Overhaul Ontology Annotations #120

HLWeil · 2024-09-06T13:50:02Z

I overhauled the specificiation of Ontology Annotations in Annotation tables. Now the specification tries to be more specific about when it talks about the header cells or the value cells. Previously, this was very confusing (see #115) or even ambiguous.

Please @UrsulaE, @StellaEggels, @Hannah-Doerpholz, @Freymaurer take a look regarding correctness of terminology and also clarity of formulation.

Check it out here: https://github.com/nfdi4plants/ARC-specification/blob/fixes/ISA-XLSX.md#ontology-annotations (So markdown is formatted)

As usual, @Brilator @muehlhaus @chgarth

closes #114 in short fix
closes #115

…notation tables

Brilator · 2024-09-09T08:19:47Z

ISA-XLSX.md

+
+The value in the main column MUST contain the name of the ontology term.
+
+The value in the `Term Source REF` column MUST either contain a short identifier for the `IDSPACE`, which identifies the ontology the term can be found in, or be left empty. 


maybe easier: "the ontology containing the term"

StellaEggels · 2024-09-09T08:21:12Z

Two small things I would change:

It says to use : , but in the examples sometimes and are separated by ":" and sometimes by "_". I would always use ":".
For Parameters, the example is "time" with Kelvin as a unit, so either change the parameter to temperature or change the unit.

StellaEggels · 2024-09-09T08:24:16Z

regarding 1.: I meant between ID SPACE and LOCAL ID (the words I copied didn't show...)

Hannah-Doerpholz · 2024-09-09T08:42:21Z

It might be good to also add that in case of columns with units, that the "main" term column is not immediately followed by the Term Source REF and Term Accession Number columns. Maybe just with a pointer that this is described in the next section. Maybe like this (line 695):
Where a value is an Ontology Annotation in an annotation table, Term Accession Number and Term Source REF columns MUST follow the main column, unless the main column contains a unit. In that case refer to the next section.

HLWeil · 2024-09-09T11:16:24Z

Two small things I would change:

It says to use : , but in the examples sometimes and are separated by ":" and sometimes by "_". I would always use ":".

For Parameters, the example is "time" with Kelvin as a unit, so either change the parameter to temperature or change the unit.

Q: "When will the world end?"
A: "I don't know exactly, but it will probably end in 10000 Kelvin"

HLWeil · 2024-09-09T11:33:21Z

Thanks a lot for your inputs, @Brilator @StellaEggels @Hannah-Doerpholz!

Could you take another look whether your remarks were incorporated as intended?

Freymaurer · 2024-09-11T09:42:37Z

ISA-XLSX.md

+The header of the main column MUST contain the structural column type followed by the `name` of the ontology term in `[]` brackets.
+There SHOULD be a `space` between the column type and the `[` bracket.
+
+The headers of the two annotation columns SHOULD contain further ontological information about the ontology term of the main header. In this case, following the static header string, separated by a single space, there MUST be a short ontology term identifier formatted as CURIEs (prefixed identifiers) of the form `<IDSPACE>:<LOCALID>` (specified [here](http://obofoundry.org/id-policy)) inside `()` brackets.


What if the header term is freetext? You are using MUST here? what is the alternative?

Then it's not an ontology term and none of this applies 😅

Edit Note: After a short meeting, I see that the original comment was referring to the case where the value is an ontology term but the header is only a name. Then the brackets should be left empty (fixed now).

Freymaurer · 2024-09-11T09:43:49Z

ISA-XLSX.md

+The value in the `Term Source REF` column MUST either contain a short identifier for the `IDSPACE`, which identifies the ontology containing the term, or be left empty. 
+
+The value in the `Term Accession Number` column MUST either contain a value formatted in one of the following formats, or be left empty:
+  - `LOCALID` of the ontology, which is only applicable if the matching `IDSPACE` is given in the `Term Source REF` column


LOCALID => do we support this in ARCtrl?

Nope, will open an Issue

Freymaurer · 2024-09-11T09:45:45Z

ISA-XLSX.md


-This implements `Ontology Annotation` from the ISA Abstract Model.
+> Note: In this example, the value in the `Term Accession Number` column is formatted as a `URL`, but shortened for the purpose of markdown-formatting.


Note
Github has a very nice markdown feature for notes 🙂

I feel like this deserves its own Issue as a discussion. OFc they look nice in GitHub but weird when not formatted in other Markdown editors.

Also there's a full spectrum of alerts than can be used. But we should use them unified across the specs.

Okay will implement it here in the isa-xlsx specs. But we still need some unification of the work Notes in the main specification file. As it's used there for actual notes but also for the specification itself.

Okay made the change. Not sure whether the side-notes are now too attention-grabbing though 😅

HLWeil added 2 commits September 6, 2024 12:55

fix assay to study copy error of datamap paragraph

e8d3ada

overhauled the formatting specification of ontology annotations in an…

423664b

…notation tables

Brilator reviewed Sep 9, 2024

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small fixes to OA and Unit sections according to requests in PR #120

3b3a295

Freymaurer requested changes Sep 11, 2024

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some adjustments to ontology annotation headers

2272b88

HLWeil mentioned this pull request Sep 11, 2024

[Feature Request] Parse LocalID OntologyAnnotation Accession Term nfdi4plants/ARCtrl#437

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Freymaurer approved these changes Sep 11, 2024

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HLWeil merged commit 3904fb1 into dev Sep 11, 2024

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Overhaul Ontology Annotations #120

Overhaul Ontology Annotations #120

HLWeil commented Sep 6, 2024 •

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Brilator Sep 9, 2024

StellaEggels commented Sep 9, 2024

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HLWeil Sep 11, 2024

HLWeil Sep 11, 2024


		The value in the main column MUST contain the name of the ontology term.

		The value in the `Term Source REF` column MUST either contain a short identifier for the `IDSPACE`, which identifies the ontology the term can be found in, or be left empty.


		This implements `Ontology Annotation` from the ISA Abstract Model.
		> Note: In this example, the value in the `Term Accession Number` column is formatted as a `URL`, but shortened for the purpose of markdown-formatting.

Overhaul Ontology Annotations #120

Overhaul Ontology Annotations #120

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HLWeil commented Sep 6, 2024 •

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