Data Submission Guidelines
- Scott Saccone
- Bill Howells
In Progress
Please note these guidelines are in progress.
Hello, if you plan to submit data to the repository please review the guidelines below.
Contents
File formats
There is no specific template for data submission. We request a reasonably structured set of tables in Excel or delimited text (comma/tab separated). If you happen to use MySQL, a dump of the database would be particularly appreciated.
Please identify subjects and biomaterials
Please make sure each subject has a unique ID. If you plan to send only a table of cell lines, there should be a subject ID column in that table. A key function of the subject ID is to identify cell lines belonging to the same subject, especially when using the "One File" approach described below. We would record your subject IDs internally but would not make them public. We generate our own public subject IDs for ordering purposes. Similarly, please ensure each cell line has a unique ID.
Do not include personally identifiable information
There should be no personally identifiable information included in your submission. Please feel free to contact us if you have questions about this.
There are at least two ways of organizing cell line data.
Two Files: (1) Subjects, and (2) Cell Lines
This is the preferred approach.
In this case one table, such an Excel sheet, would contain clinical/genetic data with a subject ID column and several clinical/genetic data columns. This table would contain one row per subject.
Another table would contain cell line data and have a cell line ID column, a subject ID (allowing multiple lines per subject) and then several cell line metadata columns. This second table would contain one row per cell line but each subject may have multiple cell lines.
One File: Combined Subjects and Cell Lines
In this case you would submit a single table containing both a subject ID column and a cell line ID column. It would also contain all the clinical and cell line metadata columns. In this approach, when a subject has multiple cell lines, all the clinical data is repeated for that subject (assuming that subject has only one set of clinical data; more elaborate systems would be required for longitudinal data).
Other Approaches
If your data does not fit into the above approaches, for example if you have longitudinal data, please feel free to contact us and we can work out a format.
Some Fields We Request
Below are some specific fields we would like to see in the data you submit.
Clinical Data
Essential Clinical Fields
Please include the following clinical fields.
| Field | Description |
|---|---|
| Disease/Condition | The disease/condition to which the diagnosis applied |
Other Clinical Fields
The NINDS Catalog Application is capable of handling extensive, heterogeneous clinical datasets. We would appreciate any clinical data that investigators would find usefuly when ordering cell lines. The system can even handle multiple data sources per subject; for example, if a subject was interviewed/tested multiple times, possibly using different diagostics.
Please see the Documents tab of our Catalog Application for some examples of types of diagnostics we currently use.
Diagnostic PDF Files
Family Data
| Field | Description |
|---|---|
| Family ID | identifier for all members in a family |
| Individual ID | unique subject id (same id and format as other data) |
| Mother's ID | unique subject id of mother (use zero for founders and married-ins) |
| Father's ID | unique subject id of father (use zero for founders and married-ins) |
Genetic Data
| Field | Description |
|---|---|
| Name of Gene | Please try to use common gene names, such as those found in the NCBI Gene database. |
Cell Line Data
| Field | Description |
|---|---|
| Cell Line ID |
|
Documentation
Please include descriptions of each of the columns in the tables.
Privacy
If there any concerns about making a particular data element publicly available, please make a note of this in the documentation.
File with Actual Diagnostics
If you happen to have a file describing the actual diagnostic used to gather clinical data, such as a PDF with the list of questions/diagnostics that were used for the patients, please include it. For example, in our Catalog Application we record those PDFs, such as for Parkinsonism, in the Documents tab. The clinical data for that PDF is then displayed in a subject’s detail such as for this subject.
