Need decisions on non-implemented rules

[pgaudet]

The following rules are not implemented; probably we don't want to implement them at this stage, but I'd like to review this on a mangers call.

Alex will tell us which rules P2GO implements:

• gorule-0000004 Reciprocal annotations for 'protein binding ; GO:0005515 : OK, already in P2GO
• gorule-0000009 Annotation Intersection Alerts: Nice to have as a report (generated by P2GO)?
• gorule-0000023 Materialize annotations for inter-branch links in the GO: DONE P2GO
• gorule-0000024 Prevent propagation of certain terms by orthology low priority
• gorule-0000025 Creating more specific annotations by reasoning over extensions low priority for a future project
• gorule-0000036 Report annotations that involve gene products where the gene product is annotated to a term 'x' and 'regulation of X' (multiple annotations involved) Nice to have as a report (generated by P2GO)?
• gorule-0000038 Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) where there exists DONE P2GO
• gorule-0000043 Check for valid combination of evidence code and GO_REF DONE P2GO TBC
• gorule-0000045 With/from: Verify that the combination of evidence (ECO) codes conform to the rules in eco-usage-constraints.yaml DONE P2GO
• gorule-0000047 With/from: ChEBI IDs in With/from can only be used with terms that are descendants of GO:0005488 (binding) OR ChEBI IDs in With/from are not allowed for annotations to GO:0005515 protein binding & children or GO:0044877 protein-containing complex binding low priority
• gorule-0000049 If the annotation has 'contributes_to' as its qualifier, verify that at least one annotation to GO:0043234 (protein complex), or one of its child terms exists DONE P2GO
• gorule-0000051 Warning Direct annotations to GO:0005488 binding require a value in the Annotation Extension field low priority
• gorule-0000053 NOT annotation should not have extension
• gorule-0000054 Genes annotated with ND should have no other annotations for that aspect Check if P2GO implements that check? (noting that 'binding' annotations should probably not count). It would be nice to generate a report of genes annotated to ND + binding
• gorule-0000056 Annotations should validate against GO shape expressions: for GO-CAM & could be used for extensions Nice to have as a report
• gorule-0000058 Filter Object extensions should conform to the extensions-patterns.yaml file in metadata: Cannot find this file

@mugitty @kltm @vanaukenk