Add missing attributes

[adamjtaylor]

Found in initial development of some pre-commit hooks in #261

The following are entries in DependsOn that do not have a matching attribute

• [x] "Barretts Esophagus Goblet Cells Present" used in component "Follow Up" is not defined in the data model - ADDED
• [x] "Pancreatitis Onset Year" used in component "Follow Up" is not defined in the data model - ADDED
• [x] "Flow" used in component "Bulk RNA-seq Level 1" is not defined in the data model --> typo, removed comma between Flow and Cell Barcode
• [x] "Cell Barcode" used in component "Bulk RNA-seq Level 1" is not defined in the data model --> typo, removed comma between Flow and Cell Barcode
• [x] "Proportion" used in component "Bulk RNA-seq Level 2" is not defined in the data model --> typo, removed comma between Proportion and Targets No Coverage
• [x] "Targets No Coverage" used in component "Bulk RNA-seq Level 2" is not defined in the data model --> typo, removed comma between Proportion and Targets No Coverage
• [x] "Genomic" used in component "scATAC-seq Level 2" is not defined in the data model --> typo, removed comma between Genomic and Reference URL
• [x] "Reference URL" used in component "scATAC-seq Level 2" is not defined in the data model --> typo, removed comma between Genomic and Reference URL
• [x] "Object ID" used in component "scATAC-seq Level 3" is not defined in the data model
• [x] "nCount Peaks" used in component "scATAC-seq Level 3" is not defined in the data model
• [x] "nFeature Peaks" used in component "scATAC-seq Level 3" is not defined in the data model
• [x] "Single Nucleus Capture" used in component "scmC-seq Level 1" is not defined in the data model - ADDED
• [x] "Median Percentage of Mitochondrial" used in component "scmC-seq Level 1" is not defined in the data model --> typo, removed comma between Median Percentage of Mitochondrial and Reads per Nucleus
• [x] "Reads per Nucleus" used in component "scmC-seq Level 1" is not defined in the data model --> typo, removed comma between Median Percentage of Mitochondrial and Reads per Nucleus
• [x] "Genomic" used in component "scmC-seq Level 2" is not defined in the data model --> typo, removed comma between Genomic and Reference URL
• [x] "Reference URL" used in component "scmC-seq Level 2" is not defined in the data model --> typo, removed comma between Genomic and Reference URL
• [x] "Proportion Coverage 10X" used in component "scDNA-seq Level 2" is not defined in the data model - typo Proportion Coverage 10x
• [x] "HTAN Parent Channel Metadata ID" used in component "Imaging Level 3 Image" is not defined in the data model
• [x] "Spots under tissue" used in component "10x Visium Spatial Transcriptomics - RNA-seq Level 3" is not defined in the data model
• [x] "HTAN Parent Channel Metadata ID" used in component "Imaging Level 4" is not defined in the data model - ADDED
• [x] "UNIPROT Protein ID Target" used in component "HTAN RPPA Antibody Table" is not defined in the data model
• [x] "Internal Ab ID" used in component "HTAN RPPA Antibody Table" is not defined in the data model
• [x] "Notes" used in component "HTAN RPPA Antibody Table" is not defined in the data model
• [x] "Instrument Make and Model" used in component "Mass Spectrometry Level 1" is not defined in the data model
• [x] "Channel QC Faliure Type" used in component "No - Channel Failed QC" is not defined in the data model
• [x] "Time between Waking and First Smoke" used in component "Yes - Smoking Exposure" is not defined in the data model

The following are attributes that appear to not be used by any component and may pair with one of the above:

• [x] Blood Tube Type is is not used by any component
• [x] Spots Under Tissue is is not used by any component
• [x] Channel QC Failure Type is is not used by any component
• [x] Workflow Type is is not used by any component
• [x] Workflow Parameters Description is is not used by any component
• [x] Antigen Retrieval is is not used by any component
• [x] Biospecimen Slide Location is is not used by any component
• [x] Staining Markers is is not used by any component
• [x] Age at Index is is not used by any component
• [x] Time Between Waking and First Smoke is is not used by any component
• [x] Anatomic Site is is not used by any component
• [x] UNIPROT Gene Symbol Target is is not used by any component
• [x] Internal Antibody ID is is not used by any component
• [x] Antibody Notes is is not used by any component
• [x] Corresponding Author is is not used by any component
• [x] Corresponding Author ORCID is is not used by any component
• [x] Other Data Type Specified is is not used by any component
• [x] scATAC-seq Object ID is is not used by any component
• [x] nCount peaks is is not used by any component
• [x] nFeature peaks is is not used by any component
• [x] MS Analyte Type is is not used by any component
• [x] MS Instrument Vendor and Model is is not used by any component
• [x] MS Instrument Metadata File is is not used by any component

[adamjtaylor]

FYI @clarisse-lau many of these are like that you spotted in #253

[adamjtaylor]

Many of these fixes are due to differences in capitalization between the DependsOn entry and the Attributes. Suggest we harmonize based on the entry in the DependsOn.

