OHDSI ATLAS

Ask an agent to

• Build a cohort of new metformin users with type 2 diabetes
• Restrict my cohort to patients aged 18 to 65
• Add an exit criterion when the drug is stopped for 30 days

28 tools

• add_criteria

  Propose adding multiple criteria to the cohort with AND/OR logic. ALWAYS provide a `name` describing the rule (e.g. "On metformin or sulfonylurea", "Excludes pregnancy"); never omit it. Prefer add_inclusion_rule when…

  name: string, group: string, logic: string, items: array

• add_criterion

  Propose adding one criterion to the cohort. The user sees a confirmation card and accepts or rejects.

  conceptId: number, conceptName: string, domain: string, group: string, includeDescendants: boolean, operator: string?, value: number?, value2: number?, … (list cut; the site may define more)

• add_demographic_criterion

  Restrict the cohort by age or sex — the criteria that have no concept set. Use for "adults", "age 18 and over", "women aged 40 to 70": pass minAge / maxAge in years and/or sex. Without this a cohort NAMED for adults…

  minAge: number?, maxAge: number?, sex: string?, name: string?

• add_exit_criterion

  Define how a patient exits the cohort. Strategy: end_of_observation = end of continuous observation period; fixed_duration = N days after entry; continuous_drug = persistence-window-driven exit.

  strategy: string, offset: number?, dateField: string?, persistenceWindow: number?, surveillanceWindow: number?, concept: object?

• add_inclusion_rule

  Add an inclusion rule: a named group of criteria with AND/OR logic and optional cardinality (AT_LEAST/AT_MOST count) or temporal window. Prefer this over add_criteria when the model needs cardinality or temporal…

  name: string, description: string?, logicType: string, count: number?, temporalWindow: object?, events: array

• add_qualifying_criterion

  Restrict the ENTRY EVENT itself rather than the person — the editor's "Restrict initial events". Use when the qualifying event must coincide with something, e.g. an inpatient visit, a diagnosis recorded on the same…

  conceptId: number, conceptName: string, domain: string, includeDescendants: boolean?, isExcluded: boolean?

• create_characterization

  Persist a NEW cohort characterization on the server. REQUIRES at least one cohort and at least one feature analysis attached. Before calling this you MUST have called search_existing_cohorts and…

  name: string, description: string?, cohorts: array, featureAnalyses: array

• create_feature_analysis

  Persist a NEW feature analysis (covariate definition) on the server. The user sees an approval card; on accept, ATLAS navigates to the editor. `type` controls the design shape: PRESET (built-in OHDSI preset id as a…

  name: string, description: string?, type: string, domain: string?, statType: string?, design?

• create_incidence_rate

  Persist a NEW incidence-rate analysis on the server. Only `name` is required; the time-at-risk window defaults to {start: StartDate +0, end: EndDate +0} which means 'from cohort start to cohort end'. Provide a custom…

  name: string, description: string?, targetIds: array?, outcomeIds: array?, timeAtRisk: object?, studyWindow: object?

• create_pathway

  Persist a NEW pathway analysis on the server. Only `name` is required; sensible OHDSI defaults are applied for the rest (combinationWindow=30, minCellCount=5, maxDepth=5, allowRepeats=false). Pass target/event cohort…

  name: string, description: string?, targetCohorts: array?, eventCohorts: array?, combinationWindow: number?, minCellCount: number?, maxDepth: number?, allowRepeats: boolean?, … (list cut; the site may define more)

• create_standalone_concept_set

  Create a NEW reusable concept set on the server via WebAPI, saved globally and usable across cohorts. This is NOT the default: criteria capabilities (set_entry_event, add_criterion, add_criteria, add_inclusion_rule)…

  name: string, description: string?, items: array

• generate_analysis

  Run a SAVED analysis against a data source, the same as clicking Generate in the editor. Use after the analysis exists (create_pathway / create_characterization / create_incidence_rate returned an id). Results appear…

  analysisType: string, analysisId: number, sourceKey: string?

• navigate_to

  Suggest moving the user to a different view in ATLAS. The user sees a 5s undo toast after the navigation is applied (no approval card). Always include a one-sentence `reason` so the toast is self-explanatory. Each…

  view: string, id: number?, sourceKey: string?, conceptId: number?, personId: number?, executionId: number?, reason: string?

