Validation reports figure

[dosumis]

https://docs.google.com/document/d/1xpzQUAJVzwGjWenLlLYrgYyinTaHRZJy_77sWdLR0AY/edit#bookmark=id.1uqyyc2pm4bd - basic example is good. Just needs updating.

• [ ] #13

[dosumis]

@aleixpuigb has regenerated manually. https://docs.google.com/presentation/d/1xSt9xhrGS5SwsijGpyJdzuyJw1zOprqkA0nXMvNI588/edit#slide=id.g29f8ccd2906_0_0

[dosumis]

I would like to be able to explain the biology behind the validation example. Taking some notes here.

keratocyte is actually recorded in CL as part of the "substantia propria of the cornea" which encompasses anterna and posterior stroma. Because "substantia propria of the cornea" is not used in the ASCT+B table, the validator suggests instead a part_of relationships to 'cornea', the most precise enclosing structure that is in the table.

The link in the ASCT+B table to anterior stroma may be justified:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819093/

But most does not mean all. Further discussion with experts is appropriate, to clarify the precise meaning of relationships in the ontology and to determine if they agree that the more general Uberon is appropriate.

In the case of telocyte - this is a much more general cell type - found in many tissues, so a part_of relationship is not appropriate.

Questions:

• are telocytes limited to the anterior stroma - not according to this paper:

  

  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706519/

• are the telocytes of the cornea sufficiently distinct, morphologically or molecularly, that they deserve a term of their own. If yes, we can add to CL and suggest this term to the experts. If not, we can use has_part relationsip to the appropriate structure. Note - another possible way to approach this is for the atlas ontology builder, in this case the human reference atlas, to define compound terms (cell type X in location Y) themselves.

[dosumis]

For figure - could combine with image of anatomy:

https://commons.wikimedia.org/wiki/File:The_human_cornea_in_cross-section..jpg - Details of attrubition on wikimedia.

Also useful to have a comparison graph with 'keratocyte' + 'substantia propria of the cornea' + 'anterior stroma of cornea', 'posterior stroma of cornea' & their relationships.