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Request for new comparison cycle with IDEA4RC DM #19

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Request for new comparison cycle with IDEA4RC DM #19

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93c296f
Update patientFollowUp-to-fhir-map.fsh
rgazzarata Sep 10, 2024
06e9644
Update Encounter-follow-up.fsh
rgazzarata Sep 10, 2024
2d308bb
Update i4rc-cancerEpisode.fsh
rgazzarata Sep 10, 2024
2388b0e
Update histologySquamous.fsh
rgazzarata Sep 10, 2024
c242f86
Update histologyAdenocarcinoma.fsh
rgazzarata Sep 10, 2024
88a32fc
Update histologyNeuroendocrine.fsh
rgazzarata Sep 10, 2024
13b66e0
Update histologyOdontogenicCarcinoma.fsh
rgazzarata Sep 10, 2024
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14 changes: 7 additions & 7 deletions input/fsh/models/idea4rc/i4rc-cancerEpisode.fsh
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Expand Up @@ -11,7 +11,7 @@ Maturity Level: 0 Draft"""
* typeOfBiopsy 1..1 CodeableConcept "Type of biopsy" """Type of biopsy performed"""
* biopsyDoneBy 1..1 string "Biopsy done by" """Describes the institution where diagnostic procedure was performed"""
* ageAtDiagnosis 1..1 integer "Age at diagnosis" """Age of the patient at the time of the diagnosis."""
* radiotherapyInducedSarcoma 1..1 boolean "Radiotherapy induced sarcoma" """radiotherapy induced if the new tumour is in the field or marginal the anatomical area that received high radiation dose; please specify the interval time from the radiotherapy treatment"""
* radiotherapyInducedSarcoma 1..1 CodeableConcept "Radiotherapy induced sarcoma" """radiotherapy induced if the new tumour is in the field or marginal the anatomical area that received high radiation dose; please specify the interval time from the radiotherapy treatment"""
* grading 0..1 CodeableConcept "Grading" """Grading of the cancer"""
* hnClassification 1..1 BackboneElement "Classification for Head and Neck tumors" """Classification for Head and Neck tumors"""
* hnClassification.histologySquamous 1..1 CodeableConcept "Histology Squamous" """Specifies the histological subgroup for squamous cancers"""
Expand Down Expand Up @@ -151,8 +151,8 @@ oxyphilic carcinoma - 4212379
oncocytic adenocarcinoma
oncocytic malignant oncocytoma
Salivary gland intraductal carcinoma (cribriform low grade adenocarcinoma) """
* hnClassification.histologyNeuroendocrine ^comment = """Small cell neuroendocrine�carcinoma (SmCC)?,Poorly differentiated neuroendocrine carcinoma, small cell (grade 3);Large cell neuroendocrine carcinoma (LCNEC)?, Poorly differentiated neuroendocrine carcinoma, large cell (grade 3);Well-differentiated neuroendocrine carcinoma, Middle ear carcinoid tumor;Moderately differentiated neuroendocrine carcinoma
Small cell neuroendocrine�carcinoma (SmCC)? - 36714029
* hnClassification.histologyNeuroendocrine ^comment = """Small cell neuroendocrine�carcinoma (SmCC)?,Poorly differentiated neuroendocrine carcinoma, small cell (grade 3);Large cell neuroendocrine carcinoma (LCNEC)?, Poorly differentiated neuroendocrine carcinoma, large cell (grade 3);Well-differentiated neuroendocrine carcinoma, Middle ear carcinoid tumor;Moderately differentiated neuroendocrine carcinoma
Small cell neuroendocrine�carcinoma (SmCC)? - 36714029
Poorly differentiated neuroendocrine carcinoma - 37018672
small cell (grade 3)
Large cell neuroendocrine carcinoma (LCNEC)? - 4029971
Expand Down Expand Up @@ -345,14 +345,14 @@ Aggressive angiomyxoma - 4239956
Angiomatoid fibrous histiocytoma - 4029526
NTRK-rearranged spindle cell neoplasm (emerging)"""
* sarcomaClassification.undifSmallRCelSarcBonAndSofTis ^comment = """Ewing sarcoma
Round cell sarcoma with�EWSR1?non-ETS fusions
Round cell sarcoma with�EWSR1?non-ETS fusions
CIC-rearranged sarcoma
Sarcoma with�BCOR�genetic alterations
Sarcoma with�BCOR�genetic alterations

