🚧 map concepts

docs/no_peeking/mappings/READMD.md

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+# Concept-Mappers between Kids First and FHIR
+
+- `Group`
+- `Patient`
+- `FamilyMemberHistory`
+- `Condition`
+- `Observation`
+- `Specimen`

docs/no_peeking/mappings/condition.py

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+def disease_onset(x):
+    """
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-onset.html
+    """
+    pass
+
+def disease_tumor_stage(x):
+    """
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-tumor-stage.html
+    """
+    pass
+
+def condition_code(x):
+    """
+    http://hl7.org/fhir/R4/valueset-condition-code.html
+    """
+    pass
+
+def body_site(x):
+    """
+    http://hl7.org/fhir/R4/valueset-body-site.html
+    """
+
+
+condition =  {
+    'resourceType': 'Condition',
+    'id': DIAGNOSIS.TARGET_SERVICE_ID
+    'disease-onset': {
+        'coding': [
+            {
+                'system': 'http://purl.obolibrary.org/obo/hp.owl',
+                'code': 'HP:0410280'
+                'display': 'Pediatric onset'
+
+            }
+        ]
+    },
+    'disease-tumor-stage': None, # disease_tumor_stage()
+    'code': {
+        'coding': None,	# condition_code()
+        'text':	DIAGNOSIS.NAME
+    },
+    'bodySite': None # body_site()
+    'subject': {
+        'reference': f'Patient/{PARTICIPANT.TARGET_SERVICE_ID}',
+        'type': 'Patient'
+    },
+    'onsetAge': DIAGNOSIS.EVENT_AGE_DAYS
+}

docs/no_peeking/mappings/family_member_history.py

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+def pedigree_node_affected_status(x):
+    """
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-pedigree-affected-status.html
+
+    """
+    if x == constants.COMMON.FALSE:
+        return {
+            'code': 'Affected',
+            'display': 'Affected'
+        }
+    elif x == constants.COMMON.TRUE:
+        return {
+            'code': 'unaffected',
+            'display': 'Unaffected'
+        }
+    elif x == constants.COMMON.UNKNOWN:
+        return {
+            'code': 'missing',
+            'display': 'Missing'
+        }
+    else:
+        raise Exception('Unknown FamilyMemberHistory pedigree-node-affected-status')
+
+def relationship(x):
+    """
+    http://hl7.org/fhir/R4/v3/FamilyMember/vs.html
+    """
+    coding = {"system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode"}
+    if x == constants.RELATIONSHIP.FATHER:
+        return coding.update({
+            'code': 'FTH',
+            'display': 'father'
+        })
+    elif x == constants.RELATIONSHIP.MOTHER:
+        return coding.update({
+            'code': 'MTH',
+            'display': 'mother'
+        })
+    else:
+        raise Exception('Unknown FamilyMemberHistory relationship')
+
+def sex(x):
+    """
+    http://hl7.org/fhir/R4/valueset-administrative-gender.html
+    """
+    if x == constants.GENDER.FEMALE:
+        return 'female'
+    elif x == constants.GENDER.MALE:
+        return 'male'
+    elif x == constants.COMMON.OTHER:
+        return 'other'
+    elif x == constants.COMMON.UNKNOWN:
+        return 'unknown'
+    else:
+        raise Exception('Unknown FamilyMemberHistory sex')
+
+
+family_member_history = {
+    'resourceType': 'FamilyMemberHistory',
+    'id': FAMILY_RELATIONSHIP.TARGET_SERVICE_ID,
+    'pedigree-node-affected-status': 
+        pedigree_node_affected_status(PARTICIPANT.IS_AFFECTED_UNDER_STUDY),
+    'pedigree-node-family-identifier': [
+        {
+            'system': None,
+            'value': FAMILY.ID
+        }
+    ],
+    'pedigree-node-individual': {
+        'reference': f'Patient/{PARTICIPANT.TARGET_SERVICE_ID}',
+        'type': 'Patient'
+    },
+    'identifier': [
+        {
+            'system': None
+            'value': FAMILY_RELATIONSHIP.ID
+        }
+    ],
+    'status': None,
+    'patient': {
+        'reference': f'Patient/{PARTICIPANT.TARGET_SERVICE_ID}',
+        'type': 'Patient'
+    },
+    'relationship': {
+        "coding": [
+            relationship(FAMILY_RELATIONSHIP.RELATION_FROM_1_TO_2)
+        ]
+        },
+    'sex': sex(PARTICIPANT.GENDER),
+}

