S5. Creating a public release of AIT99

[hkir-dev]

Epic:

Description

User: The same Scientist from Use Case 1 #98
Use Case: All the annotations are done for AIT99 from me and from the experts and we are ready to release the taxonomy publicly.
What I have:

• A link to final AIT99 file(s) with all the TDT annotations
• My starting h5ad file in AIT format, potentially with updated TDT annotations

What I need to know:

• How do I make this taxonomy public?
• I’d like to publish this taxonomy on cellxgene. Is it ready to go or do I need to do additional formatting?
• I’m submitting a paper with this taxonomy. What links should I include in it?

Tasks

• Write workflow doc for public release #114
• Task2
• Task3

[dosumis]

How do I make this taxonomy public?

1. Export to h5ad - checks will run to ensure consistency and report any problems in need of fixing before making release.
2. Press the Publish button to make a final release
3. Make the GitHub repo public (will need someone with Admin permissions - currently members of our group + some of the Allen team, including Patrick & Tim Fliss)
4. Publish AnnData file via some mechanism at Allen????

I’d like to publish this taxonomy on cellxgene. Is it ready to go or do I need to do additional formatting?

1. CxG requires a single Cell Ontology term per cell. We will provide tooling to generate this (there may be some cases where users need to choose between terms. We will support this.)
2. We don't curen

I’m submitting a paper with this taxonomy. What links should I include in it?

1. Link to final AnnData file with merged in taxonomy
2. PURL - supports reporting as DataFrames in combination with CAS-Tools - which can also pull h5ad file.
3. CxG link?

Note - one aim of all of this is to provide an infrastructure that ensures versions match across papers, platforms etc. This can be tested via embedded version links but also via tests that check for consistency between taxonomy and linked AnnData file.