Metadata convention

The Single Cell Portal Metadata Convention defines a set of metadata terms that are intended to be used in a consistent manner across participating studies within the Portal. Where possible, the Metadata Convention uses established biomedical ontologies for the communication of complex domain information in a clear and concise manner. For simpler concepts, controlled lists of terms are used to ensure the data is uniform across participating studies.

While usage of the SCP Metadata Convention is optional, it is highly encouraged as using the SCP Metadata Convention will enable your data to be discovered through our advanced search interface. When metadata files for an SCP study are validated against the SCP Metadata Convention, extra steps are applied to ensure submitted metadata conforms to the requirements of the metadata convention. Note that unconventional metadata is not stored for advanced search.

Conventional metadata file anatomy

Click to view the full-size Conventional metadata file anatomy image

Conventional metadata files must:

• have NAME and TYPE rows (as described in Legacy Metadata File Format)
• provide cell names in column 1 of the expression file, ensuring cell names exactly match cell names in other study files
• include all Required Conventional Metadata
• follow Metadata Validation Rules
• be uploaded to the Portal with Metadata Validation

Example conventional metadata file

View an example conventional metadata file

The example conventional metadata file demonstrates a study with 5 samples from 3 donors. The "mouse1" donor contributes two samples "mm1_lymph" and "mm1_blood". The sample collection had both normal (PATO_0000461) samples and disease samples. Unconventional metadata "average intensity" is included and can be used to paint cells in plots. The cells in this metadata file were annotated with the convention-optional "cell_type" metadata so that cells from this study are findable through the Cell Type facet of advanced search if the metadata file is validated against the metadata convention.

Download the example Conventional Metadata File

How to upload your metadata file with the metadata convention (File upload wizard interface):

By default the Portal requires that metadata files meet a particular convention and so the button for using that convention is defaulted to "Yes". If for some reason you are not able to use the convention there is a link to reach out for help in the upload wizard.