v3.2.3

What's Changed

• removing infores entries for automats that are no longer active by @EvanDietzMorris in #1251

Full Changelog: v3.2.2...v3.2.3

v3.2.2

What's Changed

• #1220 Add UniProt purl's for UniProt entries + Isoforms by @JervenBolleman in #1224
• add entity as a domain for id by @sierra-moxon in #1225
• added mpath mappings by @vincentvialard in #1233
• Add infores:phenio to infores catalog by @kevinschaper in #1235
• adding eRAM and TIGA infores entries by @EvanDietzMorris in #1231
• Bump markdown-it-py from 2.1.0 to 2.2.0 by @dependabot in #1229
• adding classes from Ben H, fixes #1210 by @sierra-moxon in #1222
• Added "gene fusion with" and "genetic neighborhood of" to describe genetic interactions. by @beasleyjonm in #1123
• Add pharmgkb prefixes for chemical, disease, gene, variant by @andrewsu in #1241
• add infores:aeolus by @andrewsu in #1243
• Better omnicorp URL by @cbizon in #1244
• add infores for Richards Effector Gene List by @sierra-moxon in #1246
• Add infores identifier for Columbia Clinical Data Warehouse by @CaseyTa in #1247
• maintenance and support for TRAPI 1.4 fixes #1230, fixes #1232, fixes #1238, fixes #1240, fixes #1249 by @sierra-moxon in #1248
• update smart api urls fixes #1245 by @sierra-moxon in #1250

New Contributors

• @andrewsu made their first contribution in #1241
• @CaseyTa made their first contribution in #1247

Full Changelog: v3.2.1...v3.2.2

v3.2.1

What's Changed

• add domain to biolink:type to help KGX recognize it as a node property. by @sierra-moxon in #1221

Full Changelog: v3.2.0...v3.2.1

v3.2.0

What's Changed

• add entity as a domain of name by @sierra-moxon in #1208
• Fix the regex pattern used to check for the biolink:category CURIE by @vemonet in #1213
• Add SHACL gen to the Makefile by @vemonet in #1214
• update doc to use curie form of predicates by @sierra-moxon in #1209
• make type slot multivalued by @vincentvialard in #1212
• remove cycle in permissible values, fixes #1215, remove degradation from abundance hierarchy in permissible values, fixes #1206 by @sierra-moxon in #1217
• Create publication type slot to fix SHACL validation and avoid confusion by @vemonet in #1218
• add grouping class for qualifiers, add subset translator, fix range o… by @sierra-moxon in #1219

Full Changelog: v3.1.2...v3.2.0

v3.1.2

What's Changed

• Removing stray list by @cbizon in #1189
• fix acts upstream predicate hierarchy by @vincentvialard in #1190
• fix caused by predicate hierarchy by @vincentvialard in #1191
• rename inverse of capable of predicate by @vincentvialard in #1192
• Update predicate_mapping.yaml by @cbizon in #1193
• Update predicate_mapping.yaml by @cbizon in #1194
• fixes #1199 by @sierra-moxon in #1201
• fixes #863, add loss_of_function and gain_of_function to form_or_variant qualifier enumeration by @sierra-moxon in #1202
• update dependencies via dependabot by @sierra-moxon in #1203
• fixes #1196, #1187, #1186 update domain and range of regulates hierarchy in response to the spl… by @sierra-moxon in #1197

Full Changelog: v3.1.1...v3.1.2

v3.1.1

What's Changed

• Syntax errors in example docs by @sierra-moxon in #1149
• Fixing snomed by @cmungall in #1153
• remove underscores from synonym slots by @sierra-moxon in #1172
• change semmeddb mapping case/spelling and SEMMEDDB:ASSOCIATED_WITH ma… by @colleenXu in #1169
• add fequency quantifier to the phenotypic association classes fixes #1175 by @sierra-moxon in #1174
• add an ordered prefix list per class fixes #1173 by @sierra-moxon in #1176
• fixed inverted domain/range for predicates by @vincentvialard in #1178
• fixed typo in alias of 'in taxon' by @vincentvialard in #1177
• Add original subject, original predicate and original object to Association by @kevinschaper in #1182
• fixes #1170, fixes #1167, fixes #1168, fixes #1180, fixes #1166 by @sierra-moxon in #1183
• Fix some opposite predicates should be inverses by @vincentvialard in #1179
• removing inverse and opposite from subclass, superclass predicates by @sierra-moxon in #1184
• fixing errors in id prefixes generator, removing csv generator, fixin… by @sierra-moxon in #1185

