Difference between revisions of "VRDR Testing"

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** Do you mean patient.gender?
 
** Do you mean patient.gender?
 
** Do you want to specify a value for birthsex?
 
** Do you want to specify a value for birthsex?
 +
* Address.district and address.postalCode
 +
** FHIR IG calls out postal code as (MAY, 0..1) but does not mention district
 +
** Spreadsheet data does not provide postal code (OK)
 +
** MITRE synthetic data includes district (OK)
 +
** Those are both OK by spec but not quite in sync. This could be ignored.
 
* Decedent/Mother's Maiden Name:
 
* Decedent/Mother's Maiden Name:
 
** VRDR FHIR IG: 14.3 VRDR Decedent Mother describes mother, but does not specify this is a maiden name
 
** VRDR FHIR IG: 14.3 VRDR Decedent Mother describes mother, but does not specify this is a maiden name
Line 54: Line 59:
 
** See CONF 4393-166 which states ......SHALL be selected from ValueSet abc http://www.google.co/abc
 
** See CONF 4393-166 which states ......SHALL be selected from ValueSet abc http://www.google.co/abc
 
** I don't think that is the right value set (see Table 14; is that the right value set?)
 
** I don't think that is the right value set (see Table 14; is that the right value set?)
 +
* Table 30: SSN
 +
** patient.identifier.type says "BR". I think that should be "SB". This also shows up in the conformance list below the table.
 +
* Table 30: system used to encode the SSN
 +
** Text states: 8.b. The identifier, if present, SHOULD contain zero or one [0..1] system="2.16.840.1.113883.4.1" United States of America Social Security Number (CONF:4393-28).
 +
*** If you want to use the OID the format is wrong. It should be urn:oid:.....
 +
*** MITRE data uses http://hl7.org/fhir/sid/us-ssn, so that is another difference
 
* Table 30 says there shall be a Name entry with use value nickname (cardinality 1..1)
 
* Table 30 says there shall be a Name entry with use value nickname (cardinality 1..1)
 
** Do you really mean the cardinality is 1..1?
 
** Do you really mean the cardinality is 1..1?
 
** That means that someone without a nickname is going to have an entry for nickname that is empty
 
** That means that someone without a nickname is going to have an entry for nickname that is empty
 +
* Table 30: Address
 +
** address has cardinality of 0..1 and verb SHALL
 +
** Is this combination correct (I thought SHALL implied cardinality >= 1, but I am not certain).
 +
* Table 30: address.line and address.city,state,postalCode
 +
** Why does address.line have (SHALL, 1..1) while the others are (MAY, 0..1)? Line is the least descriptive.
 
* Table 31 likely has a typo
 
* Table 31 likely has a typo
 
** http://hl7.org/fhir/us/vrdr/StructureDefinition/-VRDR-Certifier
 
** http://hl7.org/fhir/us/vrdr/StructureDefinition/-VRDR-Certifier
Line 98: Line 114:
  
 
==VRDR Canary Synthetic Data==
 
==VRDR Canary Synthetic Data==
 +
* General question for elements with cardinality 0..1
 +
** The synthetic data encodes these as arrays. When there is data present, the item in the array is populated.
 +
** Is that the norm in FHIR when the cardinality is 0..1
 +
* Patient extensions, field names
 +
** For the extensions (race, ethnicity, birthsex), the FHIR IG states the XPath for the coded value is "valueCode".
 +
** In the synthetic data, the field names are (valueCoding, valueCoding, valueCodeableConcept)
 +
* Patient extensions, structure
 +
** See the example from MITRE near the bottom of this page
 +
** In the example, the first "extension" is under resource and at the same level as resourceType ("Patient"), id, identifier, name, gender, birthdate, address, ...
 +
** That tells me there is one extension element that has an array of values.
 +
** If you look inside the array, some items are simple items like us-core-birthsex while other items have further extensions.
 +
** The second level of extensions does not make sense to me.
 +
** Is there one "extension" encoded as an array with individual items (which themselves do not have extensions)? That seems to make the most sense to me.
 +
** If not that, then what is the correct pattern? The MITRE example does not make sense, but maybe there are other rules that I have not seen.
 +
** Besides the field name difference, the structure of the encoding of birthsex is different from race and ethnicity
 +
* Patient extensions, race and birthsex
 +
** Both are encoded as arrays with a single item
 +
** In the case of birthsex, the url for ....us-core-birthsex is included within the one item
 +
** In the case of race,
 +
*** There is a url included within the item, but that url is "ombCategory"
 +
*** There is a second URL with the right value that is included "next to" the extension element.
 
