# Atlas documentation - [Start with Atlas Lyme](https://onehealthatlas.org/docs): Understand Atlas Lyme, an Epidemiologist Decision Intelligence Platform for evidence-backed tick-borne disease investigation. - [What is Atlas Lyme?](https://onehealthatlas.org/docs/what-is-atlas): Learn what Atlas Lyme is, what it helps epidemiologists investigate, and where its evidence boundaries apply. - [Who is Atlas for?](https://onehealthatlas.org/docs/who-is-atlas-for): See which public-health users Atlas Lyme is designed to support and the questions it can help them investigate. - [The Atlas decision-support workflow](https://onehealthatlas.org/docs/atlas-workflow): Follow Atlas Lyme from fragmented One Health evidence to a focused epidemiological investigation question. - [Professional workspace](https://onehealthatlas.org/docs/professional-workspace): Use the signed-in workspace for Atlas Explorer, Compare, Ask Atlas, Feed, Data Provenance, Settings, and Docs. - [Current capabilities](https://onehealthatlas.org/docs/current-capabilities): See what Atlas Lyme supports in the current public release and how each capability contributes to evidence-aware investigation. - [Investigation workflows](https://onehealthatlas.org/docs/investigation-workflows): Use Atlas Lyme to move from a surveillance question to a bounded, evidence-backed investigation next step. - [Evidence, provenance, and uncertainty](https://onehealthatlas.org/docs/evidence-and-uncertainty): Learn how to read Atlas Lyme signals, distinguish missing evidence from low observed signal, and decide what remains unknown. - [Sources and canonical evidence](https://onehealthatlas.org/docs/sources-and-canonical-evidence): How Atlas is designed to adapt governed sources into one canonical evidence model for the Web product, REST API, and MCP, and which of that design is released. - [Releases and methodology labels](https://onehealthatlas.org/docs/releases-and-methodology): Plain-language definitions for Atlas release snapshots, source periods, processing times, and scoring methodology versions. - [AI-enabled decision intelligence](https://onehealthatlas.org/docs/ai-enabled-decision-intelligence): Understand what AI means in Atlas Lyme, what is available now, and which future capabilities still require release and human review. - [API, MCP, and access](https://onehealthatlas.org/docs/api-mcp-and-access): Use the public Atlas REST API, and see the current status of MCP and API keys. - API reference - [API reference](https://onehealthatlas.org/docs/api-reference): Generated from the pinned public Atlas OpenAPI contract, with spec version, source, and the raw schema. - **Canonical Evidence** - Discovery - [Discovery](https://onehealthatlas.org/docs/api-reference/discovery): Current-release indicators and measurable variables. - [Discover indicators](https://onehealthatlas.org/docs/api-reference/discovery/indicators_v1_indicators_get): Current-release discovery with optional documented filters. page_size defaults to 100 (maximum 500); reuse opaque page_token with the same filters and release. A null next_page_token ends traversal. Cache-Control: public, max-age=60, must-revalidate. - [Get an indicator](https://onehealthatlas.org/docs/api-reference/discovery/indicator_v1_indicators__indicator_id__get): Resolve the exact governed public resource ID in the current release. Unknown IDs return 404 RESOURCE_NOT_FOUND. Preserve versions and limitations; null metadata is not inferred. Cache-Control: public, max-age=60, must-revalidate; ETag with matching If-None-Match returns an empty 304. - [Discover measures](https://onehealthatlas.org/docs/api-reference/discovery/measures_v1_measures_get): Current-release discovery with optional documented filters. page_size defaults to 100 (maximum 500); reuse opaque page_token with the same filters and release. A null next_page_token ends traversal. Cache-Control: public, max-age=60, must-revalidate. - [Get a measure](https://onehealthatlas.org/docs/api-reference/discovery/measure_v1_measures__measure_id__get): Resolve the exact governed public resource ID in the current release. Unknown IDs return 404 RESOURCE_NOT_FOUND. Preserve versions and limitations; null metadata is not inferred. Cache-Control: public, max-age=60, must-revalidate; ETag with matching If-None-Match returns an empty 304. - Observations - [Observations](https://onehealthatlas.org/docs/api-reference/observations): Bounded county observations with explicit value states. - [Query county observations](https://onehealthatlas.org/docs/api-reference/observations/observations_v1_observations_get): Current published county observations only. Ordered by measure ID, county FIPS, period start, and observation ID. Opaque page tokens bind to filters and release. Annual surveillance uses 2023. Separately enabled, reviewed January 2025 environmental measures use labeled daily periods, carry environmental_context coverage, and have no supported strata. Environmental context is descriptive weather, with no causal, disease-risk or ML claim. Surveillance context is optional and requires an admitted Data delivery; normalized_state preserves Data semantics and the publisher value remains value. Separately enabled CDC status uses start_date=end_date=2025-12-31 and CUMULATIVE grain; scapularis_status and burgdorferi_status require exact Data record admission. Annual year and other date ranges return 400 UNSUPPORTED_FILTER before data access. Missing context does not establish absence or temporal comparability. County SVI/population/insurance context requires vintage_year=2022 and retains ACS 2018-2022 periods. RUCC requires vintage_year=2023 and returns