Human cell atlas import

[bwalsh]

As an ACED stakeholder, in order to visualize how the IDP will work with single cell data, it would be useful to see representative public domain or synthetic data in the sytem.

Should we download and import a HCA project?

https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22projectId%22,%22terms%22:%5B%22a62dae2e-cd69-4d5c-b5f8-4f7e8abdbafa%22%5D%7D,%7B%22facetName%22:%22genusSpecies%22,%22terms%22:%5B%22Homo%20sapiens%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22breast%20cancer%22%5D%7D,%7B%22facetName%22:%22specimenDisease%22,%22terms%22:%5B%22breast%20cancer%22%5D%7D%5D

[bwalsh]

If we download the metadata and look at its contents you will see it lists a mixture of file types including csv files.

https://service.azul.data.humancellatlas.org/manifest/files?catalog=dcp21&format=compact&filters=%7B%22projectId%22%3A+%7B%22is%22%3A+%5B%22a62dae2e-cd69-4d5c-b5f8-4f7e8abdbafa%22%5D%7D%7D&objectKey=manifests%2F77af5fb1-d47a-592f-9216-327fe645ee7f.83e2ac44-854a-54ee-9420-b4e2f6102404.tsv

Note there are both drs:// and https:// urls.

Picking one of the csv files at random we see:

[bwalsh]

There is also a way to retrieve the data from terra. Note PFB link.

https://data.humancellatlas.org/explore/projects/a62dae2e-cd69-4d5c-b5f8-4f7e8abdbafa/export-to-terra

That data can be opened in terra and we see the full project.

Including files.

[bwalsh]

The entity types are the typical ones you would see in any study. It is encouraging to see provenance about the workflow sequencing_*

We could import this style of PFB and map it to our data model

[bwalsh]

@kellrott per our conversation about HCA and h5 matrices yesterday