The AD-DCC will provide you with a staging folder for your data, within the AD Knowledge Portal backend (a specific Synapse project). Within the staging folder, we will create a folder structure based on AD Knowledge Portal community standards. Organizing your data files in accordance with this structure will make annotation and other data management tasks easier both for you and AD-DCC staff.
Note that staging folders are not public-facing and should not be shared in manuscripts, with journal editors, or in any other public-facing capacity.
This page explains general practices for organizing data and other materials in the AD Knowledge Portal backend, which may need to be tailored to the unique needs of your study or project.
Project Folders Structure
Your Synapse project will usually be set up with this hierarchy of folders, in accordance with the conventions established by the AD-DCC:
-
Data - where files will be moved once they are ready for public release to the AD Knowledge Portal.
Do not upload any files directly to the 'Data' folder. The Data Manager will move data to this folder upon release.
-
Staging - where files are uploaded and held while undergoing data curation. These include folders organized by study and/or data type, followed by subfolders for levels of data processing ("raw data" or "processed data"), analysis, and metadata.
-
Raw or Processed - raw data or processed data.
-
Results - figures or other outputs not considered "raw data".
-
Metadata - metadata templates, data dictionaries, and optional readme files.
-
Example structure
staging_rnaSeq
├── processed
├── counts_normalized.csv
├── raw
├── sample1.fastq
├── sample2.fastq
staging_metadata
├── individualhuman.csv
├── biospecimenhuman.csv
├── rnaSeqassay.csv
└── manifest.csv
Finer organization
-
Within each data type, it is possible to group data with batches or certain other factors (i.e. tissue type, species). For example, an RNA-seq data folder may have subfolders "batch 1" and "batch 2" that were produced at different times during the project.
-
If your study includes multiple data types, you may need more than one assay folder. Name these folders by data type (for example,
[study abbreviation]_rnaSeq_assay,[study abbreviation]_snRNAseq_assay). -
Please consult with AD-DCC staff regarding any additional levels of data organization that your study or project may require.
Analysis Folder
An Analysis Folder may be added to house protocols, code, and/or derived results which are supplementary to the data and metadata files.