categorical codes/labels with null period dates. These measures reject annual/day filters; absent rows are unavailable evidence, never zero. A measure and bounded county/time selection are required; no user sorting or aggregation. After successful release/measure/query reads, an initially empty non-CDC selection returns 200 with meta.availability=UNAVAILABLE and reason=NO_PUBLISHED_RESULTS. This does not establish source coverage or biological absence. Exhausted continuation pages remain AVAILABLE. CDC admission and operational errors remain non-2xx. Known unavailable collections use Cache-Control: no-store. - Provenance - [Provenance](https://onehealthatlas.org/docs/api-reference/provenance): Governed source and methodology identities and versions. - [Get a methodology](https://onehealthatlas.org/docs/api-reference/provenance/methodology_v1_methodologies__methodology_id__get): Resolve the exact governed public resource ID in the current release. Unknown IDs return 404 RESOURCE_NOT_FOUND. Preserve versions and limitations; null metadata is not inferred. Cache-Control: public, max-age=60, must-revalidate; ETag with matching If-None-Match returns an empty 304. - [Discover sources](https://onehealthatlas.org/docs/api-reference/provenance/sources_v1_sources_get): Current-release discovery with optional documented filters. page_size defaults to 100 (maximum 500); reuse opaque page_token with the same filters and release. A null next_page_token ends traversal. Cache-Control: public, max-age=60, must-revalidate. - [Get a source](https://onehealthatlas.org/docs/api-reference/provenance/source_v1_sources__source_id__get): Resolve the exact governed public resource ID in the current release. Unknown IDs return 404 RESOURCE_NOT_FOUND. Preserve versions and limitations; null metadata is not inferred. Cache-Control: public, max-age=60, must-revalidate; ETag with matching If-None-Match returns an empty 304. - Geographies - [Geographies](https://onehealthatlas.org/docs/api-reference/geographies): Typed geography identity; delivery is not yet available. - [Get geography identity (delivery pending)](https://onehealthatlas.org/docs/api-reference/geographies/geography_v1_geographies__geography_type___geography_id__get): Validated county/state FIPS identity; currently returns 503 CANONICAL_DATA_UNAVAILABLE. No geometry is returned. - [Check canonical county geography publication availability](https://onehealthatlas.org/docs/api-reference/geographies/canonicalGeographyAvailability): Additive county-only operation. Confirms membership and release from the governed county directory before returning UNAVAILABLE/CANONICAL_GEOGRAPHY_UNPUBLISHED with null data. The canonical resource is identity metadata, not a polygon. No geometry is returned or inferred. State availability is unsupported (400). Malformed county IDs return 400; confirmed absent identities return 404. Unavailable, empty, duplicate or inconsistent directory authority remains 503. The directory uses the existing bounded snapshot cache, checked against a fresh current-release lookup; a mismatch remains 503. Responses use Cache-Control: no-store. The existing canonical resource route and county/map routes are unchanged. - **Atlas Analytics/Reports** - Atlas - [Atlas](https://onehealthatlas.org/docs/api-reference/atlas): Existing release analytics and separate display geometry. - [Get county display geometry](https://onehealthatlas.org/docs/api-reference/atlas/geometry_v1_atlas_geometry_get): Existing generalized CDC/ATSDR SVI 2022 display geometry in EPSG:4326, identified by stable five-digit county FIPS. This resource never returns internal 2025 TIGER/Line analysis polygons used for raster aggregation. - [Get Atlas release metadata](https://onehealthatlas.org/docs/api-reference/atlas/metadata_v1_atlas_metadata_get): Release metadata, source freshness and methodology; dataset_version selects an existing release. Cached publicly for 300 seconds with ETag. ETag is informational here; this route does not implement conditional 304. - [Download filtered county rankings](https://onehealthatlas.org/docs/api-reference/atlas/ranking_csv_v1_atlas_ranking_csv_get): Filtered CSV attachment for current county rankings. Existing state, text and evidence filters and score settings apply; no pagination. This route does not declare a public cache TTL. - [Get county gap scores](https://onehealthatlas.org/docs/api-reference/atlas/scores_v1_atlas_scores_get): Existing surveillance-gap scores and settings for an optional dataset_version. Scores are not individual risk estimates or diagnoses. Public cache TTL 300 seconds with informational ETag; no conditional 304. - Counties - [Counties](https://onehealthatlas.org/docs/api-reference/counties): Existing county details and versioned PDF reports. - [Get county analytics and provenance](https://onehealthatlas.org/docs/api-reference/counties/county_v1_counties__fips__get): Five-digit county FIPS with leading zeros retained. Includes release/source metadata and limitations. Optional dataset_version and score settings retain existing meanings. Public cache TTL 300 seconds with informational ETag; no conditional 304. - [Download a county report](https://onehealthatlas.org/docs/api-reference/counties/county_report_pdf_v1_counties__fips__report_pdf_get): PDF attachment using the immutable county-v1 registered template by default. Optional dataset_version and score settings bind report inputs. Opt-in county-v2 requires dataset_version, period_start, period_end and repeated measure_id (1–20, repeated or comma-separated); reads canonical evidence, lineage, value states and limitations. Missing or mismatched provenance