Metadata is standardized information about your data and will be used to annotate the data files in Synapse. Contributors must submit these These metadata files for needed for each study: Individual, Biospecimen, Assay, and Manifest. These are described below with links to the latest templates.
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A tab-delimited manifest file allows you to upload and download many data files, and set annotations, at once via the a client (Python, R, or command line clients). Each row in the manifest species the file to be uploaded and the annotations to be applied. To begin, download the manifest template and populate the relevant fields. For instance, you must specify
Template: template_manifest.xlsx
Specify:
path– the current path of the file to uploadparent(local, server, cloud)parentID– the Curator will provide a Synapse ID of the Staging/ folder where the file will be uploaded.
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Annotations are key-value pairs that associate metadata with a file and help users find and query data. For more info, see the Synapse documentation for annotations.
Provenance is a means of describing a relationship between raw and processed data. For more info, see the Synapse documentation on provenance. If you are uploading the results of an analysis, you may add a Used column to a manifest to give the Synapse ID(s) of the raw files that went into the analysis. If multiple Synapse IDs should be associated with a processed file, separate them with a semicolon
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With the three metadata CSVs and manifest TSV complete, you are ready to validate the study metadata.
Metadata Validation
Use the dccvalidator to validate your metadata files.
Once your validated metadata are ready for upload you will upload them to the parentID provided by your Curator via email.
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To standardize data submissions and quality control, we’ve built a metadata validation tool (, dccvalidator) , that will perform several data quality checks on metadata templates and manifest files.
Under Species, select ‘MODEL-AD mouse model’ button.
Under Assay type, select the assay appropriate for your data. If an appropriate assay is unavailable, leave the default selection of rnaSeq.
Use the ‘Browse’ buttons to select the individual animal metadata, biospecimen metadata, assay metadata file, and/or manifest file.
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Files that are uploaded to the Metadata Validator will be placed into a private folder on Synapse so that they can be reviewed by the MODEL-AD Data Curation team. They will only be visible to the Data Curation team and will not be shared. |
Uploading Study and Assay Descriptions
These documents should be submitted to the dccvalidator to validate the variable keys and controlled vocabulary.
Start by selecting the ‘Study Documentation’ tab on the left side of the window.
Please note, you will be unable see files after you’ve uploaded them.
The data curation team will always look at file versions and date/time stamps and take the most recent version of the file, so if in doubt, please feel free to upload a new versionValidated metadata can be uploaded to the staging location provided by the DCC Curator. See more information about uploading data.