SOCR Data AD BiomedBigMetadata

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Contents

SOCR Data - Modeling and Analysis of Clinical, Genetic and Imaging Data of Alzheimer’s Disease

Summary

These data include massive heterogeneous clinical, genetic and imaging data of Alzheimer’s disease.

Background

There are megabytes of health-related metadata some of which is incomplete, irrelevant or difficult to establish homologies between different variables or subjects. In this dataset, missing values are denoted by (“.”).

The goal is to interrogate the data using exploratory and quantitative data analysis methods and look for patterns, trends or relations that may provide cues to the diagnosis, cognitive state or prognosis of these subjects (patients and control). Specifically, one may investigate the following:

  • Identify clusters of data that agrees with specific phenotypes (e.g., Diagnosis/Dx) or traits (e.g., NPI scores).
  • Reduce the dimensionality of the data and identify linear sub-spaces that contain large between subject variations or expose common traits.
  • Plan the integration of imaging biomarkers with these clinical and demographic data. The new Pipeline mechanism for Study-Designs enables the integrated analysis of imaging and meta-data (more information on the pipeline is available here).

Although SOCR Tools may be useful for some of this analysis, most of the interesting analyses may require the use of graphical Pipeline workflows, R, Matlab, C/C++/Java and other computational libraries/tools can be compiled as stand-alone execs and wrapped in XML as Pipeline modules). This allows openly sharing of the complete protocols (pipeline.xml.pipe files) for the entire community to replicate, revise, validate, and cite.

Classroom use of this data set

Education Level (Y), Age (X) and Weight (Blob-size) of all Subjects

This data set can be used to illustrate (multivariate, logistic) regression analyses, non-parametric tests, classification/clustering approaches, and diverse array of exploratory data analyses.

Data Description

  • Subject Identifier:
    • RID: Participant roster ID N 38 digits 0
    • sid1: complete deidentified subject ID
  • Clinical measures
    • MMSCORE: TOTAL Minimental State Exam Score N 2 0..30
    • FAQTOTAL: Total Score N 2 0..30
    • GDTOTAL: Total Score N 2 0..15
    • adascog: ADAS-Cognitive Behavior
    • sobcdr: sum of boxes Clinical Dementia Rating (CDR)
    • DX: diagnosis 1=NL;2=MCI;3=AD
    • DX_Conversion: DXCONV PDXCONV Diagnostic Summary 2. Has there been a conversion or reversion to NL/MCI? N 1 1=Yes - Conversion;2=Yes - Reversion; 0=No
    • DX_Confidence: Diagnostic Summary Physician Confidence in Diagnosis: N 1 1=Uncertain; 2=Mildly Confident; 3=Moderately Confident; 4=Highly Confident
  • Demographics
    • Gender: 1=Male;2=Female
    • Married: 1=Married; 2=Widowed; 3=Divorced; 4=Never married; 5=Unknown
    • Education: Participant Education (in years, 0:20)
    • Age: in years
    • Weight_Kg: weight (kg)
  • Vital signs
