fix goref for iss

[hattrill]

fb_2022_06_EP6/PHASE2//ha9107.edit:! P32. Action - make this FBrf a secondary ID of P22 (FBrf) N :FBrf0253063 fb_2022_06_EP6/PHASE2//ha9109.edit:! P32. Action - make this FBrf a secondary ID of P22 (FBrf) N :FBrf0253063 fb_2022_06_EP6/PHASE2//ha9110.edit:! P32. Action - make this FBrf a secondary ID of P22 (FBrf) *N :FBrf0253063

yikes.

[hattrill]

• [x] make new ISS ref:ha9150.edit
• [x] submit fb_2023_01_EP5 (5th Jan)
• [x] Update ISS mapping in import and export GO pipeline via Pinglei
• [x] Obsolete FBrf0202953, FBrf0232279, FBrf0232278 (should have done this in the first place as cleaner than merging!)

[hattrill]

New ISS FBrf: FBrf0255270

[hattrill]

Pinglei has run test. Checked that FBrf0253063 had been changed to FBrf0255270 in 7227_flybase_20221102.out

kochab2:TESTLOAD hla28$ grep FBrf0255270 7227_flybase_20221102.out | wc -l 10922 kochab2:TESTLOAD hla28$ grep FBrf0253063 7227_flybase_20221102.out | wc -l 0 kochab2:TESTLOAD hla28$

kochab2:TESTLOAD hla28$ grep FBrf0253063 fb2022_06.fb | wc -l 7286 kochab2:TESTLOAD hla28$ grep FBrf0255270 fb2022_06.fb | wc -l 7290

However, issue in GAF:

kochab2:TESTLOAD hla28$ grep "GO_REF:0000024" fb2022_06.fb | wc -l 7293

From 2022_06 grep "GO_REF:0000024" fb2022_06.fb | wc -l 7290

this is because ISS lines have been duplicted: From 2022_06 136964 From TESTLOAD 144033 =7069 difference

[hattrill]

these are correct output: FB:FBrf0255270|GO_REF:0000024 this is incorrect: FB:FBrf0253063|GO_REF:0000097

FBrf0253063 is obsolete in chado - is secondary to FBrf0202953, FBrf0232279, FBrf0232278

FBrf0202953 is the one with old ISS associated, so once this is obsoleted, this issue should go away.

TESTLOAD hla28$ grep "GO_REF:0000097" fb2022_06.fb | wc -l 7286 LOAD hla28$ grep "GO_REF:0000097" fb2022_06.fb | wc -l 0

This is because the rule is: The script adds external refs in a preference order:

1. FBrf -> PMID

2. FBrf -> doi

3. FBrf -> GO_REF (note: this can be a many:one, in this direction)

4. Non-of the above is available and the publication type is a "Personal communication to FlyBase" then add GO_REF:0000097

5. If none of the above, then add GO_REF:0000095

and FBrf0202953 is a pub_type: FlyBase analysis

[hattrill]

Obsoletion records for FB_2023_01_EP7: ha9155.edit: FBrf0232278

ha9154.edit:FBrf0232279

ha9153.edit:FBrf0202953 (this will fix issue)

[hattrill]

• [x] Pull request for updating goref: https://github.com/geneontology/go-site/pull/1951

[hattrill]

done