docs/no_peeking/mappings/group.py

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+def group_type(x):
+    """
+    http://hl7.org/fhir/R4/valueset-group-type.html
+    """
+    if x in {constants.SPECIES.DOG}:
+        return 'animal'
+    elif x == constants.SPECIES.HUMAN:
+        return 'person'
+    else:
+        raise Exception('Unknown Group type')
+
+def family_member_type(x):
+    '''
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-family-member-type.html
+    '''
+    if x == constants.COMMON.TRUE:
+        return {
+            'code': 'proband',
+            'display': 'Proband'
+        }
+    elif x == constants.COMMON.FALSE:
+        return {
+            'code': 'relative',
+            'display': 'Relative'
+        }
+    else:
+        raise Exception('Unknown Group family-member-type')
+
+
+group = 'Group': {
+    'resourceType': 'Group',
+    'id': FAMILY.TARGET_SERVICE_ID,
+    'identifier': [
+        {
+            'system': None
+            'value': FAMILY.ID
+        }
+    ],
+    'type': group_type(PARTICIPANT.SPECIES or constants.SPECIES.HUMAN),
+    'actual': constants.COMMON.TRUE or constants.COMMON.FALSE, # defaults to True
+    'member': [
+        {
+            'id': PARTICIPANT.ID,
+            'family-member-type': {
+                'coding': [
+                    family_member_type(PARTICIPANT.IS_PROBAND)
+                ]
+            },
+            # 'family-member-phenopacket': {},
+            'entity': {
+                'reference': f'Patient/{PARTICIPANT.KF_ID}',
+                'type': 'Patient'
+            },
+        }
+    ]
+}

docs/no_peeking/mappings/observation.py

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+def status(x):
+    """
+    http://hl7.org/fhir/R4/valueset-observation-status.html
+    """
+    pass
+
+def interpretation(x):
+    """
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-phenotypic-feature-interpretation.html
+
+    """
+    if x == constants.PHENOTYPE.OBSERVED.NO:
+        return {
+            'code': 'NEG',
+            'display': 'Negative'
+        }
+    elif x == constants.PHENOTYPE.OBSERVED.YES:
+        return {
+            'code': 'POS',
+            'display': 'Positive'
+        }
+    else:
+        raise Exception('Unknown Observation interpretation')
+
+
+observation = {
+    'id': PHENOTYPE.TARGET_SERVICE_ID,
+    'phenotypic-feature-severity': None,
+    'phenotypic-feature-modifier': None,
+    'phenotypic-feature-onset': {
+        'valueAge':  PHENOTYPE.EVENT_AGE_DAYS
+    },
+    'evidence': None,
+    'identifier': [
+        {
+            'system': None,
+            'value': PHENOTYPE.ID
+        }
+    ],
+    'status': 'registered', # defaults to 'registered'
+    'code': {
+        'text': PHENOTYPE.NAME
+    },
+    'subject': {
+        'reference': f'Patient/{PARTICIPANT.TARGET_SERVICE_ID}',
+        'type': 'Patient'
+    },
+    'interpretation': {
+        'coding': [
+            interpretation(PHENOTYPE.OBSERVED)
+        ]
+    },
+    'bodySite': None # body_site()
+}

