\n\n### Running Locally via Node + Python\n\n##### Requirements\n\n-   Node \u003e= 16.0.0\n-   npm \u003e= 8.0.0\n-   Python \u003e= 3.9.0\n-   pip \u003e= 21.0.0\n-   text2term \u003e= 4.1.2\n\n**\\*** These are the versions I have that work; while I know Python 3.9 or higher is necessary, the others may not strictly require the listed versions.\n\n**\\*\\*** If you are running this locally on Google Chrome, you will likely run into issues with CORS (Cross-Origin Requests) that I have been unable to completely resolve. I would recommend using a different browser, using the Docker method, or finding some way to disable CORS on Chrome while running this.\n\n#### Instructions\n\n##### Initial Setup\n\nWhen first cloned, run the command:\n\n\n```\nnpm install\n```\n\nto install all necessary packages for the React frontend.\n\nNext, go into the `flask-api` folder (perhaps by running `cd flask-api`) and run\n\n```\npip install -r requirements-flask.txt\n```\n\nto install necessary packages for the Flask api.\n\n##### Running\n\nTo run, make sure you are in the root of the repository and run, in two separate command line instances, the command\n\n```\nnpm start\n```\n\nto start the front-end, which can be seen at `localhost:3000`, and the command\n\n```\nnpm run flask-api\n```\n\nto start the back-end, which can be interacted with at `localhost:5000`.\n\n### Running Locally via Docker\n\n#### Requirements\n\n-   Docker\n\n#### Instructions\n\n##### Initial Setup\n\nBefore running, make sure you have the latest version of the repository built by running the command\n\n```\ndocker-compose build\n```\n\nDocker should build two images:\n\n-   `ontology-mapper-api`: the Flask backend API\n-   `ontology-mapper-client`: the React frontend\n\n##### Running\n\nTo run the website, run the command:\n\n```\ndocker-compose up\n```\n\nDocker should build two containers corresponding to the two images.\n\nIn a browser, navigate to `localhost:8602` to see the front-end.\n\n### Acknowledgements\n\nInitial setup of React and Flask and Dockerization aided by an [article series](https://blog.miguelgrinberg.com/post/how-to-dockerize-a-react-flask-project) by Miguel Grinberg.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fccb-hms%2Fontology-mapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fccb-hms%2Fontology-mapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fccb-hms%2Fontology-mapper/lists"}