> For the complete documentation index, see [llms.txt](https://docs.biobox.io/guide/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.biobox.io/guide/how-to.md).

# How To

- [Configure your Knowledge Graph Schema](https://docs.biobox.io/guide/how-to/configure-your-knowledge-graph-schema.md): How to customize your knowledge graph schema
- [Format Internal Data For Uploading](https://docs.biobox.io/guide/how-to/configure-your-knowledge-graph-schema/format-internal-data-for-uploading.md): How to use our python data adapters to format internal data to upload.
- [Upload Internal Data](https://docs.biobox.io/guide/how-to/configure-your-knowledge-graph-schema/upload-internal-data.md): How to add internal data to your graph through the creation of a data package.
- [Create delta reports to compare prioritization frameworks](https://docs.biobox.io/guide/how-to/create-delta-reports-to-compare-prioritization-frameworks.md): Understand how changes in scientific criteria and data availability impact ranking and prioritization across your organization. Explore how and why previous decisions were made.
- [Create Prioritization Graph Models](https://docs.biobox.io/guide/how-to/create-prioritization-graph-models.md): How to create a graph model to prioritize data points
- [Generate Reports](https://docs.biobox.io/guide/how-to/create-prioritization-graph-models/generate-reports.md): How to leverage you graph models to generate reports for the purposes of target prioritization, indication selection and more.
- [Pathway Enrichment](https://docs.biobox.io/guide/how-to/create-prioritization-graph-models/pathway-enrichment.md): How to run pathway enrichment analysis on the genes returned in you graph model report.
- [Use the Graph Explorer](https://docs.biobox.io/guide/how-to/use-the-graph-explorer.md): How to traverse your knowledge graph to explore specific objects
- [Running Graph Algorithms](https://docs.biobox.io/guide/how-to/use-the-graph-explorer/running-graph-algorithms.md): How to run graph algorithms to identify paths and prioritize data points.
- [Save Graph Explorer Sessions](https://docs.biobox.io/guide/how-to/use-the-graph-explorer/save-graph-explorer-sessions.md): How to save sessions and access previously saved sessions
- [Ask multi-modal questions](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions.md): How to use Query Language or Natural Language to interrogate your custom knoweldge graph
- [Ask questions with Natural Language (GraphRAG)](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-natural-language-graphrag.md): How to use GraphRAG to ask questions with natural language.
- [Use Agent Orion to generate a query with Natural Language](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-natural-language-graphrag/use-agent-orion-to-generate-a-query-with-natural-language.md): How to use natural language to generate complex biological queries with Agent Orion
- [Use Agent Iris to converse with your data](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-natural-language-graphrag/use-agent-iris-to-converse-with-your-data.md): How to converse with your data
- [Ask questions with Query Language](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language.md): A comprehensive breakdown of how to use the query language
- [Customize the data table returned with your query](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/customize-the-data-table-returned-with-your-query.md): How to customize the data table returned with your query.
- [Explore and understand your results](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/explore-and-understand-your-results.md): How to explore and interpret the results returned from the Query Language
- [Visualize data returned in Query Language](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/visualize-data-returned-in-query-language.md): How to visualize the data returned in a query language search in an interactive plot.
- [Modify Queries using the Query Editor](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/modify-queries-using-the-query-editor.md): How to edit queries using the Query Editor
- [Use the MCP to connect your agents to BioBox](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude.md): Connect your agents to the BioBox platform and ask grounded questions in plain language — read-only and scoped to your organization.
- [Connect Claude (sign in)](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/connect-claude.md): Add the BioBox connector to Claude on the web, in Claude Code, or in Claude Desktop, and sign in with your BioBox account.
- [Example](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/quickstart.md): Connect an agent to BioBox and ask your first grounded question
- [Tool Reference](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools.md): The full set of tools the agent can call against your BioBox graph — what each does, its parameters, and an example response.
- [list\_entity\_types — List entity types](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/list-entity-types.md): List entity types
- [describe\_entity\_type — Describe entity type](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/describe-entity-type.md): Describe entity type
- [get\_graph\_schema — Get graph schema](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-graph-schema.md): Get graph schema
- [search\_entities — Search entities by name](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/search-entities.md): Search entities by name
- [get\_entity — Get entity](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-entity.md): Get entity
- [get\_entity\_connections — Get entity connections](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-entity-connections.md): Get entity connections
- [find\_paths — Find shortest path](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/find-paths.md): Find shortest path
- [run\_graph\_query — Run a read-only graph query](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/run-graph-query.md): Run a read-only graph query
- [list\_reports — List scoring reports](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/list-reports.md): List scoring reports
- [get\_report\_scores — Get report scores](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-report-scores.md): Get report scores
- [get\_evidence — Get evidence for a scored entity](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-evidence.md): Get evidence for a scored entity
- [where\_entity\_ranks — Where entity ranks](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/where-entity-ranks.md): Where entity ranks
- [list\_delta\_reports — List delta reports](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/list-delta-reports.md): List delta reports
- [get\_delta\_report — Get a delta report](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-delta-report.md): Get a delta report
- [get\_delta\_report\_target — Compare a target within a delta report](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-delta-report-target.md): Compare a target within a delta report
- [list\_reasoning\_modules — List reasoning modules](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/list-reasoning-modules.md): List reasoning modules
- [get\_reasoning\_module — Get reasoning module config](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-reasoning-module.md): Get reasoning module config
- [list\_profile\_models — List profile models](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/list-profile-models.md): List profile models
- [get\_profile\_model — Get profile graph model config](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/get-profile-model.md): Get profile graph model config
- [search\_models — Search reasoning models](https://docs.biobox.io/guide/how-to/ask-biobox-with-claude/tools/search-models.md): Search reasoning models