NCI - Multiple Term Requests

[ssyeds3]

The NCI Cancer Research Data Commons (CRDC) Program (https://datacommons.cancer.gov/) is developing data standards for submitting data to the CRDC ecosystem. As part of this effort, the CRDC Data Standards Service (DSS) Team is identifying industry standards that can be leveraged for this harmonization and standardization effort. For the data element ‘Specimen Anatomic Site’, we will be referencing UBERON. The DSS team is requesting 49 terms, to be included in UBERON, that are needed by one or more CRDC repositories. We could not find these terms in UBERON. For the 49 terms we have provided the equivalent NCI Thesaurus terms and the concept codes. Please let us know if you have any questions.

UBERON Term Suggestion Submission.xlsx

[cmungall]

Thanks @ssyeds3, we would be happy to add any missing terms that are in scope.

Note that Uberon is for gross anatomy. It is designed to work in concert with CL (for cell types) and GO (subcellular compartments).

We could not find these terms in UBERON

I believe all of the gross anatomy terms in your list are present. Note we also have NCIT xrefs for these. Can you specify how you went about determining these terms are missing? I am worried you are using some kind of interface that is masking synonyms or mappings. We have many tools to help with mappings if you are interested.

Requested Term	NCIt Concept Code	NCIt Concept Name	NCIt Concept Definition
Antrum	Antrum	C97102	A chamber formation in an organ.

Are you sure this is really the concept you want? This is a very very general abstract term, we typically avoid concepts that don't have any biological unity.

I suspect the person at CRDC meant phyloric antrum when they said "antrum" and this was mistakenly mapped to C97102

Requested Term	NCIt Concept Code	NCIt Concept Name	NCIt Concept Definition
Hepatic	Hepatic	C13308	"Pertaining to, affecting, or associated with the liver."

I don't think you really want this term. This is an adjective. I assume you want the term for liver here? This is of course in uberon

Requested Term	NCIt Concept Code	NCIt Concept Name	NCIt Concept Definition
Cell-Line	Cell Line	C16403	A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space.

This is not in scope. I suggest CLO:0000031

Requested Term	NCIt Concept Code	NCIt Concept Name	NCIt Concept Definition
Mitochondria	Mitochondrion	C13258	"Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Mitochondria contain distinctive ribosomes, transfer RNAs, amino acyl t-RNA synthetases, and elongation and termination factors. Mitochondria depend upon genes within the nucleus for many essential messenger RNAs. Mitochondria consist of two sets of membranes, a smooth continuous outer coat and an inner membrane arranged in tubules or more often in folds that form platelike double membranes (cristae). Mitochondria are the principal energy source of the cell and contains the cytochrome enzymes of terminal electron transport and the enzymes of the citric acid cycle, fatty acid oxidation, and oxidative phosphorylation. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP."

Use GO for subcellular components

Requested Term	NCIt Concept Code	NCIt Concept Name	NCIt Concept Definition
Islet Cells	Islet Cell	C32885	A pancreatic cell that produces and secretes hormones such as insulin and glucagon.

this is in CL

For many other terms e.g. hippocampus, muscle, they are all there, I suspect you are using a tool that doesn't search on synonyms

You also have terms like "Other" and "Unknown". These are not anatomical terms.

[ssyeds3]

You response was very helpful. Thanks Chris! I understand that Uberon works in concert with CL & GO, does Uberon also work with other ontologies such as BSPO, RO, and CLO?

[ssyeds3]

Thanks @ssyeds3, we would be happy to add any missing terms that are in scope.

Note that Uberon is for gross anatomy. It is designed to work in concert with CL (for cell types) and GO (subcellular compartments).

We could not find these terms in UBERON

I believe all of the gross anatomy terms in your list are present. Note we also have NCIT xrefs for these. Can you specify how you went about determining these terms are missing? I am worried you are using some kind of interface that is masking synonyms or mappings. We have many tools to help with mappings if you are interested.

Requested Term NCIt Concept Code NCIt Concept Name NCIt Concept Definition Antrum Antrum C97102 A chamber formation in an organ. Are you sure this is really the concept you want? This is a very very general abstract term, we typically avoid concepts that don't have any biological unity.

