From f1be2219f3ea2d27ecd7401c8e47141651235297 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Sun, 14 Jul 2024 07:44:02 -0700 Subject: [PATCH 1/5] add goals to generate a mapping change diff report --- src/ontology/mondo.Makefile | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile index 45aa1db667..f2a75579fa 100644 --- a/src/ontology/mondo.Makefile +++ b/src/ontology/mondo.Makefile @@ -638,6 +638,38 @@ release_diff: reports/mondo_release_diff.md all: reports/mondo_release_diff.md all: reports/mondo_obsoletioncandidates.tsv +################## +### KGCL Diff #### +################## + +KGCL_ONTOLOGY=mondo-base.obo + +prepare_release: kgcl-diff + +.PHONY: kgcl-diff +kgcl-diff: kgcl-diff-release-base + +.PHONY: kgcl-diff-release-base +kgcl-diff-release-base: reports/difference_release_base.yaml \ + reports/difference_release_base.tsv \ + reports/difference_release_base.md + +tmp/mondo-released.obo: + wget http://purl.obolibrary.org/obo/mondo.obo -O tmp/mondo-released.obo + +reports/difference_release_base.md: tmp/mondo-released.obo $(KGCL_ONTOLOGY) + runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type md + +reports/difference_release_base.tsv: tmp/mondo-released.obo $(KGCL_ONTOLOGY) + runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) \ + -o $@ --output-type csv --statistics --group-by-property oio:hasOBONamespace + +reports/difference_release_base.txt: tmp/mondo-released.obo $(KGCL_ONTOLOGY) + runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type kgcl + +reports/difference_release_base.yaml: tmp/mondo-released.obo $(KGCL_ONTOLOGY) + runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type yaml + ########################### ## MONDO VIEW GENERATION ## ########################### From 1bfd0092a637490c9a8f050afd4579e461be0033 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Thu, 18 Jul 2024 21:13:39 -0700 Subject: [PATCH 2/5] Update src/ontology/mondo.Makefile Co-authored-by: Nico Matentzoglu --- src/ontology/mondo.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile index f2a75579fa..e2b3df6e3e 100644 --- a/src/ontology/mondo.Makefile +++ b/src/ontology/mondo.Makefile @@ -644,7 +644,7 @@ all: reports/mondo_obsoletioncandidates.tsv KGCL_ONTOLOGY=mondo-base.obo -prepare_release: kgcl-diff +all: kgcl-diff .PHONY: kgcl-diff kgcl-diff: kgcl-diff-release-base From 5c56c7d7a4567dabdedee223d269dcfc7e67d68b Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Thu, 18 Jul 2024 21:14:02 -0700 Subject: [PATCH 3/5] Update src/ontology/mondo.Makefile Co-authored-by: Nico Matentzoglu --- src/ontology/mondo.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile index e2b3df6e3e..8dd2ae1369 100644 --- a/src/ontology/mondo.Makefile +++ b/src/ontology/mondo.Makefile @@ -654,7 +654,7 @@ kgcl-diff-release-base: reports/difference_release_base.yaml \ reports/difference_release_base.tsv \ reports/difference_release_base.md -tmp/mondo-released.obo: +tmp/mondo-released.obo: .FORCE wget http://purl.obolibrary.org/obo/mondo.obo -O tmp/mondo-released.obo reports/difference_release_base.md: tmp/mondo-released.obo $(KGCL_ONTOLOGY) From d90d4e54e605bae5d2c39687621374408a3cee0a Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Thu, 18 Jul 2024 21:15:05 -0700 Subject: [PATCH 4/5] Update src/ontology/mondo.Makefile Co-authored-by: Nico Matentzoglu --- src/ontology/mondo.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile index 8dd2ae1369..e6e790c3bd 100644 --- a/src/ontology/mondo.Makefile +++ b/src/ontology/mondo.Makefile @@ -655,7 +655,7 @@ kgcl-diff-release-base: reports/difference_release_base.yaml \ reports/difference_release_base.md tmp/mondo-released.obo: .FORCE - wget http://purl.obolibrary.org/obo/mondo.obo -O tmp/mondo-released.obo + wget http://purl.obolibrary.org/obo/mondo/$(KGCL_ONTOLOGY) -O $@ reports/difference_release_base.md: tmp/mondo-released.obo $(KGCL_ONTOLOGY) runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type md From 51851bb0cfc6fd739e0044b66c1be9616ac729c8 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 23 Jul 2024 12:51:14 +0300 Subject: [PATCH 5/5] Remove txt KGCL output This output was not needed for the Mondo DIFF pipeline --- src/ontology/mondo.Makefile | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile index e6e790c3bd..4f3123d3ad 100644 --- a/src/ontology/mondo.Makefile +++ b/src/ontology/mondo.Makefile @@ -664,9 +664,6 @@ reports/difference_release_base.tsv: tmp/mondo-released.obo $(KGCL_ONTOLOGY) runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) \ -o $@ --output-type csv --statistics --group-by-property oio:hasOBONamespace -reports/difference_release_base.txt: tmp/mondo-released.obo $(KGCL_ONTOLOGY) - runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type kgcl - reports/difference_release_base.yaml: tmp/mondo-released.obo $(KGCL_ONTOLOGY) runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type yaml