pantherdb fullgo_paint_update issues

pantherdb / fullgo_paint_update

Update of Panther and PAINT DBs with monthly GO release data

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IBA GAF creation should output species taxon for S. japonicus

#62 dustine32 opened 1 week ago
1
Add do_not_annotate field to go_classification table

#61 dustine32 opened 3 months ago
1
IBA GAF creation should output species taxon for S. pombe

#60 dustine32 closed 4 months ago
2
Change PMID:21873635 reference to GOREF:0000033

#59 dustine32 closed 1 year ago
0
Emit GOREF in PAINT GAF reference field instead of PMID

#58 dustine32 closed 9 months ago
3
Fix MGI reference ID parsing in update pipeline

#57 dustine32 opened 2 years ago
0
Output only most specific term IBA in GAF generation

#56 dustine32 closed 2 years ago
3
Annotation ids in go_aggregate table are not unique for qualifiers

#55 mugitty opened 2 years ago
3
Improve logging during DB update query execution

#54 dustine32 opened 3 years ago
0
Publish README release notes for each IBA release

#53 dustine32 opened 3 years ago
3
Convert PAINT tool IBA XML to GAF

#52 dustine32 opened 3 years ago
3
IRD without NOT qualifier

#51 huaiyumi closed 3 years ago
3
Bump pyyaml from 3.12 to 5.4

#50 dependabot[bot] opened 3 years ago
0
Generate PAINT data as GPAD files

#49 pgaudet opened 3 years ago
2
Standard test for detecting drastic changes in overrepresentation results

#48 dustine32 opened 4 years ago
0
Add date column to fullgo_version table to track DB load date

#47 dustine32 opened 4 years ago
2
Obsolete Uniprot entries should be filtered at each PAINT release

#46 pgaudet closed 4 months ago
15
Handle qualifiers for new GAF 2.2 spec

#45 dustine32 opened 4 years ago
12
Paint refactor

#44 dustine32 closed 4 years ago
0
Report stats comparing PAINT release versions

#43 dustine32 opened 4 years ago
4
Add the latest ‘PAINT curation status’ notes for each release/update

#42 dustine32 opened 4 years ago
0
Include paint_other.gaf in GO release GAF load

#41 dustine32 opened 4 years ago
3
Display GO release DOI and release date (correctly)

#40 dustine32 closed 4 years ago
1
Prevent leaf-specific IBA propagation if NOT qualifiers do not match

#39 dustine32 opened 5 years ago
5
Bump pyyaml from 3.12 to 5.1

#38 dependabot[bot] closed 3 years ago
1
Fix handling of obsoleted terms

#37 dustine32 closed 4 years ago
4
IBD should not have been auto-obsoleted because other supporting exp annotation exists

#36 dustine32 closed 4 years ago
1
Obsolete redundant IBDs on same node

#35 dustine32 opened 5 years ago
11
Create folder structure for versioning IBA GAF releases

#34 dustine32 opened 5 years ago
11
Integrate IBA GAF generation into GO pipeline

#33 dustine32 opened 5 years ago
8
Using UniProt ID when EcoGene. For issue #29

#32 dustine32 closed 5 years ago
0
Log paint annotation change counts for each update

#31 dustine32 opened 5 years ago
5
Prevent IBA propagation to leaves having conflicting qualifiers (NOT)

#30 dustine32 opened 5 years ago
2
Output UniProt identifiers in EcoCyc IBA GAF

#29 dustine32 closed 5 years ago
8
Recording changes to paint annotations in comments

#28 dustine32 opened 5 years ago
5
ID part of full taxon IDs missing in GAF

#27 kltm closed 5 years ago
2
Errors with identifiers

#26 pgaudet opened 6 years ago
6
Maintain archive of genelist_agg table in Panther

#25 dustine32 opened 6 years ago
0
Add comment when IBD paint_annotation is obsoleted due to loss of EXP evidence

#24 dustine32 opened 6 years ago
1
IBD to PTN000###### for annotation ####### to term GO:000#### does not have associated experimental evidence

#23 dustine32 opened 6 years ago
12
Centralize where update process determines which evidence codes are experimental

#22 dustine32 opened 6 years ago
0
"using with evidence (an annotation id) #### is invalid, since there is no information about annotation id ####"

#21 dustine32 opened 6 years ago
4
Implement taxon constraints checking

#20 dustine32 closed 2 years ago
6
These PAINT annotations are in amigo but not in PAINT GAFs

#19 dustine32 closed 6 years ago
4
Write flowchart of PAINT update pipeline

#18 dustine32 opened 6 years ago
2
Create paint_aggregate materialized view

#17 dustine32 closed 6 years ago
1
Auto-pull correct date for comments_status update SQL

#16 dustine32 opened 6 years ago
0
Create test DB refresh procedure for PAINT DB

#15 dustine32 opened 6 years ago
1
GO evidence records not imported from GAFs for HDA annotations

#14 dustine32 closed 6 years ago
4
Place PANTHER:PTN as first value in IBA GAF with column

#13 dustine32 closed 6 years ago
11