Library Source Material - CDE 14808227 (retired)

[GeoffLyle]

caDSR Link: 14808227

Definition: "The cellular source of the double stranded DNA fragments analyzed by high-throughput sequencing."

[GeoffLyle]

Note: Splitting this from previous discussion #46, as that discussion was tracking both library source material and library source molecule. As library source material has been approved by the data harmonization team for implementation, a separate discussion to track its implementation status is warranted.

[Ssandor13]

From October 04, 2024 meeting:

Although this CDE was approved by the harmonization subgroup, we are re-opening this CDE to discuss what the next steps should be to map heme samples.

Per the discussion in #46 it was agreed to map to Bulk Tissue, however, the Federation agreed to not map heme samples in the meantime until 1) a new PV is agreed upon and accepted or 2) we find that one of the PV in the current caDSR CDE is adequate enough to map to.

At this time, mapping to Bulk Tissue seems as too much of a stretch to map to and thus this use case will be re-interviewed.

[Ssandor13]

Based on the provided permissible values for this CDE, none seem to directly correspond to blood as a cellular material source, as we discussed. Blood typically contains multiple cell types like red blood cells, white blood cells (buffy coat), and platelets, and can be processed into different preparations like bulk blood cells or plasma.

A potential new permissible value could be:
VM Long Name: Bulk Blood Cells
Definition: A biospecimen derived from whole blood consisting of multiple cell types, intended to be analyzed as a pool.
This definition would capture the essence of blood as a source while aligning it with the format of other permissible values like "Bulk Cells" and "Bulk Tissue. @jknable @GeoffLyle

[dunnpa]

Uberon has 'blood
http://purl.obolibrary.org/obo/UBERON_0000178
which can be interpreted as whole blood vs the many blood related derivatives.

I suggest not using bulk blood as that conflates the bulk vs single cell classification with the anatomic site or specimen type.

[Ssandor13]

From October 18th, 2024 meeting:

The team further discussed this and agreed with the consensus to map Blood to Bulk Tissue for this CDE.

[GeoffLyle]

@dunnpa
I'm seeing that "Other" is not a permissible value on the caDSR website (
https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14808227%20and%20ver_nr=1).

When we implement this CDE, we will not be adding "Other" as it is not a listed permissible value. Is "Other" going to be added to this CDE?

[dunnpa]

I think this PV list is pretty good as is.
Janice and Maureen, what are your thoughts on adding "Other" as a PV?

[dunnpa]

From: "Ryan, Maureen (NIH/NCI) [C]" maureen.ryan2@nih.gov

Hi Geoff,

The term “Blood Bulk Cells” is actually combining the specimen, blood, with the source material, bulk cells. There are two separate CDEs for these two properties.

• For the specimen, blood, please use CDE 12445832 Specimen Material Category.
• For the library source material, bulk cells, please use CDE 14808227 Library Source Material.

[GeoffLyle]

At November 1, 2024, meeting it was decided to use the new CDE #119. CDE 14808227 will not be implemented in the CCDI Federation open API.