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CDCWonder_NNDSS_InfectiousAnnual PR #1164

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CDCWonder_NNDSS_InfectiousAnnual PR #1164

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64368d7
CDCWonder_NNDSS_InfectiousAnnual PR
shapateriya Jan 2, 2025
e9b8c8a
updated mapping file
shapateriya Jan 3, 2025
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36 changes: 36 additions & 0 deletions scripts/us_cdc/nndss_annual_tables/README.md
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# CDCWonder NNDSS InfectiousAnnual Import

## About the Dataset
Notifiable Infectious Diseases Data: Annual tables from CDC WONDER which has the incident counts of different infectious diseases per year and are aggregated based on demographic factors. The statistics are reported by the 50 states, New York City, the District of Columbia, and the U.S. territories

### Download URL

Source URL {https://wonder.cdc.gov/nndss/nndss_annual_tables_menu.asp}.


To download the latest versions of ALL datasets available, run the following command. Files will be downloaded and extracted to a nndss_Annual_data folder.

### License

This dataset is available for public use, license is available at https://www.cdc.gov/other/agencymaterials.html


### Downloading and Processing Data


To download the data run the below command

```bash
python3 download_annual_data.py
```
To process the data, execute the below command:

Running this command generates input_fles and csv, mcf, tmcf files

```bash
A. python3 process_annual_demographics.py
B. python3 process_annual_reporting.py
```