* Ethnicity
 
* Ethnicity
 
** Generated document uses wrong value for system for the coded value
 
** Generated document uses wrong value for system for the coded value
Line 110: Line 147:
 
** Synthetic data uses the wrong value for system: http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex
 
** Synthetic data uses the wrong value for system: http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex
 
** Correct value is: urn:oid:2.16.840.1.113883.5.1
 
** Correct value is: urn:oid:2.16.840.1.113883.5.1
 +
* Patient Address City Limits Indicator extension
 +
** Not included in MITRE data
 
* Occupation
 
* Occupation
 
** FHIR IG requires a component with code=21847-9
 
** FHIR IG requires a component with code=21847-9
Line 147: Line 186:
 
** Proper code system is SNOMED-CT or NullFlavor
 
** Proper code system is SNOMED-CT or NullFlavor
  
 +
==Patient Extension JSON Example from MITRE==
 +
<nowiki>
 +
      "extension": [
 +
          {
 +
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
 +
            "valueCodeableConcept": {
 +
              "coding": [
 +
                {
 +
                  "system": "http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex",
 +
                  "code": "M",
 +
                  "display": "Male"
 +
                }
 +
              ]
 +
            }
 +
          },
 +
          {
 +
            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
 +
            "valueAddress": {
 +
              "city": "Campello",
 +
              "district": "Plymouth",
 +
              "state": "Massachusetts",
 +
              "country": "United States"
 +
            }
 +
          },
 +
          {
 +
            "extension": [
 +
              {
 +
                "url": "ombCategory",
 +
                "valueCoding": {
 +
                  "system": "urn:oid:2.16.840.1.113883.6.238",
 +
                  "code": "2186-5",
 +
                  "display": "Not Hispanic or Latino"
 +
                }
 +
              },
 +
              {
 +
                "url": "text",
 +
                "valueString": "Not Hispanic or Latino"
 +
              }
 +
            ],
 +
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
 +
          },
 +
          {
 +
            "extension": [
 +
              {
 +
                "url": "ombCategory",
 +
                "valueCoding": {
 +
                  "system": "urn:oid:2.16.840.1.113883.6.238",
 +
                  "code": "2106-3",
 +
                  "display": "White"
 +
                }
 +
              },
 +
              {
 +
                "url": "text",
 +
                "valueString": "White"
 +
              }
 +
            ],
 +
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
 +
          }
 +
        ],
 +
 +
 +
</nowiki>
  
 
==Reference==
 
==Reference==

Latest revision as of 12:25, 28 December 2019

Notes/items for VRDR testing

Fourquet Test Data / Spreadsheet

  • Alias
    • Spreadsheet uses the value Alias in column B
    • FHIR IG: Table 30 has an entry for "nickname". When you state Alias, do you mean to use "nickname"?
  • Race of Cancer Patient
  • Ethnicity
  • Your spreadsheet says sex
    • Do you mean patient.gender?
    • Do you want to specify a value for birthsex?
  • Address.district and address.postalCode
    • FHIR IG calls out postal code as (MAY, 0..1) but does not mention district
    • Spreadsheet data does not provide postal code (OK)
    • MITRE synthetic data includes district (OK)
    • Those are both OK by spec but not quite in sync. This could be ignored.
  • Decedent/Mother's Maiden Name:
    • VRDR FHIR IG: 14.3 VRDR Decedent Mother describes mother, but does not specify this is a maiden name
    • Is there any place else in the document that describes mother's maiden name?
  • Education of Cancer patient (and others)
    • You have english values that make sense, but are not part of the value set.
    • Are you expecting documents to use the proper encoding? I assume so.
  • Industry of Cancer patient
  • Language
    • Spreadsheet has a row for Language, but I do not see that in the FHIR IG
  • Place of death
    • For Cancer patient, spreadsheet says "nursing home"
    • How does this map to Table 10. Is this ?
      • description
      • type
      • physicalType
  • Date signed, date pronounced dead, time pronounced dead
    • I am not sure where to pull these values from the death report.
    • I did find what I believe to be the date and time of death, but these values are not the same thing.
    • Table 2 in the FHIR IG has separate fields for date and time, but there is no description that does with these to make it clear to me what these are. The Canary Tool uses the term "Certified Time" and I assume uses the data from Table 2. Since I am not in this business, the different naming without cross reference leads me to guessing (not what I want to do).
  • Cause of Death
    • Is this to be sent as a string or as a coded value?

