File
A File represents a single data unit within a dataset, such as a document, spreadsheet, or image. In research and data management, files are essential for storing and organizing raw or processed data. They provide the foundation for data analysis, sharing, and compliance with storage policies. Properly formatted file entries ensure data can be retrieved, validated, and referenced consistently across projects.
The attributes in this model describe key metadata about each file, including its format, assay type, species, and associated dataset. These details help maintain file traceability and usability within data repositories.
Why You Should Contribute File Entries¶
Contributing file entries ensures that critical data files are accessible, organized, and easily retrievable. By documenting your files with key metadata, you enhance their usability in research workflows and support data sharing and collaboration. Accurate and detailed file entries also help prevent data loss, streamline future analyses, and facilitate compliance with research data management policies.
Who Should Be Contributing File Entries?¶
- Researchers – Share and organize key datasets and processed results to improve reproducibility and collaboration across projects.
- Data Managers – Maintain an organized structure for large-scale data repositories by documenting file attributes like formats, assays, and species.
- Project Leads – Ensure data generated by your research projects is categorized and described, making it easier for teams to access and reuse.
- Bioinformaticians and Data Analysts – Provide detailed metadata to streamline data integration, analysis pipelines, and compatibility with downstream tools.
- Collaborative Consortia Members – Contribute shared resources to foster data transparency, enabling broader collaboration and multi-institution research efforts.
Download Template¶
Use the file entry template to streamline your data entry process. The template contains pre-defined required fields.
Example Data Entry¶
The table below includes sample values to demonstrate proper attribute usage.
Example Data Entry (Biology-Focused)¶
| Attribute | Example Value |
|---|---|
| File Description | CSV file containing gene expression data for breast cancer samples |
| File Design | CSV (Comma-separated values) |
| File Url | https://www.example.com/files/breast_cancer_expression_data.csv |
| Assay | RNA Sequencing |
| File Level | Level 3: Processed summary data, like gene expression counts or coverage statistics (e.g., CSV files) |
| Species | Human |
| Tumor Type | Breast Carcinoma |
| Tissue | Breast |
| File View | List View |
| FileView_id | FileView_789012 |
| File Format | CSV |
| File Alias | Breast_Cancer_Gene_Expression.csv |
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | CDE | Examples |
|---|---|---|---|---|---|---|---|---|
| FileView_id | Unique ID associated with a File entry, used as a key for record linking and updates. This should be equivalent to File Alias unless otherwise directed. | True | string | None | ^syn\d{7,8}$ | None | CDE:14528010 | "SynapseID_123456" |
| Biospecimen Key | Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | -B\d{1,9} | None | ||
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | ||
| DatasetView Key | Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | ||
| Filename | The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet. | False | string | None | None | None | CDE:11284037, CRDC_CDE:11284037 | |
| File Alias | A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs. | True | string | None | None | None | "SynapseID_123456" | |
| File Description | Description of the file. | False | string | None | None | None | CDE:11280338, CRDC_CDE:11280338 | "CSV file containing gene expression data for breast cancer" |
| File Design | The overall design of the file. | False | string | None | None | None | "Gene expression values derived from RNA sequencing of tumor and normal tissue samples, processed using STAR aligner and featureCounts. Samples collected from 100 patients at diagnosis." | |
| File Batch Identifier | An identifier for the batch or group of files processed together (e.g. an extract batch, library prep batch, or sequencing run), used to support downstream analysis of batch effects. Free text, not a fixed list. | False | string | None | None | None | ||
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | Level 3 | |
| Assay | The assay the dataset, file, or publication is representative of. Multiple values permitted, comma separated. | True | string_list | None | None | View | ||
| Species | The species of origin corresponding to the model, or from which the biospecimen originates. | True | string_list | None | None | View | ||
| Tissue | Tissue type(s) associated with the dataset, file, or publication. Multiple values permitted, comma separated. | False | string_list | None | None | View | ||
| Tumor Type | The tumor type(s), if applicable, associated with the dataset, file, or publication. Multiple values permitted, comma separated. | False | string_list | None | None | View | ||
| File Url | The url of where the file is stored. | True | string | uri | None | None | CDE:11556141 | https://www.example.com/files/breast_cancer_expression_data.csv |
| File Format | The format of the file described by this entry. | True | string | None | None | View | CDE:11416926, CRDC_CDE:11416926 | CSV |
| File Assay Category | The broad category of experimental method used to generate the file, per NCI caDSR CDE 12373576 (Research Activity Experimental Method Type). | False | string | None | None | View | CRDC_CDE:12373576 | |
| Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/shared/#attribute-data-use-codes | False | string_list | None | None | View | CDE:0002001 | |
| File Longitudinal Group | A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment | False | string | None | None | None | Patient Cohort A - Baseline | |
| File Longitudinal Event Type | The type of event to which File Longitudinal Total Time Elapsed is related (e.g. Enrollment, Baseline). Free text, not a fixed list. | False | string | None | None | None | Baseline | |
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). | False | string | None | None | None | 10-9876543210-12 | |
| File Longitudinal Time Elapsed Unit | The unit of time associated with Sequential and Total Time Elapsed attributes. | False | string | None | None | None | Seconds | |
| File Longitudinal Total Time Elapsed | The total time elapsed between the first and current files contained this longitudinal group. | False | number | None | None | None | "990000s" | |
| File Data Category | A broad classification of the contents of a data file generated from an experiment or a study. | False | string | None | None | None | CRDC_CDE:14824731 | |
| File Data Checksum Type | The method by which the file checksum was calculated. | False | string | None | None | None | CRDC_CDE:11475057 | |
| File Data Checksum Value | A small-sized block of data derived from a file for the purpose of detecting errors that may have been introduced during file transmission and/or storage and used to verify data integrity. | False | string | None | None | None | CRDC_CDE:11480133 | |
| File Data Compression Status | The state of data when saved to storage space or during data transmission. | False | string | None | None | None | CRDC_CDE:11387114 | |
| File Data Size | The measure (in bytes) of how much space a data file takes up on a storage medium. | False | number | None | None | None | CRDC_CDE:11479876 |