    • VSBPSYS: Systolic - mmHg N 3 76..250
    • VSBPDIA: Diastolic - mmHg N 3 36..130
    • VSPULSE: 4. Seated Pulse Rate (per minute) N 3 40..130
    • VSRESP: 5. Respirations (per minute) N 2 6..40
    • VSTEMP: 6a. Temperature N 4,1 0
  • Symptoms:
    • SymptomSeverety: 1=Mild; 2=Moderate; 3=Severe
    • SymptomChronicity: 1= Single Occurrence; 2= Intermittent; 3= Persistent
  • Baseline check:
    • BCNAUSEA: 1. Nausea N 1 1=Absent; 2=Present
    • BCVOMIT: 2. Vomiting N 1 1=Absent; 2=Present
    • BCDIARRH: 3. Diarrhea N 1 1=Absent; 2=Present
    • BCCONSTP: 4. Constipation N 1 1=Absent; 2=Present
    • BCABDOMN: 5. Abdominal discomfort N 1 1=Absent; 2=Present
    • BCSWEATN: 6. Sweating N 1 1=Absent; 2=Present
    • BCDIZZY: 7. Dizziness N 1 1=Absent; 2=Present
    • BCENERGY: 8. Low energy N 1 1=Absent; 2=Present
    • BCDROWSY: 9. Drowsiness N 1 1=Absent; 2=Present
    • BCVISION: 10. Blurred vision N 1 1=Absent; 2=Present
    • BCHDACHE: 11. Headache N 1 1=Absent; 2=Present
    • BCDRYMTH: 12. Dry mouth N 1 1=Absent; 2=Present
    • BCBREATH: 13. Shortness of breath N 1 1=Absent; 2=Present
    • BCCOUGH: 14. Coughing N 1 1=Absent; 2=Present
    • BCPALPIT: 15. Palpitations N 1 1=Absent; 2=Present
    • BCCHEST: 16. Chest pain N 1 1=Absent; 2=Present
    • BCURNDIS: 17. Urinary discomfort (e.g., burning) N 1 1=Absent; 2=Present
    • BCURNFRQ: 18. Urinary frequency N 1 1=Absent; 2=Present
    • BCANKLE: 19. Ankle swelling N 1 1=Absent; 2=Present
    • BCMUSCLE: 20. Musculoskeletal pain N 1 1=Absent; 2=Present
    • BCRASH: 21. Rash N 1 1=Absent; 2=Present
    • BCINSOMN: 22. Insomnia N 1 1=Absent; 2=Present
    • BCDPMOOD: 23. Depressed mood N 1 1=Absent; 2=Present
    • BCCRYING: 24. Crying N 1 1=Absent; 2=Present
    • BCELMOOD: 25. Elevated mood N 1 1=Absent; 2=Present
    • BCWANDER: 26. Wandering N 1 1=Absent; 2=Present
    • BCFALL: 27. Fall N 1 1=Absent; 2=Present
    • BCOTHER: 28. Other N 1 1=Absent; 2=Present
    • CTWHITE: White Blood Cell Count N 4 0..100
    • CTRED: Red Blood Cell Count N 4 0
    • PROTEIN: Protein Results N 3 0
    • GLUCOSE: Glucose Results N 3 0
  • Genetics
    • ApoEGeneAllele1: ApoE Genotyping: Allele 1- Results (2:4)
    • ApoEGeneAllele2: ApoE Genotyping: Allele 2 - Results (2:4)
  • Clinical Dementia measures:
    • CDMEMORY: Clinical Dementia Rating Score N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • CDORIENT: Score N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • CDJUDGE: Score N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • CDCOMMUN: Score N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • CDHOME: Score N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • CDCARE: Score N 2,1 0.0=0.0;1.0=1.0;2.0=2.0;3.0=3.0
    • CDGLOBAL: Global CDR N 2,1 0.0=0.0;0.5=0.5;1.0=1.0;2.0=2.0;3.0=3.0
    • COT1SCOR: Total N 2 0..10
    • COT2SCOR: Total N 2 0..10
    • COT3SCOR: Total N 2 0..10
    • COT4TOTL: ADAS-Cognitive Behavior Total N 2 0..10
    • CONMCXLA: 14a. Number of targets hit (range = 0-49) N 2 0..49
    • NPISCORE: Total Score N 2 0..36

