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geneontology
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pipeline
Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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Add documentation for MGI upstreams pipeline
#326
kltm
closed
2 months ago
10
BOOKKEEPING: Retained for holding on to confinement-325 files until the MGI imports are done.
#325
kltm
opened
1 year ago
14
For #1944 assigned-by reports
#324
mugitty
closed
1 year ago
1
Experiment: try and load AmiGO (and reason) within a single ontology
#323
kltm
opened
1 year ago
1
Modify Jenkinsfile to use new go-amigo.owl
#322
balhoff
opened
1 year ago
0
(Some?) ontology builds fail due to upstream changes in tzdata setup
#321
kltm
closed
1 year ago
2
Document recent pipeline changes
#320
kltm
closed
1 year ago
6
Rename products/annotations to products/upstream_and_raw_data to help avoid user confusion
#319
kltm
closed
1 year ago
25
Update to ODK 1.4
#318
balhoff
closed
1 year ago
3
Update GORULE:0000029 (IEA life) to start filtering at three (3) years
#317
kltm
opened
1 year ago
2
In some cases, the pipeline fails due to container not stopping fast enough
#316
kltm
opened
1 year ago
3
Add monitor to builds to prevent "failed" loads from going live
#315
kltm
closed
1 year ago
3
Modified Jenkins to generate assigned by files
#314
mugitty
closed
1 year ago
0
Proteoform annotations are missing from the mouse gaf
#313
ukemi
opened
1 year ago
14
NEO having trouble building in most cases
#312
kltm
opened
1 year ago
2
In some cases, the ontology build gets dirty and uses old artifacts during build
#311
kltm
closed
1 year ago
5
Old go.json file getting propagated into new releases
#310
kltm
closed
1 year ago
9
Add monitor to NEO build to prevent "failed" loads from going live
#309
kltm
closed
1 year ago
3
Switch PANTHER trees to version 17.0
#308
dustine32
closed
1 year ago
0
Test and merge PANTHER / PAINT 17 into pipeline
#307
kltm
closed
1 year ago
8
Fold new GO-CAM-related pipeline items to main pipeline
#306
kltm
opened
1 year ago
1
Slow and unstable downloads from EBI upstreams increasing pipeline failures
#305
kltm
closed
10 months ago
36
Switch EBI URLs in the metadata from ftp to http(s) schema
#304
kltm
closed
1 year ago
6
Apply causalmf param to fetch causal gocam-models.json
#302
dustine32
closed
1 year ago
1
Create branch to generate Reactome pathway GO-CAMs
#301
dustine32
opened
1 year ago
1
Add stats for number of genes per MOD for which IBAs get dropped on the floor
#300
cmungall
opened
1 year ago
3
Issues with Zenodo are preventing release completion [replacement issue]
#299
kltm
closed
1 year ago
3
Revert or fix changes to mail necessary to temporarily patch pipeline to functionality
#297
kltm
closed
1 year ago
2
Pipelines no longer build due to ChEBI's .obo form containing unparsable data
#296
kltm
closed
1 year ago
3
Remove *-src.gpi files from the release /annotations directory
#295
kltm
closed
1 year ago
2
An unexpected increase in MGI annotations (duplicates showing up)
#294
kltm
closed
1 year ago
14
Add JSON for metadata/eco-usage-constraints.yaml in releases
#293
kltm
closed
1 year ago
2
Update ODK to latest, v1.3.1
#292
balhoff
closed
1 year ago
0
Revert changes for pinned CL version once CL is fixed
#291
kltm
opened
2 years ago
2
Revert changes for pinned uberon version once uberon is fixed
#290
kltm
closed
1 year ago
2
Look into systematizing the noctua-models migration SOP into a pipeline
#289
kltm
opened
2 years ago
6
Experimental go-cam site JSON builder fails after addition of imported data
#288
kltm
closed
2 years ago
1
Explore adding "continuous" ontology building
#287
kltm
closed
2 years ago
12
Pipeline currently fails due to python lib certifi changing requirements (floating requirement for requests-toolbelt)
#286
kltm
closed
2 years ago
5
Look into unblocking GO jenkins for public viewing to help communicate status
#285
kltm
closed
1 year ago
2
Remove remaining ROBOT from non-dockerized portions of the pipeline
#284
kltm
opened
2 years ago
5
When converting emitting GAF (from Noctua model sources), some ECO codes do not seem to map up correctly
#283
kltm
closed
2 years ago
18
Severe annotation drop reported in release pipeline
#282
kltm
closed
2 years ago
4
Suppress or remove owltools *-summary.txt files from pipeline reports
#281
kltm
closed
1 year ago
6
GORULE:0000028 fails for GPAD; ensure that GPAD files can make it through QC without failing GAF-specific rules
#280
kltm
closed
2 years ago
5
Pipeline currently fails due to antlr4 changing requirements
#279
kltm
closed
2 years ago
2
Storing noctua model in github has reached its first limit
#278
kltm
closed
2 years ago
2
Xenbase upstream data file not available
#277
kltm
closed
2 years ago
6
Typo in the mgi-prediction file?
#276
ukemi
closed
2 years ago
4
Task list and timing to complete MGI import
#275
ukemi
closed
2 years ago
18
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