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pantherdb / fullgo_paint_update

Update of Panther and PAINT DBs with monthly GO release data
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Add comment when IBD paint_annotation is obsoleted due to loss of EXP evidence #24

Open dustine32 opened 6 years ago

dustine32 commented 6 years ago

I think comments are being added for certain obsoletion scenarios when terms are obsoleted/merged and there are update queries for lost leaf experimental evidence comments but somehow it missed adding a comment for when IBDs PTHR24089:AN615, PTHR24089:AN555, PTHR24089:AN544 to GO:0015217 were obsoleted on May 7th, 2018 due to missing leaf experimental evidence.

So this ticket is mainly to find out why no comment was added for these obsoletions and fix the queries.

dustine32 commented 6 years ago 
select remark from comments cm
join classification c on c.classification_id = cm.classification_id
where c.classification_version_sid = 24
and c.accession = 'PTHR24089'

Current comment is:

2018-02-04: Due to PANTHER library version update from PANTHER12 to PANTHER13.1, PANTHER12 families PTHR24089 contained nodes PTN000641105can not be directly mapped to Panther13 nodes by PTN but their direct child nodes PTN001184311,PTN001184320,PTN001942513 can be directly mapped to Panther13 nodes in PANTHER13 family PTHR24089 by PTN these nodes were annotated with GO terms GO:0015217,GO:0015228,GO:0015866,GO:0035349,GO:0080122.\n\n2018-02-04: Due to PANTHER library version update from PANTHER12 to PANTHER13.1, PANTHER13.1 family PTHR24089 lost some paint annotations because in PANTHER12 family PTHR24089 some nodes PTN001943061,PTN002377725 annotated with GO termsGO:0005476,GO:0005762,GO:0015226,GO:0015879 can not be mapped to PANTHER13.1.\n\n2018-04-22: GO:0000066 is alternative accession to GO:1990575 , this is a merge, so annotation to PTN000639825 is updated with primary GO accession GO:1990575.\n\n2018-05-07: PAINT_EXP annotation to node PTN001942513 with GO:0015228 was obsoleted because there was no supporting leaf node experimental go annotation left after PANTHER library version update.\n\n2018-06-02: GO:0000066 is alternative accession to GO:1990575 , this is a merge, so annotation to PTN000639825 is updated with primary GO accession GO:1990575.\n