Upload data in AnnData mode

How to upload AnnData during study creation

The following guide assumes you have chosen the AnnData upload experience.

Step 1. Fill in the "Expression matrices" form fields

1. Select the species for the file being uploaded.
2. Choose the experimental input type of the biosample -- one of "Whole-cell", "Single Nuclei" or "Bulk".
3. Choose the library preparation protocol used for the uploaded matrix file. If the library preparation protocol you need is not available, contact us.
4. Choose the modality of the expression data. If the modality you need is not available, contact us.
5. Optionally enter a description of the file.
6. Optionally enter an axis label.

Step 2. Ensure the adata.obs dataframe conforms to SCP metadata convention

1. Clicking the metadata tab will reveal an image for the format that the metadata for your file must follow. No upload or form fields are required at this step. Successful metadata upload assumes  adata.obs dataframe has all the required conventional metadata listed in the SCP metadata convention (except NAME which will be automatically extracted from adata.obs_names).  For more information about conventional names. 

Step 3. Fill in the Clustering form fields

1. Choose a clustering from your data that you want to represent in the visualizations created on the portal. Enter that clustering’s name in the Name field.  The name will be displayed in Clustering drop-down menus in the Portal.
2. Enter the name of the corresponding .obsm key name (also known as the
   Multi-dimensional observations annotations .obsm "attribute" key names for clusterings)
3. Enter a description of the ordination (optional). The description should comment on the biology being displayed and the method of generating the plot. 
4. Enter axis labels for the plot:
   • The Z-axis is optional and only used for 3D plots. 
   • You can also optionally provide the range of each axis (domain min/max) if you would like your plots to render a certain way. If not, the portal will size each plot automatically based on the input data provided.

You can choose as many clusterings as your data contains. Each clustering corresponding to one .obsm key name.

Step 4. Upload the AnnData (.h5ad) file

1. Choose your AnnData file, formatted with a file extension like .h5ad, .h5, or
   .hdf5.
2. Optionally enter a description of the file.

Click "Save & Upload" to begin the process of uploading the file. All the form fields you filled in for Expression, Metadata and Clusterings will be parsed from this single AnnData file as appropriate. Please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal. 

The following file types under the section "Other files" are all optional. To jump past these descriptions click here.

Coordinate labels

1. Choose a coordinate label file to upload. This is not a cluster file but an annotation for overlaying on top of a scatter plot.
2. Select the corresponding cluster/spatial data. The coordinates of the label must be in the same range as the corresponding data for them to show.
3. Optionally add a description (which will appear below the image)

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Seurat data files

1. Choose a Seurat data file to upload. These files will not be used to power visualizations on the portal but can be added as for reference or as supplemental data. 
2. Optionally add a description of the file.

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Documentation & other files

If you would like to share a file we have not mentioned so far, please share it here. 

1. Upload a file
2. Choose the file type, such as "Documentation", if the file type you would like to add is not listed please contact us.
3. Optionally add a description of the file.

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. File validation and data ingest will take at least 10 minutes and up to several hours, depending on file size. A series of emails will follow to update you on the status of loading your data into the portal.

Finished!

Once you are satisfied with your uploaded files you can click “View study” to view your study summary page.

If you loaded the required visualization files you may click on "Explore" and explore your data online!

Known issue: AnnData ingest currently does not automatically update the "Cell count" field in Study settings. Please update Cell count to reflect the size of your dataset.

If you want to come back to your study to add, update, or remove files you can do so by clicking  your study’s “Settings” tab and then the “Upload/Edit data” section. The settings tab will also show a summary of your study, including uploaded files, some information in your files like clusters, and study permissions, as well as links to your study in the portal and in Terra.