geneontology pathways2GO issues

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)

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Activity node for reaction should be a process if GO BP is curated at Reactome

#318 dustine32 opened 3 weeks ago
5
Experiment: Only include chemicals that are causally connected in a model.

#317 ukemi opened 3 months ago
2
Only include reactions that are part of a pathway in the GO-CAM imports

#316 ukemi opened 3 months ago
0
Fatty AcylCoA biosynthesis

#315 deustp01 closed 2 months ago
4
To discuss: how to handle Reactome and Yeast Pathways imported GO-CAMs wrt input/output data updates

#314 vanaukenk opened 3 months ago
0
Allow shared intermediate small molecules for Reactome

#313 dustine32 closed 2 weeks ago
4
Reactome: amino acid and PTM mismatches

#312 nataled opened 4 months ago
0
GO-CAM reaction labels don't match the Reactome pathway browser

#311 ukemi opened 5 months ago
0
R-HSA-163765 "ChREBP activates metabolic gene expression" cleanup

#310 deustp01 opened 6 months ago
1
Sub-sequence termini revisions/review

#309 nataled opened 6 months ago
4
Switch on intermediate small molecule instance sharing for Reactome

#308 dustine32 opened 7 months ago
9
Connect branched and cyclical YeastPathways models

#307 dustine32 closed 7 months ago
0
Complexes & Sets - info needed for PRO

#306 nataled opened 7 months ago
0
Suspicious sequence range for UniProtKB:P43251 derived EWASes

#305 nataled closed 7 months ago
1
Signal/Transit peptides in Reactome (12 confirmed cases)

#304 nataled opened 7 months ago
3
Representation of an unknown enabler in Reactome and GO-CAM

#303 huaiyumi opened 7 months ago
6
Represent enzymatic complex enablers according to GO-CAM spec

#302 thomaspd opened 8 months ago
11
Remove explicit causal relation if rxns connected via same input/output instance

#301 dustine32 closed 8 months ago
0
Third step: Use Textpresso-like resource to identify papers that could provide evidence for statements that aren't supported by evidence from existing annotations.

#300 ukemi opened 8 months ago
1
Second step: Add existing evidence to imported pathways

#299 ukemi opened 8 months ago
1
First step: Import Reactome Pathways for MOD species

#298 ukemi opened 8 months ago
6
Review the causal flow between EGFR(s) activity and Src activity

#297 ukemi opened 8 months ago
0
Prioritization of Steps in Converting Molecular Events

#296 ukemi opened 8 months ago
7
Define proper way of passing Drug type info from Reactome in BioPAX

#295 dustine32 opened 8 months ago
1
Remove intervening Molecular Event between MFs and black box BPs

#294 vanaukenk opened 8 months ago
2
If an input to a binding reaction contains the enabler, remove the corresponding input from the MF

#293 vanaukenk opened 8 months ago
1
Add code to disentangle downstream events when the active unit is the same in two different reactions

#292 vanaukenk closed 8 months ago
3
Carnitine synthesis (R-HSA-71262)

#291 ukemi opened 9 months ago
0
Heme biosynthesis (R-HSA-189451)

#290 ukemi opened 9 months ago
0
TNFR1-mediated ceramide production (R-HSA-5626978)

#289 ukemi opened 9 months ago
0
TNF signaling (R-HSA-75893) and TNFR1-induced proapoptotic signaling (R-HSA-5357786)

#288 ukemi opened 9 months ago
0
TNF signaling (R-HSA-75893) and TNFR1-induced NF-kappa-B signaling pathway (R-HSA-5357956)

#287 ukemi closed 9 months ago
1
GPAD export erroneous line for molecular_event as subject

#286 dustine32 opened 9 months ago
1
Make appropriate pathways cyclical

#285 suzialeksander closed 3 months ago
4
Exclude "molecular event" for reactions that don't occur in yeast

#284 suzialeksander closed 9 months ago
2
Add NAS evidence code & reference to all Yeast Pathway models

#283 suzialeksander closed 3 months ago
6
We need the ability to load Reactome biopax test files into Noctua-dev

#282 ukemi closed 8 months ago
1
Apply manuscript changes from geneontology/pathways2GO#214 to master

#281 dustine32 closed 9 months ago
0
Reactome - duplicate EWAS?

#280 nataled closed 7 months ago
2
Reactome - Discrepancy between internal database and web presentation?

#279 nataled opened 9 months ago
3
Emit correct datatype for date field (and maybe other fields)

#278 dustine32 opened 9 months ago
4
Fix transport direction with ChEBI bug in Reactome

#277 dustine32 closed 9 months ago
0
Remove extraneous edges in imported models

#276 suzialeksander opened 9 months ago
5
Load YeastPathways as development state into Noctua

#275 suzialeksander closed 3 months ago
4
There are still orphan entities in some models

#274 ukemi opened 10 months ago
0
occurs_in for Yeast Pathways is incorrect

#273 suzialeksander closed 9 months ago
2
Fill in missing yeast xrefs

#272 dustine32 closed 10 months ago
2
Prevent emitting entities if drug

#271 dustine32 closed 11 months ago
1
The direction of a transport reaction is backwards in the new import

#270 ukemi closed 8 months ago
12
Imported pathways missing protein/activity unit, inputs, chemicals

#269 suzialeksander opened 11 months ago
5