Skip to content

Commit

Permalink
For #1658
Browse files Browse the repository at this point in the history
  • Loading branch information
@mugitty
mugitty committed Oct 12, 2023
1 parent 3d0bc79 commit 6a9a244
Show file tree
Hide file tree
Showing 6 changed files with 20 additions and 20 deletions.
8 changes: 4 additions & 4 deletions ontobio/io/assocparser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
8 changes: 4 additions & 4 deletions ontobio/io/differ.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion ontobio/io/qc.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
12 changes: 6 additions & 6 deletions ontobio/rdfgen/gocamgen/gocamgen.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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",
}

Expand Down
8 changes: 4 additions & 4 deletions ontobio/rdfgen/relations.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion tests/resources/test-qualifiers-2.2.gaf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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

0 comments on commit 6a9a244

Please sign in to comment.