geneontology/pathways2GO

Issues

• Extract and emit UniProt classes for proteins

  #326 opened 9 days ago by dustine32
  1

• Discuss possible rules for using 'is small molecule activator/inhibitor' relations in the conversion

  #325 opened 9 days ago by vanaukenk
  0

• Removing molecular events - merging successive reactions with the same enabler and GO MF term

  #324 opened 9 days ago by vanaukenk
  0

• Include downstream reaction and process in imported process models

  #323 opened 9 days ago by vanaukenk
  0

• Add Biological Process for upstream reactions using 'part of' relation

  #322 opened 9 days ago by vanaukenk
  0

• Only include reactions that are part of a pathway in the GO-CAM imports

  #316 opened 9 days ago by ukemi
  0

• To discuss: how to handle Reactome and Yeast Pathways imported GO-CAMs wrt input/output data updates

  #314 opened 8 months ago by vanaukenk
  3

• Represent enzymatic complex enablers according to GO-CAM spec

  #302 opened a year ago by thomaspd
  12

• The direction of transport in model R-HSA-6787639 is backwards

  #319 opened 3 months ago by ukemi
  1

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

  #318 opened 5 months ago by dustine32
  5

• Fatty AcylCoA biosynthesis

  #315 opened 7 months ago by deustp01
  4

• Switch on intermediate small molecule instance sharing for Reactome

  #308 opened a year ago by dustine32
  9

• Experiment: Only include chemicals that are causally connected in a model.

  #317 opened 8 months ago by ukemi
  2

• Add NAS evidence code & reference to all Yeast Pathway models

  #283 opened 8 months ago by suzialeksander
  6

• Make appropriate pathways cyclical

  #285 opened 8 months ago by suzialeksander
  4

• Load YeastPathways as development state into Noctua

  #275 opened 8 months ago by suzialeksander
  4

• Remove extraneous edges in imported models

  #276 opened a year ago by suzialeksander
  5

• R-HSA-163765 "ChREBP activates metabolic gene expression" cleanup

  #310 opened a year ago by deustp01
  1

• Reactome: amino acid and PTM mismatches

  #312 opened 9 months ago by nataled
  0

• GO-CAM reaction labels don't match the Reactome pathway browser

  #311 opened 10 months ago by ukemi
  0

• Sub-sequence termini revisions/review

  #309 opened a year ago by nataled
  4

• Signal/Transit peptides in Reactome (12 confirmed cases)

  #304 opened a year ago by nataled
  3

• Suspicious sequence range for UniProtKB:P43251 derived EWASes

  #305 opened a year ago by nataled
  1

• Complexes & Sets - info needed for PRO

  #306 opened a year ago by nataled
  0

• Representation of an unknown enabler in Reactome and GO-CAM

  #303 opened a year ago by huaiyumi
  6

• Define proper way of passing Drug type info from Reactome in BioPAX

  #295 opened a year ago by dustine32
  1

• Heme biosynthesis (R-HSA-189451)

  #290 opened a year ago by ukemi
  0

• Carnitine synthesis (R-HSA-71262)

  #291 opened a year ago by ukemi
  0

• Reactome - Discrepancy between internal database and web presentation?

  #279 opened a year ago by nataled
  3

• Reactome - duplicate EWAS?

  #280 opened a year ago by nataled
  2

• Prioritization of Steps in Converting Molecular Events

  #296 opened a year ago by ukemi
  7

• TNF signaling (R-HSA-75893) and TNFR1-induced proapoptotic signaling (R-HSA-5357786)

  #288 opened a year ago by ukemi
  0

• First step: Import Reactome Pathways for MOD species

  #298 opened a year ago by ukemi
  6

• 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 opened a year ago by ukemi
  1

• Second step: Add existing evidence to imported pathways

  #299 opened a year ago by ukemi
  1

• Review the causal flow between EGFR(s) activity and Src activity

  #297 opened a year ago by ukemi
  0

• If an input to a binding reaction contains the enabler, remove the corresponding input from the MF

  #293 opened a year ago by vanaukenk
  1

• We need the ability to load Reactome biopax test files into Noctua-dev

  #282 opened a year ago by ukemi
  1

• The direction of a transport reaction is backwards in the new import

  #270 opened a year ago by ukemi
  12

• Add code to disentangle downstream events when the active unit is the same in two different reactions

  #292 opened a year ago by vanaukenk
  3

• Remove intervening Molecular Event between MFs and black box BPs

  #294 opened a year ago by vanaukenk
  2

• GPAD export erroneous line for molecular_event as subject

  #286 opened a year ago by dustine32
  1

• Exclude "molecular event" for reactions that don't occur in yeast

  #284 opened a year ago by suzialeksander
  2

• TNFR1-mediated ceramide production (R-HSA-5626978)

  #289 opened a year ago by ukemi
  0

• TNF signaling (R-HSA-75893) and TNFR1-induced NF-kappa-B signaling pathway (R-HSA-5357956)

  #287 opened a year ago by ukemi
  1

• Emit correct datatype for date field (and maybe other fields)

  #278 opened a year ago by dustine32
  4

• occurs_in for Yeast Pathways is incorrect

  #273 opened a year ago by suzialeksander
  2

• There are still orphan entities in some models

  #274 opened a year ago by ukemi
  0

• Imported pathways missing protein/activity unit, inputs, chemicals

  #269 opened a year ago by suzialeksander
  5

• Test load of Mouse and Fly Reactome Pathways

  #268 opened a year ago by ukemi
  8