Overall Project info page changes.

[cjvillar]

Page Project

Change ordering of sections to: The preferred order of categories Project Wrangling Submission steps Post submission tracking

We feel a need to remove the star system (can discuss with Clay if needed) Consent to use boolean "Yes" or "No" Sample type → with enums Add “library preparation methods” Add organ, organ_part, disease, cell count to this section Combine Pubs, people & pay into one on the page.

[pnejad]

sample type enums:

• primary tissue
• organoid
• stem cell derived
• cell line

[pnejad]

library preparation methods enums

[JimKent]

Paris - how are we going to tell if it's frozen or fresh? Maybe what I'm wanting to capture in this field is spread across many in the spreadsheets.

[pnejad]

@JimKent that would be captured by 'preservation_method', which has the following enums:

"cryopreservation in liquid nitrogen (dead tissue)", "cryopreservation in dry ice (dead tissue)", "cryopreservation of live cells in liquid nitrogen", "cryopreservation, other", "formalin fixed, unbuffered", "formalin fixed, buffered", "formalin fixed and paraffin embedded", "hypothermic preservation media at 2-8C", "fresh"

[JimKent]

Thanks @pnejad. I added a preservation_method field hooked up to a vocab in the x table of the same name. I just populated it with fresh. I also replaced "fresh sample" in the "sample type" table with "primary tissue."

WHen I release the next version, possibly later today, could you edit the sample_type table inside of Tuatara to match your list, and add the ones (or at least the ones you think we'll see) from the preservation method? Thanks!

[JimKent]

Ok, the dev version has all the stuff from the initial ticket that I agree with and can change. A few things are reworked enough I'd like you to just have another look, and let me know if you like it.

For the concent I am not using the yes/no. I feel like we are overloading this field trying to make it serve both "concent from donor" and "concent from researcher". With this one I am just trying to capture concent from donor. Also I want to capture the donor concent in a slightly more nuanced way than just yes/no.

The AssayType is now called cDNA library prep. I have not edited out the SE and PE from the smart-seq2, and honestly am tempted not to, as currently the distinction is important, but apparently both SE and PE smartseq2 is going to be handled soon if not already by the pipeline, so we could just merge the fields at that point.

In terms of combining a bunch of stuff into the Overall section, please look at the new arrangement, and let me know if you would still like to. I did rearrange the Overall section quite a bit.

[pnejad]

@JimKent how often do we anticipate tracking a dataset where the donor has not given consent?

If consent has not been given by the donor, it should not be added to tuatara in the first place. I can only see this being useful in a scenario where the researchers are going back to the donors to request consent.

The consent that wranglers need to worry about is from the researchers (not applicable to GEO wrangling). We can not accept metadata or data files until the data contributor agrees to the terms in this form: tinyurl.com/HCA-Terms-Conditions

[pnejad]

@JimKent

The AssayType is now called cDNA library prep. I have not edited out the SE and PE from the smart-seq2, and honestly am tempted not to, as currently the distinction is important, but apparently both SE and PE smartseq2 is going to be handled soon if not already by the pipeline, so we could just merge the fields at that point.

Where would I see the SE and PE?

[JimKent]

It is still right after smart-seq2 in library prep controlled vocab.

[JimKent]

In terms of tracking stuff without consent - I do think we'll want to track some projects before we get the T&C. Historically we have done so with some from Aviv Regev's lab I believe for instance.