Submission File

Back to Submission Requirements

Column Name

Type

Format / Value Checks

Additional Comments

ind_id

string

Checks:

Must match exactly with Subject Code submitted to Sampled (formerly IBX).

Field is a required field and cannot be left empty.

Values in the field should be unique.

Definition: The unique individual id submitted to Sampled (formerly IBX) with the biospecimen.

Comments: IMPORTANT —This id is used to verify subject \ NRGR_BIO_ID pairs at Sampled (formerly IBX). Therefore, the id you submit here should match exactly the subject-code submitted to Sampled (formerly IBX).

nrgr_bio_id

string(14)

Checks:

Values in the field should be unique.

Definition: Sampled sample id, "NRGR_BIO_ID", formerly RUID

Sample value: 03C19340

For subjects with multiple samples at Sampled (formerly IBX), please include the blood sample in the main submission file. Additional sample IDs can be submitted in the Alternate ID (_id) file. For timepoint studies where multiple blood draws were used in analysis.

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

site_id

integer(5)

Definition: Submitting site within a study.

Sample value: 101

This is a required field. Empty strings and "NULL" are both considered invalid values.

study_id

integer(3)

Definition: Study number assigned by the NIMH RGR

Sample value: 22

This is a required field. Empty strings and "NULL" are both considered invalid values.

father_id

string

Checks:

Must match exactly with Subject Code submitted to Sampled (formerly IBX).

Definition: Id for the father of this individual in the specified format

in Sample value: 22-132-90000

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

mother_id

string

Checks:

Must match exactly with Subject Code submitted to Sampled (formerly IBX).

Definition: Id for the mother of this individual in the specified format

Sample value: 22-132-90001

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

fam_id

string

Format:

Field is a required field and cannot be left empty.

Definition: Family id of this individual in the specified format

Sample value: 132

subject_type

string(1)

Valid Values:

P=Primary Subject

S=Secondary Subject

C=Control

E=Excluded from Study

I=Informant

L=Linker

Definition: Subject type, including primary, secondary, control, linker, and excluded individuals. See below for details.

Sample value: P

This is a required field. Empty strings and "NULL" are both considered invalid values.

Comments:

P - Primary Subject - Individual is a primary subject for a given study. In family studies this will most often be the proband. Primary subjects typically have a biospecimen and will be included in most, if not all, applicable clinical assessments.

S - Secondary Subject - Individual is a secondary subject for a given study. In family studies this will most often be non probands. Secondary subjects typically have a biospecimen and may or may not be included in any applicable clinical assessments.

C - Control - Individual is a control.

E - Excluded from Study - Individuals who met exclusion criteria from a given study, but still have a biospecimen, consent, and at least some demographic information available and therefore may be of use to other investigators.

I - Informant - Individual provided information on a study participant. Informants have limited demographic information and no biospecimen. This subject_type should only be used for individuals who do not meet the requirements for P, S, C or E as described above.

L - Linker - Individual needed to construct a pedigree (ex. parents in the case of twin studies), has limited demographic information available and no biospecimen.

zygosity

string,multi_encoded

Valid Values:

AI=Adopted In

AO=Adopted Out

S=Singleton

MZ=Twin, Monozygotic

DZ=Twin, Dizygotic

UZ=Twin, Unknown Zygosity

MZMZ=Triplet, Monozygotic and Monozygotic

MZDZ=Triplet, Monozygotic and Dizygotic

MZUZ=Triplet, Monozygotic and Unknown Zygosity

DZDZ=Triplet, Dizygotic and Dizygotic

DZUZ=Triplet, Dizygotic and Unknown Zygosity

UZUZ=Triplet, Unknown Zygosity and Unknown Zygosity

NULL=Missing, Not Applicable, or Unknown

Definition: Zygosity of this individual

Sample value: AI|MZ

Use a '|' to add multiple values. For twins, a single zygosity value (e.g. 'MZ') should be used. For triplets, a concatenated zygosity value (e.g. 'MZDZ') should be used and each zygosity within that value should describe the relationship between the current individual and each of the other members of the birth cohort. When using a concatenated value, the hierarchy is 'MZ' > 'DZ' > 'UZ' (e.g. use 'MZDZ' not 'DZMZ').

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL.

Note: NULL may not be used when there are multiple values.

sex

string(1)

Valid Values:

M=Male

F=Female

I=Intersex

NULL=Missing or not applicable or unknown

Definition: Sex

Sample value: F

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

race

string(3)

Valid Values:

W=White

I=American Indian

A=Asian

B=Black

P=Pacific Islander

M=Mixed

RES=Not collected due to externally imposed restrictions (EU, IRB, etc)

REF=Refused

NULL=Missing or not applicable or unknown

Definition: Race according to the NIH Policy on Reporting Race and Ethnicity Data for Subjects In Clinical Research

Sample value: P

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

ethnicity

string(3)

Valid Values:

H=Hispanic

N=Not Hispanic

RES=Not collected due to externally imposed restrictions (EU, IRB, etc)

REF=Refused

NULL=Missing or not applicable or unknown

Definition: Ethnicity according to the NIH Policy on Reporting Race and Ethnicity Data for Subjects In Clinical Research

Sample value: H

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

Submissions for Autism

age_months

integer(4)

Format:

Age (months).

