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
Example | Definitition | Restrictions/Rules | Notes |
---|---|---|---|
ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
01 | Study Code | 2 Numerals | Typically '01', unless describing divisions within a project |
CMH | Site Code | 3 Uppercase Letters | Must 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
Example | Definitition | Restrictions/Rules | Notes |
---|---|---|---|
ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
01 | Study Code | 2 Numerals | Typically '01', unless describing divisions within a project |
CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
00000001 | Subject Code | 4-8 Alphanumeric Characters | See 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
Example | Definitition | Restrictions/Rules | Notes |
---|---|---|---|
ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
01 | Study Code | 2 Digits | Typically '01', unless describing divisions within a project |
CMH | Site Code | 3 Uppercase Letters | Must be chosen from Site Code list HERE |
00000001 | Participant Code | 4-8 Alphanumeric Characters | See Participant Code Guidelines |
02 | Visit Code | 2 Digits | Increment each visit |
BED | Specimen Code | 3 Uppercase Letters | See Specimen Code List |
01 | Vial (Aliquot) Number | 2 Digits | The 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.
Description | Specimen Code | Primary Specimen | Additive | Derivative |
---|---|---|---|---|
Oragene saliva for DNA | OSD | Saliva | OrageneDNA | DNA |
Norgen saliva DNA | NSD | Saliva | NorgenDNA | DNA |
Blood EDTA for DNA | BED | Blood (Whole) | EDTA | DNA |
Lymphoblasts for DNA | LBD | Lymphoblast | N/A | DNA |
Buccal swabs for DNA | BSD | Buccal swab | N/A | DNA |
Fibroblasts for DNA | FBD | Fibroblast | N/A | DNA |
Oragene microbiome for DNA | OMD | Stool | OrageneMicrobiome | DNA |
Blood EDTA for Buffy for DNA | BBD | Buffy | EDTA | DNA |
PAXgene for RNA | BPR | Blood (Whole) | PAXgene | RNA |
Oragene saliva for RNA | OSR | Saliva | OrageneRNA | RNA |
Blood EDTA for plasma | BEP | Blood (Whole) | EDTA | Plasma |
Blood Citrate plasma | BCP | Blood (Whole) | Citrate | Plasma |
Blood Heparin plasma | BHP | Blood (Whole) | Heparin | Plasma |
Blood for Serum | BSR | Blood (Whole) | Serum | |
PBMC Cells | PBC | PBMC | PBMC | |
PBMC Dry Pellet | PBP | PBMC | PBMC Pellet | |
Culture Supernatant | CLS | Culture | Culture | |
Blood Citrate plasma Extracellular Vesicles (EV) | BCE | Blood (Whole) | Citrate | Plasma EV |
Blood Citrate plasma positive control | BCC | Blood (Whole) | Citrate | Plasma Positive Control |
Ear Punch DNA | EPD | Ear Punch | N/A | DNA |
Blood EDTA for RNA | BER | Blood (Whole) | EDTA | RNA |
Urine (unpreserved) | URN | Urine | ||
DNA purified by Ethanol Precipitation | DED | DNA | Ethanol precipitation | DNA |
Saliva (unpreserved) for DNA | SLD | Saliva | N/A | DNA |
Blood with unknown additive for DNA | BXD | Blood (Whole) | Unknown | DNA |