docs/no_peeking/mappings/patient.py

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+def individual_texonomy(x):
+    """
+    https://aehrc.github.io/fhir-phenopackets-ig/ValueSet-taxonomy.html
+    """
+    if x == constants.SPECIES.DOG:
+        return {
+            'code': 'NCBITaxon_9615',
+            'display': 'Canis lupus familiaris'
+        }
+    elif x == constants.SPECIES.HUMAN:
+        return {
+            'code': 'NCBITaxon_9606',
+            'display': 'Homo sapiens'
+        }
+    else: 
+        raise Exception('Unknown Patient individual-taxonomy')
+
+def gender(x):
+    """
+    http://hl7.org/fhir/R4/valueset-administrative-gender.html
+    """
+    if x == constants.GENDER.FEMALE:
+        return 'female'
+    elif x == constants.GENDER.MALE:
+        return 'male'
+    elif x == constants.COMMON.OTHER:
+        return 'other'
+    elif x == constants.COMMON.UNKNOWN:
+        return 'unknown'
+    else:
+        raise Exception('Unknown Patient gender')
+
+
+patient = {
+    'resourceType': 'Patient'
+    'id': PARTICIPANT.TARGET_SERVICE_ID,
+    'individual-age': {
+        'valueAge':  PARTICIPANT.ENROLLMENT_AGE_DAYS
+    },
+    'individual-karyotypic-sex': None,
+    'individual-taxonomy': {
+        'coding': [
+            individual_texonomy(PARTICIPANT.SPECIES or constants.SPECIES.HUMAN)
+        ]
+    },
+    'identifier': [
+        {
+            'system': None,
+            'value': PARTICIPANT.ID
+        }
+    ],
+    'gender': gender(PARTICIPANT.GENDER),
+    'birthDate': None
+}

docs/no_peeking/mappings/specimen.py

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+def status(x):
+    """
+    http://hl7.org/fhir/R4/valueset-specimen-status.html
+    """
+    if x == constants.COMMON.FALSE:
+        return 'unavailable'
+    elif x == constants.COMMON.TRUE:
+        return 'available'
+    else:
+        raise Exception('Unknown Specimen status')
+
+def specimen_type(x):
+    """
+    http://hl7.org/fhir/R4/v2/0487/index.html
+    """
+    if x == constants.SPECIMEN.COMPOSITION.BLOOD:
+        return	{
+            'coding': 'BLD',
+            'display': 'Whole blood'
+        }
+    elif x == constants.SPECIMEN.COMPOSITION.SALIVA:
+        return	{
+            'coding': 'SAL',
+            'display': 'Saliva'
+        }
+    elif x == constants.SPECIMEN.COMPOSITION.TISSUE:
+        return	{
+            'coding': 'TISS',
+            'display': 'Tissue'
+        }
+    else:
+        raise Exception('Unknown Specimen type')
+
+
+specimen = {
+    'resourceType': 'Specimen',
+    'id': BIOSPECIMEN.TARGET_SERVICE_ID,
+    'biosample-individual-age-at-collection': None,
+    'biosampe-histological-diagnosis': None,
+    'biosample-tumor-progression': None,
+    'biosample-tumor-grade': None,
+    'biosample-control': True or False, # defaults to True
+    'identifier': [
+        {
+            'system': None,
+            'value': BIOSPECIMEN.ID
+        }
+    ],
+    'accessionIdentifier': [
+        {
+            'system': None,
+            'value': BIOSPECIMEN.ID
+        }
+    ],
+    'status': status(BIOSPECIMEN.VISIBLE),
+    'type': {
+        'coding': [
+            specimen_type(BIOSPECIMEN.COMPOSITION)
+        ],
+        'text': BIOSPECIMEN.COMPOSITION
+    },
+    'subject': {
+        'reference': f'Patient/{PARTICIPANT.TARGET_SERVICE_ID}',
+        'type': 'Patient'
+    }
+}