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(warning) Using proper KCNI naming convention to label projects, participants, experiments, and files is extremely important as data is routed through the Neuroinformatics Platform according to these labels. Please take great case in ensuring data is properly labelled at every level, codes are consistent throughout the project life cycle and typos are avoided. Thank you!



Project ID



The project ID must be a 3 character project code, followed by a two digit study code, followed by an underscore and finally a 3 character site code.

Ex. ABC01_CMH

ExampleDefinititionRestrictions/RulesNotes
ABCProject Code3 Uppercase LettersChosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project.
01Study Code2 NumeralsTypically '01', unless describing divisions within a project
CMHSite Code3 Uppercase LettersMust be chosen from site code list HERE


A Project Code will be assigned when you meet with the Neuroinformatics Platform Admin at your initial project on-boarding meeting. If you already use a project code in some other capacity (including but not limited to NGDB or TIGR Lab XNAT), please share this at the meeting as it is best to keep the same project code across platforms/databases.

The Study Code is used to distinguish unique studies within a larger project, including sub-studies or study variations. Some big projects or labs will have multiple studies under the same project.

One or more Site Codes will be used based on the location(s) of the study. See the Standardized Site Codes table for a list of current study sites and their corresponding site codes.

Study Participant ID (LabKey Participant IDs)



It is important that each project Subject is assigned exactly 1 Subject ID that is unique across the project. In multi-site or multi-modality projects, care must be taken to ensure the same Subject is not assigned multiple Subject IDs at different sites or across different modalities. Of equal importance is the precise Subject ID entry at every data entry occurence. A Subject ID typo can have significant consequences throughtout the Neuroinformatics Platform system.

The Subject ID must be the concatenation of the Project ID, an underscore and a Subject Code.

Ex. ABC01_CMH_00000001

ExampleDefinititionRestrictions/RulesNotes
ABCProject Code3 Uppercase LettersChosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project.
01Study Code2 NumeralsTypically '01', unless describing divisions within a project
CMHSite Code3 Uppercase LettersMust be chosen from the Site Code List
00000001Subject Code4-8 Alphanumeric CharactersSee Subject Code Guidelines

The Subject Code denotes a specific person (or animal) within the study.

Guidelines for choosing an appropriate Subject Code:

  • must be 4 to 8 characters long
  • preferably contains only numeric digits, but can include uppercase letters if needed
  • recomended to start at 00000001 and increment as necessary
  • must not contain lowercase letters, symbols, or whitespace (spaces, tabs, etc)
  • must not include PHI (e.g., diagnosis), case/control status, or other sensitive information
  • must not contain the characters 'PHA' in positions 4-6, since these indicate "phantom" (non-human) images in XNAT
  • must not contain any coding related to location, visit, or any other code that is not representative of the participant. (eg. BAD: ABC01_CMH_V10001 - where V1 represents the first visit)

If you have already started collecting data and your participants do not follow this naming convention, please indicate this at your Neuroinformatics Platform project on-boarding meeting as a name conversion script might need to be implemented.


Note that for LabKey Study Participant IDs, it is highly recommended that the Participant code is fully numeric (rather than alphanumeric). 

Biosample ID (Specimen Label)

Please ensure the BiosampleIDs are entered correctly at all data entry occurrences, as a misspelled labels can have significant consequences throughout the Neuroinformatics Platform system.

Biosample IDs will be created automatically for users entering specimens through the Specimen Entry form. They consist of the following parts:

Ex. ABC01_CMH_00000001_02_BED_01

ExampleDefinititionRestrictions/RulesNotes
ABCProject Code3 Uppercase LettersChosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project.
01Study Code2 DigitsTypically '01', unless describing divisions within a project
CMHSite Code3 Uppercase LettersMust be chosen from Site Code list HERE
00000001Participant Code4-8 Alphanumeric CharactersSee Participant Code Guidelines
02Visit Code2 DigitsIncrement each visit
BEDSpecimen Code3 Uppercase LettersSee Specimen Code List
01Vial (Aliquot) Number2 DigitsThe vial number of the specimen collection


The Visit Code is 2 integers that represent the visit number. For example, 01 is first baseline visit, 02 is a follow-up visit, etc..

The Specimen Code is the type of the specimen collected from the participant. This is a predefined list from the Biobank and Molecular Core Facility. See the Specimen Code list below.

The Vial Number is 2 integers that represent the vial or aliquot number of the specimen. For example, 01 will always be first vial for the specimen collection, 02 would be second vial from the collection, etc. LabKey allows for a maximum of 10 vials per collection.


Specimen Codes 


When entering specimens, ensure the correct specimen code is entered in the Specimen Entry form and included in the LabKey Biosample ID.


DescriptionSpecimen CodePrimary SpecimenAdditiveDerivative
Oragene saliva for DNAOSDSalivaOrageneDNADNA
Norgen saliva DNANSDSalivaNorgenDNADNA
Blood EDTA for DNABEDBlood (Whole)EDTADNA
Lymphoblasts for DNALBDLymphoblastN/ADNA
Buccal swabs for DNABSDBuccal swabN/ADNA
Fibroblasts for DNAFBDFibroblastN/ADNA
Oragene microbiome for DNAOMDStoolOrageneMicrobiomeDNA
Blood EDTA for Buffy for DNABBDBuffyEDTADNA
PAXgene for RNABPRBlood (Whole)PAXgeneRNA
Oragene saliva for RNAOSRSalivaOrageneRNARNA
Blood EDTA for plasmaBEPBlood (Whole)EDTAPlasma
Blood Citrate plasmaBCPBlood (Whole)CitratePlasma
Blood Heparin plasmaBHPBlood (Whole)HeparinPlasma
Blood for SerumBSRBlood (Whole)
Serum
PBMC CellsPBCPBMC
PBMC
PBMC Dry PelletPBPPBMC
PBMC Pellet
Culture SupernatantCLSCulture
Culture
Blood Citrate plasma Extracellular Vesicles (EV)BCEBlood (Whole)CitratePlasma EV
Blood Citrate plasma positive controlBCCBlood (Whole)CitratePlasma Positive Control
Ear Punch DNAEPDEar PunchN/ADNA
Blood EDTA for RNABERBlood (Whole)EDTARNA
Urine (unpreserved)URNUrine



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