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obophenotype / brain_data_standards_ontologies

A repository for co-ordinating work on ontologies for the Brain Data Standards Project
Apache License 2.0
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Update build pipeline to support denormalized markers #42

Closed dosumis closed 3 years ago

dosumis commented 3 years ago

2 branches needed

Branch 1: EquivalentClass definitions link directly to anatomical individuals

Built from:

TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS)) # Taxonomy as OWL individuals TEMPLATE_CLASS_FILES = $(patsubst %, ../templates/%_class.tsv, $(JOBS)) # Partially curated class files MARKER_FILES = $(patsubst %, ../templates/%_markers.tsv, $(JOBS)) # Normalised markers EQUIVALENT_CLASS_REIFICATION_FILES = $(patsubst %, ../templates/%_equivalent_reification.tsv, $(JOBS)) #EquivalentClass axioms - generated

Branch2: EquivalentClass definitions used denormalised markers

TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS)) # As branch 1 TEMPLATE_CLASS_FILES = $(patsubst %, ../templates/%_class.tsv, $(JOBS)) # Partially Curated, shared with branch 1 MARKER_DENORMALIZED_FILES = $(patsubst %, ../templates/%_markers_denormalized.tsv, $(JOBS)) # EquivalentClass axioms

dosumis commented 3 years ago

The Makefile under dendograms, which build ROBOT templates can be the same in both branches, building all templates. The 2 branches should differ in the main build makefile: https://github.com/obophenotype/brain_data_standards_ontologies/blob/master/src/ontology/bdscratch.Makefile reflecting the different templates used to generate OWL for the final product.

dosumis commented 3 years ago

To build

cd src/ontology sh ./run.sh make prepare_release MIR=false

hkir-dev commented 3 years ago

Related braches created: Branch 1: https://github.com/obophenotype/brain_data_standards_ontologies/tree/ec_individuals Branch 2: https://github.com/obophenotype/brain_data_standards_ontologies/tree/ec_denormalised_markers

BAevermann commented 3 years ago

Hey David!

I was wondering what the status of Branch2 is? I was looking to get involved in extending the templates to generate marker derived definitions of form used in the pCL.

Thanks!

b.

dosumis commented 3 years ago

Hi @BAevermann - see comment on https://github.com/obophenotype/brain_data_standards_ontologies/pull/41