Ewing sarcoma - 45766528
Round cell sarcoma with�EWSR1?non-ETS fusions
Round cell sarcoma with�EWSR1?non-ETS fusions
CIC-rearranged sarcoma
Sarcoma with�BCOR�genetic alterations
Sarcoma with�BCOR�genetic alterations
"""
* sarcomaClassification.estAndRelatedTumours ^comment = """Endometrial stromal sarcoma, high grade
Endometrial stromal sarcoma, low grade
Expand Down
2 changes: 1 addition & 1 deletion input/fsh/models/idea4rc/patientFollowUp-to-fhir-map.fsh
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Expand Up @@ -153,7 +153,7 @@ Details in the referred Condition"
* group[=].element[=].target.display = ""
* group[=].element[=].target.equivalence = #equivalent

* group[=].element[+].code = #PatientFollowUp.
* group[=].element[+].code = #PatientFollowUp.lastContact
* group[=].element[=].display = "Patient Follow Up date"
* group[=].element[=].target.code = #Observation.valueDateTime
* group[=].element[=].target.display = ""
Expand Down
2 changes: 1 addition & 1 deletion input/fsh/profiles/Encounter-follow-up.fsh
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Expand Up @@ -17,7 +17,7 @@ Description: "This profile defines how to represent the Patient follow-up model
* insert SubjectRules
* episodeOfCare only Reference(EpisodeOfCareI4rc)
* reasonReference only Reference(ConditionPrimaryCancerI4rc)
* reasonReference 1..
* reasonReference 0..
* ^short = "Reference to the first Primary Cancer"
* diagnosis ^short = "Typically used for the discharge diagnosis"
* condition only Reference(ConditionPrimaryCancerI4rc)
Expand Down
62 changes: 48 additions & 14 deletions input/fsh/terminologies/cancerEvent/histologyAdenocarcinoma.fsh
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Expand Up @@ -8,43 +8,54 @@ Description: "Codes identifying codindins beloging to the Histology Adenocarcino

// Missing "NOS, non–intestinal-type (sinonasal)"
// Missing * $athena# "Endolymphatic sac low grade, "
* $athena#4312929 "Intestinal-type (salivary gland)"
* $athena#4050978 "cystoadenocarcinoma"
* $athena#4247921 "mucinous"
* $athena#4238334 "Ceruminous (only in ear)"
* $athena#605208 "Nasopharyngeal papillary adenocarcinoma"
* $athena#4097305 "Adenocarcinoma, intestinal type"
* $athena#37152526 "Adenocarcinoma"
//* $athena#4312929 "Intestinal-type (salivary gland)"
* $athena#4050978 "Cystoadenocarcinoma"
//* $athena#4247921 "mucinous"
* $athena#4247921 "Mucinous adenocarcinoma"
//* $athena#4238334 "Ceruminous (only in ear)"
* $athena#4238334 "Ceruminous adenocarcinoma"
* $athena#4172953 "Papillary adenocarcinoma"
//* $athena#605208 "Nasopharyngeal papillary adenocarcinoma"
// * $athena# "thyroid like low grade nasopharingeal papillary adenocarcinoma"
* $athena#4022895 "Adenoid cystic carcinoma"
// * $athena# "Adenoid cystic carcinoma: solid type (> 30% solid)"
* $athena#4253608 "Mucoepidermoid carcinoma"
// * $athena# "Polymorphous"
// * $athena#THERE IS NO MINOR BUT MAJOR SALIVARY GLANDS "Cribriform of minor salivary glands"
* $athena#4030121 "Polymorphous (low grade)"
//* $athena#4030121 "Polymorphous (low grade)"
* $athena#4030121 "Polymorphous low grade adenocarcinoma"
// * $athena#NOT SURE "terminal duct carcinoma"
* $athena#4232456 "lobular carcinoma"
//* $athena#4232456 "lobular carcinoma"
* $athena#4164740 "Acinic cell carcinoma"
* $athena#4148292 "Clear cell carcinoma"
// * $athena# "hyalinising clear cell carcinoma"
* $athena#4146684 "Basal cell adenocarcinoma"
* $athena#4221403 "Infiltrating duct carcinoma"
* $athena#4224593 "Juvenile carcinoma of the breast"
* $athena#4323699 "Paget's disease, extramammary (except Paget's disease of bone)"
// * $athena#NOT SURE "malignant dermal analog tumor"
* $athena#4287334 "Salivary duct carcinoma"
//* $athena#4287334 "Salivary duct carcinoma"
// * $athena# "high grade ductal carcinoma"
* $athena#37116978 "Salivary secretory adenocarcinoma (mammary analog, MASC)"
//* $athena#37116978 "Salivary secretory adenocarcinoma (mammary analog, MASC)"
// * $athena#LOOKS LIKE NO MAPPING IN SNOMED "Secretory carcinoma"
* $athena#4029680 "Myoepithelial carcinoma, malignant myoepithelioma"
//* $athena#4029680 "Myoepithelial carcinoma, malignant myoepithelioma"
* $athena#4029680 "Malignant myoepithelioma"
* $athena#4321002 "Epithelial-myoepithelial carcinoma"
* $athena#4066512 "Carcinoma ex pleomorphic adenoma"
// * $athena# "Carcinoma ex pleomorphic adenoma: NOS, Intracapsular, minimally invasive, largely invasive"
* $athena#4182993 "Sebaceous adenocarcinoma"
* $athena#37116976 "Sebaceous lymphadenocarcinoma"
//* $athena#37116976 "Sebaceous lymphadenocarcinoma"
* $athena#4271564 "Carcinosarcoma"
// * $athena# "Oncocytic carcinoma"
* $athena#4212379 "Oxyphilic carcinoma"
// * $athena# "oncocytic adenocarcinoma"
// * $athena# "oncocytic malignant oncocytoma"
// * $athena# "Salivary gland intraductal carcinoma (cribriform low grade adenocarcinoma) "