• remove_entry_event

  Remove one entry event from the cohort being edited, identified by the concept it was built from. Use when the cohort qualifies on several entry events and the user wants one dropped. To replace the entry event…

  conceptId: number?, conceptName: string?

• remove_inclusion_rule

  Remove an inclusion rule from the cohort being edited, by its name (as shown in the editor) or its id. Use this when the user asks to drop, delete or undo a rule you added — do not rebuild the cohort to get rid of one…

  name: string?, id: string?

• save_cohort

  Persist the CURRENTLY OPEN cohort to the WebAPI so it gets a stable id. Call this AFTER the user has accepted the cohort's entry event + criteria, and BEFORE creating any analysis (incidence rate / pathway /…

  name: string?, description: string?

• set_censor_event

  Add a censoring criterion that ends a patient's time-at-risk when the event occurs.

  conceptId: number, conceptName: string, domain: string, includeDescendants: boolean?, isExcluded: boolean?

• set_censor_window

  Bound the study period with fixed dates (YYYY-MM-DD): nobody is followed before startDate or after endDate, whatever their observation. Use when the user names a study window ('2015 to 2019') — without it the cohort…

  startDate: string?, endDate: string?

• set_entry_event

  Set the cohort's primary qualifying entry event. Replaces any existing entry event.

  conceptId: number, conceptName: string, domain: string, includeDescendants: boolean?, isExcluded: boolean?

• set_era_collapse

  Gap in days below which two stretches of cohort membership are merged into one era (the editor's era collapse). Default 0 — a person who leaves and re-enters counts as two episodes. Raise it when brief gaps should not…

  gapDays: number

• set_event_limits

  Choose which qualifying events count, per person. 'first' is the new-user / first-diagnosis design — one row per person at their earliest qualifying event; 'all' (the default) puts a person in the cohort once per…

  entryEvents: string?, qualifyingEvents: string?, inclusionRuleEvents: string?

• set_observation_window

  Set the prior + post observation window (in days) around the entry event. priorDays = days of continuous observation required BEFORE entry; postDays = days of continuous observation required AFTER entry.

  priorDays: number, postDays: number

• update_characterization

  Apply a partial edit to an existing characterization: rename, change description, replace or extend cohorts/featureAnalyses. Each cohort and feature-analysis ref is {id, name} from search_existing_* results.

  id: number, name: string?, description: string?, cohorts: array?, cohortsToAdd: array?, featureAnalyses: array?, featureAnalysesToAdd: array?

• update_concept_set

  Apply a partial edit to an existing standalone concept set: rename, change description, append items, or replace items. Mutates the open editor; user clicks Save to persist. Use itemsToAdd to append (skips duplicate…

  id: number, name: string?, description: string?, items: array?, itemsToAdd: array?

• update_feature_analysis

  Apply a partial edit to an existing feature analysis: rename, change description, change type/domain/statType, or replace the design payload. Mutates the open editor; user clicks Save to persist.

  id: number, name: string?, description: string?, type: string?, domain: string?, statType: string?, design?

• update_incidence_rate

  Apply a partial edit to an existing incidence-rate analysis: rename, change description, replace or extend target/outcome cohort ids, tweak timeAtRisk or studyWindow.

  id: number, name: string?, description: string?, targetIds: array?, targetIdsToAdd: array?, outcomeIds: array?, outcomeIdsToAdd: array?, timeAtRisk: object?, … (list cut; the site may define more)

• update_pathway

  Apply a partial edit to an existing pathway analysis: rename, change description, replace or extend target/event cohorts, tweak combinationWindow / minCellCount / maxDepth / allowRepeats.

  id: number, name: string?, description: string?, targetCohorts: array?, targetCohortsToAdd: array?, eventCohorts: array?, eventCohortsToAdd: array?, combinationWindow: number?, … (list cut; the site may define more)

• use_concept_set

  Use an EXISTING saved concept set in the cohort being built, by its id from search_existing_concept_sets. Prefer this over rebuilding the same set concept by concept: it reuses the definition the user already curated…

  conceptSetId: number, group: string?, name: string?