New Contributors

• @vincentvialard made their first contribution in #1178

Full Changelog: v3.1.0...v3.1.1

v3.1.0

What's Changed

• Some (new?) inverse predicates are missing their is_a property connection to the predicate hierarchy by @RichardBruskiewich in #1095
• Updating biolink-model.yaml to include new classes for epigenomic ent… by @beasleyjonm in #1102
• fixes #1111 - exposure_event is_a: ontology_class by @sierra-moxon in #1113
• fixes #1101, fixes #1100, fixes #1098 add subject of investigation mixin to many different organism level c… by @sierra-moxon in #1115
• Association and Predicates for Gene to Gene Family relationships by @RichardBruskiewich in #945
• Supporting publications fixes #1107 by @sierra-moxon in #1114
• remove obsolete GAMMA predicates by @EvanDietzMorris in #1117
• Move deprecated mappings to examples/biolink3_migration/predicate_mappings.yaml by @sierra-moxon in #1116
• fixes #1088 - make macromolecular complex a class, add mappings by @sierra-moxon in #1125
• fixes #1096 - add Study, Variable, CommonDataElement by @sierra-moxon in #1126
• fixes #1124 adding canonical tags to response predicates, deprecating increase/de… by @sierra-moxon in #1127
• updating orphanet prefix, fixes #1122 by @sierra-moxon in #1128
• fixes #1119 by @sierra-moxon in #1129
• remove mixin tag from regulates, fixes #1094 by @sierra-moxon in #1130
• adding documentation and examples on qualifiers partially fixes #1133 by @sierra-moxon in #1134
• fixing unknown prefix artifact regeneration error by @sierra-moxon in #1135
• update doc gen to not include yamlfile by @sierra-moxon in #1136
• replace spaces with underscores in enumerations by @sierra-moxon in #1137
• add infores catalog as a nodes tsv file by @sierra-moxon in #1139
• fixes #1132 : include mappings and id prefixes for "chemical role" by @sierra-moxon in #1142
• refactor Sequence Variant to make it more clear that CNVs are a sublc… by @sierra-moxon in #1141
• refactor helpdesk template to include contact information, fixes #1138 by @sierra-moxon in #1146

New Contributors

• @beasleyjonm made their first contribution in #1102
• @EvanDietzMorris made their first contribution in #1117

Full Changelog: v3.0.3...v3.1.0

v3.0.3

What's Changed

• add UMLS as a prefix for organism fixes #1084 by @sierra-moxon in #1086
• Mappings for KGX category assignment fixes #1082 by @sierra-moxon in #1087
• Migrate mappings qualifiers by @sierra-moxon in #1089
• add missing inverses or missing symmetric tag by @sierra-moxon in #1090

Full Changelog: v3.0.2...v3.0.3

v3.0.2

What's Changed

• add side-effect, deprecate causes adverse event fixes #1051 by @sierra-moxon in #1057
• deprecate original knowledge source? by @sierra-moxon in #1079
• Activity or abundance by @sierra-moxon in #1083

Full Changelog: v3.0.1...v3.0.2

v3.0.1

What's Changed

• Trapi examples by @sierra-moxon in #1067
• S-P-O annotation of annotation of diseases or phenotypic features with mode of inheritance. by @RichardBruskiewich in #1068
• fixes #1075, add mappings to organism, virus, and cellular organism by @sierra-moxon in #1076
• add exact, narrow, broad, related synonym slots to the model fixes #1073 by @sierra-moxon in #1077
• adding supporting data properties, fixes #1074 by @sierra-moxon in #1078
• fix typos in enumerated gene->chemical terms by @sierra-moxon in #1080

Full Changelog: v3.0.0...v3.0.1