gorule-0000027 must check that DBs are in the db-xref file and use the 'name' field

pgaudet commented 10 months ago

gorule-0000027 states that all identifiers must be valid, but this is vague.

We will first check

Column 1 & 2: entity

[x] DB (GAF column 1) value should be in the "database" field db-xref = GORULE:0000027 - TEST 1
[ ] database names or synonyms should be REPAIRED to value should be in the "database" field, and error reported = GORULE:0000027 - TEST 6
[ ] id_syntax (GAF column 2) should be checked, if defined in db-xref = GORULE:0000027 - TEST 7
[ ] Column 1 and column 2 cardinality = 1; pipes are not allowed = GORULE:0000027 - TEST 8

Column 8 "with" and Column 16 (extensions)

[ ] cardinality 0-n; values are pipe-separated = GORULE_TEST:0000027-9 (PASS), GORULE_TEST:0000027-10, GORULE_TEST:0000027-11
[ ] values that contain DB:ID : same as column 1 & 2:
[ ] DB (GAF column 1) value should be in the "database" field db-xref = GORULE:0000027 - TEST 12, GORULE:0000027 - TEST 13
[ ] id_syntax (GAF column 2) should be checked, if defined in db-xref = GORULE:0000027 - TEST 14

References GAF - column 6, GPAD column 5

[ ] cardinality 1-n; values are pipe-separated GORULE:0000027 - TEST 15 (PASS), GORULE:0000027 - TEST 16****
[ ] These have to be in db-xref and syntax has to be checked against syntax_id if possible. GORULE:0000027 - TEST 17**

Assigned_by field (GAF column 15; GPAD column 10)

[ ] checked against groups.yaml = GORULE:0000027 - TEST 18 (PASS), GORULE:0000027 - TEST 19**

LATER

[ ] errors should be FILTERED (to do later, once we are sure this is working correctly)

kltm commented 10 months ago

@pgaudet Looking at this and https://github.com/geneontology/go-site/issues/1873#issuecomment-1858134410, I think that we're pushing the bounds of what I would consider "low-hanging fruit"; there are some things here that require further discussion on the software side. I think we should roll these into a new project that is digging a little deeper in.

pgaudet commented 9 months ago

For id_syntax, @kltm asks that @mugitty does a test for speed, to make sure that this is not too intense computationally.

pgaudet commented 3 months ago

Correctly failing test

GORULE:0000027: SGDDB is not present in groups reference--`UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P GORULE_TEST:0000027-2 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB

pgaudet commented 3 months ago

Need to add more tests to check all points mentioned in initial comment

pgaudet commented 3 months ago

Add test

[ ] Assigned_by field (GAF column 15; GPAD column 10) should be checked against groups.yaml >> GO-OWL is not allowed, for example (currently we have 42 annotations in AmiGO)
[ ] Added more tests for all cases in the initial comment
[ ] Noting that FB:FBrf0193169 is incorrectly picked up as an error by gorule-0000027 (FB refs were recently added this to the dbxef file, this should be fixed once the change is incorporated in @mugitty 's local version for testing)

mugitty commented 2 months ago

@pgaudet , It is working on http://skyhook.berkeleybop.org/go-site-2210-gorule-0000027-id-syntax/reports/assigned-by-gorule-report.html

Update has to be tested on a build that is based on ontobio version 2.9.7 or greater. However, we have reverted to build 2.9.2 on Aug 28, 2024.

kltm commented 2 months ago

@mugitty You can continue with the newer (latest) ontobio. The temporary reversion was to see if we could get a snapshot through to support ontology and GAF (annotation) updates while we work on the ontobio fixes for release.

mugitty commented 2 months ago

Thanks @kltm! The updates for this ticket are already merged into the latest ontobio release.

geneontology / go-site

gorule-0000027 must check that DBs are in the db-xref file and use the 'name' field #2210