VRDR FHIR IG: VRDR Death Certificate Document

  • Table 10 describes the Death Location
    • description: The only constraint is that this is a string. Is there anything else to say about this? Might be enough
    • type: Constraint says this is a codeable concept, but there is no information on the code/coding system. Just use constraints from a FHIR Location?
    • physicalType: Constraint says this is a codeable concept, but there is no information on the code/coding system. Just use constraints from a FHIR Location?
  • Table 14: Manner of Death
    • See CONF:4393-345 which states: 7. VALUECODEABLECONCEPT, which SHALL be selected from ValueSet DispositionTypeVS http://hl7.org/fhir/ValueSet/DispositionTypeVS DYNAMIC (CONF:4393-345)
    • Selecting from a Disposition Value Set does not make sense to me
  • Table 18 has a row for effectiveDateTime but no text/requirement to go with it. There is a line below the table, but it does the same. It just says effectiveDateTime.

Table 20: Disposition Method

    • See CONF 4393-166 which states ......SHALL be selected from ValueSet abc http://www.google.co/abc
    • I don't think that is the right value set (see Table 14; is that the right value set?)
  • Table 30: SSN
    • patient.identifier.type says "BR". I think that should be "SB". This also shows up in the conformance list below the table.
  • Table 30: system used to encode the SSN
    • Text states: 8.b. The identifier, if present, SHOULD contain zero or one [0..1] system="2.16.840.1.113883.4.1" United States of America Social Security Number (CONF:4393-28).
  • Table 30 says there shall be a Name entry with use value nickname (cardinality 1..1)
    • Do you really mean the cardinality is 1..1?
    • That means that someone without a nickname is going to have an entry for nickname that is empty
  • Table 30: Address
    • address has cardinality of 0..1 and verb SHALL
    • Is this combination correct (I thought SHALL implied cardinality >= 1, but I am not certain).
  • Table 30: address.line and address.city,state,postalCode
    • Why does address.line have (SHALL, 1..1) while the others are (MAY, 0..1)? Line is the least descriptive.
  • Table 31 likely has a typo
  • Sections 3.1 and 3.2 are confusing
    • Both have the title: VRDR Cause Of Death Condition
    • Section 3.1 says code is a codeable concept, but does not break it down further. The example from canary has code/text
    • Section 3.1 has this condition: http://hl7.org/fhir/us/vrdr/StructureDefinition/-VRDR-Cause-Of-Death-Condition
      • Is the - before VRDR-Cause-Of-Death-Condition a typo or on purpose?
    • Section 3.2 states: SHALL contain exactly one [1..1] onset[x], where onset[x]
      • and then it stops. Section 3.1 actually fills this in, but that is in 3.1
    • Requirements are slightly different
  • Section 3.3 has typo in the title of the section.
  • Sections 11.1 and 11.2, are these duplicates?
    • Both sections discuss VRDR Certifier
    • They have slightly different requirements
  • LOINC as a coding system

VRDR Supplement

  • Table 6.3.1.D1.4.1-1, Pregnancy
    • Supplement says: Where value data type is CD and uses values from value set: (CodeSystem: 2.16.840.1.114222.4.11.6003 Pregnancy Status (NCHS))
    • 2.16.840.1.114222.4.11.6003 is the identifier for a value set and not for a code system
    • See https://phinvads.cdc.gov/vads/ViewValueSet.action?id=98603205-77AC-448A-ABBD-A43D5B34E627
    • PHIN VADS says coding system is "PHIN VS (CDC Local Coding System)" but does not give a value that one would use for "system", at least on that page. Google tells me the right value for system would be: urn:oid:2.16.840.1.114222.4.5.274. But, that is based on a random page I found. Would like to find a definite reference.
  • Table 6.3.1.D1.4.1-1, Tobacco Use
    • Supplement says: Contributory Tobacco Use (NCHS) [Observation: templateId 2.16.840.1.114222.4.11.6004]
      • Not sure that the OID listed qualifies as a template ID. It is the OID of a value set (see next item).
    • Supplement says: Where value data type is CD and uses values from value set: (CodeSystem: 2.16.840.1.114222.4.11.6004 Contributory Tobacco Use (NCHS)),

