NTR: cancer cell

[markwoon]

label: cancer cell definition: A cell that has undergone transformation to become cancerous. is_a: CL_0000000 (cell)

[addiehl]

Hi Mark,

This term is not in scope for the CL at this time, as we primarily curate "native cell" types into the CL at the moment. I, and others, are interested in developing a cancer cell ontology, of which this class might be considered the root.

I think I would recommend the the CL editorial group might discuss whether we should add this class to the CL at a high level, as a sibling to cell in vitro and native cell. I would be in favor of adding it, but want make sure that I am aware of all efforts regarding cancer cells first, so we don't step on any one's toes. We might prefer the term "transformed cell," although that needs discussion as well

Also the Brenda Tissue Ontology does represent various cancer cell types, but doesn't seem to provide a root term.

-- Alex

[mellybelly]

consider requesting from NCIT, where there is a lot of work being done to relate cancers to their anatomical sources, parts.

On Oct 5, 2016, at 12:39 PM, addiehl notifications@github.com<mailto:notifications@github.com> wrote:

Hi Mark,

This term is not in scope for the CL at this time, as we primarily curate "native cell" types into the CL at the moment. I, and others, are interested in developing a cancer cell ontology, of which this class might be considered the root.

I think I would recommend the the CL editorial group might discuss whether we should add this class to the CL at a high level, as a sibling to cell in vitro and native cell. I would be in favor of adding it, but want make sure that I am aware of all efforts regarding cancer cells first, so we don't step on any one's toes. We might prefer the term "transformed cell," although that needs discussion as well

Also the Brenda Tissue Ontology does represent various cancer cell types, but doesn't seem to provide a root term.

-- Alex

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[markwoon]

We're not looking for an in-depth cancer cell ontology, we're just looking for a way to indicate that a cell is cancerous.

Adding this at the root level would suit us just fine and hopefully this would not interfere with any other efforts to classify and represent the wide range of cancer cell types since it could ultimately then represent the parent term for an entire new branch. We would also be fine with the term transformed cell.

The Beta Cell Genomics Ontology does have the term "cancer cell" that is a sibling to native cell and in vitro cell along with other cell types that they are interested in. We could use this but prefer to constrain our tool to use only cell ontology as the gold standard for cell types.

[markwoon]

Any chance this might get reconsidered?

Or is a high-level term out of the question as well?

[cmungall]

We could use this but prefer to constrain our tool to use only cell ontology as the gold standard for cell types.

I think it's a very good idea to use only gold standard ontologies rather than an ad-hoc mix of multiple terminologies.

Who do we contact about vetting NCIT to be the gold standard source for cancer cells?

[markwoon]

If there's hope for this, could you please re-open this issue so it doesn't get lost?

[nicolevasilevsky]

Maybe Sherri De Coronado at NCIT?

[addiehl]

I suggest that we should provide a limited set of terms compatible with NCIT and BCG, such as abnormal cell <- neoplastic cell <- malignant cell/cancer cell. NCIT provides a large listing of neoplastic and cancer cell types types, and may be considered a gold standard of enumerating these types, although with a somewhat different approach to ontology development than CL, with missing many definitions and having numerous unfulfilled possibilities for interesting axiomatization.

We discussed several years ago in regards to CLO and ReO, that the CL should be the parent ontology for all cell types, even if we really only curate vertebrate cell types any more. It seems to me that adding these terms, with appropriate reference to their NCIT is appropriate. Also, this leaves open the possibility of developing a cancer cell type ontology that is more in the BFO/OBO style.

[cfthorn]

The terms you mention above would definitely be sufficient for our needs at PharmGKB. Its like adding a doorway that someone could then open at a later date when ready to curate what goes beyond it.

[addiehl]

Here are some proposed definitions for the cell types ‘abnormal cell’, ‘neoplastic cell’, ‘malignant cell’, developed by me and William Duncan and Carmelo Gaudioso of the Roswell Park Cancer Institute.

abnormal cell: A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.

neoplastic cell: An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.

malignant cell: A neoplastic cell that is capable of entering a surrounding tissue or metastasizing to a regional or distant bodily location.

Notes: The labels are identical to the NCIT labels, but the definitions are substantially different. The NCIT definition of ‘Abnormal Cell’, “An abnormal human cell type which can occur in either disease states or disease models,” makes no attempt to define what abnormality means in this context, and defines this cell type as necessarily human, which is far too restrictive for the CL. As this is the parent of the other two cell types, this is not appropriate.

We define ‘neoplastic cell’ based on its specific phentotype, rather than its origin. The NCIT definition of ‘Neoplastic Cell’, “Cells of, or derived from, a tumor,” is unnecessarily broad in that normal cell types can be found in tumors (vascular cells, TILs, etc.), but also too restrictive, as neoplastic cells can occur outside of tumors.

We define ‘malignant cell’ in reference to the definition of the NCIT term ‘Malignant’, “Cancerous. Malignant cells can invade and destroy nearby tissue and spread to other parts of the body,” rather than the NCIT term ‘Malignant Cell’, “Cells of, or derived from, a malignant tumor.”

We welcome comments on the suggested definitions for these cell types.

Thanks, Alex

[cmungall]

do you want to suggest taxon constraints for these?

[cfthorn]

Thanks. This would certainly fit our needs.

[addiehl]

As far as taxon constraints for these terms, I prefer to be fairly liberal. For 'abnormal cell' I suggest constraining usage to eukaryotic cells (or having no constraint at all). For 'neoplastic cell' and 'malignant cell' I suggest constraining usage to multicellular organisms, including plants, (PMID:17745128 provides early evidence for plants, for instance).

[cfthorn]

So what else needs to happen for an accession number to be assigned? thanks

[addiehl]

I will try to do this later this week. I'm out of town at the moment.

[cfthorn]

thank you

[addiehl]

These cell types will appear in the next public release of CL: 'abnormal cell' = http://purl.obolibrary.org/obo/CL_0001061 'neoplastic cell' = http://purl.obolibrary.org/obo/CL_0001063 'malignant cell' = http://purl.obolibrary.org/obo/CL_0001064