Form Structure: Biomarker Assay Data Form
This form structure is an organized set of data definitions for a form that has not been copyrighted
Resource:
FITBIR
Title:
Biomarker Assay Data Form
Short Name:
BiomarkerAssayDataForm
Description:
Standard form for protein and microRNA biomarker assay data.
Disease:
General (For all diseases)
Traumatic Brain Injury
Organization:
FITBIR
Required Program Form:
No
Standardization:
Standard NINDS CDE
Labels:
Form Type:
Genomics
Publication Date:
2016-10-26
Version:
1.1
Date Created:
2016-02-26
Owner:
Number of Data Elements:
75
eForms:
N
Logically grouped data elements with defined frequency at which they repeat.
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | GUID | Global Unique ID which uniquely identifies a subject | GUID | Required | CDE |
| 2 | Subject identifier number | An identification number assigned to the participant/subject within a given protocol or a study. | SubjectIDNum | Optional | CDE |
| 3 | Age in years | Value for participant's subject age recorded in years. | AgeYrs | Recommended | CDE |
| 4 | Vital status | Status of participant/subject as alive or dead | VitStatus | Optional | CDE |
| 5 | Visit date | Actual interview or visit date | VisitDate | Recommended | CDE |
| 6 | Site name | The name of the site for the study | SiteName | Recommended | CDE |
| 7 | Days since baseline | The number of days since baseline | DaysSinceBaseline | Optional | CDE |
| 8 | Case control indicator | Indicator of whether subject is in the case or control arm of the study. | CaseContrlInd | Optional | CDE |
| 9 | General notes text | General notes | GeneralNotesTxt | Optional | CDE |
Additional Element Groups
Listed below are your additional element groups.
Form Administration (Appears Up To 1 Time)
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | Context type | The context to which the questions were answered | ContextType | Recommended | CDE |
| 2 | Context type other text | The free-text related to ContextType specifying other text | ContextTypeOTH | Recommended | CDE |
| 3 | Data source | Source of the data provided on the case report form | DataSource | Recommended | CDE |
| 4 | Data source other text | The free-text field related to Data source specifying other text. Source of the data provided on the case report form | DataSourceOTH | Recommended | CDE |
Analyte and Test Result (Appears Up To 1 Time)
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | Analyte name | The molecule or molecular entity that is measured in an analytical procedure or assay. | AnalyteNam | Required | UDE |
| 2 | HGNC gene symbol | Official gene symbol that has been approved by Human Genome Organization Nomenclature Committee (HGNC) | HGNCGeneSymbl | Recommended | UDE |
| 3 | Analyte annotation identifier(s) | The list of analyte annotation IDs contains references to well-known public resources such as dbGaP, HGNC, NCBI, OMIM, UniProt, or other Proprietary Database. See Guidelines for more details | AnalyteAnnotatnIDs | Optional | UDE |
| 4 | Lab test result score type | Indication of whether the reported lab test result value is raw or calculated value | LabTestResultScoreTyp | Recommended | UDE |
| 5 | Lab test result value | Result of the laboratory test | LabTestResltVal | Recommended | CDE |
| 6 | Lab test result unit of measure | Unit of measure for the laboratory test result | LabTestResltUoM | Recommended | CDE |
| 7 | Limit of detection | The lowest quantity of a substance that can be distinguished from the absence of that substance (a blank value) within a stated confidence limit (generally 1%). | LimitOfDetectn | Optional | UDE |
| 8 | Limit of detection unit of measure | Limit of detection unit of measure | LimitDetectnUoM | Optional | UDE |
| 9 | Laboratory test lowest range value | Lowest possible value in the range of the lab test | LabTestLowRangeVal | Optional | UDE |
| 10 | Laboratory test highest range value | Highest possible value in the range of the lab test | LabTestHighRangeVal | Optional | UDE |
| 11 | Coefficient of variation(CV) in percentage | The standardized measure of dispersion of a probability distribution or frequency distribution, expressed as a percentage. | CVinPercentage | Optional | UDE |