275 changes: 275 additions & 0 deletions scripts/us_cdc/nndss_annual_tables/config.py
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_PV_MAP = {
'confirmed': {
'medicalStatus': 'dcs:ConfirmedCase'
},
'probable': {
'medicalStatus': 'dcs:ProbableCase'
},
'deaths': {
'medicalStatus': 'dcs:PatientDeceased'
},
'pediatric mortality': {
'medicalStatus': 'dcs:PediatricMortality'
},
'all serotypes': {
'serotype': 'dcs:AllSerotypes'
},
'serotype b': {
'serotype': 'dcs:SerotypeB'
},
'unknown serotype': {
'serotype': 'dcs:UnknownSerotype'
},
'non-b serotype': {
'serotype': 'dcs:NonSerotypeB'
},
'other serogroups': {
'serogroup': 'dcs:OtherSerogroups'
},
'nontypeable': {
'serogroup': 'dcs:OtherSerogroups'
},
'unknown serogroup': {
'serogroup': 'dcs:UnknownSerogroups'
},
'all groups': {
'serogroup': 'dcs:AllSerogroups'
},
'all serogroups': {
'serogroup': 'dcs:AllSerogroups'
},
'serogroups acwy': {
'serogroup': 'dcs:ACWYSerogroup'
},
'serogroup b': {
'serogroup': 'dcs:SerogroupB'
},
'group a': {
'serogroup': 'dcs:SerogroupA'
},
'perinatal infection': {
'medicalCondition': 'dcs:PerinatalInfection'
},
'acute': {
'medicalCondition': 'dcs:AcuteCondition'
},
'chronic': {
'medicalCondition': 'dcs:ChronicCondition'
},
'imported': {
'medicalStatus': 'dcs:ImportedCase'
},
'indigenous': {
'medicalStatus': 'dcs:IndigenousCase'
},
'clinical': {
'medicalStatus': 'dcs:ClinicalCase'
},
'neuroinvasive': {
'medicalCondition': 'dcs:NeuroinvasiveDisease'
},
'non-neuroinvasive': {
'medicalCondition': 'dcs:NonNeuroinvasiveDisease'
},
'congenital': {
'medicalCondition': 'dcs:CongenitalDisease'
},
'non-congenital': {
'medicalCondition': 'dcs:NonCongenitalDisease'
},
'drug resistant': {
'medicalCondition': 'dcs:DrugResistantDisease'
},
'nondrug resistant': {
'medicalCondition': 'dcs:NonDrugResistantDisease'
},
'invasive disease': {
'medicalCondition': 'dcs:InvasiveDisease'
},
'post-diarrheal': {
'medicalCondition': 'dcs:PostDiarrheal'
},
'<1 yr': {
'age': '[- 1 Years]'
},
'1-4 yrs': {
'age': '[1 4 Years]'
},
'5-14 yrs': {
'age': '[5 14 Years]'
},
'15-24 yrs': {
'age': '[15 24 Years]'
},
'25-39 yrs': {
'age': '[25 39 Years]'
},
'40-64 yrs': {
'age': '[40 64 Years]'
},
'≥65 yrs': {
'age': '[65 - Years]'
},
'age <5 years': {
'age': '[- 5 Years]'
},
'age not stated': {
'age': 'dcs:USC_AgeNotStated'
},
'male': {
'gender': 'dcs:Male'
},
'female': {
'gender': 'dcs:Female'
},
'sex not stated': {
'gender': 'dcs:CDC_GenderUnknownOrNotStated'
},
'american indian or alaska native': {
'race': 'dcs:AmericanIndianAndAlaskaNativeAlone'
},
'american indian or alaska native': {
'race': 'dcs:AmericanIndianAndAlaskaNativeAlone'
},
'asian or pacific islander': {
'race': 'dcs:AsianOrPacificIslander'
},
'asian or pacific islander': {
'race': 'dcs:AsianOrPacificIslander'
},
'black or african american': {
'race': 'dcs:BlackOrAfricanAmericanAlone'
},
'black': {
'race': 'dcs:Black'
},
'white': {
'race': 'dcs:White'
},
'other race': {
'race': 'dcs:CDC_OtherRace'
},
'other or multi-race ¶': {
'race': 'dcs:CDC_OtherRace'
},
'race not stated': {
'race': 'dcs:CDC_RaceUnknownOrNotStated'
},
'hispanic': {
'ethnicity': 'dcs:HispanicOrLatino'
},
'hispanic or latino': {
'ethnicity': 'dcs:HispanicOrLatino'
},
'non-hispanic/latino': {
'ethnicity': 'dcs:NotHispanicOrLatino'
},
'non-hispanic': {
'ethnicity': 'dcs:NotHispanicOrLatino'
},
'ethnicity not stated': {
'ethnicity': 'dcs:CDC_EthnicityUnknownOrNotStated'
},
'confirmed': {
'medicalStatus': 'dcs:ConfirmedCase'
},
'probable': {
'medicalStatus': 'dcs:ProbableCase'
},
'pediatric mortality': {
'medicalStatus': 'dcs:PediatricMortality'
},
'deaths': {
'medicalStatus': 'dcs:PatientDeceased'
},
'age <5': {
'age': '[- 5 Years]'
},
'age < 5': {
'age': '[- 5 Years]'
},
'age <5 years': {
'age': '[- 5 Years]'
},
'age < 5 years': {
'age': '[- 5 Years]'
},
'all serotypes': {
'serotype': 'dcs:AllSerotypes'
},
'serotype b': {
'serotype': 'dcs:SerotypeB'
},
'unknown serotype': {
'serotype': 'dcs:UnknownSerotype'
},
'non-b serotype': {
'serotype': 'dcs:NonSerotypeB'
},
'other serogroups': {
'serogroup': 'dcs:OtherSerogroups'
},
'nontypeable': {
'serogroup': 'dcs:OtherSerogroups'
},
'unknown serogroup': {
'serogroup': 'dcs:UnknownSerogroups'
},
'all groups': {
'serogroup': 'dcs:AllSerogroups'
},
'all serogroups': {
'serogroup': 'dcs:AllSerogroups'
},
'serogroups acwy': {
'serogroup': 'dcs:ACWYSerogroup'
},
'serogroup b': {
'serogroup': 'dcs:SerogroupB'
},
'group a': {
'serogroup': 'dcs:SerogroupA'
},
'perinatal infection': {
'medicalCondition': 'dcs:PerinatalInfection'
},
'acute': {
'medicalCondition': 'dcs:AcuteCondition'
},
'chronic': {
'medicalCondition': 'dcs:ChronicCondition'
},
'imported': {
'medicalStatus': 'dcs:ImportedCase'
},
'indigenous': {
'medicalStatus': 'dcs:IndigenousCase'
},
'clinical': {
'medicalStatus': 'dcs:ClinicalCase'
},
'neuroinvasive': {
'medicalCondition': 'dcs:NeuroinvasiveDisease'
},
'non-neuroinvasive': {
'medicalCondition': 'dcs:NonNeuroinvasiveDisease'
},
'congenital': {
'medicalCondition': 'dcs:CongenitalDisease'
},
'non-congenital': {
'medicalCondition': 'dcs:NonCongenitalDisease'
},
'drug resistant': {
'medicalCondition': 'dcs:DrugResistantDisease'
},
'nondrug resistant': {
'medicalCondition': 'dcs:NonDrugResistantDisease'
},
'invasive disease': {
'medicalCondition': 'dcs:InvasiveDisease'
},
'post-diarrheal': {
'medicalCondition': 'dcs:PostDiarrheal'
}
}
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