{"id":25843068,"url":"https://github.com/incatools/oakx-grape","last_synced_at":"2025-03-01T06:37:59.295Z","repository":{"id":59343127,"uuid":"531307316","full_name":"INCATools/oakx-grape","owner":"INCATools","description":"Experimental OAK plugin for Grape","archived":false,"fork":false,"pushed_at":"2023-02-10T16:23:41.000Z","size":4242,"stargazers_count":5,"open_issues_count":13,"forks_count":2,"subscribers_count":7,"default_branch":"main","last_synced_at":"2024-05-09T00:21:43.044Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://incatools.github.io/oakx-grape/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/INCATools.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}},"created_at":"2022-09-01T00:35:43.000Z","updated_at":"2022-11-15T02:52:07.000Z","dependencies_parsed_at":"2023-01-30T01:15:35.914Z","dependency_job_id":null,"html_url":"https://github.com/INCATools/oakx-grape","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Foakx-grape","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Foakx-grape/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Foakx-grape/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Foakx-grape/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/INCATools","download_url":"https://codeload.github.com/INCATools/oakx-grape/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241329396,"owners_count":19944982,"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":[],"created_at":"2025-03-01T06:37:58.784Z","updated_at":"2025-03-01T06:37:59.289Z","avatar_url":"https://github.com/INCATools.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# oakx-grape\n\n🌳 🍇 Grape wrapper for OAK 🌳 🍇\n\n**ALPHA**\n\n## Usage\nMacbook users with M1 processor need to do a few extra steps as follows:\n\n - Download [Anaconda](https://www.anaconda.com/products/distribution).\n - `conda create --name oakx-grape-env python=3.9`\n - `conda activate oakx-grape-env`\n - `pip install poetry`\n - `poetry install`\n\nThe steps below are common to everyone.\n```\npip install oakx-grape\npoetry run runoak -i grape:sqlite:obo:pato relationships --direction both shape\n```\n### Install NVM + NPM\nThese [instructions](https://dev.to/ms314006/how-to-install-npm-through-nvm-node-version-manager-5gif) help setup nvm and npm on one's system.\n\n### Install GraphViz and OboGraphViz\n- `brew install graphviz`\n- `npm install -g obographviz`\n\n## How it works\n\nThis plugin implements a grape wrapper. The wrapper in fact wraps two adapters:\n\n1. An adaptor to ensmallen/grape, for performing performance-intensive graph operations\n2. An OAK adapter for handling everything else, including lookup by labels, search, predicate filtering, etc\n\nThere are two choices of selector:\n\n1. `grape:kgobo:{go,pato,uberon,...}`\n2. `grape:OAK-SELECTOR`\n\nwith the first pattern, the grape graph is loaded from kgobo, and the oak adapter is loaded from semantic sql\n\nwith the second, you can most existing existing OAK adapters:\n\n- sqlite/semsql\n- obo\n- rdf/owl\n\nNote you CANNOT use a backend like ubegraph or bioportal that relies on API calls\n\nThe idea is we will be able to run a notebook like this:\n\nhttps://github.com/INCATools/ontology-access-kit/blob/main/notebooks/Monarch/PhenIO-Tutorial.ipynb\n\nWith the semsim part handled by OAK\n\n## Acknowledgements\n \nThis [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [oakx-plugin-cookiecutter](https://github.com/INCATools/oakx-plugin-cookiecutter) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fincatools%2Foakx-grape","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fincatools%2Foakx-grape","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fincatools%2Foakx-grape/lists"}