Data Table

RIDsidMMSCOREFAQTOTALGDTOTALadascogsobcdrDXDX_ConversionDX_ConfidenceGenderMarriedEducationAgeWeight_KgVSBPSYSVSBPDIAVSPULSEVSRESPVSTEMPSymptomeSeveretySymptomeChronicityBCNAUSEABCVOMITBCDIARRHBCCONSTPBCABDOMNBCSWEATNBCDIZZYBCENERGYBCDROWSYBCVISIONBCHDACHEBCDRYMTHBCBREATHBCCOUGHBCPALPITBCCHESTBCURNDISBCURNFRQBCANKLEBCMUSCLEBCRASHBCINSOMNBCDPMOODBCCRYINGBCELMOODBCWANDERBCFALLBCOTHERCTWHITECTREDPROTEINGLUCOSEApoEGeneAllele1ApoEGeneAllele2CDMEMORYCDORIENTCDJUDGECDCOMMUNCDHOMECDCARECDGLOBALCOT1SCORCOT2SCORCOT3SCORCOT4TOTLCONMCXLANPISCORE
2011_S_0002280110.6701041216798911080602096.3121111111111111211121221111111....3300000005775120
3011_S_000320101224.53031118817414870601897.922111111111111112111121211111102645834011110.503452201
5011_S_000529008.6701041116748815080521896.73311121111121111111222111111112143593300000005776160
6100_S_0006250018.670.52042113806912376552097121111111111111111111111111111....3300.5000003463260
8011_S_0008280050103221884601247480209623111211111111111112111111111134415723000000081098230
10011_S_00102411212.335203211274681408072209623111111121111111211111121111106635523401111103560173
15100_S_00152900701041118818715571582097131111111111111111121121111111....3400000008888322
19067_S_0019290330104211873651326965189721111111111111111111111111112200335423000000010101010220
29067_S_00292110121.3341041118647014385641696.6-4-4111111111111111111111111111100316034010.510.5100230100
30023_S_003029611011042119806119792641696.3211112212211111111111111111111....3300.500.50005430181
31023_S_003130001.6701042118777214881861697.7121112111211211211211111111111116037633300000008101010240
33035_S_0033296217.67210411208384120594816362311121111112111111112121111222146632300.500.50.50.503764177
35100_S_0035300060104001877951408578249711111121112111121111111111111134967923300000006878200
38067_S_0038251411.3313041112769814687601697.3121121111111112111111111111111-1-1-1-13300.500.50005546184
40099_S_004029008.3302041118737812668602096.92311111111111111111111111111110030723300000006776230
41007_S_0041254218.331.51042114715310464601696.9-4-411111111111111111111111111112039574400.50.5000.501250230
42023_S_0042302170.52041117739313984611696.913111111111111111111121111112220551003300.5000004655310
43018_S_00432900701041116766112270601898.6-4-4111111111111111111111111111106234552300000005888220
44022_S_004426441721042116865414084681297.9121111222211111111111111211111....3300.50.50.500.504560220
45067_S_0045291115.33110411188647122756816971211111112111111111111111111111040603400.50.500005753184
47100_S_00473000801041120848911261811896.5-4-411111111111111111111111111110041632300000004988220
50123_S_005026130183.5104-4-41677809664561897.6121121111121111111111111111111....3300.5110.50.50666454
51099_S_005127219.6711041118667811870601696.93211111111111111111211111111111247624400.500.50004663183
53011_S_00532312518.3343031112807514052681896112112112222121121111111111111....33010.5110.50326484
54099_S_00542712220.332.51042120817014090601697.4231111111221112121111211111111....3300.50.50.50.50.502450163
55018_S_005529115.3301041120759412470701897.62211111121111111111111111111113370086743300000005788182
57018_S_0057277215.671.520311207773128786618981311111111111211111211111111111034633400.500.500.502477184
58023_S_005830004.6702011216707215773821896.7121111111111211111111221111122....3400000005596200
60099_S_006027211412031120708113480601697.5211111111111111111111111111111....3400.500.50004565261
66022_S_006630003.3302031118746211570681698131111211111111211121111111111432525723000000088108271
67010_S_006727005.6702031117746713078582535131111111111111111111111111111....2300000005896282
68007_S_00683001202042112746914284601897.5-4-41111111111111111111111111111....330000000710109220
69100_S_006928008.3301041116727314274622096.4-4-41111111111111111111111111111....3300000004554201
70007_S_007027019.67010412147410013084642096.3-4-411111111111111111111111111111757593300000005655280
72123_S_007228005.33010311167010614191721897.911111112111111111111121111111100003300000005786290
74027_S_00743000702041120788213969651436.3-4-41111111111111111111111111111....3300000005676290
76067_S_0076257214.6741041112786011671622096.4-4-41111111111111111111111111111105059340110.510.502351181
78023_S_0078249117.3332042118767115572612095131121122211212211111211111122....34010.50.50.50.502332213
80018_S_00802715141.51031118856511860601898121111111111111111111112111111....3400.500.500.503453260
81023_S_00813000401041118707715881791697.4121111111111111111111112111111....34000000059109280
83023_S_00832291182.51041217736613575632497.112112111121111111111111111111100286144010.50.500.502220252
84023_S_0084241001421032114756814378631896.313111111121111111111111122111112224493400.50.50.500.502551282
86136_S_008630011.6701042118816814878682096.8111111111111111111111111121111073656330000000691010290
