From 6a9a244e9d364fdb1a4dc863bd4212705868708d Mon Sep 17 00:00:00 2001 From: Anushya Muruganujan Date: Thu, 12 Oct 2023 12:40:55 -0700 Subject: [PATCH] For #1658 --- ontobio/io/assocparser.py | 8 ++++---- ontobio/io/differ.py | 8 ++++---- ontobio/io/qc.py | 2 +- ontobio/rdfgen/gocamgen/gocamgen.py | 12 ++++++------ ontobio/rdfgen/relations.py | 8 ++++---- tests/resources/test-qualifiers-2.2.gaf | 2 +- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/ontobio/io/assocparser.py b/ontobio/io/assocparser.py index 28728900..c3ec3e5d 100644 --- a/ontobio/io/assocparser.py +++ b/ontobio/io/assocparser.py @@ -105,11 +105,11 @@ class Qualifier2_2(ColumnValidator): "contributes_to", "involved_in", "acts_upstream_of", - "acts_upstream_of_positive_effect", - "acts_upstream_of_negative_effect", + "acts_upstream_of,_positive_effect", + "acts_upstream_of,_negative_effect", "acts_upstream_of_or_within", - "acts_upstream_of_or_within_positive_effect", - "acts_upstream_of_or_within_negative_effect", + "acts_upstream_of_or_within,_positive_effect", + "acts_upstream_of_or_within,_negative_effect", "located_in", "part_of", "is_active_in", diff --git a/ontobio/io/differ.py b/ontobio/io/differ.py index c3ec7bd2..74303301 100644 --- a/ontobio/io/differ.py +++ b/ontobio/io/differ.py @@ -371,11 +371,11 @@ def get_column_count(data_frame, file) -> (pd, pd): "RO:0002326": "contributes_to", "RO:0002331": "involved_in", "RO:0002263": "acts_upstream_of", - "RO:0004034": "acts_upstream_of_positive_effect", - "RO:0004035": "acts_upstream_of_negative_effect", + "RO:0004034": "acts_upstream_of,_positive_effect", + "RO:0004035": "acts_upstream_of,_negative_effect", "RO:0002264": "acts_upstream_of_or_within", - "RO:0004032": "acts_upstream_of_or_within_postitive_effect", - "RO:0004033": "acts_upstream_of_or_within_negative_effect", + "RO:0004032": "acts_upstream_of_or_within,_postitive_effect", + "RO:0004033": "acts_upstream_of_or_within,_negative_effect", "RO:0001025": "located_in", "BFO:0000050": "part_of", "RO:0002432": "is_active_in", diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py index 0f39878c..cb3f3153 100644 --- a/ontobio/io/qc.py +++ b/ontobio/io/qc.py @@ -163,7 +163,7 @@ def message(self, state: RepairState) -> str: if state == RepairState.REPAIRED: message = "Found violation of: `{}` but was repaired".format(self.title) elif state == RepairState.FAILED: - message = "Found violatoin of: `{}` and could not be repaired".format(self.title) + message = "Found violation of: `{}` and could not be repaired".format(self.title) return message diff --git a/ontobio/rdfgen/gocamgen/gocamgen.py b/ontobio/rdfgen/gocamgen/gocamgen.py index 0936eb4a..c5be7c36 100644 --- a/ontobio/rdfgen/gocamgen/gocamgen.py +++ b/ontobio/rdfgen/gocamgen/gocamgen.py @@ -82,8 +82,8 @@ def contract_uri_wrapper(id): "acts_upstream_of_or_within": "RO:0002264", "acts upstream of or within, positive effect": "RO:0004032", "acts upstream of or within, negative effect": "RO:0004033", - "acts_upstream_of_positive_effect": "RO:0004034", - "acts_upstream_of_negative_effect": "RO:0004035", + "acts_upstream_of,_positive_effect": "RO:0004034", + "acts_upstream_of,_negative_effect": "RO:0004035", } HAS_REGULATION_TARGET_RELATIONS = { # WB:WBGene00013591 involved_in GO:0042594 @@ -230,12 +230,12 @@ class GoCamModel: "contributes_to": "RO:0002326", "part_of": "BFO:0000050", "acts_upstream_of": "RO:0002263", - "acts_upstream_of_negative_effect": "RO:0004035", + "acts_upstream_of,_negative_effect": "RO:0004035", "acts_upstream_of_or_within": "RO:0002264", - "acts_upstream_of_positive_effect": "RO:0004034", + "acts_upstream_of,_positive_effect": "RO:0004034", "acts