returns 503; unknown observations return 404. V1 rejects observation selectors with 422. V2 responses use no-store and revalidate authoritative context before cache/304. ETag/If-None-Match supports 304; V1 public cache TTL 300 seconds with revalidation. Unknown templates return 422; resource limits 413; renderer failure/timeout 503. - [Get persisted Tier 1 model-assisted surveillance review priority](https://onehealthatlas.org/docs/api-reference/counties/county_tier1_surveillance_priority_get): Returns the approved persisted county result from the current Tier 1 batch. This is surveillance review priority, not Lyme disease risk, predicted incidence, probability, clinical risk, or diagnosis. LOW is a scored tier; evidence sufficiency is separate. Percentile is relative to the scored batch and population. A county without a persisted result returns 404; an unavailable current view or malformed result returns 503. Public cache TTL 60 seconds; generated_at_utc is the model batch time, not request time. - [Get Tier 1 result availability and persisted data](https://onehealthatlas.org/docs/api-reference/counties/county_tier1_surveillance_priority_availability_get): Additive availability contract for current supported county geographies. A successful lookup returns AVAILABLE with the exact persisted result, or UNAVAILABLE with reason NO_PUBLISHED_MODEL and null data after the current geography release and Tier 1 projection have both been read successfully. geography_release_id identifies the release used to validate the FIPS. This endpoint does not turn null into zero or synthesize model output. NOT_ESTIMABLE is a persisted result state and is distinct from no published model result. Malformed FIPS returns 422; an identity outside the current geography release returns typed 404; dependency or malformed-data failures return 503. Public cache TTL 60 seconds. - States - [States](https://onehealthatlas.org/docs/api-reference/states): Existing state PDF reports. - [Download a state report](https://onehealthatlas.org/docs/api-reference/states/state_report_pdf_v1_states__state__report_pdf_get): PDF attachment using the immutable state-v1 registered template by default. State is a two-letter code. Optional dataset_version and score settings bind report inputs. ETag/If-None-Match supports 304; public cache TTL 300 seconds with revalidation. Unknown templates return 422; resource limits 413; renderer failure/timeout 503. - [Review a state's county evidence](https://onehealthatlas.org/docs/api-reference/states/state_review_v1_states__state__review_get): Versioned county Review result. Current rules are disabled. Lineage gaps are separate. Public cache TTL is 60 seconds. - [Schemas](https://onehealthatlas.org/docs/api-reference/schemas): Component schema names and descriptions from the pinned public Atlas OpenAPI contract. - [FAQ and troubleshooting](https://onehealthatlas.org/docs/faq-and-troubleshooting): Get practical answers about Atlas Lyme interpretation, loading, filters, data availability, and the public HelpDocs experience. - Developers - [Developer overview](https://onehealthatlas.org/docs/develop): Start here for anonymous Atlas REST reads, the guide map, and the limits of the public contract. - [Quickstart](https://onehealthatlas.org/docs/develop/quickstart): Make one anonymous current-release observation request and read every response state that request can return. - [REST API](https://onehealthatlas.org/docs/develop/rest): Call the anonymous Atlas HTTP contract, page collections, and handle the declared errors, cache headers, and version fields. - [Geography](https://onehealthatlas.org/docs/develop/geography): Identify Atlas counties by FIPS, stay within the lower 48 and DC, and request display polygons while identity delivery is pending. - [Indicators, measures, and observations](https://onehealthatlas.org/docs/develop/resources): Discover current-release indicators and measures, then query county observations with explicit value states. - [Provenance and evidence](https://onehealthatlas.org/docs/develop/provenance): Read source, methodology, release, freshness, and value-state fields together before citing an Atlas observation. - [Workflow guides](https://onehealthatlas.org/docs/develop/workflows): Query one county, compare counties, read environmental context, choose a county PDF template, and cite the observation you actually received. - [Observation queries](https://onehealthatlas.org/docs/develop/observation-queries): Checked observation slices, including annual land cover, and the temporal parameters each slice accepts or rejects. - [Tier 1 availability](https://onehealthatlas.org/docs/develop/tier1-availability): Choose the Tier 1 availability read or the persisted priority read, and keep sufficient, insufficient, abstention, no published model, and an unknown FIPS apart. - [MCP clients](https://onehealthatlas.org/docs/develop/mcp-clients): Connect Claude Desktop, Cursor, or a custom client to production Atlas MCP, and copy the interpretation guardrails agents must keep. - [OpenAPI, GitHub, and support](https://onehealthatlas.org/docs/develop/support): Open the public Atlas contract, the GitHub repositories that own it, and the fields to include when you ask for help. ## Exports - [llms.txt](https://onehealthatlas.org/llms.txt): This index of the current documentation pages. - [llms-full.txt](https://onehealthatlas.org/llms-full.txt): Every current documentation page in one Markdown file, generated from the docs source for this deployment. - Append `.md` to a page URL for that page's processed Markdown. - Append `.mdx` to a page URL for that page's current MDX source.