87018_S_0087293118.671.53031114758416080741897.1211111111111111111111111111111....3300.500.50.5002650241
88123_S_00882129124.673104-4-48659914070681898121111111111111111111121221111....4400.50.50.50.51023201311
89073_S_008930002.6701031120669411556561636.2121111111111111111112211111111-1-1-1-1330000000691010190
90099_S_009029005.3301031120698415090681697.5221111111111111111111111111111....44000000089910260
91123_S_00912512011.3332041120627312281561895.812211112222121111111121111111141248593300.50.50.50.510356583
93023_S_00932320222.6782032116776113161611897.412221111221211111111111222112203436553402111211330914
94123_S_00942128326.675303-4-414707415179561898.81121122121211111111112112111111037573401111101240133
95032_S_00952600701031112718912880642098.1121111111111111211111121111111018347612300000004899260
96022_S_00963000301041219798413080681697.81211121111112111111211121111110549503300000006999230
97020_S_009730011.670103211472541358080149812111111111111111111111211111104425423000000069109271
98067_S_0098264510.6723142116855520193752498.5331112111211121111111112211111....3400.500.50.50.5056842011
101007_S_0101270070.51031118738612084721696.5-4-4111111111111111111111111111121249544400.5000004866282
102130_S_010225NA216.671.51042120706813070722098-4-411111111111111111111111111111334573400.500.50.5003764160
103018_S_0103242018.671.52041118877212060751895-4-411111111111111111111111111110439603400.500.500.502472232
106123_S_010630028030421157413712382561697.21211122211222121121122222211224026763300000004686270
107136_S_0107280220.51032119617613077721698.61211212111111111111111111111110036583300.50000089109270
108123_S_0108271121321041118797312872521897.2131121211221112211221212111111....3400.500.50.50.502342292
109068_S_0109257111.6732032116706112079601697.8121122111111111211121212211111....34010.510.5003373110
110067_S_011023521941032110836814377702098-4-41111111111111111111111111111....3301110.50.503571310
111099_S_01112411112.672.52022116765011874561697.92211111111111111111111111111112039553400.50.510.5003250101
112127_S_0112300161.51041118717712276591635.5-4-411111111111111111111111111115149662400.50.50.50006788211
113123_S_01132804401031120767611864841696.312112221212211111212121111111100002300000006788260
116027_S_0116301211.330.52041118798214070521036.6-4-41111111111111111111111111111....3300.5000003686240
118027_S_011829126.33010400208111314485852237.71211111121111211111112111111112049693300000004885200
120027_S_012030029.3301041120728110871781036.2-4-4111111111111111111111111111102137633400000004586371
123131_S_01233002402041120746411270561297.4-4-411111111111111111111111111110062603300000004899400
125041_S_0125290050...11207411216885572897.8131111111111111111111111111111....3300000003876280
126023_S_012625029.6712042114787613165672097.313111111111111111111121111111101438523400.50.500005775300
127068_S_012729115.67020411177113512280722098.12221221122211122121222222111112055773300000006586210
128007_S_0128290110.670.53040020657114084681896.5121111111111111111111212111111....4400.5000004664261
129022_S_0129229120.674.51042116816110660761898.6121111111211111111111211111111004355330110.51102560221
130022_S_01303001601041116747611880802297.5-4-4111111211111111111121111111121042653300000006999300
135128_S_013529157.6712022118838714073681236.61211112112211121111222111111111054623300.50.50000688661
138128_S_01382702511041116879013675631498111111211212111211112211111111....3300.50.500006998200
139023_S_01392510114.333.52022113666114571622098.2121111111221211111112211111111133234744010.510.50.503562282
141021_S_0141279112.6732041112828314686652036.7121111112111111111121111111111....34010.50.50.50.505773280
142018_S_014229007.330.52041114807316070701897.6-4-41111111111111111111111111111....3400.5000004674162
147032_S_01472520434.334.51042118607012476601297.512111111121111121111111121111111742463330110.5110011078
149098_S_01492011120.334.51041116887517180641696111111211111111111111111111111103359330110.51103442203
150037_S_0150274111.330.51041112748412464561297.91112211112211112111112211111112946553300.5000006680222
155018_S_0155282311.331.51041116816512060601897.8121121111111111111221211211111....24010.500003682271
156035_S_015630006.6703041117758914683761697.8211111111112111111121211111111....3300000006888250
158137_S_015829136.331.5104-4-413817012764802099.21111111111111111111111111111111031572300.50.50.50004887180
159021_S_015930024.330...2116788813569731635.9-4-4111111111111111111111111111161641335633000000088109250
160098_S_016027011511031116767414482701696.8231111111111111111111211111111....3400.50.500003452191
162123_S_01622401121.51041118728012691681698.2131111111111111111121111111122....3400.500.500.503451340
166114_S_0166300016.3301042118735014698821497.8-4-4111111111111111111111111111100003400000004888330
167128_S_0167262412.674.52021116779317979481896.8121111112221111111112111111111....3401010.5114455163