Checks:

Age should be between 0 and 1560.

Definition: Age of individual in months at time of first study assessment

Sample value: 240

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

age_onset_months

integer(4)

Format:

Age of Onset (months).

Checks:

Age should be between 0 and 1560.

Definition: Age of individual in months at time of onset of disorder

Sample value: 200

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

Submissions for Other Disorders

age_years

integer(3)

Format:

Age (years).

Checks:

Age should be between 0 and 130.

Definition: Age of individual in years at time of first study assessment

Sample value: 24

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

age_onset_years

integer(3)

Format:

Age of Onset (years).

Checks:

Age should be between 0 and 130.

Definition: Age of individual in years at time of onset of disorder

Sample value: 20

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

yob

integer(4)

Checks:

Year of Birth should be between 1800 and <current_year>.

Definition: Year of birth

Sample value: 1999

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

deceased

string(1)

Valid Values:

Y=Yes

N=No

NULL=Missing or not applicable or unknown

Definition: Whether individual is deceased

Sample value: N

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

yod

integer(4)

Valid Values:

0=Not Dead/Not Applicable

Year of Death should be between 1800 and <current_year>.

Definition: Year of Death

Sample value: 2005

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

dx_study

string

Valid Values:

Only values specified in the 'dx_study' column of the Diagnosis File Format are allowed here.

A value is required if and only if subject_type is P, S, or C. If subject_type is L, this value should be NULL.

Definition: Investigator-provided overall primary diagnosis.

Sample value: SADD

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

Comments: The dx provided in the column is meant to allow future investigators to match the dx's described in corresponding publications with the data stored in the repository. For example, if in your paper you describe 4 dx groups: Schizophrenia, Schizophrenia-spectrum, Bipolar, Bipolar-spectrum, this is where you would indicate how subjects in your study were grouped into those 4 categories. (In this case, the dx_system would be "Other" and a corresponding _dx dictionary would describe what criteria were used in grouping)

dx_confidence

integer

A value is required if and only if subject_type is P, S, or C, or subject_type is E and a value for dx_study is specified.

Valid Values:

1=Unknown; dx_study value asserted but completeness of diagnosis status and supporting information is unknown

2=Low; only some diagnostic criteria met for dx study as defined in the _dx file

3=Medium; all criteria met for dx study as defined in the _dx file, no supporting information

4=High; all criteria met for dx study as defined in the _dx file, and has supporting information

NULL=Not applicable

Definition: Confidence on the diagnosis in dx_study field

Sample value: 4

Note: a dx_confidence vale of "4" IS compatible with a dx_external_support value of "E"

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

dx_external_support

string(1)

A value is required if and only if subject_type is P, S, or C, or subject_type is E and a value for dx_study is specified.

Valid Values:

I=Submitted to NRGR and/or NDA

E=Not submitted to NRGR or NDA

NULL=Missing or not applicable or unknown

Definition: Diagnosis based on information that is not (or cannot be) submitted to the Center. This missing information overrules some information that was submitted to the Center. For example, medical records, interviews with family members, etc.

Sample value: I

Note: dx based on any source or instrument, even one administered by the study itself, should be coded E=external, if not deposited.

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

genetic_dx

string

Study-reported genetic variants.

consent

string(3)

A value is required unless subject_type is 'L' or 'I'.

Valid Values:

GRU=General Research Use

HMB=Health/Medical/Biomedical

REL=Related Mental Health Conditions

DIS=Specific Disorder Only

Definition: The type of consent granted by the subjects on the use of their data.

Sample value: REL

Detailed definition of "REL": Related Mental Health Conditions - Use of the data must be related to mental health research only. Use for methods development is permitted provided there is sufficient evidence that the methodology will further mental health research.

For more information about the valid values, see the consent definitions.

consent_modifier

string,multi_encoded

Valid Values:

IRB=IRB Approval required

PUB=Publication Required

COL=Collaboration required

NPU=Non-profit use only

MDS=Methods

GSO=Genetic Studies Only

NAE=No Animal Engraftment

RPU=Restrictions on for-profit use of samples

NTC=No Therapeutic Cloning

NULL=Missing or not applicable or unknown

Additional consent modifiers.

The user can specify more than one value for consent_modifier by separating them using a pipe "|".

Empty string is considered an invalid value.

Empty strings should be represented with the value NULL

For more information about the valid values, see the consent definitions.