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geneontology
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pathways2GO
Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Test load of Mouse and Fly Reactome Pathways
#268
ukemi
opened
1 year ago
8
Molybdenum cofactor biosynthesis (R-HSA-947581)
#267
ukemi
opened
1 year ago
0
Biotin transport and metabolism (R-HSA-196780)
#266
ukemi
opened
1 year ago
0
Vitamins B6 activation to pyridoxal phosphate (R-HSA-964975)
#265
ukemi
opened
1 year ago
0
Not all drug reaction elements are deleted from model
#264
dustine32
closed
8 months ago
26
Update SGD prefix in source to SGD_PWY for #254
#263
dustine32
closed
1 year ago
0
Delete non small mol regulator individuals
#262
dustine32
closed
1 year ago
0
Vitamin B5 (pantothenate) metabolism (R-HSA-199220)
#261
ukemi
closed
11 months ago
0
Parse manually curated file and map YeastPathway IDs to BPs
#260
dustine32
closed
1 year ago
2
YeastPathways - Intermediate molecules share same instances
#259
dustine32
closed
1 year ago
2
YeastPathways - Intermediate small molecules shared between reactions
#258
dustine32
closed
9 months ago
11
Change YeastCyc- to YeastPathways_ in model ID, filename
#257
dustine32
closed
1 year ago
0
Make source URL comment more comment-like
#256
dustine32
closed
1 year ago
0
Merge manually-curated YeastPathways2BP into conversion code
#255
suzialeksander
closed
9 months ago
1
YeastPathways models have imaginary DB ref
#254
suzialeksander
closed
9 months ago
4
Vitamin B2 (riboflavin) metabolism (R-HSA-196843)
#253
ukemi
opened
1 year ago
6
Work with Reactome to modify the Reactome2GO xref file.
#252
ukemi
opened
1 year ago
1
Prepend YeastCyc- to model ID and filename
#251
dustine32
closed
1 year ago
0
Fix null source prefix for #242
#250
dustine32
closed
1 year ago
4
Add contributor_link comment for #126
#249
dustine32
closed
1 year ago
0
DUPLICATE: Vitamin B1 (thiamin) metabolism (R-HSA-196819)
#248
ukemi
closed
1 year ago
0
Vitamin B1 (thiamin) metabolism (R-HSA-196819)
#247
ukemi
opened
1 year ago
0
EGFR Downregulation (R-HSA-182971)
#246
ukemi
opened
1 year ago
0
Triglyceride catabolism (R-HSA-163560)
#245
ukemi
opened
1 year ago
0
Header on the "clone evidence" popup has a gomodel: that doesn't match the model title
#244
suzialeksander
closed
9 months ago
3
providedBy: URLs inconsistent between users from same group
#243
suzialeksander
closed
1 year ago
3
YeastPathways import: "source: null:*pathway-name" instead of "source: SGD:*pathway-name*"
#242
suzialeksander
closed
1 year ago
4
fix errors in fructose metabolism R-HSA-5652084
#241
deustp01
closed
1 year ago
2
Cleanup of an ChEBI non pH7.3 chemicals
#240
ukemi
opened
1 year ago
0
Analysis of missing ChEBI identifiers
#239
ukemi
opened
1 year ago
0
Add starting locations for transported molecules
#238
ukemi
opened
1 year ago
1
Orphan gene products are showing up in pathways
#237
ukemi
closed
1 year ago
3
Report for missing ChEBI IDs in release 83 work
#236
ukemi
closed
1 year ago
9
Infer has_small_molecule_regulator for #204
#235
dustine32
closed
1 year ago
0
Fix bad IRIs from obsolete replacements
#234
balhoff
closed
1 year ago
0
Move all transport/localization reaction inputs/outputs to has_primary_input
#233
dustine32
closed
1 year ago
0
Reactome proteoforms that point to deleted UniProt entries
#232
deustp01
closed
1 year ago
4
Triglyceride biosynthesis (R-HSA-75109)
#231
ukemi
opened
1 year ago
1
Regulation of ChREBP (MLXIPL) ( R-HSA-163765, R-HSA-163680, R-HSA-163358, R-HSA-163767)
#230
ukemi
opened
1 year ago
1
Reaction intermediates: out of scope?
#229
nataled
opened
1 year ago
1
Representation questions (more to add later; didn't want to lose the notes)
#228
nataled
opened
1 year ago
0
Same entity?
#227
nataled
opened
1 year ago
0
Deprecated or suboptimal UniProtKB accessions referenced in Reactome
#226
nataled
closed
1 year ago
7
Regulation of glycolysis by fructose 2,6-bisphosphate metabolism (R-HSA-9634600)
#225
ukemi
opened
1 year ago
0
Extract ChEBI ID for all small molecules
#224
dustine32
closed
1 year ago
0
Something is weird about the import of Regulation of glycolysis by fructose 2,6-bisphosphate metabolism - imported from: Reactome
#223
ukemi
opened
1 year ago
4
Aspartate and asparagine metabolism (R-HSA-8963693)
#222
ukemi
opened
1 year ago
0
Convert chemicals to ChEBI rather than Reacto
#221
ukemi
closed
1 year ago
7
Reactome: EWASs with wrong modified residues
#220
deustp01
opened
1 year ago
3
Clean up EWASs with wrong modifiedResidue annotations
#219
deustp01
closed
1 year ago
0
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