GO Rules: Add example passing/failing data to go rules

[dougli1sqrd]

Now that we have a yaml schema in place for the go rules to add example passing and failing data (#956) we can add the data to the go rules. This data can be read by software to perform the comparison test.

[dougli1sqrd]

@pgaudet has created many examples already here: https://drive.google.com/drive/folders/12H6Kz9BsFEhtllx7CMy9OW29FeiC8GwQ

[pgaudet]

File is here https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gaf

[kltm]

@pgaudet @mugitty What test suite is this part of? The file should be in /tests/, not user documentation. If the test suite is not in go-site, that will complicate testing and this should probably be in the appropriate repository.

[mugitty]

@kltm, as the rules are implemented, they will be included as part of the standard suite of tests in the pipeline

[kltm]

@mugitty What pipeline are we talking about here? The main "pipeline" pipeline has no test suite. Is there operating code in go-site/pipeline that is under consideration that is separate from ontobio code?

[pgaudet]

Tests for implemented GORULES:

• GORULE:0000001 - GAF lines are parsed according to GAF 2.2 specifications
• Need more tests
• Need to decide which checks are warnings, which are errors, see Modify gorule-0000002 to also include No NOT annotations to 'GO:0005488 binding' #2079 - no gene symbol (col3); should lines be filtered because of this?
• GORULE:0000002 - No 'NOT' annotations to 'protein binding ; GO:0005515'
• Needs to be updated - see Modify gorule-0000002 to also include No NOT annotations to 'GO:0005488 binding' #2079
• All tests are already in the test GAF
• GORULE:0000006 - IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC
• possible bug: see gorule-0000006 IEP and HEP restricted usage- small bug #2081
• GORULE:0000007 - No IPI with 'catalytic activity' or descendants
• GORULE:0000008 - Do not annotate terms
• GORULE:0000011 - ND should not be used for root term annotations
• GORULE:0000013 - Taxon constraints - approved but cannot be tested since it is not implemented in onto-bio
• GORULE:0000015 - Dual species check
• false positives in http:https://release.geneontology.org/2023-07-27/reports/assigned-by-UniProt-report.html#gorule-0000015; added a 'should pass test in the test GAF, see gorule-0000015 gives some false positives errors #2089
• GORULE:0000016 - IC required a with/from value
• GORULE:0000017 - with/from not allowed with IDA
• GORULE:0000018 - with/from mandatory with IPI
• Need to re-run the test errors; data had were not formatted correctly
• GORULE:0000019 - Generic Reasoner Validation Check currently not reported
• GORULE:0000020 - Repair or filter of obsolete terms
• Need to re-run the test errors; 2 new tests for extensions (currently, GO term and 'with' are being tested)
• GORULE:0000026 - IBA annotations should come from the PAINT pipeline
• ok not reported in snapshot/release
• what is the difference between gorule-0000026 and gorule-0000037?
• GORULE:0000027 - Each identifer in GAF is valid
• some tests not failing ; looks like this rule is only checking GOIDs in column 5?
• GORULE:0000028 - GO aspect (column 9) should match GO term
• To rerun: added a test for missing value (test 4)
• GORULE:0000029 - IEAs should be less than one year old
• To rerun: added a test older annotations (should be filtered)
• GORULE:0000030 - Deprecated GOREFs are not allowed
• test not failing, see gorule-0000030 test is not failing  #2093
• see also Change gorule-0000030 to an error #1423
• GORULE:0000031 - Annotation relations are replaced when not provided by source - not reported; where is this implemented?
• GORULE:0000037 - IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference -- isn't this the implementation of GORULE:0000026? Are both active? No error on snapshot; test errors not failing
• GORULE:0000039 - Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants
• GORULE:0000042 - IKR requires a NOT qualifier
• GORULE:0000043 Check for valid combination of evidence code and GO_REF
• marked as proposed but being reported in reports, but no results; also need to make tests, see Add ECO code mappings to GO_REF files (gorule-0000043) #1177
• GORULE:0000046 - The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms
• rerun TEST2, had format problem
• GORULE:0000050 - ISS , ISA and ISO annotations should not be self-referential
• GORULE:0000051 - Some GO terms require a value in the Annotation Extension field
• GORULE:0000055 - References should have only one ID per ID space
• GORULE:0000057 Group specific filter rules should be applied to annotations -> marked as proposed, present in the REPORTS file, with no errors found anywhere. No tests
• GORULE:0000058 Object extensions should conform to the extensions-patterns.yaml file in metadata -> marked as proposed, present in the REPORTS file, with no errors found anywhere. No tests
• GORULE:0000059 - GAF Version 2.0 and 2.1 are converted into GAF Version 2.2
• close gorule-0000059 Upgrade 2.1 GAF files with GAF 2.2 default formula #1558 ?
• GORULE:0000061 - Allowed gene product to term relations (gp2term)
• Some tests not failing see gorule-0000061 update implementation to reflect new rule wording updates #1658 (comment)