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Analysis of Parkinson's Progressive Markers Initiative Data

Home Page: http://www.ppmi-info.org/

Makefile 0.02% Python 4.76% Jupyter Notebook 94.64% Shell 0.58%

parkinsons-disease ppmi

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yttik1470 vipul105 alexlilloo cseas voyagertherapeutics ramku31 horizonailab guaponi cuckoong akshayayadav antonellamadauni jgockley62 okshashank

ppmi's Issues

import ppmilib

Hello,

I am trying to use your database but i have a problem.
When i execute the next command:
· "python scripts/create_ppmi_database.py"
This error appears:

Traceback (most recent call last):
File "scripts/create_ppmi_database.py", line 8, in
import ppmilib
ImportError: No module named ppmilib

I do not know how to install this lib. When i execute that:

·"sudo pip3 install ppmilib"

This error appears:

Collecting ppmilib
ERROR: Could not find a version that satisfies the requirement ppmilib (from versions: none)
ERROR: No matching distribution found for ppmilib

And i dont know where can i download the requirements.

Can you help me please?

Thank you very much.

Alejandro.

New filename causes missing tables

It seems the PPMI updated its file list since the scripts have been created. When running the create scripts, multiple files are not processed correctly.
I have the following output showing all the files being processed but some tables are not created because of change in filename or new files.

I pasted my output of the create script below.

