Uscdi flat specs

SUMMARY.md

@@ -68,9 +68,11 @@
     * [Care Team Members](data-integration/uscdi/care-team.md)
     * [Allergies and Intolerances](data-integration/uscdi/allergies.md)
     * [Problems](data-integration/uscdi/conditions.md)
+    * [Medications](data-integration/uscdi/medications.md)
+    * [Laboratory](data-integration/uscdi/labs.md)
     * [Immunizations](data-integration/uscdi/immunizations.md)
     * [Goals](data-integration/uscdi/goals.md)
-    * [Unique Device Identifiers](data-integration/uscdi/devices.md)
+    * [Device](data-integration/uscdi/devices.md)
     * [Encounter Information](data-integration/uscdi/encounters.md)
     * [Procedures](data-integration/uscdi/procedures.md)
     * [Assessment and Plan of Treatment](data-integration/uscdi/care-plans.md)

docs/data-integration/README.md

@@ -20,7 +20,7 @@ graph LR
 
 | Rule | Detail |
 |---|---|
-| Format | Agreed per engagement. If you deliver CSV: UTF-8, comma-delimited, RFC 4180 quoting, first row is the headers, named exactly as in the tables. |
+| Format | Agreed per engagement. If you deliver CSV: UTF-8, comma-delimited, first row is the headers, named exactly as in the tables. |
 | Delivery | Arranged per engagement. PHI: encrypted in transit and at rest under the executed BAA. |
 | History (USCDI feed) | Date of service on or after January 1, 2016. Send active and historical records; the status columns mark which is which. |
 | Code systems | Every coded column has a companion `_system` column holding the code system URI: `substance_code` with `substance_system`, `vaccine_code` with `vaccine_system`, and so on. Leave it blank to accept the default named in that column's row. |