| 12 | Lab test result status | Status of the laboratory test result, usually based upon the comparison of the test result to the normal range for the lab test performed | LabTestResltStatus | Optional | CDE |
| 13 | Test assay result abnormality subtype | The subtypes that provide further details on the abnormality condition for a given test assay result | TestAssyResltAbnrmlySubtyp | Optional | UDE |
| 14 | Data file content type | Indicator as to whether or not the attached data file contains the raw data, processed data, both raw and processed data, or unknown | DataFileContntTyp | Recommended | UDE |
| 15 | Molecular data file | Molecular data file | MolDataFile | Recommended | UDE |
| 16 | Assay data - Platform quality control indicator | Indicator for the quality control for the platform that is used to carry out a molecular laboratory or computational experiment. | PlatformQualContInd | Recommended | UDE |
| 17 | Assay data - Platform quality control text | Description of the quality control for the platform that is used to carry out a molecular laboratory or computational experiment. | PlatformQualContTxt | Recommended | UDE |
| 18 | Assay data - Concentration type | Concentration type that is used to carry out a molecular laboratory or computational experiment. | ConcentrationTyp | Recommended | UDE |
| 19 | Assay data - Concentration value | Concentration values that is used to carry out a molecular laboratory or computational experiment. | ConcentrationVal | Recommended | UDE |
| 20 | Unit of measurement type | A unit of measurement is a definite magnitude of a quantity, defined and adopted by convention or by law, that is used as a standard for measurement of the same quantity. | UnitOfMeasTyp | Recommended | UDE |
| 21 | Unit of measurement type other text | The text to describe a unit of measure that is not captured in the permissible values of the UnitOfMeasTyp data element. | UnitOfMeasTypOthTxt | Recommended | UDE |
Experiment Sample (Appears Up To 1 Time)
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | Organism NCBI Taxonomy Identifier | Organism NCBI Taxonomy Identifier | OrganismNCBITaxonID | Recommended | UDE |
| 2 | Study sample name | Sample name assigned within a study where the sample is used. | StudySmplNam | Recommended | UDE |
| 3 | Lab specimen type | Type of specimen collected for the laboratory test | LabSpecmnTyp | Recommended | CDE |
| 4 | Lab specimen collection date and time | Date (and time if applicable and known) when the specimen was collected | LabSpecmnCollDateTime | Optional | CDE |
| 5 | Biosample repository name | Biosample repository name | BioSampReposNam | Optional | UDE |
| 6 | Biorepository sample name | Sample name assigned by the biorepository. | BiorepositorySmplNam | Optional | UDE |
| 7 | Experiment sample name | Sample name assigned by the genotyping or sequencing service provider. | ExprmntSmplNam | Optional | UDE |
| 8 | Quality control sample indicator | Indicator of whether the sample is used for quality-control in an experiment. | CntrlSmplInd | Recommended | UDE |
| 9 | NCBI Biosample identifier | Biosample ID assigned by NCBI BioSample Database where the sample is registered with its metadata. | NCBIBioSmplID | Optional | UDE |
| 10 | Sample identifier assigned by dbGaP | The sample identifier assigned by the database of Genotypes and Phenotypes (dbGaP) for the submitted subject sample. | dbGaPSmplID | Optional | UDE |
| 11 | Molecule biological type | The type of molecule that was extracted from the biological material. Molecules can be DNA, RNA, and protein. | MolBioTyp | Optional | UDE |
| 12 | DNA subtype | The subtype of a DNA molecule. | DNASubTyp | Optional | UDE |
| 13 | RNA subtype | The subtype of an RNA molecule | RNASubTyp | Optional | UDE |
Assay and Reagent (Appears Up To 1 Time)
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | Lab test LOINC code | Identifier name given to a test performed on body fluid(s) and tissues. Test names are typically comprised of the analyte name, properties (%, Ratio, etc.), the type of body fluid tested, and any special instructions. | LabTestLOINCCode | Optional | CDE |
