Add specifications for 0.1 draft #2

caroott · 2024-07-08T07:38:09Z

Add specifications for 0.1 draft based upon Workflow RO-Crate profile and Workflow Run Crate with an extension for LabProcess. This PR references #1

profile/arc_cwl_ro_crate.md

floWetzels · 2024-07-19T11:14:06Z

profile/arc_cwl_ro_crate.md

 | Property | Required | Expected Type | Description |
 |----------|----------|---------------|-------------|
-| | | | |
+|about|SHOULD|[schema.org/PropertyValue](https://schema.org/PropertyValue)|The computational processes encoded in this workflow|


I suggest to drop this as well, like for the Run, and make the Workflow of double type ComputationalWorkflow and LabProtocol.

floWetzels · 2024-07-19T11:16:12Z

profile/arc_cwl_ro_crate.md

 | Property | Required | Expected Type | Description |
 |----------|----------|---------------|-------------|
-| | | | |
+|about|SHOULD|[schema.org/PropertyValue](https://schema.org/PropertyValue)|The computational processes encoded in this workflow|


Then, I would add the hasPart to allow hierarchical modelling of workflows (e.g. also model processing units within a workflow as Workflows/LabProtocols).

floWetzels · 2024-07-26T08:10:51Z

profile/arc_cwl_ro_crate.md

@@ -32,32 +32,31 @@ flowchart TD
        D["Assay=Dataset"] -- "processSequence" --> C
        D -- "hasPart" --> E
 ```
-When adding the workflow run execution context, the "hasPart" field contains all files that are part of the invoced workflow. The "inputs" and "outputs" of the "ComputationalWorkflow" 
-MAY point to the "objects" and "results" of "CreateAction" via "workExample", while the latter point to the former via "exampleOfWork".
+The "inputs" and "outputs" of the "ComputationalWorkflow" MAY point to the "objects" and "results" of "CreateAction" via "workExample", while the latter point to the former via "exampleOfWork".


I would suggest to put these terms into code snippets instead of quotation marks

floWetzels · 2024-07-26T08:13:04Z

profile/arc_cwl_ro_crate.md

@@ -23,11 +23,14 @@ To continue staying consisten with the [ISA RO-Crate Profile](https://github.com

 ```mermaid
 flowchart TD
-        A["File\nSoftwareSourceCode\nComputationalWorkflow"] -- "input\noutput" --> B["FormalParameter"]
-        A -- "instrument" --> C["CreateAction"]
+        A["File\nSoftwareSourceCode\nComputationalWorkflow\nLabProtocol"] -- "input\noutput" --> B["FormalParameter"]


In my opinion, this reads like a list of options for the type. Maybe annotate it as [File,SoftwareSourceCode,...]? This holds for all multi types of course.

floWetzels · 2024-07-26T08:16:40Z

profile/arc_cwl_ro_crate.md

-        A -- "instrument" --> C["CreateAction"]
+        A["File\nSoftwareSourceCode\nComputationalWorkflow\nLabProtocol"] -- "input\noutput" --> B["FormalParameter"]
+        A -- "instrument" --> C["CreateAction\nLabProcess"]
+        C -- "executes" --> A
        C -- "agent" --> D["Person or Organization"]
        B -- "exampleOfWork" --> E["File or Property Value"]
        C -- "object result" --> E


Why are File and PropertyValue merged here? To me, it doesn't make sense for the object/result to be a PropertyValue.

This is part of the original process run crate:
Entities referenced by an action’s object or result SHOULD be of type File (an RO-Crate alias for MediaObject) for files, Dataset for directories and Collection for multi-file datasets, but MAY be a CreativeWork for other types of data (e.g. an online database); they MAY be of type PropertyValue to capture numbers/strings that are not stored as files.

That's interesting, and also makes a lot of sense for some kinds of workflows. It doesn't fit with the ISA model though. However, in an ARC, CWL workflows are clearly separated from the ISA process graph. So I'm not sure how we should handle this. Do we want to allow/encourage such workflows that do not produce files? If we do not, it is ok to diverge in a derived profile.

Any opinions on that @HLWeil, @muehlhaus?

I think it makes sense in processing steps/workflows, that are part of a wf/nested wf. But in the ARC, we recommend to annotate higher level wfs (see here. Those shouldn't return results that are not files.

So the use of PropertyValue here implies some kind of inline data, mixed into the annotation?

Not easy to judge whether we can/should/must allow this option in the profile. Maybe open an issue as a place for a postponed discussion?

floWetzels · 2024-07-26T08:21:03Z

profile/arc_cwl_ro_crate.md

        C -- "agent" --> D["Person or Organization"]
        B -- "exampleOfWork" --> E["File or Property Value"]
        C -- "object result" --> E
+        D["Assay=Dataset"] -- "processSequence" --> C


At the moment, the property processSequence of an Assay has not been added to the bioschemas specification and has been mapped to about.

HLWeil

Thanks for tackling this significant task!