I suspect the person at CRDC meant phyloric antrum when they said "antrum" and this was mistakenly mapped to C97102

Requested Term NCIt Concept Code NCIt Concept Name NCIt Concept Definition Hepatic Hepatic C13308 "Pertaining to, affecting, or associated with the liver." I don't think you really want this term. This is an adjective. I assume you want the term for liver here? This is of course in uberon

Requested Term NCIt Concept Code NCIt Concept Name NCIt Concept Definition Cell-Line Cell Line C16403 A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. This is not in scope. I suggest CLO:0000031

Requested Term NCIt Concept Code NCIt Concept Name NCIt Concept Definition Mitochondria Mitochondrion C13258 "Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Mitochondria contain distinctive ribosomes, transfer RNAs, amino acyl t-RNA synthetases, and elongation and termination factors. Mitochondria depend upon genes within the nucleus for many essential messenger RNAs. Mitochondria consist of two sets of membranes, a smooth continuous outer coat and an inner membrane arranged in tubules or more often in folds that form platelike double membranes (cristae). Mitochondria are the principal energy source of the cell and contains the cytochrome enzymes of terminal electron transport and the enzymes of the citric acid cycle, fatty acid oxidation, and oxidative phosphorylation. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP." Use GO for subcellular components

Requested Term NCIt Concept Code NCIt Concept Name NCIt Concept Definition Islet Cells Islet Cell C32885 A pancreatic cell that produces and secretes hormones such as insulin and glucagon. this is in CL

For many other terms e.g. hippocampus, muscle, they are all there, I suspect you are using a tool that doesn't search on synonyms

You also have terms like "Other" and "Unknown". These are not anatomical terms.

We have cleaned up our list based on the above and would like to suggest a few new terms to Uberon. Please find the suggestions in the attached document which includes a corresponding NCIt concept code for the term (if it exists) and comments.

Uberon Term Suggestions - Updated for Submission.xlsx

[cmungall]

the list is getting better. I think it's small enough that it makes sense to just discuss the items directly rather than attaching spreadsheets

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

NCIt Concept Code | Uberon Term Suggestion -- | -- Dome of the Bladder (C12332) | "dome of bladder" or "superior surface of the bladder" Fibroadipose Tissue (Code C155770) | fibroadipose tissue Mixed (C25259) | mixed Minimantle Radiation Field (C53632) | mini mantle (No equivalent NCIt concept was found) | fundus uteri (No equivalent NCIt  concept was found) | intraocular (No equivalent NCIt  concept was found) | serosal surface

Note there is no such anatomical structure as "mixed"

"intraocular" is an adjective. If you want eye or eye adnexa we have these terms

the radiation field request is interesting, this is what is in NCIT

• NCIT:C12219 Anatomic Structure, System, or Substance A human biological structure, fluid or other substance; excludes single molecular entities.
  • NCIT:C12507 Mantle Field A type of extended radiation field that includes lymph node areas in the neck, chest, and axilla.
    • NCIT:C53632 Minimantle Radiation Field A radiation field that includes the bilateral cervical, supraclavicular, and axillary lymph nodes.
      • NCIT:C54648 Radiation Field The area of the body exposed to radiation during radiation therapy.
        • NCIT:C33904 Other Anatomic Concept None

[ssyeds3]

the list is getting better. I think it's small enough that it makes sense to just discuss the items directly rather than attaching spreadsheets

NCIt Concept Code Uberon Term Suggestion Dome of the Bladder (C12332) "dome of bladder" or "superior surface of the bladder" Fibroadipose Tissue (Code C155770) fibroadipose tissue Mixed (C25259) mixed Minimantle Radiation Field (C53632) mini mantle (No equivalent NCIt concept was found) fundus uteri (No equivalent NCIt  concept was found) intraocular (No equivalent NCIt  concept was found) serosal surface Note there is no such anatomical structure as "mixed"

"intraocular" is an adjective. If you want eye or eye adnexa we have these terms

the radiation field request is interesting, this is what is in NCIT

• NCIT:C12219 Anatomic Structure, System, or Substance A human biological structure, fluid or other substance; excludes single molecular entities.

  • NCIT:C12507 Mantle Field A type of extended radiation field that includes lymph node areas in the neck, chest, and axilla.

  • NCIT:C53632 Minimantle Radiation Field A radiation field that includes the bilateral cervical, supraclavicular, and axillary lymph nodes.

    • NCIT:C54648 Radiation Field The area of the body exposed to radiation during radiation therapy.

    • NCIT:C33904 Other Anatomic Concept None

Thank you Chris, no problem, and this is very helpful. We will take note of your feedback and also re-evaluate the terms using the tool recommended by Jim.

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