168011_S_01682612100.51041213906114471842096.5221111211111111211121111111111....3300.5000006696200
169014_S_0169290213.670.51042116726211076701897.433111111111111111111111221111100003400.5000004875234
171098_S_017130008.3303042117796015678491696131112112111111111111111211111....3300000002666231
172098_S_017229007.6701042118716317191731697131111111111111111111211111111116543573300000004666220
173114_S_0173300013.6701031118747213285821298-4-4111111111111111111111111111111605233000000069109270
176067_S_0176285211.3311031119757513672481897.31211111121111221111221112111110160823400.50.500003772181
177067_S_017729045.6702022114754613578781896.61211212112211221221222112111111028573300000007999250
178021_S_017829204.331.51041120658414795761836.6221111111111111111121111111111....3300.500.500.506775322
179027_S_0179245011.330.51031116818513676611637.5221111111111111111111212111111....3400.5000003441131
182037_S_018229511221042112646112474681297.1121111121111111111111211111111....3400.50100.502254154
183011_S_01832113212.674.5103-4-414736712870601897.9121111112211121111111111211111....34011110.506790266
184136_S_018429004.6701042114798816084841899.2121111111111111111111111111111....34000000069109210
186136_S_018627026.670.53042116818814090781698.71311111211111111111111111111110463454330000.50005897231
187032_S_018728311311041116789413060601697.2121121111111112211122212211111....4400.500.50003544152
188128_S_0188279042202-4-416877113273551698.21311111111111211111111111111112247913400.500.50.50.506787203
190100_S_01902710114.6723131118798712761701896.813111111111111111111111111111118845743400.50.50.500.504541181
194136_S_019424822333032112814712482641897.5231111111111111111111111111111-1-1-1-13300.50.510.50.503663139
195136_S_01952522162.51031118805411060541496.7-4-41111111111111111111111111111....3400.5010.50.504565147
196136_S_019629115.6703032118788312888601698.21211111111111111111111111111113029643300000006888231
204035_S_0204253210.331.51032216726213163651435.51111111111112211111111111211111128593300.50.50.50004553224
205128_S_020530003.330.51042118675812271682097121111111121121211111111111111....3300.50000098910360
210068_S_021029005.6702042113737313080761898.71211111111112112111222211111111522432300000005687220
213020_S_0213245212.3341031118636713070601498.2-4-4111111111111111111111111111110455523010.510.510356570
214032_S_0214275114.3312041120658314082602097.21211211112111111111112111121111237724400.500.50003565275
216128_S_0216258211.3331041116858315271681898.8111112111211111111121211111111....3300.50.50.500.511553143
217023_S_021727009.3313032118845214669852097.2121111111111111211121111111111....3300.50.500002541350
221005_S_02212022024730311186811012870641697.123112112122111111111121111211102455844011112124302013
222005_S_022225100103104-4-418867813884761698.41211111122221121111212111111111135725733010.50.50.50.503663193
223005_S_022330006.3301042118786113278681698.11211111111111111111121121111111146553400000006778150
225128_S_022528019.6723142117837114973831636.1121111111111111111111121111111....3300.50.50.500.504877260
227128_S_0227240113.332.53042112806414976631697.6-4-4111111111111111111111111111124527534400.50.50.50015695151
228114_S_0228202402881042110815812273751498.9-4-41111111111111111111111111111....3301211213453190
229128_S_02293002002042116758119064661698121111121111112111112221111111....34000000010101010210
230128_S_02302900801041120809514259651498.4121111111111121111121111111111....3300000007988250
231021_S_023129648.331.51041118618114171531837.3121111111111111111111211211111144471573300.50.50.50003651230
232130_S_023229616.67020211207810114484811697.6-4-411111111111111111111111111113088873300000007786211
240013_S_0240283112.331.51041116896017776582497.21211112112221221111211111111110356553300.5000016896200
243067_S_02432820112.672104-4-415686215380581697-4-411111111111111111111111111110623593400.50.50.500.505684196
245128_S_0245270390.51042110748315065761897131111112211122212112112211111....330000.50005885285
249007_S_024929627.671.52042116725912084561697.1131111111111121111111211111111....3400.500.50.5004572281
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See also

References

  • Sergi G. Costafreda, Ivo D. Dinov, Zhuowen Tu, Yonggang Shi, Cheng-Yi Liu, Iwona Kloszewska, Patrizia Mecocci, Hilkka Soininen, Magda Tsolaki, Bruno Vellas, Lars-Olof Wahlund, Christian Spenger, Arthur W. Toga, Simon Lovestone, Andrew Simmons (2011) Automated hippocampal shape analysis predicts the onset of dementia in mild cognitive impairment, NeuroImage, 56(1):212-219, DOI: 10.1016/j.neuroimage.2011.01.050.
  • Dinov I, Lozev K, Petrosyan P, Liu Z, Eggert P, et al. (2010) [www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013070 Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline]. PLoS ONE 5(9): e13070. doi:10.1371/journal.pone.0013070.



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