> 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/ask-biobox-with-claude/tools.md).

# Tool Reference

When you ask a question, the agent chooses from the tools below and calls the ones it needs. You don't call these directly — the agent does — but this reference shows exactly what each tool does, what it accepts, and what it returns, so you can understand (and trust) how an answer was built.

{% hint style="info" %}
These pages are **generated automatically** from the BioBox MCP tool definitions, so they always match what the agent actually sees. Every tool is **read-only** and scoped to your organization.
{% endhint %}

## The tools, by what they're for

**Get oriented in the graph**

* [`list_entity_types`](/guide/how-to/ask-biobox-with-claude/tools/list-entity-types.md) — what kinds of things (genes, diseases, drugs, …) exist in the graph
* [`describe_entity_type`](/guide/how-to/ask-biobox-with-claude/tools/describe-entity-type.md) — the properties and relationships of one entity type
* [`get_graph_schema`](/guide/how-to/ask-biobox-with-claude/tools/get-graph-schema.md) — the overall shape of the graph
* [`get_concept_relationships`](/guide/how-to/ask-biobox-with-claude/tools/get-concept-relationships.md) — which ontology relationships can connect two entity types
* [`find_intermediate_concept`](/guide/how-to/ask-biobox-with-claude/tools/find-intermediate-concept.md) — a bridging concept between two groups that don't connect directly

**Find and inspect entities**

* [`search_entities`](/guide/how-to/ask-biobox-with-claude/tools/search-entities.md) — resolve a name or symbol (e.g. "ERBB4") to graph nodes
* [`search_entities_fulltext`](/guide/how-to/ask-biobox-with-claude/tools/search-entities-fulltext.md) — full-text search over entity names in the ontology
* [`search_entities_fuzzy`](/guide/how-to/ask-biobox-with-claude/tools/search-entities-fuzzy.md) — typo-tolerant search when the spelling isn't exact
* [`get_entity`](/guide/how-to/ask-biobox-with-claude/tools/get-entity.md) — full detail for one entity
* [`get_entity_connections`](/guide/how-to/ask-biobox-with-claude/tools/get-entity-connections.md) — what an entity is connected to
* [`find_paths`](/guide/how-to/ask-biobox-with-claude/tools/find-paths.md) — the shortest path between two entities
* [`expand_anchor`](/guide/how-to/ask-biobox-with-claude/tools/expand-anchor.md) — broaden a too-specific entity up its is-a hierarchy to a parent with more data
* [`run_graph_query`](/guide/how-to/ask-biobox-with-claude/tools/run-graph-query.md) — a read-only graph query for advanced questions

**Prioritization reports & evidence**

* [`list_reports`](/guide/how-to/ask-biobox-with-claude/tools/list-reports.md) — the scoring reports available to you
* [`list_profile_reports`](/guide/how-to/ask-biobox-with-claude/tools/list-profile-reports.md) — the profile (monopartite) scoring reports available to you
* [`get_report_scores`](/guide/how-to/ask-biobox-with-claude/tools/get-report-scores.md) — the ranked scores in a report
* [`get_evidence`](/guide/how-to/ask-biobox-with-claude/tools/get-evidence.md) — the evidence behind a scored entity
* [`where_entity_ranks`](/guide/how-to/ask-biobox-with-claude/tools/where-entity-ranks.md) — where a specific entity ranks in a report

**Compare reports (delta reports)**

* [`list_delta_reports`](/guide/how-to/ask-biobox-with-claude/tools/list-delta-reports.md) — the saved report-to-report comparisons available to you
* [`get_delta_report`](/guide/how-to/ask-biobox-with-claude/tools/get-delta-report.md) — the per-target diff (biggest movers) within a comparison
* [`get_delta_report_target`](/guide/how-to/ask-biobox-with-claude/tools/get-delta-report-target.md) — how one target changed between the compared runs

**Reasoning models**

* [`list_reasoning_models`](/guide/how-to/ask-biobox-with-claude/tools/list-reasoning-models.md) — the reasoning models in your organization, across both topologies
* [`get_reasoning_model`](/guide/how-to/ask-biobox-with-claude/tools/get-reasoning-model.md) — the configuration of one reasoning model, whichever topology it is
* [`search_models`](/guide/how-to/ask-biobox-with-claude/tools/search-models.md) — find a reasoning model by name

**Dashboards**

* [`list_dashboards`](/guide/how-to/ask-biobox-with-claude/tools/list-dashboards.md) — the dashboards in your organization
* [`list_object_dashboards`](/guide/how-to/ask-biobox-with-claude/tools/list-object-dashboards.md) — the dashboards pinned to a specific entity
* [`get_dashboard`](/guide/how-to/ask-biobox-with-claude/tools/get-dashboard.md) — the widgets on one dashboard
* [`get_widget_data`](/guide/how-to/ask-biobox-with-claude/tools/get-widget-data.md) — run one dashboard widget's saved query and return its data

**Query building & guidance**

* [`run_bxql`](/guide/how-to/ask-biobox-with-claude/tools/run-bxql.md) — run a read-only BxQL pattern query directly
* [`validate_bxql`](/guide/how-to/ask-biobox-with-claude/tools/validate-bxql.md) — check a BxQL query parses before relying on it
* [`ground_query`](/guide/how-to/ask-biobox-with-claude/tools/ground-query.md) — resolve a fuzzy mention to a real, data-backed value for a query
* [`get_ql_instructions`](/guide/how-to/ask-biobox-with-claude/tools/get-ql-instructions.md) — your organization's query-building instructions
* [`find_guidance`](/guide/how-to/ask-biobox-with-claude/tools/find-guidance.md) — find guidance playbooks for a question's intent
* [`get_concept_guidance`](/guide/how-to/ask-biobox-with-claude/tools/get-concept-guidance.md) — the guidance playbooks attached to a concept
* [`list_query_templates`](/guide/how-to/ask-biobox-with-claude/tools/list-query-templates.md) — the reusable query templates your organization has
* [`get_query_template`](/guide/how-to/ask-biobox-with-claude/tools/get-query-template.md) — one reusable query template by id
* [`list_evidence_catalog`](/guide/how-to/ask-biobox-with-claude/tools/list-evidence-catalog.md) — your organization's catalog of canonical evidence lines

Browse any page for the details.