From 72c9cba03c7985b786912f480c41a9e935dc396b Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 28 Aug 2023 17:19:03 -0500 Subject: [PATCH] remove unnecessary files --- Makefile | 5 +++-- tmp/mondo_validate_full.tsv | 10 +++++----- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/Makefile b/Makefile index 51b12ca..b9a16d5 100644 --- a/Makefile +++ b/Makefile @@ -22,9 +22,10 @@ tmp/mondo_edit.obo: tmp/mondo.owl: tmp/mondo_edit.obo robot convert -i $< --output $@ -tmp/mondo.db: +tmp/mondo.db: tmp/mondo.owl semsql make $@ - rm .template.db + rm -f .template.db + rm -f tmp/mondo-relation-graph.tsv.gz tmp/mondo_lexmatch.sssom.tsv: tmp/mondo.db runoak -i sqlite:$< lexmatch -o $@ -R $(RULES_FILE) diff --git a/tmp/mondo_validate_full.tsv b/tmp/mondo_validate_full.tsv index 7037fc0..a576e79 100644 --- a/tmp/mondo_validate_full.tsv +++ b/tmp/mondo_validate_full.tsv @@ -356,7 +356,7 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000200 ERROR None obo: http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000200 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0000508 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000208 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0018320 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000211 ERROR None ICEO:0000115 None None None Unknown pred (ICEO:0000115) = None An adult-onset movement disorder characterized by bradykinesia, dysarthria and muscle rigidity. -http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000212 ERROR None ICEO:0000115 None None None Unknown pred (ICEO:0000115) = None A hypercalcemia disease that occurs between 28 days to one year of life.. +http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000212 ERROR None ICEO:0000115 None None None Unknown pred (ICEO:0000115) = None A hypercalcemia disease that occurs between 28 days to one year of life. http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000212 ERROR None ICEO:0000233 None None None Unknown pred (ICEO:0000233) = None https://github.com/monarch-initiative/mondo/issues/2926 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000212 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0019743 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0000218 ERROR None ICEO:0000231 None None None Unknown pred (ICEO:0000231) = OMO:0001000 None @@ -549,7 +549,7 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001147 ERROR None obo: http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001149 ERROR None ICEO:0000589 None None None Unknown pred (ICEO:0000589) = None microcephaly (disease) http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001149 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0002320 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001150 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0005559 None -http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001153 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 +http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001153 ERROR None ICEO:0000231 None None None Unknown pred (ICEO:0000231) = OMO:0001000 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001156 ERROR None ICEO:0000589 None None None Unknown pred (ICEO:0000589) = None borderline personality disorder (disease) http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001170 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0002602 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001175 ERROR None obo:mondo#excluded_subClassOf None None None Unknown pred (obo:mondo#excluded_subClassOf) = MOP:0004847 None @@ -558,7 +558,6 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001271 ERROR None ICEO http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001303 ERROR None ICEO:0000589 None None None Unknown pred (ICEO:0000589) = None abnormal pupillary function (disease) http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001306 ERROR None ICEO:0000231 None None None Unknown pred (ICEO:0000231) = OMO:0001000 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001319 ERROR None obo:mondo#excluded_synonym None None None Unknown pred (obo:mondo#excluded_synonym) = None Lateral Wall of bladder -http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001321 ERROR None ICEO:0000231 None None None Unknown pred (ICEO:0000231) = OMO:0001000 None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001321 ERROR None ICEO:0000589 None None None Unknown pred (ICEO:0000589) = None scleral staphyloma (disease) http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001328 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/general/qc-single-child.sparql None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001338 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/general/qc-single-child.sparql None @@ -566,6 +565,7 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001342 ERROR None ICEO http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001583 ERROR None obo:mondo#confidence None None None Unknown pred (obo:mondo#confidence) = None 0.3333333333333335 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001595 ERROR None obo:mondo#confidence None None None Unknown pred (obo:mondo#confidence) = None 0.4999999999999998 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001676 ERROR None obo:mondo#confidence None None None Unknown pred (obo:mondo#confidence) = None 0.045454545454545414 +http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001693 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/general/qc-single-child.sparql None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001706 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/general/qc-single-child.sparql None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0001724 ERROR None obo:mondo#excluded_synonym None None None Unknown pred (obo:mondo#excluded_synonym) = None supraglottis http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0002009 ERROR None obo:mondo#confidence None None None Unknown pred (obo:mondo#confidence) = None 0.23106060606060574 @@ -680,9 +680,7 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0008438 ERROR None obo: http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0008731 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/mondo/qc-omim-subsumption.sparql None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0008807 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-10-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0008855 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = MOP:0018814 None -http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0008858 ERROR None obo:mondo#excluded_from_qc_check None None None Unknown pred (obo:mondo#excluded_from_qc_check) = obo:mondo/sparql/qc/general/qc-single-child.sparql None http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0010204 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 -http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0011380 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0011499 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0011940 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2022-10-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0013742 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 @@ -723,6 +721,8 @@ http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015334 ERROR None ICEO http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015337 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-10-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015338 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015359 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 +http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015360 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2022-09-01 +http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015361 ERROR None ICEO:0006012 None None None Unknown pred (ICEO:0006012) = None 2023-09-01 http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0015364 ERROR None obo:mondo#excluded_synonym None None None Unknown pred (obo:mondo#excluded_synonym) = None familial dysautonomia, type II http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0020066 ERROR None obo:mondo#excluded_synonym None None None Unknown pred (obo:mondo#excluded_synonym) = None Cutis hyperelastica http://www.w3.org/ns/shacl#ClosedConstraintComponent MOP:0020066 ERROR None obo:mondo#excluded_synonym None None None Unknown pred (obo:mondo#excluded_synonym) = None India rubber skin