List of processed files

Processing Prodromal_Diagnostic_Questionnaire.csv Processing FBB_Analysis_Data.csv Processing University_of_Pennsylvania_Smell_ID_Test.csv Processing FOUND_RFQ_Calcium_Channel_Blockers.csv Processing Lexical_Fluency.csv Processing Wearable_and_Sensor_Eligibility.csv Processing Features_of_REM_Behavior_Disorder.csv Processing Epworth_Sleepiness_Scale.csv Processing Letter_-_Number_Sequencing__PD_.csv Processing Florbetaben_Eligibility.csv Processing AV-133_Image_Metadata.csv Processing Diagnostic_Features.csv Processing Clinical_Diagnosis_and_Management.csv Processing FOUND_RFQ_Height___Weight.csv Processing Clinical_Labs.csv Processing Skin_Biopsy.csv Processing Page_Descriptions.csv Processing Determination_of_Falls.csv Processing General_Medical_History.csv Processing Contact_Information_Brain_Bank.csv Processing Upper_Extremity_Function-_Short_Form.csv Processing MDS_UPDRS_Part_I__Patient_Questionnaire.csv Processing Use_of_PD_Medication.csv Processing Participation_in_Other_Clinical_Trials.csv Processing AV-133_Imaging.csv Processing TAP-PD_OPDM_Use_Questionnaire.csv Processing Conclusion_of_Study_Participation.csv Processing ST_CATALOG.csv Processing Skin_Biopsy_Eligibility.csv Processing RBD_PSG_Eligibility.csv Processing DaTscan_Imaging.csv Processing SPECT_Scan_Information_Source_Document.csv Processing Olfactory_UPSIT.csv Processing General_Physical_Exam.csv Processing FOUND_RFQ_Head_Injury.csv Processing DATScan_Analysis.csv Processing Concomitant_Medications.csv Processing Inclusion_Exclusion.csv Processing Current_Biospecimen_Analysis_Results.csv Processing AV-133_Subject_Eligibility.csv Processing Genetic_Testing_Results.csv Processing General_Neurological_Exam.csv Processing Primary_Diagnosis.csv Processing Whole_Blood_Sample_Collection.csv Processing REM_Sleep_Disorder_Questionnaire.csv Processing Patient_Status.csv Processing Cognitive_Assessments.csv Processing FOUND_RFQ_Pesticides_at_Work.csv Processing FOUND_RFQ_Caffeine.csv Processing TAP-PD_Conclusion.csv Processing Socio-Economics.csv Processing FOUND_RFQ_Occupation.csv Processing FOUND_RFQ_Female_Reproductive_Health.csv Processing MDS_UPDRS_Part_I.csv Processing Current_Medical_Conditions_Log.csv Processing PASE_-_Household_Activity.csv Processing iPSC_Blood_Sample.csv Processing FOUND_RFQ_Smoking_History.csv Processing Gait_Data___Arm_swing.csv Processing Adverse_Event_Log.csv Processing Pilot_Biospecimen_Analysis_Results.csv Processing MDS-UPDRS_Tagging_Status.csv Processing Family_History__PD_.csv Processing Initiation_of_PD_Medication-_incidents.csv Processing Code_List.csv Processing Modified_Boston_Naming_Test.csv Processing MDS_UPDRS_Part_IV.csv Processing Signature_Form.csv Processing Laboratory_Procedures.csv Processing Communication-Short_Form.csv Processing SCOPA-AUT.csv Processing Cognitive_Categorization.csv Processing Screening___Demographics.csv Processing Laboratory_Procedures_with_Elapsed_Times.csv Processing Modified_Schwab_+_England_ADL.csv Processing FOUND_RFQ_Dictionary.csv Processing Hopkins_Verbal_Learning_Test.csv Processing FOUND_Enrollment_Status.csv Processing AV-133_SBR_Results.csv Processing Lumbar_Puncture_Sample_Collection.csv Processing Montreal_Cognitive_Assessment__MoCA_.csv Processing IUSM_BIOSPECIMEN_CELL_CATALOG.csv Processing 151_Project_Extra___Buffer_and_Calibrator_Data.csv Processing Lower_Extremity_Function__Mobility_.csv Processing Derived_Variable_Definitions_and_Score_Calculations.csv Processing Semantic_Fluency.csv Processing MDS_UPDRS_Part_III.csv Processing Deprecated_Biospecimen_Analysis_Results.csv Processing Geriatric_Depression_Scale__Short_.csv Processing Trail_Making_A_and_B.csv Processing Blood_Chemistry___Hematology.csv Processing Device_Placement_Log.csv Processing Wearable_and_Sensor_Participation_Status.csv Processing TAP-PD_OPDM_Assessment.csv Processing Symbol_Digit_Modalities.csv Processing State-Trait_Anxiety_Inventory.csv Processing FOUND_RFQ_Alcohol.csv Processing TAP-PD_Kinetics_Device_Testing.csv Processing DNA_Sample_Collection.csv Processing Center-Subject_List.csv Processing Data_Dictionary.csv Processing Contact_Information_FOUND.csv Processing FOUND_Self-Reported_Dx.csv Processing Pregnancy_Form.csv Processing Benton_Judgment_of_Line_Orientation.csv Processing Research_Advance_Directive.csv Processing FOUND_RFQ_Pesticides_Non-Work.csv Processing Magnetic_Resonance_Imaging.csv Processing FOUND_RFQ_Toxicant_History.csv Processing PASE_-_Leisure_Time_Activity.csv Processing Cognition_Function-Short_Form.csv Processing FOUND_RFQ_Anti-Inflammatory_Meds.csv Processing MDS_UPDRS_Part_II__Patient_Questionnaire.csv Processing TAP-PD_Subject_Eligibility.csv Processing Surgery_for_Parkinson_Disease.csv Processing Randomization_table.csv Processing FOUND_RFQ_Residential_History.csv Processing Neurological_Exam_-_Cranial_Nerves.csv Processing DTI_Regions_of_Interest.csv Processing Genetic_and_Registry_Diagnostic_Questionnaire.csv Processing PD_Features.csv Processing FOUND_RFQ_Physical_Activity.csv Processing Vital_Signs.csv Processing DaTSCAN_SPECT_Visual_Interpretation_Assessment.csv Processing IUSM_CATALOG.csv Processing FBB_Metadata.csv Processing MRI_Imaging_Data_Transfer_Information_Source_Document.csv Processing QUIP_Current_Short.csv

