Advanced Architecture.md

Advanced Pipeline Architecture

Purpose

• This is a model of the pipeline used in OBI's Makefile by James Overton: https://github.com/obi-ontology/obi/blob/master/Makefile
• This pipeline runs automated tests, builds reports, creates modules from templates, and builds base, release, and core versions of the ontology.
• Differences with the basic ontology pipeline:
  • "Templates" are used for quickly adding many terms at once
    • "Template Modules" are then generated and merged together with the "Edited Ontology", then tested
  • A "Base Build" removes imports and only a "Base Report" is created
  • A "Core Build" contains a selected subset of "Core Terms"
  • "SPARQL Constructs" are inserted terms

Classification

• "Edited Ontology" is a http://purl.obolibrary.org/obo/IAO_8000002 "editors ontology module"
• "Release Build" is a http://purl.obolibrary.org/obo/IAO_8000003 "main release ontology module"
• "Base Build" is a http://purl.obolibrary.org/obo/IAO_8000001 "base ontology module"
• "Core Build" is a http://purl.obolibrary.org/obo/IAO_8000014 "generated ontology module"
• "Imported Modules" are instances of http://purl.obolibrary.org/obo/IAO_8000005 "import ontology module"
• "Template/Temporary/Merged Modules" are instances of http://purl.obolibrary.org/obo/IAO_8000015 "template generated ontology module"

Diagram Key

• Hexagons are ontologies
• Rectangles are SPARQL or text files
• Rounded boxes are spreadsheets
• Dotted lines involve automated tests
• ":" prefix means ROBOT command

graph
	%%%% Entities
	Edited{{Edited Ontology}}
	Merged{{Merged Build}}
	Release{{Release Build}}
	Base{{Base Build}}
	ImportedModules{{Imported Modules}}
	Core{{Core Build}}

	Constructs[SPARQL Constructs]
	Queries[SPARQL Queries]
	ImportedTerms[Imported Terms]
	Templates[Templates]

	TemplateModules{{Template Modules}}
	PhonyModules{{Temporary Modules}}
	MergedModules{{Merged Modules}}

	BaseReport(Base Report)


	%%%% Relations
	ImportedTerms --> |OntoFox:export| ImportedModules
	Edited --> |owl:import| ImportedModules

	Edited --> |:merge| TemplateModules
	Templates --> |:merge, :template, :annotate| TemplateModules
		TemplateModules --> |:remove annotations| PhonyModules
			PhonyModules --> |:remove imports, :merge, :reason ELK| MergedModules
			Edited --> |:merge| MergedModules
			Queries -.-> |:verify| MergedModules

	Edited ----> |:merge| Merged
	TemplateModules --> |:merge| Base
	Constructs --> |:merge| Merged
		Merged -.-> |:reason ELK| Merged
		Queries -.-> |:verify| Merged
			Merged --> |:reason HermiT, :annotate | Release
			Merged --> |:remove imports, :annotate| Base
				Base -.-> |:report| BaseReport

	CoreTerms[Core Terms] --> |:extract core terms| Core
	Release --> |:remove terms, :annotate| Core

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