docs/data-integration/uscdi/README.md

@@ -8,27 +8,27 @@ description: >-
 
 | # | Dataset | USCDI v3.1 data class | US Core 6.1.0 target profile(s) |
 |---|---|---|---|
-| 1 | [`patients`](patient-demographics.md#patients) | [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3) | [US Core Patient](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-patient.html) (+ race, ethnicity, sex, tribal extensions) |
-| 2 | [`related_persons`](patient-demographics.md#related-persons) | [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3) | [US Core RelatedPerson](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-relatedperson.html) |
-| 3 | [`practitioners`](care-team.md#practitioners) | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3) (ref), may come from [Provider Directory](../provider-directory/README.md#providers) | [US Core Practitioner](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-practitioner.html), [US Core PractitionerRole](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-practitionerrole.html) |
-| 4 | `organizations` | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3) (ref), may come from [Provider Directory](../provider-directory/README.md#facilities) | [US Core Organization](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-organization.html) |
-| 5 | [`locations`](encounters.md#locations) | [Encounter Information](https://isp.healthit.gov/taxonomy/term/2986#uscdi-v3) (ref), may come from [Provider Directory](../provider-directory/README.md#facilities) | [US Core Location](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-location.html) |
-| 6 | [`allergies`](allergies.md#allergies) | [Allergies and Intolerances](https://isp.healthit.gov/taxonomy/term/2941#uscdi-v3) | [US Core AllergyIntolerance](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-allergyintolerance.html) |
-| 7 | [`conditions`](conditions.md#conditions) | [Problems](https://isp.healthit.gov/taxonomy/term/3066#uscdi-v3) | [US Core Condition Problems and Health Concerns](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-condition-problems-health-concerns.html), [US Core Condition Encounter Diagnosis](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-condition-encounter-diagnosis.html) |
-| 8 | `medications` | [Medications](https://isp.healthit.gov/taxonomy/term/3036#uscdi-v3) | [US Core MedicationRequest](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medicationrequest.html), [US Core Medication](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medication.html) |
-| 9 | `medication_dispenses` | [Medications](https://isp.healthit.gov/taxonomy/term/3036#uscdi-v3) (Fill Status) | [US Core MedicationDispense](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medicationdispense.html) |
-| 10 | [`immunizations`](immunizations.md#immunizations) | [Immunizations](https://isp.healthit.gov/taxonomy/term/3021#uscdi-v3) | [US Core Immunization](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-immunization.html) |
-| 11 | [`procedures`](procedures.md#procedures) | [Procedures](https://isp.healthit.gov/taxonomy/term/3071#uscdi-v3) | [US Core Procedure](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-procedure.html) |
-| 12 | [`service_requests`](procedures.md#service-requests) | [Procedures](https://isp.healthit.gov/taxonomy/term/3071#uscdi-v3) (Referral, SDOH Interventions) | [US Core ServiceRequest](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-servicerequest.html) |
-| 13 | [`encounters`](encounters.md#encounters) | [Encounter Information](https://isp.healthit.gov/taxonomy/term/2986#uscdi-v3) | [US Core Encounter](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-encounter.html) |
-| 14 | [`care_team`](care-team.md#care-team) | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3) | [US Core CareTeam](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-careteam.html) |
-| 15 | [`care_plans`](care-plans.md#care-plans) | [Assessment and Plan of Treatment](https://isp.healthit.gov/taxonomy/term/2946#uscdi-v3) | [US Core CarePlan](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-careplan.html) |
-| 16 | [`goals`](goals.md#goals) | [Goals](https://isp.healthit.gov/taxonomy/term/3006#uscdi-v3) | [US Core Goal](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-goal.html) |
-| 17 | [`coverage`](health-insurance.md#coverage) | [Health Insurance Information](https://isp.healthit.gov/taxonomy/term/3016#uscdi-v3) | [US Core Coverage](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-coverage.html) |
-| 18 | [`documents`](clinical-notes.md#documents) | [Clinical Notes](https://isp.healthit.gov/taxonomy/term/2961#uscdi-v3) | [US Core DocumentReference](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-documentreference.html) |
-| 19 | [`diagnostic_reports`](clinical-notes.md#diagnostic-reports) | [Clinical Notes](https://isp.healthit.gov/taxonomy/term/2961#uscdi-v3), [Laboratory](https://isp.healthit.gov/taxonomy/term/3026#uscdi-v3), [Diagnostic Imaging](https://isp.healthit.gov/taxonomy/term/2971#uscdi-v3) | [US Core DiagnosticReport Lab](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-diagnosticreport-lab.html), [US Core DiagnosticReport Note](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-diagnosticreport-note.html) |
-| 20 | [`devices`](devices.md#devices) | [Unique Device Identifier(s)](https://isp.healthit.gov/taxonomy/term/3126#uscdi-v3) | [US Core Implantable Device](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-implantable-device.html) |
-| 21 | [`vital_signs`](vital-signs.md#vital-signs) | [Vital Signs](https://isp.healthit.gov/taxonomy/term/3131#uscdi-v3) | [US Core Vital Signs](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-vital-signs.html) |
-| 22 | `labs` | [Laboratory](https://isp.healthit.gov/taxonomy/term/3026#uscdi-v3) | [US Core Laboratory Result Observation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-lab.html), [US Core Specimen](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-specimen.html) |
-| 23 | [`social_history`](patient-demographics.md#social-history) | [Health Status Assessments](https://isp.healthit.gov/taxonomy/term/4401#uscdi-v3), [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3) (Occupation) | [US Core Smoking Status](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-smokingstatus.html), [US Core Observation Occupation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-occupation.html), [US Core Observation Pregnancy Status](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-pregnancystatus.html), [US Core Observation Pregnancy Intent](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-pregnancyintent.html) |
-| 24 | [`clinical_observations`](clinical-tests.md#clinical-observations) | [Clinical Tests](https://isp.healthit.gov/taxonomy/term/2976#uscdi-v3), [Diagnostic Imaging](https://isp.healthit.gov/taxonomy/term/2971#uscdi-v3), [Health Status Assessments](https://isp.healthit.gov/taxonomy/term/4401#uscdi-v3) | [US Core Observation Clinical Result](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-clinical-result.html), [US Core Observation Screening Assessment](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-screening-assessment.html), [US Core Simple Observation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-simple-observation.html) |