	basename	pat_id	pag_cnt	table_name
0	Prodromal_Diagnostic_Questionnaire.csv	True	2	None
3	FOUND_RFQ_Calcium_Channel_Blockers.csv	False	0	None
13	FOUND_RFQ_Height___Weight.csv	False	0	None
22	Use_of_PD_Medication.csv	True	2	None
34	FOUND_RFQ_Head_Injury.csv	False	0	None
38	Current_Biospecimen_Analysis_Results.csv	True	0	None
42	Primary_Diagnosis.csv	True	3	None
46	Cognitive_Assessments.csv	True	2	None
47	FOUND_RFQ_Pesticides_at_Work.csv	False	0	None
48	FOUND_RFQ_Caffeine.csv	False	0	None
51	FOUND_RFQ_Occupation.csv	False	0	None
52	FOUND_RFQ_Female_Reproductive_Health.csv	False	0	None
57	FOUND_RFQ_Smoking_History.csv	False	0	None
58	Gait_Data___Arm_swing.csv	True	0	None
60	Pilot_Biospecimen_Analysis_Results.csv	True	0	None
75	FOUND_RFQ_Dictionary.csv	False	0	None
77	FOUND_Enrollment_Status.csv	True	0	None
82	151_Project_Extra___Buffer_and_Calibrator_Data...	False	0	None
84	Derived_Variable_Definitions_and_Score_Calcula...	False	0	None
85	Semantic_Fluency.csv	True	2	None
86	MDS_UPDRS_Part_III.csv	True	4	None
87	Deprecated_Biospecimen_Analysis_Results.csv	True	0	None
96	FOUND_RFQ_Alcohol.csv	False	0	None
102	FOUND_Self-Reported_Dx.csv	True	0	None
106	FOUND_RFQ_Pesticides_Non-Work.csv	False	0	None
108	FOUND_RFQ_Toxicant_History.csv	False	0	None
111	FOUND_RFQ_Anti-Inflammatory_Meds.csv	False	0	None
116	FOUND_RFQ_Residential_History.csv	False	0	None
121	FOUND_RFQ_Physical_Activity.csv	False	0	None
122	Vital_Signs.csv	True	2	None

Setup issue

Hi this repo looks really useful! I'm recieving an error in the setup script and wondered if you had any advice as wo what I may be doing wrong!

> python3 scripts/create_ppmi_database.py 
Processing Code_List.csv
Processing Data_Dictionary.csv
Processing Derived_Variable_Definitions_and_Score_Calculations.csv
Processing Page_Descriptions.csv
Processing Skin_Biopsy.csv
....
Processing ambulatory.csv
                                              basename  pat_id  pag_cnt table_name
2    Derived_Variable_Definitions_and_Score_Calcula...   False        0       None
7                            Gait_Data___Arm_swing.csv    True        0       None
10                          IUSM_ASSAY_DEV_CATALOG.csv   False        0       None
12                         FOUND_Enrollment_Status.csv    True        0       None
13                            FOUND_RFQ_Dictionary.csv   False        0       None
..                                                 ...     ...      ...        ...
214                                      pulserate.csv   False        0       None
215                                            prv.csv   False        0       None
216                                        onwrist.csv   False        0       None
217                                     inbedtimes.csv   False        0       None
218                                     ambulatory.csv   False        0       None

[152 rows x 4 columns]
Maximum Table name is larger than 8
Traceback (most recent call last):
  File "/home/ec2-user/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3361, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 76, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: True

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "scripts/create_ppmi_database.py", line 158, in <module>
    print (pd_results[tmax > 8])
  File "/home/ec2-user/.local/lib/python3.7/site-packages/pandas/core/frame.py", line 3458, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3363, in get_loc
    raise KeyError(key) from err
KeyError: True

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