
====== Phenotype database info ======


The following serves as a documentation of the planned PostgreSQL database (NoDa) for phenotypes.



===== Columns for phenotype database on TSD =====


==== SubjID ====

Unique participant id. This is the **only** ID that connects across data sets.

==== deCODE_ID ====

deCODE id (FID) if present. A single **SubjID** may correspond to multiple  **deCODE_ID** as individuals can have been chipped/genotyped several times.

==== DNA_ID ====

DNA sample ID if present.

==== MRI_ID ====

If exists.

May have multiple ids per individual

==== cohort_group ====

  Psychiatric cohorts
  Miscellaneous cohorts
  MoBa cohort
  Dementia Norwegian cohorts
  Dementia European cohorts
  

====cohort====

  === Psychiatric cohort (by prefix used in Subj_ID) ===

  TOP (U, A, D, O, S, I, KSU, T, SIK (Control(K))
  U_TOP (BUP, TGV, TPB, (Control(BUPK))
  BRAIN (AA, FR, ST, NT, NN, RH, BR, SF, GJ, RS, OP, MO, BG, US, LI, BHCR(Agitation (AG))
  EPHAPS (JE)
  Hjertefrisk(HF)
  Fysakt (FA)
  TIPS (SU, POP)
  Bergen_bp
  BUPGEN (OS, AU, VV, HU, SI, SOH, UNN, SIV, MR)
  Clozapine (CLZ) 
   
  (Miscellaneous cohorts)
  STROKE (UMR, (Control(UMRK))
  NONSTOP (PP)
  Blood_donor (BBD)
  NORCOR (?)
  NORDOC (LU)
  LifeSpan (ID, dev)
  Bergen_adhd
  MedGen_Gervin (?)
  
  (MoBa cohort)
  subclinical ADHD (2012)
  controls (Dec14 Singletons)
  trios (population based controls) May16
  HARVEST (n=33000)
  ADHD trios (Nov_2016_ADHD)
  MoBa 1479 Phasing   
  
  (Dementia norwegian cohort)
  norcog
  padr
  demvest
  ahus
  ddi
  nordnorge
  namsos/hunt
  cognorm
  oslo_pd_study
  tronderbrain
  NORCOAST
  nursing_home
  
  (Dementia european cohort)
  brno
  adrc
  karolinska
  UK BioResources
  Ljubliana (E-DLB)
  Barcelona (E-DLB)
  Strasbourg (E-DLB)
  Amsterdam (E-DLB)
  Malmø/Lund (E-DLB)
  Thessaloniki (E-DLB)
  St. Petersburg (E-DLB)
  Genova(E-DLB)
  KCL_OPTIMA
  TEC/Protect
  Kassel
  Paris
  Halle(E-DLB)
 
    

==== CASE_CONTROL ====


==== DIAGNOSIS_MAIN ====


  AD - Alzheimer's Disease
  ANX - Anxiety Disorder
  ASD - Autism
  BD - Bipolar
  CTRL - Control
  DEM - Dementia
  DEP - Depression
  INT - Intellectual Disability
  MOOD - Other Mood Disorders
  PERSON - Personality Disorder
  PSY - Other psychosis Disorder
  SCZ - Schizophrenia
  MIX - Other mental disorder
  PROD - Prodromal


==== DIAGNOSIS_SUB ====

  AD
    /Alzheimers Disease/ADRD/DLB/VaD/MCI
  ANX
    /Anxiety disorder/
  ASD
    /Autism/Child_autism/Atypical_autism/ASD
  BD
    /Bipolar_I/Bipolar_II/Bipolar_III/Bipolar_IV/Bipolar_NOS
  CTRL
    /Control
  DEM
    /AD/Afasia/Alcoholic_dementia/Ataxia/CBD/Cortibasal_degeneration/Ct/Dementia_NOS/DLB/DLB_AD/
    /Down_syndrome_and_AD/FTD_Behavioral/FTD_Language/FTD_not_specified/FTLD_ALS/Huntigton/MCI/
    /Mixed_AD_VaD/NPH/PCA/PD/PD_MCI/PD_SCI/possAD/possDLB/possVaD/probAD_D/probAD_MCI/probDLB/
    /probPDD/probVaD/PSP/SCI/solvent_encephalopathy
  DEP
    /Brief_Recurrent_Depression/Depression_NOS/Major_Depressive_Disorder/
    /Mild_Depressive_Disorder/Moderate_depressive_disorder/Unipolar depression
  INT
    /Intellectual disability/Neurodevelopmental disorder/General learning disability
  MOOD
    /Dysthymia/Atypical depression/
  PERSON
    /Borderline personality disorder/Schizoid personality disorder/Schizotyp/  
  PSY
    /Delusion/Paranoia/Psychosis_Alcohol_Related/Psychosis_Drug_Related/Psychosis_NOS/Psychosis_Other/
    /Psychosis_outside_specter
  SCZ
    /schizophrenia/schizophreniform/schizoaffective/Paranoid_schizophrenia


==== YEAR_BIRTH ====

0000

==== AGE_BASELINE ====
Age at baseline diagnosis



==== SEX ====


  male
  female
  NA

==== ETHNICITY ====

  Common categories
 
==== ---------GENETIC DATA-------------- ====


==== BATCH_IMPUTATION ====


  Apr16
  Jul15
  etc...

==== BATCH_CHIP ====

See this overview

https://docs.google.com/spreadsheets/d/1cJ1Ri7-FJisSQ3vBSJvgZNlmlx_z-xbB2x3KZ8mxQqA/edit#gid=0

==== CHIP_NUMBER ====

Number of chip plate. (?)

==== TS_INSERTION ====

Timestamp of when subject was inserted into the database

==== TS_REMOVAL ====

Timestamp for removal. If present, indicates if and when the subject
no longer can be used.

==== COMMENTS ====

String of comments "comment 1;  comment 2;"