* $athena#4050978 "Cystadenocarcinoma"

/*

" Intestinal-type (sinonasal) adenocarcinoma - CHECK WHICH SON
NOS, non–intestinal-type (sinonasal) - FROM HERE?,
Endolymphatic sac low grade,
Expand Down Expand Up @@ -81,6 +92,29 @@ oxyphilic carcinoma - 4212379
oncocytic adenocarcinoma
oncocytic malignant oncocytoma
Salivary gland intraductal carcinoma (cribriform low grade adenocarcinoma) "
*/


/* 10/09/2024 New codes
Adenocarcinoma, intestinal type - 4097305
Adenocarcinoma - 37152526
Cystoadenocarcinoma - 4050978
Mucinous adenocarcinoma - 4247921
Ceruminous adenocarcinoma - 4238334
Papillary adenocarcinoma - 4172953
Adenoid cystic carcinoma - 4022895
Mucoepidermoid carcinoma - 4253608
Polymorphous low grade adenocarcinoma - 4030121
Acinar cell carcinoma - 4164740
Clear cell adenocarcinoma - 4148292
Basal cell adenocarcinoma - 4146684
Infiltrating duct carcinoma - 4221403
Juvenile carcinoma of the breast - 4224593
Paget's disease, extramammary (except Paget's disease of bone) - 4323699
Malignant myoepithelioma - 4029680
Epithelial-myoepithelial carcinoma - 4321002
Carcinoma ex pleomorphic adenoma - 4066512
Sebaceous adenocarcinoma - 4182993
Carcinosarcoma - 4271564
Oxyphilic adenocarcinoma - 4212379
Cystadenocarcinoma - 4050978
*/
15 changes: 14 additions & 1 deletion input/fsh/terminologies/cancerEvent/histologyNeuroendocrine.fsh
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Expand Up @@ -7,13 +7,17 @@ Description: "Codes identifying codindins beloging to the Histology Neuroendocri
* ^experimental = false

* $athena#36714029 "Small cell neuroendocrine carcinoma (SmCC)"
* $athena#37018672 "Poorly differentiated neuroendocrine carcinoma"
//* $athena#37018672 "Poorly differentiated neuroendocrine carcinoma"
* $athena#37018672 "Malignant poorly differentiated neuroendocrine carcinoma"
// * $athena# "small cell (grade 3)"
* $athena#4029971 "Large cell neuroendocrine carcinoma (LCNEC)"
// * $athena# "Poorly differentiated neuroendocrine carcinoma, large cell (grade 3)"
/* * $athena# "Well-differentiated neuroendocrine carcinoma, "
* $athena# "Middle ear carcinoid tumor"
* $athena# "Moderately differentiated neuroendocrine carcinoma" */
* $athena#4133828 "Neuroendocrine tumor grade 1"
* $athena#4133297 "Neuroendocrine tumor grade 2"



