Investigation Ontology: Investigation Person ORCID misses follows relationship

[omaus]

ARCTokenization/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo

Lines 236 to 241 in 2dfd46f

	[Term]
	id: INVMSO:00000094
	name: Comment[Investigation Person ORCID]
	def: ""
	synonym: "Comment[<Investigation Person ORCID>]" EXACT []
	relationship: part_of INVMSO:00000021 ! INVESTIGATION CONTACTS

misses a follows relationship to INVMSO:00000093. This is needed in arc-validate to check the Investigation file's schema.

Same goes for

ARCTokenization/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo

Lines 228 to 234 in 2dfd46f

	[Term]
	id: INVMSO:00000093
	name: Comment[<Investigation Person ORCID>]
	def: ""
	synonym: "Comment[Investigation Person ORCID]" EXACT []
	is_obsolete: true
	relationship: part_of INVMSO:00000021 ! INVESTIGATION CONTACTS

[kMutagene]

As we discussed previously it was not clear if that term even has a specific position. However @HLWeil told me that it should always appear at the end of the contacts section, meaning it should follow Investigation Person Roles Term Source REF

[kMutagene]

should be fixed via 587eafb

[HLWeil]

@kMutagene, @omaus
Quick heads-up. The comments do not have to appear at a certain position within a section.
Just that our tools will put the comment at the end after read and write.

[omaus]

@kMutagene, @omaus Quick heads-up. The comments do not have to appear at a certain position within a section. Just that our tools will put the comment at the end after read and write.

I'd suggest to pin this at the specification because it's easier to test if it's always at the same position. Opinions? @HLWeil @kMutagene

Or maybe we give it follows to every other key in the Inv. Contacts section? @kMutagene

[HLWeil]

Well this is part of the standard ISA-Tab specification.
In general we definitely need some kind of ISA-XLSX specification. It's on my near-future bucket list.

[omaus]

Ok but would you rather suggest following the ISA-Tab specs or change this in our ISA-XLSX specs? @HLWeil

[kMutagene]

Since we invented this term and our tooling is the only source that writes this term, can we just use the convention of always writing this at a specific position to make our own lives easier? @HLWeil

[kMutagene]

Or maybe we give it follows to every other key in the Inv. Contacts section? @kMutagene

this is the worst imaginable solution, i would only implement that if we have no other choice

[HLWeil]

Well, we didn't invent the isa comment "Comment". It is specified as followed in ISA-Tab:

Rows where the label Comment[<comment name>] appear can also appear within any of the section blocks. Where these appear, the comment name must be unique within the context of a single block (e.g. you cannot have multiple occurences of Comment[external DB REF] within STUDY ASSAYS. Also, the value cells MUST match the number of values indicated by the rest of the section in context.

So no constraint on any positioning in a section. Our tools follow this specification by reading anything that follows this specification and writing with the comments at the end of the section (just for ease of implementation).

Why should we constrain this, to allow comments only at the end?

[kMutagene]

We invented the term in the sense that it is a mandatory line in our Investigation metadata files. Since we already "break" the pure ISA schema by requiring an optional field, we can also make sure to write it at a specific location to not make our lives miserable