upstream of, negative effect": "RO:0004035", - "acts_upstream_of_or_within_negative_effect": "RO:0004033", - "acts_upstream_of_or_within_positive_effect": "RO:0004032", + "acts_upstream_of_or_within,_negative_effect": "RO:0004033", + "acts_upstream_of_or_within,_positive_effect": "RO:0004032", "located_in": "RO:0001025", } diff --git a/ontobio/rdfgen/relations.py b/ontobio/rdfgen/relations.py index 07066c75..7753f86e 100644 --- a/ontobio/rdfgen/relations.py +++ b/ontobio/rdfgen/relations.py @@ -61,10 +61,10 @@ def curie_to_obo_uri(curie, base=None) -> str: "colocalizes with": "http://purl.obolibrary.org/obo/RO_0002325", "contributes to": "http://purl.obolibrary.org/obo/RO_0002326", "acts upstream of or within": "http://purl.obolibrary.org/obo/RO_0002264", - "acts upstream of or within positive effect": "http://purl.obolibrary.org/obo/RO_0004032", - "acts upstream of or within negative effect": "http://purl.obolibrary.org/obo/RO_0004033", - "acts upstream of negative effect": "http://purl.obolibrary.org/obo/RO_0004035", - "acts upstream of positive effect": "http://purl.obolibrary.org/obo/RO_0004034", + "acts upstream of or within, positive effect": "http://purl.obolibrary.org/obo/RO_0004032", + "acts upstream of or within, negative effect": "http://purl.obolibrary.org/obo/RO_0004033", + "acts upstream of, negative effect": "http://purl.obolibrary.org/obo/RO_0004035", + "acts upstream of, positive effect": "http://purl.obolibrary.org/obo/RO_0004034", "located in": "http://purl.obolibrary.org/obo/RO_0001025", "is active in": "http://purl.obolibrary.org/obo/RO_0002432", "exists during": "http://purl.obolibrary.org/obo/GOREL_0000032", diff --git a/tests/resources/test-qualifiers-2.2.gaf b/tests/resources/test-qualifiers-2.2.gaf index 34905a1f..2c622926 100644 --- a/tests/resources/test-qualifiers-2.2.gaf +++ b/tests/resources/test-qualifiers-2.2.gaf @@ -6,6 +6,6 @@ PomBase SPAC1296.02 cox4 contributes_to GO:0004129 PAINT_REF:10122 ISO PANTHER:P PomBase SPAC25B8.17 ypf1 involved_in GO:1990578 GO_REF:0000024 ISO SGD:S000001583 C intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase PomBase SPBC1711.04 mtd1 NOT GO:0004488 PAINT_REF:10025 ISO PANTHER:PTN000002254 F methylenetetrahydrofolate reductase Mtd1 (predicted) UniProtKB:Q9P786|PTN000002263 protein NCBITaxon:4896 20120921 GO_Central PomBase SPBC1711.04 mtd1 NOT|involved_in GO:0004477 PAINT_REF:10025 IMP PANTHER:PTN000002254 F methylenetetrahydrofolate reductase Mtd1 (predicted) UniProtKB:Q9P786|PTN000002263 protein NCBITaxon:4896 20120921 GO_Central -PomBase SPBC1703.04 mlh1 acts_upstream_of_negative_effect GO:0000795 PAINT_REF:10073 IC GO:1234567|PANTHER:PTN000008207 C MutL family protein Mlh1 (predicted) UniProtKB:Q9P7W6|PTN000008215 protein NCBITaxon:4896 20120921 GO_Central +PomBase SPBC1703.04 mlh1 acts_upstream_of,_negative_effect GO:0000795 PAINT_REF:10073 IC GO:1234567|PANTHER:PTN000008207 C MutL family protein Mlh1 (predicted) UniProtKB:Q9P7W6|PTN000008215 protein NCBITaxon:4896 20120921 GO_Central PomBase SPCC736.14 dis1 colocalizes with GO:0035371 PAINT_REF:12609 IMP PANTHER:PTN000288762 C TOG/XMAP14 microtubule-associated protein Dis1 UniProtKB:Q09933|PTN000288823 protein NCBITaxon:4896 20161005 GO_Central PomBase SPAC1296.02 cox4 contributes_to|enables GO:0004129 PAINT_REF:10122 ISO PANTHER:PTN000012880 F cytochrome c oxidase subunit IV (predicted) UniProtKB:P79010|PTN000012940 protein NCBITaxon:4896 20160819 GO_Central