{"id":19388863,"url":"https://github.com/linkml/linkml-store","last_synced_at":"2026-01-24T01:03:24.388Z","repository":{"id":231799337,"uuid":"782765842","full_name":"linkml/linkml-store","owner":"linkml","description":"wrapper for multiple linkml storage engines","archived":false,"fork":false,"pushed_at":"2025-03-13T23:07:18.000Z","size":10506,"stargazers_count":20,"open_issues_count":2,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-02T22:23:25.698Z","etag":null,"topics":["data-lake","data-stack","database-wrapper","duckdb","hdf5","linkml","mongo","mongodb","nosql-database","rdf","semweb","triplestore","vector-database"],"latest_commit_sha":null,"homepage":"https://linkml.io/linkml-store","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/linkml.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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":"2024-04-06T01:28:43.000Z","updated_at":"2025-03-17T13:47:34.000Z","dependencies_parsed_at":"2024-04-06T02:32:29.347Z","dependency_job_id":"5e3a26d4-5eab-46a6-a21b-7db502a438dd","html_url":"https://github.com/linkml/linkml-store","commit_stats":null,"previous_names":["linkml/linkml-store"],"tags_count":24,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Flinkml-store","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Flinkml-store/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Flinkml-store/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Flinkml-store/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linkml","download_url":"https://codeload.github.com/linkml/linkml-store/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250532125,"owners_count":21446122,"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":["data-lake","data-stack","database-wrapper","duckdb","hdf5","linkml","mongo","mongodb","nosql-database","rdf","semweb","triplestore","vector-database"],"created_at":"2024-11-10T10:13:54.713Z","updated_at":"2026-01-24T01:03:24.382Z","avatar_url":"https://github.com/linkml.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# linkml-store\n\nAn AI-ready data management and integration platform. LinkML-Store\nprovides an abstraction layer over multiple different backends\n(including DuckDB, MongoDB, Neo4j, and local filesystems), allowing for\ncommon query, index, and storage operations.\n\nFor full documentation, see [https://linkml.io/linkml-store/](https://linkml.io/linkml-store/)\n\nSee [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false\u0026loop=false\u0026delayms=3000) for a high level overview.\n\n__Warning__ LinkML-Store is still undergoing changes and refactoring,\nAPIs and command line options are subject to change!\n\n## Quick Start\n\nInstall, add data, query it:\n\n```\npip install linkml-store[all]\nlinkml-store -d duckdb:///db/my.db -c persons insert data/*.json\nlinkml-store -d duckdb:///db/my.db -c persons query -w \"occupation: Bricklayer\"\n```\n\nIndex it, search it:\n\n```\nlinkml-store -d duckdb:///db/my.db -c persons index -t llm\nlinkml-store -d duckdb:///db/my.db -c persons search \"all persons employed in construction\"\n```\n\nValidate it:\n\n```\nlinkml-store -d duckdb:///db/my.db -c persons validate\n```\n\n## Basic usage\n\n* [Command Line](https://linkml.io/linkml-store/tutorials/Command-Line-Tutorial.html)\n* [Python](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)\n* API\n* Streamlit applications\n\n## The CRUDSI pattern\n\nMost database APIs implement the **CRUD** pattern: Create, Read, Update, Delete.\nLinkML-Store adds **Search** and **Inference** to this pattern, making it **CRUDSI**.\n\nThe notion of \"Search\" and \"Inference\" is intended to be flexible and extensible,\nincluding:\n\n* Search\n   * Traditional keyword search\n   * Search using LLM Vector embeddings (*without* a dedicated vector database)\n   * Pluggable specialized search, e.g. genomic sequence (not yet implemented)\n* Inference (encompassing  *validation*, *repair*, and inference of missing data)\n   * Classic rule-based inference\n   * Inference using LLM Retrieval Augmented Generation (RAG)\n   * Statistical/ML inference\n\n## Features\n\n### Multiple Adapters\n\nLinkML-Store is designed to work with multiple backends, giving a common abstraction layer\n\n* [MongoDB](https://linkml.io/linkml-store/how-to/Use-MongoDB.html)\n* [DuckDB](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)\n* [Solr](https://linkml.io/linkml-store/how-to/Query-Solr-using-CLI.html)\n* [Neo4j](https://linkml.io/linkml-store/how-to/Use-Neo4j.html)\n* **Ibis** - Universal database adapter supporting DuckDB, PostgreSQL, SQLite, BigQuery, Snowflake, and many more\n\n* Filesystem\n\nComing soon: any RDBMS, any triplestore, HDF5-based stores, ChromaDB/Vector dbs ...\n\nThe intent is to give a union of all features of each backend. For\nexample, analytic faceted queries are provided for *all* backends, not\njust Solr.\n\n### Composable indexes\n\nMany backends come with their own indexing and search\nschemes. Classically this was Lucene-based indexes, now it is semantic\nsearch using LLM embeddings.\n\nLinkML store treats indexing as an orthogonal concern - you can\ncompose different indexing schemes with different backends. You don't\nneed to have a vector database to run embedding search!\n\nSee [How to Use-Semantic-Search](https://linkml.io/linkml-store/how-to/Use-Semantic-Search.html)\n\n### Use with LLMs\n\nTODO - docs\n\n### Validation\n\nLinkML-Store is backed by [LinkML](https://linkml.io), which allows\nfor powerful expressive structural and semantic constraints.\n\nSee [Indexing JSON](https://linkml.io/linkml-store/how-to/Index-Phenopackets.html)\n\nand [Referential Integrity](https://linkml.io/linkml-store/how-to/Check-Referential-Integrity.html)\n\n## Web API\n\nThere is a preliminary API following HATEOAS principles implemented using FastAPI.\n\nTo start you should first create a config file, e.g. `db/conf.yaml`:\n\nThen run:\n\n```\nexport LINKML_STORE_CONFIG=./db/conf.yaml\nmake api\n```\n\nThe API returns links as well as data objects, it's recommended to use a Chrome plugin for JSON viewing\nfor exploring the API. TODO: add docs here.\n\nThe main endpoints are:\n\n* `http://localhost:8000/` - the root of the API\n* `http://localhost:8000/pages/` - browse the API via HTML\n* `http://localhost:8000/docs` - the Swagger UI\n\n## Streamlit app\n\n```\nmake app\n```\n\n## Background\n\nSee [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false\u0026loop=false\u0026delayms=3000) for more details\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinkml%2Flinkml-store","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinkml%2Flinkml-store","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinkml%2Flinkml-store/lists"}