Hi all,
I am trying to download a small subset of single-cell multiomics but have difficult to find out how after reading related paper and navigate this website. Would you please have a guidance? I went to https://knowledge.brain-map.org/ and select 10X Genomics Multiome but seems I still can’t download. Thank you so much.
Hi @Chris_D,
Thanks for reaching out and apologies for the delayed response.
The answer is going to depend on a number of factors, e.g. are the files at an archive or in one of our S3 buckets, etc.
Could you share more details on which specific data you’re interested in downloading? This will allow us to advise better.
Cheers,
Sven
Hi Sven,
Thank you for your response. I found two datasets, but not in a systematic way. At this stage, I just want to explore what data are accessible, so I don’t have any additional criteria for the data. A few other examples of multi-omics data that people can access would be helpful.
Best,
Chris
Hi Chris,
Glad you found what you needed for now.
It’d be helpful what kind of search-to-download process you’d expected to guide future product development. So any feedback you have would be much appreciated.
I’ll approach the rest of my answer as how I’d encourage folks to navigate the Brain Knowledge Platform’s (BKP) data ecosystem. I hope this helps 
Finding the right projects
I’d encourage anybody to start with the BKP’s Data Catalog on Brain Knowledge Platform and use the faceted search and text search options to narrow things down to projects that may fit your interests.
Tutorials for how to use them can be found here:
The result may look something like this:
Navigating projects, data collections and their files
Projects include data collections that capture their files. How many data collections and what other types of resources are associated with a project is visible via the content chips highlighted below.
The first example includes four data collections. The second includes only one data collection but also offers data visualizations via ABC Atlas.
One you click into a given project, you’ll see the list of data collections and their corresponding metadata. In most cases they include links to the data archives or S3 buckets where you can download the relevant files.
Archive example: Brain Knowledge Platform
S3 bucket example: Brain Knowledge Platform
Projects with detailed specimen inventories and file manifests
Some projects include detailed specimen inventories and file manifests that allow for more integrated subsetting of the data in BKP already.
Example: Brain Knowledge Platform
After you’ve filtered down to the specimens of interest, you can down the associated file manifest:
Once you have the manifest in hand, you can follow processes like this one to download the files.
What’s currently not possible
You currently can’t define a set of projects in Data Catalog, e.g. Technique = “10X Genomics Multiome”, check a box, and click a download button that downloads all the files at their respective locations.