+| 1 | [`patients`](patient-demographics.md#patients) | [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3-1) | [US Core Patient](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-patient.html) (+ race, ethnicity, sex, tribal extensions) |
+| 2 | [`related_persons`](patient-demographics.md#related-persons) | [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3-1) | [US Core RelatedPerson](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-relatedperson.html) |
+| 3 | [`practitioners`](care-team.md#practitioners) | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3-1) (ref), may come from [Provider Directory](../provider-directory/README.md#providers) | [US Core Practitioner](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-practitioner.html), [US Core PractitionerRole](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-practitionerrole.html) |
+| 4 | [`organizations`](care-team.md#organizations) | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3-1) (ref), may come from [Provider Directory](../provider-directory/README.md#facilities) | [US Core Organization](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-organization.html) |
+| 5 | [`locations`](encounters.md#locations) | [Encounter Information](https://isp.healthit.gov/taxonomy/term/2986#uscdi-v3-1) (ref), may come from [Provider Directory](../provider-directory/README.md#facilities) | [US Core Location](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-location.html) |
+| 6 | [`allergies`](allergies.md#allergies) | [Allergies and Intolerances](https://isp.healthit.gov/taxonomy/term/2941#uscdi-v3-1) | [US Core AllergyIntolerance](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-allergyintolerance.html) |
+| 7 | [`conditions`](conditions.md#conditions) | [Problems](https://isp.healthit.gov/taxonomy/term/3066#uscdi-v3-1) | [US Core Condition Problems and Health Concerns](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-condition-problems-health-concerns.html), [US Core Condition Encounter Diagnosis](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-condition-encounter-diagnosis.html) |
+| 8 | [`medications`](medications.md#medications) | [Medications](https://isp.healthit.gov/taxonomy/term/3036#uscdi-v3-1) | [US Core MedicationRequest](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medicationrequest.html), [US Core Medication](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medication.html) |
+| 9 | [`medication_dispenses`](medications.md#medication-dispenses) | [Medications](https://isp.healthit.gov/taxonomy/term/3036#uscdi-v3-1) (Fill Status) | [US Core MedicationDispense](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-medicationdispense.html) |
+| 10 | [`immunizations`](immunizations.md#immunizations) | [Immunizations](https://isp.healthit.gov/taxonomy/term/3021#uscdi-v3-1) | [US Core Immunization](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-immunization.html) |
+| 11 | [`procedures`](procedures.md#procedures) | [Procedures](https://isp.healthit.gov/taxonomy/term/3071#uscdi-v3-1) | [US Core Procedure](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-procedure.html) |
+| 12 | [`service_requests`](procedures.md#service-requests) | [Procedures](https://isp.healthit.gov/taxonomy/term/3071#uscdi-v3-1) (Referral, SDOH Interventions) | [US Core ServiceRequest](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-servicerequest.html) |
+| 13 | [`encounters`](encounters.md#encounters) | [Encounter Information](https://isp.healthit.gov/taxonomy/term/2986#uscdi-v3-1) | [US Core Encounter](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-encounter.html) |
+| 14 | [`care_team`](care-team.md#care-team) | [Care Team Members](https://isp.healthit.gov/taxonomy/term/2956#uscdi-v3-1) | [US Core CareTeam](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-careteam.html) |
+| 15 | [`care_plans`](care-plans.md#care-plans) | [Assessment and Plan of Treatment](https://isp.healthit.gov/taxonomy/term/2946#uscdi-v3-1) | [US Core CarePlan](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-careplan.html) |
+| 16 | [`goals`](goals.md#goals) | [Goals](https://isp.healthit.gov/taxonomy/term/3006#uscdi-v3-1) | [US Core Goal](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-goal.html) |
+| 17 | [`coverage`](health-insurance.md#coverage) | [Health Insurance Information](https://isp.healthit.gov/taxonomy/term/3016#uscdi-v3-1) | [US Core Coverage](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-coverage.html) |
+| 18 | [`documents`](clinical-notes.md#documents) | [Clinical Notes](https://isp.healthit.gov/taxonomy/term/2961#uscdi-v3-1) | [US Core DocumentReference](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-documentreference.html) |
+| 19 | [`diagnostic_reports`](clinical-notes.md#diagnostic-reports) | [Clinical Notes](https://isp.healthit.gov/taxonomy/term/2961#uscdi-v3-1), [Laboratory](https://isp.healthit.gov/taxonomy/term/3026#uscdi-v3-1), [Diagnostic Imaging](https://isp.healthit.gov/taxonomy/term/2971#uscdi-v3-1) | [US Core DiagnosticReport Lab](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-diagnosticreport-lab.html), [US Core DiagnosticReport Note](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-diagnosticreport-note.html) |
+| 20 | [`devices`](devices.md#devices) | [Unique Device Identifier(s)](https://isp.healthit.gov/taxonomy/term/3126#uscdi-v3-1) | [US Core Implantable Device](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-implantable-device.html) |
+| 21 | [`vital_signs`](vital-signs.md#vital-signs) | [Vital Signs](https://isp.healthit.gov/taxonomy/term/3131#uscdi-v3-1) | [US Core Vital Signs](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-vital-signs.html) |
+| 22 | [`labs`](labs.md#labs) | [Laboratory](https://isp.healthit.gov/taxonomy/term/3026#uscdi-v3-1) | [US Core Laboratory Result Observation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-lab.html), [US Core Specimen](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-specimen.html) |
+| 23 | [`social_history`](patient-demographics.md#social-history) | [Health Status Assessments](https://isp.healthit.gov/taxonomy/term/4401#uscdi-v3-1), [Patient Demographics/Information](https://isp.healthit.gov/taxonomy/term/3061#uscdi-v3-1) (Occupation) | [US Core Smoking Status](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-smokingstatus.html), [US Core Observation Occupation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-occupation.html), [US Core Observation Pregnancy Status](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-pregnancystatus.html) |
+| 24 | [`clinical_observations`](clinical-tests.md#clinical-observations) | [Clinical Tests](https://isp.healthit.gov/taxonomy/term/2976#uscdi-v3-1), [Diagnostic Imaging](https://isp.healthit.gov/taxonomy/term/2971#uscdi-v3-1), [Health Status Assessments](https://isp.healthit.gov/taxonomy/term/4401#uscdi-v3-1) | [US Core Observation Clinical Result](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-clinical-result.html), [US Core Observation Screening Assessment](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-observation-screening-assessment.html), [US Core Simple Observation](https://hl7.org/fhir/us/core/STU6.1/StructureDefinition-us-core-simple-observation.html) |

