issues
search
geneontology
/
gopreprocess
MIT License
3
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
remove silver from URL downloads and tests, remove unused pypi GH action
#72
sierra-moxon
closed
3 months ago
0
remove print statements
#71
sierra-moxon
closed
4 months ago
0
refactor code to support gzip format of final output
#70
sierra-moxon
closed
4 months ago
0
remove print statements that clog the jenkins log
#69
sierra-moxon
closed
4 months ago
0
Issue 369 rename output gaf and compress resulting merged file
#68
sierra-moxon
closed
5 months ago
0
added documentation image
#67
sierra-moxon
closed
5 months ago
0
regenerate the static noctua mgi src file used in the full-issue-325-gopreprocess pipeline to catch changes David made in noctua to the "with" field of ISS annotations
#66
sierra-moxon
closed
4 months ago
0
push mgi-merged.gaf (silver-issue-325-gopreprocess) up to the mirror when successful
#65
sierra-moxon
closed
5 months ago
1
update validate command to send diff snippets through GO Rules
#64
sierra-moxon
closed
5 months ago
0
do not change date for annotation in protein to go file
#63
sierra-moxon
closed
5 months ago
0
Do not set the date annotated on the Protein to GO annotations, instead inherit this date from the original files.
#62
sierra-moxon
closed
5 months ago
1
MGI provided by then exclude
#61
sierra-moxon
closed
5 months ago
0
tighten the constraint aroudn MGI provided_by in GOA laod
#60
sierra-moxon
closed
5 months ago
0
noctua annotations being duplicated
#59
sierra-moxon
closed
5 months ago
8
RGD annotations being imported via orthology file correctly, but duplicated by the protein to GO load (and consequently these duplicates are provided_by "MGI")
#58
sierra-moxon
closed
5 months ago
8
remove non mouse, human, wb from full-issue-325-pipeline to speed up full run
#57
sierra-moxon
closed
5 months ago
2
set "provided_by" to "GO_Central" for orthology upstreams
#56
sierra-moxon
closed
5 months ago
1
date change resulted in thousands of errors at the end of the full-issue-325 pipeline - badly formatted date
#55
sierra-moxon
closed
5 months ago
1
go-ontology-dev is down, snapshot files are unavailable, release files don't work, preventing go.json from being used in silver/full pipelines for this project
#54
sierra-moxon
closed
5 months ago
1
latest run that includes a relaxed check for "skipping GO annotations made by GO_Central, GOC, and GO_REF:0000033 increased output by 200K
#53
sierra-moxon
closed
5 months ago
1
tweak evidence code filtering in p2g
#52
sierra-moxon
closed
5 months ago
0
lint and clean
#51
sierra-moxon
closed
5 months ago
0
remove debugging, simplify method, remove duplicate method
#50
sierra-moxon
closed
5 months ago
0
update date in gopreprocess orthology converted annotations to be the date the "pipeline" runs
#49
sierra-moxon
closed
5 months ago
1
revert loosened check for GO_Central with REF 00033 for ortho, keep f…
#48
sierra-moxon
closed
5 months ago
0
mock test files
#47
sierra-moxon
closed
5 months ago
0
condense makefile
#46
sierra-moxon
closed
5 months ago
0
add goref 33 processing to p2g
#45
sierra-moxon
closed
5 months ago
0
validate resulting merged GAF using ontobio ahead of pipeline checks
#44
sierra-moxon
closed
5 months ago
0
add a validate GAF method to return error status if errors found in r…
#43
sierra-moxon
closed
5 months ago
0
date_assigned, provider, IKR annotation inclusion fixes
#42
sierra-moxon
closed
6 months ago
0
set provider back to MGI to see if that fixes the missing annotations
#41
sierra-moxon
closed
6 months ago
0
change annotation date to current date this preprocessing script runs
#39
sierra-moxon
closed
6 months ago
0
investigate missing annotations from MGI imports pipeline - EXP "GO_Central", and "GOC" annotations should not have been exluded from the load
#38
sierra-moxon
closed
5 months ago
8
use loaded date instead of original date in rat/human->mouse orthology load
#37
sierra-moxon
closed
6 months ago
2
Should GPAD association writer in ontobio, use GPI files and isoform protein identifiers in associations to modify the subject of annotation in GPAD output?
#36
sierra-moxon
closed
5 months ago
7
move original annotation source from MGI to GO_Central
#35
sierra-moxon
closed
6 months ago
0
ensure validate.py can run locally with new ontobio changes
#34
sierra-moxon
closed
6 months ago
2
ensure gpad2.0 produced by the pipeline
#33
sierra-moxon
closed
6 months ago
1
ensure mgi.gpad and mgi.gaf produced by the pipeline have equivalent output
#32
sierra-moxon
closed
5 months ago
16
lint and add docstrings
#31
sierra-moxon
closed
6 months ago
0
add some download retries here
#30
sierra-moxon
closed
6 months ago
0
get ontology file from snapshot to speed silver pipeline
#29
sierra-moxon
closed
6 months ago
0
updating makefile commands
#28
sierra-moxon
closed
6 months ago
0
fixing goref for human/mouse ortho
#27
sierra-moxon
closed
7 months ago
0
string double MGI namespace
#26
sierra-moxon
closed
8 months ago
0
update file location with change in pipeline name
#25
sierra-moxon
closed
8 months ago
0
remove debugging statements
#24
sierra-moxon
closed
8 months ago
0
fixing up subject id in p2go transformer from PR to MGI
#23
sierra-moxon
closed
8 months ago
0
fixing up PR id mappings
#22
sierra-moxon
closed
8 months ago
0
Next