| 2 | Assay plate name | The assay plate name represents the plate or array name where standard curves, control samples, and experiment samples were collected and assayed. | AssayPlatNam | Recommended | UDE |
| 3 | Assay kit name | Assay kit name | AssyKitNam | Optional | UDE |
| 4 | Reagent name | The reagent name | ReagntNam | Optional | UDE |
| 5 | Reagent description | The assay reagent description provides further details on the nature and purpose of the reagent. | ReagntDesc | Optional | UDE |
| 6 | Reagent antibody registry identifier | Reference to AntibodyRegistry.org to describe antibody based reagents | ReagntAnibodyRegistryID | Optional | UDE |
| 7 | Reagent manufacturer | Name of the reagent manufacturer. | ReagentManuFacturer | Optional | UDE |
| 8 | Reagent lot number | Lot Number from the reagent manufacturer. | ReagentLotNumTxt | Optional | UDE |
| 9 | Reagent catalog number | Identifier for the reagent in the vendor catalog. | ReagentCatelogNumTxt | Optional | UDE |
Experiment Metadata (Appears Up To 1 Time)
| # | Title | Short Description | Variable Name | Required? | Type |
|---|---|---|---|---|---|
| 1 | Molecular study laboratory name | Name of laboratory that performed the molecular study | MolecularStdyLabName | Recommended | CDE |
| 2 | Experiment name | A user provided name for the experiment configuration | ExprmntName | Recommended | UDE |
| 3 | Experiment purpose | The experiment purpose describes the nature of the data that will be collected. | ExprmntPurpose | Recommended | UDE |
| 4 | Molecular platform vendor | The name of the company, facility or laboratory where the molecular platform was manufactured or produced. | MolPltfmVndr | Recommended | UDE |
| 5 | Molecular platform vendor other text | Molecular platform vendor other text | MolPltfmVndrOTH | Optional | UDE |
| 6 | Molecular platform name | The specific platform name or technology that is used to carry out a molecular laboratory or computational experiment. | MolPltfmName | Recommended | UDE |
| 7 | Molecular platform version | The version of platform that is used to carry out a molecular laboratory or computational experiment. | MolPltfmVer | Optional | UDE |
| 8 | Molecular platform distribution | The operational process by which a molecular platform is manufactured and made available. | MolPltfmDist | Recommended | UDE |
| 9 | Assay classification category based on output type | Assay classification category based on output type | OutputTypAssyClass | Optional | UDE |
| 10 | Experiment measurement technology type | Experiment measurement technology type | ExprmntMeasmntTechTyp | Recommended | UDE |
| 11 | Experiment measurement technology type other text | Experiment measurement technology type other text | ExprmntMeasmntTechTypOTH | Optional | UDE |
| 12 | Single- or multiplexing assay type | Indication of single- or multiplexing assay used in the experiment | AssayPlexingTyp | Optional | UDE |
| 13 | Name of analysis software used on molecular data | Name of analysis software used on molecular data | MolDataAnlysisSftwrNam | Optional | UDE |
| 14 | Dilution factor | The dilution factor is the ratio of aliquot volume to the final volume. It indicates how much a sample was diluted before it was assayed. | DilutionFactor | Optional | UDE |
| 15 | Replication number | The number of times the experiment has been repeated for a biological sample. | ReplicationNum | Optional | UDE |
| 16 | Laboratory protocol type | Types of laboratory protocols that are used in the design and implementation of experiments, also known as standard operations procedure(SOP). | LabProtlTyp | Required | UDE |
| 17 | Laboratory protocol type other text | The free-text field related to 'Laboratory protocol type' specifying other text. It is a preferred list of terms to characterize the protocol's content. | LabProtlTypOTH | Optional | UDE |
| 18 | Laboratory protocol file(s) | A single or collection of protocols that have been used in the design and implementation of experiments | LabProtlFiles | Required | UDE |
| 19 | Laboratory test comment | Comments on the laboratory test | LabTestComment | Optional | UDE |
Keywords
