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Question on high level validation, ruleId=pd10112: if there are compartments defined, top-level glyphs must have a compartmentRef.

Open ibalaur opened this issue 6 years ago • 2 comments

The high level validation (using libSBGN 3.0) failed due to not having all top-level glyphs referring to a compartment. Please see the attached files: input SBGN-ML and output validation message. However, the input SBGN-ML file validates with SBGN-ED. Users often draw diagrams without taking subcellular locations into account at that stage, and some molecules could be from extracellular space, some on the membrane and some inside cell. Maybe in the validation it should not be that strict and required information on compartments?

Could you please advise on this difference/ further use? Thank you very much.

F014-carnitine-SBGNv02.sbgn.zip MR_F014-carnitine_SBGN_Validation.docx

ibalaur avatar May 26 '19 10:05 ibalaur

I second that. It would not be unusual to develop a diagram without thinking about the compartments yet. We can not force or assume some default compartment in my opinion.

amazein avatar May 26 '19 10:05 amazein

Just as a quick comment. SBGN-ED does not validate the SBGN-ML. SBGN-ED just validates SBGN itself.

tczauderna avatar Jun 13 '19 23:06 tczauderna