[aclayton555]

@elv-sb just checking in on this?

[elv-sb]

• [x] Blood Tube Type DELETED together with "Other Blood Tube Type-specify" and "Blood Tube Type Other" - not used anywhere --> Is it needed for Blood Biospecimen Type?
• [x] Spots Under Tissue - used in 10x Visium Spatial Transcriptomics - RNA-seq Level 3 (Spots under tissue)
• [x] Channel QC Failure Type - Typo
• [x] Workflow Type DELETED - not used anywhere --> Required TRUE
• [x] Workflow Parameters Description DELETED - not used anywhere --> Required TRUE
• [x] Antigen Retrieval DELETED - not used anywhere - was removed from RFC Biospecimen Tier 2 --> Required FALSE
• [x] Biospecimen Slide Location DELETED - not used anywhere - was removed from RFC Biospecimen Tier 1 --> Required FALSE
• [x] Staining markers DELETED - not used anywhere - was removed from RFC Imaging Level 1 - v1 --> Required FALSE
• [x] Age at Index DELETED - not used anywhere --> Required FALSE
• [x] Time Between Waking and First Smoke - used in Yes, Smoking Exposure (Time between Waking and First Smoke)
• [x] Anatomic Site DELETED - not used anywhere --> Required FALSE
• [x] UNIPROT Gene Symbol Target - not used anywhere --> Could it have been mixed up with UNIPROT Protein ID Target - Yes, in Antibody Table RPPA
• [x] Internal Antibody ID - not used anywhere --> Typo for Internal Ab ID used in HTAN RPPA Antibody Table
• [x] Antibody Notes - not used anywhere --> should replace "Notes" in Antibody Table RPPA
• [x] Corresponding Author - not used anywhere --> Should be in Publication according to RFC Publication
• [x] Corresponding Author ORCID - not used anywhere --> Should be in Publication according to RFC Publication
• [x] Other Data Type Specified - not used anywhere - "Other Data Type" in RFC Publication
• [x] scATAC-seq Object ID - not used anywhere --> Required FALSE --> added to Mass Spec Level 3
• [x] nCount peaks - used in scATAC-seq Level 3 (nCount Peaks)
• [x] nFeature peaks - used in scATAC-seq Level 3 (nFeature Peaks)
• [x] MS Analyte Type DELETED - not used anywhere --> should replace "Analyte Type" in Mass Spec Level 1 --> Required TRUE --> added valid values of MS Analyte Type (protein, metabolite, lipid) to Analyte Type
• [x] MS Instrument Vendor and Model - not used anywhere --> should replace "Instrument Make and Model" in Mass Spec Level 1
• [x] MS Instrument Metadata File - not used anywhere - in RFC Mass Spec --> changed required to FALSE and added to Mass Spec Level 1

[aclayton555]

@elv-sb thanks for looking into these. Let's discuss in our sprint close-out next week...I'm curious how some of these are happening. Anyway, I expect that efforts to tidy this will spill into our next sprint

[aclayton555]

Complete fixes in one giant PR in next sprint.

Are any attributes that are currently 'not used anywhere' - are any of these required? If so, this will cause a validation error.

Are there any attributes that will now have validation and trigger issues.

Check what has been submitted - MS - Stanford

[elv-sb]

@adamjtaylor could you please take a look at the ones below? I recommend removing them from the model

• [ ] Workflow Type - not used anywhere --> Required TRUE
• [ ] Workflow Parameters Description - not used anywhere --> Required TRUE
• [ ] Antigen Retrieval - not used anywhere - was removed from RFC Biospecimen Tier 2 --> Required FALSE
• [ ] Biospecimen Slide Location - not used anywhere - was removed from RFC Biospecimen Tier 1 --> Required FALSE
• [ ] Staining markers - not used anywhere - was removed from RFC Imaging Level 1 - v1 --> Required FALSE
• [ ] Age at Index - not used anywhere --> Required FALSE
• [ ] Anatomic Site - not used anywhere --> Required FALSE

[adamjtaylor]

@elv-sb happy for all of those to be removed from the model.