LinkML-Store documentation

Contents:

• About
  • Installation
  • Quickstart
  • Data Model
  • Adapters
  • Indexing
  • Metadata and Configuration
• Tutorials
  • Tutorial: Using the Command Line Interface
    • Top level command
    • Inserting objects from a file
    • Querying
    • Describing the data set
    • Facet Counts
    • Search
    • Indexing using an LLM (OPTIONAL)
    • Schemas
    • Configuration Files and Explicit Schemas
    • Validation
  • Tutorial: Using the Python API
    • Create a Client object
    • Attach and populate a DuckDB in-memory database
    • Querying
    • Faceting
    • Plotting
    • Complex objects
    • Schemas
    • Asserting schemas
    • Other adapters
    • Indexing
• How-To Guides
  • How to use MongoDB with LinkML-Store
    • Creating a client and attaching to a database
    • Creating a collection
    • Preparing data to load
    • Inserting objects
    • Queries
    • Facet counts
    • Creating an LLM embedding index
  • How to use Semantic Search
    • Background
    • Obtaining upstream files
    • Storing the JSON
    • Creating an LLMIndexer
    • Searching using the index
    • How it works
  • How to query the Monarch-KG
  • How to query Solr using the Command Line
    • Specifying a Solr backend on the command line:
    • Using a configuration
    • Search
  • How to Check Referential Integrity
    • Inserting invalid data
  • Example: Storing an ontology
  • How to index Phenopackets with LinkML-Store
    • Use pystow to download phenopackets
    • Creating a client and attaching to a database
    • Creating a collection
    • Inserting objects into the store
    • Check contents
    • Query faceting
    • Semantic Search
    • Semantic Search
    • Validation
    • Command Line Usage
  • How to index GO-CAMs with LinkML-Store
    • Creating a client and attaching to a database
    • Creating a collection
    • Inserting objects into the store
    • Check contents
    • Query faceting
    • Semantic Search
    • Semantic Search
    • Validation
    • Command Line Usage
• Reference
  • linkml_store

Indices and tables

• Index

• Module Index

• Search Page