Common assay template changes

[handemcginty]

created "assay tissue" field for the common assay template, in prep for tissue axioms from DTO and also because of previous requests for it.

[gedeck]

Something is odd here. There individual commits have changes however the Files Changed tab shows none.

[gedeck]

I see. You reverted

[handemcginty]

yes, I thought I was able to create a pull request for a branch?

[handemcginty]

This is currently on hold. Because assay tissue, we realized that the tissues actually come with different association rules to the other annotations in the template. For example we have tissue information in the assay because it’s noted as the cell line’s tissue. The axioms in DTO are there because the tissue is associated with the protein. So what do you guys think about a set of new sub-annotations for the cell lines and proteins (target) in the common assay template and then adding the “assay tissue” to the phenotype template that we have been thinking about? Because it seems like in the phenotype assays, the assays might be performed on actual tissues in addition to cell lines, cells or organisms.

Cell line A

   |

   |>Tissue B

   |>Organism O

Protein P1

   |

   |>Tissue B

   |> Organism O

Assay Tissue in Common Phenotype Assay Template

Another idea from Samantha :

What might make sense is to make broader category, "Assay Material", that has multiple subgroupings under it. Thinking of expandability, if we have a broad category of "Assay Material" and then have a customer that has some unique material (ie: reconstituted organelles), we could add the field under the same general "Assay material" heading, without having to create a whole new parent field in the main template. I'm not sure if that makes sense from an axiom/ontology building standpoint, but from the scientific standpoint it would nice to at least have a category already present so we can just nest "unique" terms if they come up.

Example:

Assay Material ....Cell ........Organism ...................Homo sapiens ...........Type ....................Fibroblast ............Disease ....................Melanoma .............Tissue ....................Lung .............Line/Identifier ....................ATCC PCS2010101 ....Tissue ........Organism ...................Homo sapiens ............Disease ....................Melanoma .............Tissue ....................Lung .............Line/Identifier ....................Patient 0238401 ....Organism ...................Pseudomonas aeruginosa ...........Type ....................Bacteria .............Strain ....................PA071 .............Line/Identifier ....................ATCC BA2038410 ....Organ ........Type ..................Heart ........Organism ...................Mus musculus ............Disease ....................Normal .............Line/Identifier ....................Mouse Strain C2038

Peter's suggestion was to just change the label of the assignment to 'cell line or tissue’.

We might need to separate BRENDA cell lines and tissues and use them separately too. This issue needs more discussion and is on hold for now.

[handemcginty]

with further discussion we opted for leaving the common assay template as is for now.