Added some comments to the specification part specifically. Will look into the example separately.

profile/arc_cwl_ro_crate.md

HLWeil · 2024-07-29T08:50:02Z

profile/arc_cwl_ro_crate.md

-        A -- "instrument" --> C["CreateAction"]
+        A["File\nSoftwareSourceCode\nComputationalWorkflow\nLabProtocol"] -- "input\noutput" --> B["FormalParameter"]
+        A -- "instrument" --> C["CreateAction\nLabProcess"]
+        C -- "executes" --> A
        C -- "agent" --> D["Person or Organization"]
        B -- "exampleOfWork" --> E["File or Property Value"]
        C -- "object result" --> E


So the use of PropertyValue here implies some kind of inline data, mixed into the annotation?

Not easy to judge whether we can/should/must allow this option in the profile. Maybe open an issue as a place for a postponed discussion?

HLWeil · 2024-07-29T08:54:40Z

profile/arc_cwl_ro_crate.md

 ```
+The `inputs` and `outputs` of the `ComputationalWorkflow` MAY point to the `objects` and `results` of `CreateAction` via `workExample`, while the latter point to the former via `exampleOfWork`.


Where do these fields come from?

FormalParameters (inputs/outpus) don't have such a field workExample.

This is defined in the Requirements section of Workflow Run Crate:

Is this a thing, @floWetzels? (Fields in Profile which are not defined in Type)

profile/arc_cwl_ro_crate.md

HLWeil · 2024-07-29T09:04:43Z

profile/arc_cwl_ro_crate.md

 | Property | Required | Expected Type | Description |
 |----------|----------|---------------|-------------|
-| | | | |
+| @type | MUST | [Text](https://schema.org/Text) | MUST be of type [File](https://schema.org/MediaObject), [SoftwareSourceCode](https://schema.org/SoftwareSourceCode), [ComputationalWorkflow](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE) and [LabProtocol](https://github.com/nfdi4plants/isa-ro-crate-profile/blob/main/profile/isa_ro_crate.md#labprotocol)|


Regarding the MUST multityping of File, SoftwareSourceCode and ComputationalWorkflow:

I know this stems from the workflow-run-crate-profile, but there I could only find it specified in this way in the graph.

Wouldn't this logically make more sense to be an OR between these types instead of an AND? Like in, either it's a tool execution or a workflow execution?

Maybe this isn't the right place here to discuss this, but just noticed it.

profile/arc_cwl_ro_crate.md

kMutagene · 2024-08-27T06:55:30Z

@caroott @HLWeil @floWetzels is there still something blocking this since the review from last month and subsequent commits? Or does it just need another review?

HLWeil

Honestly, I would say this looks stable enough. For further improvements, having this merged and then Issues opened on it seems more manageable.

caroott added 8 commits July 4, 2024 19:42

start adding wf example #1 🚧

844c5c4

start adding wf invocation example based on wf run crate #1 🚧

424640e

add wf requirements and short description

87b3c95

add wf run mermaid

f209466

add combined wf and wf run example

8d305a7

add short description for when addin invocation to wf

dbe56ed

small corrections

c780ff3

add example metadata

b7b72b7

caroott requested review from kMutagene and HLWeil July 8, 2024 07:38

caroott self-assigned this Jul 8, 2024

Remove done TODO

e77fe7a

caroott requested a review from floWetzels July 8, 2024 08:05

kMutagene linked an issue Jul 9, 2024 that may be closed by this pull request

Base profile on existing workflow run crates #1

Closed

kMutagene marked this pull request as ready for review July 9, 2024 06:51

caroott added 3 commits July 16, 2024 14:33

update mermaid chart

22ca6d1

change LabProcess in Workflow about to Property value #1

cf653cc

add short description for design choice

ed52380

floWetzels reviewed Jul 19, 2024

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floWetzels reviewed Jul 19, 2024

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floWetzels reviewed Jul 19, 2024

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caroott added 6 commits July 24, 2024 18:11

update descriptions 🚧

41d3284

update mermaid graph

3216753

update descriptions and modifications

c9642b5

revert instrument arrow

2881f89

fix tables

44c4f9c

add workflow/run relationship

edab610

floWetzels reviewed Jul 26, 2024

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caroott added 3 commits July 26, 2024 11:03

correct mermaid charts

94642fb

put fields in code boxes

8f8f793

Change Assay=Dataset to Run=Dataset

72601d8

HLWeil requested changes Jul 29, 2024

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caroott added 2 commits July 29, 2024 13:57

fix typos

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clarification

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HLWeil approved these changes Aug 27, 2024

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caroott merged commit e00a5af into main Aug 28, 2024

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Add specifications for 0.1 draft #2

Add specifications for 0.1 draft #2

caroott commented Jul 8, 2024 •

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kMutagene commented Aug 27, 2024

HLWeil left a comment

		```
		The `inputs` and `outputs` of the `ComputationalWorkflow` MAY point to the `objects` and `results` of `CreateAction` via `workExample`, while the latter point to the former via `exampleOfWork`.

Add specifications for 0.1 draft #2

Add specifications for 0.1 draft #2

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caroott commented Jul 8, 2024 • edited Loading

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caroott commented Jul 8, 2024 •

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