Modify SenNet Breast organ

[maxsibilla]

Currently we have the following entry in organs for "Breast" from the UBKG:

    {
        "code": "C030027",
        "organ_cui": "C0006141",
        "organ_uberon": "UBERON:0000310",
        "rui_code": "BS",
        "sab": "SENNET",
        "term": "Breast"
    }

After discussing with the team from Indiana we learned that the RUI tool supports “Mammary Gland (Left)” and “Mammary Gland (Right)“.

Is it possible to modify this existing entry into a left and right breast? Are there UBERON and CUI codes to support that? Would it be better to change this to be "Mammary Gland" instead of "Breast"?

@bhonick @AlanSimmons @shirey

[maxsibilla]

Notes regarding the RUI tool

• The 2 digit code is not required, it is used on the HuBMAP side as a quick lookup for the UBERON or FMA term (https://github.com/hubmapconsortium/ingest-ui/blob/5bce9fba3162a64faf0433a541fd8a465a883f87/src/src/constants.jsx#L139)
• The UBERON code for "Mammary Gland" is http://purl.obolibrary.org/obo/UBERON_0001911
  • An FMA code is required to specify left or right and would need to be stored instead
  • Mammary Gland L -http://purl.org/sig/ont/fma/fma57991
  • Mammary Gland R - http://purl.org/sig/ont/fma/fma57987

[AlanSimmons]

Issues to consider

1. Downward/cross-platform compatibility: HuBMAP datasets previously registered for breast would use the existing UBERON code. If we change from one code (UBERON:0000310) to two FMA codes, wouldn't we need to reindex or reregister? Because we wouldn't have laterality for existing HUBMAP datasets, how would we map?
2. A breast contains mammary glands. Is it possible to have a sample of breast tissue that was not from the mammary gland?
3. More of a Pandora's Box than an issue: In addition to codes for left and right mammary gland, FMA has left and right mammary glands for both female and male. It seems a bit overdetermined to use the sex/location-specific codes instead of the location-specific codes, because we can obtain the sex from the donor metadata.

Proposal

1. Keep the existing UBERON code for breast for cross-platform compatibility.
2. Add the location-specific FMA codes for left and right mammary glands.
3. Ask an anatomy subject matter expert (at Indiana) whether we can assume that "breast" means mammary gland, at least for the particular case of sample registration.

[maxsibilla]

After discussing with the Indiana team I have applied a band-aid fix to allow for RUI registration of Breast Blocks. I have added a check for this organ and set the RUI organ to be "Mammary Gland, L"

[AlanSimmons]

So, do we add codes for left and right mammary glands and delete the code for breast in SenNet?

[maxsibilla]

@AlanSimmons I added this as an agenda item for the CODCC meeting tomorrow

[AlanSimmons]

In source

SENNET:C030082 - Mammary gland (left) - cross-referenced to FMA:57991 SENNET:C030083 - Mammary gland (right) - cross-referenced to FMA:57987

These will be available in the next release of the HuBMAP/SenNet UBKG.