/* "Small cell neuroendocrine carcinoma (SmCC)​,Poorly differentiated neuroendocrine carcinoma, small cell (grade 3);Large cell neuroendocrine carcinoma (LCNEC)​, Poorly differentiated neuroendocrine carcinoma, large cell (grade 3);Well-differentiated neuroendocrine carcinoma, Middle ear carcinoid tumor;Moderately differentiated neuroendocrine carcinoma
Expand All @@ -26,3 +30,12 @@ Well-differentiated neuroendocrine carcinoma,
Middle ear carcinoid tumor
Moderately differentiated neuroendocrine carcinoma"
*/

/*10/09/2024 New codes
Small cell neuroendocrine carcinoma (SmCC)​ - 36714029
Malignant poorly differentiated neuroendocrine carcinoma - 37018672
Large cell neuroendocrine carcinoma (LCNEC)​ - 4029971
Neuroendocrine tumor grade 1 - 4133828
Neuroendocrine tumor grade 2 - 4133297

*/
23 changes: 16 additions & 7 deletions input/fsh/terminologies/cancerEvent/histologyOdontogenicCarcinoma.fsh
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Expand Up @@ -6,12 +6,21 @@ Description: "Codes identifying codindins beloging to the Histology Odontogenic

* ^experimental = false

* $athena#4098585 "Odontogenic carcinoma, NOS"
* $athena#37153944 "Ameloblastic carcinoma"
* $athena#37158144 "Dedifferentiated intraosseous ameloblastic carcinoma"
* $athena#37153976 "Dedifferentiated peripheral ameloblastic carcinoma"
* $athena#37117009 "Primary intraosseous carcinoma"
* $athena#37116887 "Intraosseous carcinoma developed on odontogenic cyst"
//* $athena#4098585 "Odontogenic carcinoma, NOS"
* $athena#4098585 "Odontogenic tumor, malignant"
//* $athena#37153944 "Ameloblastic carcinoma"
//* $athena#37158144 "Dedifferentiated intraosseous ameloblastic carcinoma"
//* $athena#37153976 "Dedifferentiated peripheral ameloblastic carcinoma"
//* $athena#37117009 "Primary intraosseous carcinoma"
//* $athena#37116887 "Intraosseous carcinoma developed on odontogenic cyst"
// Sclerosing odontogenic carcinoma
* $athena#37116966 "Clear cell odontogenic carcinoma"
* $athena#37312303 "Gosht cell odontogenic carcinoma"
//* $athena#37312303 "Gosht cell odontogenic carcinoma"
* $athena#4005818 "Malignant odontogenic ghost cell tumor"


/*10/09/2024
Odontogenic tumor, malignant - 4098585
Clear cell odontogenic carcinoma - 37116966
Malignant odontogenic ghost cell tumor - 4005818
*/
61 changes: 50 additions & 11 deletions input/fsh/terminologies/cancerEvent/histologySquamous.fsh
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Expand Up @@ -6,19 +6,37 @@ Description: "Codes identifying codindins beloging to the Histology Squamous gro
*/
* ^experimental = false

* $athena#4078953 "Keratinizing squamous cell carcinoma, epidermoid carcinoma"
* $athena#4147603 "Non-keratinizing squamous cell carcinoma"
// * $athena#1 Non-keratinizing squamous cell carcinoma: SMARCB1 (INI-1)-deficient Sinonasal Carcinoma - (This should be a modifier? not clear)
* $athena#4206785 "Non-keratinizing squamous cell carcinoma: Transitional (cylindrical cell, Schneiderian) carcinoma"
* $athena#4277415 "Spindle cell (sarcomatoid) squamous cell carcinoma"
// * $athena#1 Spindle cell (sarcomatoid) squamous cell carcinoma: SMARCB1 (INI-1)-deficient Sinonasal Carcinoma - (This should be a modifier? not clear)
* $athena#4247661 "Lymphoepithelial carcinoma, lymphoepithelioma like carcinoma"
//* $athena#4078953 "Keratinizing squamous cell carcinoma, epidermoid carcinoma"
* $athena#4078953 "Squamous cell carcinoma, keratinizing"
* $athena#4166826 "Squamous cell carcinoma, large cell, nonkeratinizing"
//* $athena#4206785 "Non-keratinizing squamous cell carcinoma: Transitional (cylindrical cell, Schneiderian) carcinoma"
* $athena#4206785 "Schneiderian carcinoma"
* $athena#4009590 "Squamous cell carcinoma, spindle cell"
//* $athena#4247661 "Lymphoepithelial carcinoma, lymphoepithelioma like carcinoma"
* $athena#4247661 "Lymphoepithelial carcinoma"
* $athena#4029973 "Basaloid squamous cell carcinoma"
* $athena#4298030 "Verrucous squamous cell carcinoma: NOS, cuniculatum carcinoma/Ackerman tumor"
* $athena#4191609 "Papillary squamous cell carcinoma"
* $athena#37156145 "Squamous cell carcinoma"
* $athena#37204531 "Squamous cell carcinoma: HPV-positive"
* $athena#37204532 "Squamous cell carcinoma: HPV-negative"
* $athena#4312219 "Adenoid squamous cell carcinoma"
* $athena#4052146 "Squamous cell carcinoma, microinvasive"
* $athena#4175678 "Giant cell carcinoma"
* $athena#4233949 "Verrucous carcinoma"
* $athena#4191609 "Papillary squamous cell carcinoma"
//* $athena#37204531 "Squamous cell carcinoma: HPV-positive"
* $athena#37204531 "Human papillomavirus positive squamous cell carcinoma"
//* $athena#37204532 "Squamous cell carcinoma: HPV-negative"
* $athena#37204532 "Human papillomavirus negative squamous cell carcinoma"