VRDR Canary Synthetic Data

Patient Extension JSON Example from MITRE

       "extension": [
          {
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
            "valueCodeableConcept": {
              "coding": [
                {
                  "system": "http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex",
                  "code": "M",
                  "display": "Male"
                }
              ]
            }
          },
          {
            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
            "valueAddress": {
              "city": "Campello",
              "district": "Plymouth",
              "state": "Massachusetts",
              "country": "United States"
            }
          },
          {
            "extension": [
              {
                "url": "ombCategory",
                "valueCoding": {
                  "system": "urn:oid:2.16.840.1.113883.6.238",
                  "code": "2186-5",
                  "display": "Not Hispanic or Latino"
                }
              },
              {
                "url": "text",
                "valueString": "Not Hispanic or Latino"
              }
            ],
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
          },
          {
            "extension": [
              {
                "url": "ombCategory",
                "valueCoding": {
                  "system": "urn:oid:2.16.840.1.113883.6.238",
                  "code": "2106-3",
                  "display": "White"
                }
              },
              {
                "url": "text",
                "valueString": "White"
              }
            ],
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
          }
        ],

Reference

Code Systems

Concept ValueSet System Web page
Race NA urn:oid:2.16.840.1.113883.6.238 https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238
Ethnicity NA urn:oid:2.16.840.1.113883.12.189 https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.12.189
Birth Sex NA urn:oid:2.16.840.1.113883.5.1 https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.5.1


Marital Status XX http://terminology.hl7.org/CodeSystem/v3-MaritalStatus https://www.hl7.org/fhir/valueset-marital-status.html
Education Level FHIR MaritalStatus http://hl7.org/fhir/vs/marital-status http://hl7.org/fhir/v3/EducationLevel https://www.hl7.org/fhir/valueset-marital-status.html
Occupation http://hl7.org/fhir/ValueSet/Usual-occupation urn:oid:2.16.840.1.114222.4.5.314 https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.114222.4.5.314
Industry Industry-cdc-census-2010 http://hl7.org/fhir/ValueSet/Industry-cdc-census-2010 urn:oid:2.16.840.1.114222.4.5.315 https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.114222.4.5.315
Date/Time Pronounced Dead XX http://loinc.org NA
Location: Type http://terminology.hl7.org/ValueSet/v3-ServiceDeliveryLocationRoleType http://terminology.hl7.org/CodeSystem/v3-RoleCode http://hl7.org/implement/standards/fhir/v3/ServiceDeliveryLocationRoleType/vs.html
Location: Physical Type http://hl7.org/fhir/ValueSet/location-physical-type http://terminology.hl7.org/CodeSystem/location-physical-type https://www.hl7.org/fhir/valueset-location-physical-type.html
Cause of Death http://hl7.org/fhir/ValueSet/condition-code http://snomed.info/sct https://www.hl7.org/fhir/valueset-condition-code.html
Manner of Death XX http://snomed.info/sct
Autopsy Performed v2-0532 http://hl7.org/fhir/ValueSet/v2-0532 http://terminology.hl7.org/CodeSystem/v2-0136 https://www.hl7.org/fhir/v2/0532/index.html
Disposition Method DispositionTypeVS http://hl7.org/fhir/ValueSet/DispositionTypeVS http://snomed.info/sct https://phinvads.cdc.gov/vads/ViewValueSet.action?id=F4C8B6A9-0DCB-E711-ACE2-0017A477041A
Pregnancy PregnancyStatusVS http://hl7.org/fhir/ValueSet/PregnancyStatusVS urn:oid:2.16.840.1.114222.4.5.274 https://phinvads.cdc.gov/vads/ViewValueSet.action?id=98603205-77AC-448A-ABBD-A43D5B34E627
Tobacco Use ContributoryTobaccoUseVS http://hl7.org/fhir/ValueSet/ContributoryTobaccoUseVS http://snomed.info/sct http://hl7.org/fhir/us/vrdr/2019May/TobaccoUseContributedToDeath.html and https://phinvads.cdc.gov/vads/ViewValueSet.action?id=FF7F17AE-3D20-473D-9068-E77A08491242


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