{"id":19448612,"url":"https://github.com/neurodata/ndontology","last_synced_at":"2025-10-19T06:04:08.795Z","repository":{"id":140563162,"uuid":"104658342","full_name":"neurodata/ndontology","owner":"neurodata","description":"Manage/query/update a MongoDB that contains the Allen Research Atlas Ontology","archived":false,"fork":false,"pushed_at":"2017-10-05T19:44:17.000Z","size":61,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-25T08:54:13.440Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/neurodata.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":"2017-09-24T16:18:21.000Z","updated_at":"2017-10-03T22:46:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"c96654eb-3e8f-45b0-9531-ef246ebb65f3","html_url":"https://github.com/neurodata/ndontology","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/neurodata/ndontology","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fndontology","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fndontology/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fndontology/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fndontology/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/neurodata","download_url":"https://codeload.github.com/neurodata/ndontology/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fndontology/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270702562,"owners_count":24630877,"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":"2025-08-16T02:00:11.002Z","response_time":91,"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":"2024-11-10T16:27:52.217Z","updated_at":"2025-10-19T06:04:03.763Z","avatar_url":"https://github.com/neurodata.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ndaraontology\nManage/query/update a MongoDB in Docker that contains the \n* Allen Research Atlas Ontology\n* Waxholm Rat Atlas.\n\nThese tools run in python 3.5+, require a mongo database to talk to.\nYou need to install a late version of mongo clients (3.4.9).\nPlease `pip/pip3 install -r requirements.txt` to configure your python or virtualenv.\n\nSee README.md in ./docker for run instructions\n    \n\nThe docker-compose file will load the databases.  It can be done manually on any running mongo instance.\n\n```\nRun the load scripts to put ontology databases onto local mongodb.  You need to have PTYHONPATH set to the root directory of this repository, e.g. /home/XXXX/ndontology\n```\n    cd arascripts\n    ./load_ara.sh\n    cd ../whsscripts\n    ./load_whs.sh\n    cd ..\n```\nRun the unit tests\n```\n    py.test \n```\n\n## What you get\n\nA MongoDB instance running in docker that has the following databases:\n* Allen Reference Atlas\n    * atlases.ara -- DB of ROIs supports lookup by id, atlas\\_id, details, and descendants\n    * atlases.ara\\_nametree -- contains one object with hierarchical tree of all objects\n* Waxholm Rat Atlas\n    * atlases.whs -- DB of ROIs supports lookup by id, details, and descendants\n    * atlases.whs\\_nametree -- contains one object with hierarchical tree of all objects\n\nReference queries are in the unit tests and ontology.py/araonotology.py\n\nAll of the tests and reference queries assume that Mongo runs on localhost.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodata%2Fndontology","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurodata%2Fndontology","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodata%2Fndontology/lists"}