model revisions/updates

[jmvera255]

• change Clinical to Demographics???
  • I've added a 'just' demographics template to the clinical context and created a draft template for 'just' clinical-related details. My main concern at this time is that a contributor will have to create multiple files with several columns redundant between the two, namely 'individualID', 'program', 'project' and that seems annoying, though they can just copy/paste so perhaps it's not so burdensome after all.
  • the plus i see here is that this creates flexibility in studies with multiple clinical visit, like AMP RA/SLE, where the demographics details aren't collected each visit nor need to be reported each visit.
  • perhaps the best approach is just to wait until we need to support this particular use case? it strikes me that it's not entirely clear to me which of the "demographics" data would or wouldn't be collected across multiple visits (i'm thinking weight mostly)
• review BDM metadata file annotation template
  • going forward I believe there's only need for the contributor template, so the BDM template has been removed
• create a contributor metadata file annotation template
• add 'notes' to Clinical metadata template
• add tentative new 'project' valid vals for AMP AIM
  • the model already has the LOCKIT, STAMP, etc. project valid values. for this update I'm adding EDP1, EDP2, and METRO but only at this time to the all_attributes. For clinical and biospecimen I'll use the same list minus the EDP options since I don't know/think that there's as clear delineation of patients btwn EDP but there is for the other project designations.
• remove conditional dependency btwn synovial fluid and synovialCollectionProcedure
• consider expanding Dataset Annotation template to include Synapse Homepage Data Catalog table details as annotations
• issue change year validation rule to integer with range #65 ??
• consider adding conditional behavior for datasetType == "publication"
• revise conditional trigger of biospecimenType == "cell line" to instead trigger 'userDefinedCellType' in place of 'cellType'? we would then harmonize internally to the best of our ability to use only CL terms in 'cellType' since that's what the 'cellType' column is for.
  • i am reconsidering this idea mostly b/c cell lines have pretty well establish names and so I wouldn't expect much difference btwn user-defined and the actual cell line name
  • also less concerned about making this change b/c we can sanity check the provide cellType and replace with a standard name if needed and provide the original provided name to userDefinedCellType.
• remove 'fibroblast-derived synoviocyte' from biospecimenType enum and utilize higher-level classification for biospecimenType along with additional existing fields to capture this level of detail
  • for this case I think it makes sense that biospecimenType would be set to 'cell line' or 'primary cell culture' and then the cellType would be 'fibroblast-like synoviocyte'
  • i've created issue add cellType valid values #90 to address this
• add 'html' as valid val for fileFormat in scRNA-seq processed data annotation template
• add 'alignment metrics' as valid value for 'metadataType'
• replace 'frozen tissue' with 'frozen tissue/fluid' as valid value for biospecimenSubtype