docs/data-integration/uscdi/allergies.md

@@ -26,7 +26,7 @@ allergies.csv Data template with example rows
 |---|---|---|---|
 | `record_id` | Yes | your stable key for this allergy | `AL-0001` |
 | `patient_identifier` | Yes | patient key | `MRN-4471903` |
-| `substance_code` | Yes | RxNorm ingredient or SNOMED CT code, with `substance_system`; RxNorm if omitted [Common substances for allergy and intolerance documentation including refutations](https://healthsamurai.github.io/fhir-valueset-viewer/#url=http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1186.8) | `7980` penicillin G |
+| `substance_code` | Yes | RxNorm ingredient or SNOMED CT code, with `substance_system` (RxNorm assumed when empty) [Common substances for allergy and intolerance documentation including refutations](https://healthsamurai.github.io/fhir-valueset-viewer/#url=http%3A%2F%2Fcts.nlm.nih.gov%2Ffhir%2FValueSet%2F2.16.840.1.113762.1.4.1186.8) | `7980` penicillin G |
 | `clinical_status` | Yes, unless `verification_status` is `entered-in-error` | `active`, `inactive`, `resolved` [allergyintolerance-clinical](https://healthsamurai.github.io/fhir-valueset-viewer/#url=http://hl7.org/fhir/ValueSet/allergyintolerance-clinical%7C4.0.1) | `active` |
 | `verification_status` | Recommended | `unconfirmed`, `confirmed`, `refuted`, `entered-in-error` [allergyintolerance-verification](https://healthsamurai.github.io/fhir-valueset-viewer/#url=http://hl7.org/fhir/ValueSet/allergyintolerance-verification%7C4.0.1) | `confirmed` |
 | `category` | If available | `food`, `medication`, `environment`, `biologic` [allergy-intolerance-category](https://healthsamurai.github.io/fhir-valueset-viewer/#url=http://hl7.org/fhir/ValueSet/allergy-intolerance-category%7C4.0.1) | `medication` |
@@ -35,7 +35,6 @@ allergies.csv Data template with example rows
 | `onset_date` | If available | datetime | `2019-05-02` |
 | `is_deleted` | If retracting | `true` retracts this row | `true` |
 
-- `substance_code` is the one coded field with no fallback: a row without it cannot become an AllergyIntolerance. Send `substance_system` as `http://www.nlm.nih.gov/research/umls/rxnorm` or `http://snomed.info/sct`.
 - **For a medication, send the ingredient (`substance_code`).** Every RxNorm code the value set accepts is an ingredient, single or combination. A code for a specific product or pack, whether an NDC or an RxNorm drug-level code from a pharmacy claim, is not accepted, so roll it up to the ingredient first. For an allergy recorded against a whole drug class, send the SNOMED CT class code.
 - A row that carries a reaction needs at least one `reaction_manifestation_code`. Manifestation is mandatory inside a reaction.
 - `clinical_status` and `verification_status` are coupled: FHIR requires `clinical_status` on every row whose `verification_status` is not `entered-in-error`, and forbids it on rows that are. A row that leaves both empty is rejected. Sending `active` on live rows and `resolved` or `inactive` on closed ones satisfies this.