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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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For #887 #669

Closed mugitty closed 7 months ago

mugitty commented 7 months ago

Testing with the following GAF lines: ! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed
UniProtKB O76187 darA enables GO:0005515 PMID:9802899 ISS UniProtKB:P34149 F GORULE_TEST:0000005-1 Darlin darA protein taxon:44689 20100205 GO_Central
! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed
UniProtKB O76187 darA enables GO:0005515 PMID:9802899 ISO UniProtKB:P34149 F GORULE_TEST:0000005-2 Darlin darA protein taxon:44689 20100205 GO_Central
! TBC FAILS GORULE:0000005 - TEST 3 - incorrect evidence codes for 'protein binding ; GO:0005515' - IBA not allowed
UniProtKB O76187 darA enables GO:0005515 GO_REF:0000033 IBA UniProtKB:P34149 F GORULE_TEST:0000005-3 Darlin darA protein taxon:44689 20100205 GO_Central

Resulted in the following errors: "gorule-0000005": [ { "level": "WARNING", "line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tPMID:9802899\tISS\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-1 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n", "type": "Violates GO Rule", "message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'", "obj": "", "taxon": "", "rule": 5 }, { "level": "WARNING", "line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tPMID:9802899\tISO\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-2 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n", "type": "Violates GO Rule", "message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'", "obj": "", "taxon": "", "rule": 5 }, { "level": "WARNING", "line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tGO_REF:0000033\tIBA\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-3 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n", "type": "Violates GO Rule", "message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'", "obj": "", "taxon": "", "rule": 5 } ],

Also, unrelated IBA for PAINT error "gorule-0000026": [ { "level": "ERROR", "line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tGO_REF:0000033\tIBA\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-3 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n", "type": "Violates GO Rule", "message": "GORULE:0000026: IBA evidence codes should be filtered from main MOD gaf sources", "obj": "", "taxon": "", "rule": 26 },

mugitty commented 7 months ago

@dustine32 thanks for reviewing quickly.