//* $athena#4147603 "Non-keratinizing squamous cell carcinoma"
// * $athena#1 Non-keratinizing squamous cell carcinoma: SMARCB1 (INI-1)-deficient Sinonasal Carcinoma - (This should be a modifier? not clear)
//* $athena#4206785 "Non-keratinizing squamous cell carcinoma: Transitional (cylindrical cell, Schneiderian) carcinoma"
//* $athena#4277415 "Spindle cell (sarcomatoid) squamous cell carcinoma"
// * $athena#1 Spindle cell (sarcomatoid) squamous cell carcinoma: SMARCB1 (INI-1)-deficient Sinonasal Carcinoma - (This should be a modifier? not clear)
//* $athena#4247661 "Lymphoepithelial carcinoma, lymphoepithelioma like carcinoma"
//* $athena#4298030 "Verrucous squamous cell carcinoma: NOS, cuniculatum carcinoma/Ackerman tumor"
//* $athena#4191609 "Papillary squamous cell carcinoma"
//* $athena#37204531 "Squamous cell carcinoma: HPV-positive"
//* $athena#37204532 "Squamous cell carcinoma: HPV-negative"

/*Keratinizing squamous cell carcinoma, epidermoid carcinoma - 4078953
Non-keratinizing squamous cell carcinoma - 4147603
Expand All @@ -34,3 +52,24 @@ Verrucous squamous cell carcinoma: NOS, cuniculatum carcinoma/Ackerman tumor - 4
Squamous cell carcinoma - 4103543
Squamous cell carcinoma: HPV-positive - 37204531
Squamous cell carcinoma: HPV-negative - 37204532*/

/*10/09/2024 New codes
Squamous cell carcinoma, keratinizing - 4078953
Squamous cell carcinoma, large cell, nonkeratinizing - 4166826
Schneiderian carcinoma - 4206785
Non-keratinizing squamous cell carcinoma: SMARCB1 (INI-1)-deficient Sinonasal Carcinoma - CUSTOM CODE -> TO ADD WHEN UNAI WILL PROVIDE US THE CODE
Non-keratinizing squamous cell carcinoma: Transitional (cylindrical cell, Schneiderian) carcinoma - CUSTOM CODE -> TO ADD WHEN UNAI WILL PROVIDE US THE CODE
Squamous cell carcinoma, spindle cell - 4009590
Spindle cell (sarcomatoid) squamous cell carcinoma: SMARCB1 (INI-1) - CUSTOM CODE -> TO ADD WHEN UNAI WILL PROVIDE US THE CODE
Lymphoepithelial carcinoma - 4247661
Basaloid squamous cell carcinoma - 4029973
Squamous cell carcinoma - 37156145
Adenoid squamous cell carcinoma - 4312219
Squamous cell carcinoma, microinvasive - 4052146
Giant cell carcinoma - 4175678
Verrucous carcinoma - 4233949
Papillary squamous cell carcinoma - 4191609
Squamous cell carcinoma - 37156145
Human papillomavirus positive squamous cell carcinoma - 37204531
Human papillomavirus negative squamous cell carcinoma - 37204532
*/