Phenotype cloning? - Githubissues

sbgn / process-descriptions

SBGN PD specification

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Phenotype cloning? #124

Open cannin opened 14 years ago

cannin commented 14 years ago

In the SBGN PD1.1 spec, it says phenotype can be cloned. Cloning is only allowed for EPNs, isn't it? If Phenotype is a Process Node, why can it have connections attached?

It would be helpful to have more examples how the phenotypes are used in the actual pathway model.

Reported by: *anonymous

cannin commented 14 years ago

labels: --> SBGN Issues
status: open --> pending

Original comment by: lenov

cannin commented 14 years ago

I agree that there is a problem. There is an inconsistency between the parts "glyphs" and "syntax and semantics". We need to discuss the issue in depth.

Original comment by: lenov

cannin commented 13 years ago

assigned_to: nobody --> stumoodie
status: pending --> open

Original comment by: stumoodie

cannin commented 13 years ago

I can't see any inconsistency. I think the confusion may arise from an ambiguity about the collective term Process Nodes that describes a category of nodes and "Process Node" that refers to the process glyph. Section 3.5.2 in the spec is titles "Process Node Rules" renaming it to "Process Nodes" may help make this distinction clearer.

Original comment by: stumoodie

cannin commented 13 years ago

Changed title in Semantics section.

Original comment by: stumoodie

cannin commented 13 years ago

status: open --> closed

Original comment by: stumoodie

cannin commented 13 years ago

Changed title in Semantics section.

Original comment by: stumoodie

cannin commented 13 years ago

status: closed --> pending

Original comment by: stumoodie

cannin commented 13 years ago

Closed in error. Should get a third opinion.

Original comment by: stumoodie

cannin commented 13 years ago

status: pending --> open

Original comment by: stumoodie

cannin commented 13 years ago

Should have changed to pending for reconsideration.

Original comment by: stumoodie

cannin commented 13 years ago

I'll exclude from V1.2. I think this is really a request for clarity as much as anything else. The spec is pretty clear in my opinion that phenotypes can be cloned. The bug also requests more usage examples. We should probably do this.

Original comment by: stumoodie

cannin commented 13 years ago

status: open --> pending

Original comment by: stumoodie

cannin commented 13 years ago

Fix in V2.0. No cannot be cloned.

Original comment by: stumoodie

adrienrougny commented 8 months ago

Still inconsistent in V2.0 (table in section 3.5.3: Phenotype can be cloned; section 2.3.3: clone markers apply for EPNs only).