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Fix definitions containing '2-trans,6-trans-farnesyl diphosphate ' to align with RHEA term label #28835

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pgaudet opened this issue Sep 4, 2024 · 1 comment
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@pgaudet
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pgaudet commented Sep 4, 2024

The following terms use '2-trans,6-trans-farnesyl diphosphate' in their definitions, while RHEA uses '(2E,6E)-farnesyl diphosphate'

  • GO:0047461 (+)-delta-cadinene synthase activity
  • GO:0102879 (+)-thujopsene synthase activity
  • GO:0080016 (-)-E-beta-caryophyllene synthase activity
  • GO:0061923 (2S,3R,6S,9S)-(-)-protoillud-7-ene synthase activity
  • GO:0102145 (3R)-(E)-nerolidol synthase activity
  • GO:0120086 (3S)-(+)-asterisca-2(9),6-diene synthase activity
  • GO:0052683 (Z)-gamma-bisabolene synthase activity
  • GO:0102931 (Z,E)-alpha- farnesene synthase activity
  • GO:0102698 5-epi-aristolochene synthase activity
  • GO:0102906 7-epi-alpha-selinene synthase activity
  • GO:0097269 all-trans-decaprenyl-diphosphate synthase activity
  • GO:0052681 alpha-bisabolene synthase activity
  • GO:0102886 alpha-chamigrene synthase activity
  • GO:0102877 alpha-copaene synthase activity
  • GO:0102885 alpha-cuprenene synthase activity
  • GO:0052578 alpha-farnesene synthase activity
  • GO:0080017 alpha-humulene synthase activity
  • GO:0102066 alpha-patchoulene synthase activityy
  • GO:0102884 alpha-zingiberene synthase activity
  • GO:0034006 amorpha-4,11-diene synthase activity
  • GO:0102063 beta-curcumene synthase activity
  • GO:0102889 beta-elemene synthase activity
  • GO:0102887 beta-sesquiphellandrene synthase activity
  • GO:0102888 delta-cuprenene synthase activity
  • GO:0052682 epi-cedrol synthase activity
  • GO:0052680 epi-isozizaene synthase activity
  • GO:0047887 farnesyl diphosphate kinase activity
  • GO:0102064 gamma-curcumene synthase activity
  • GO:0034004 germacradienol synthase activity
  • GO:0102904 germacrene C synthase activity
  • GO:0034005 germacrene-A synthase activity
  • GO:0102880 isobazzanene synthase activity
  • GO:0102356 isoitalicene synthase activity
  • GO:0102065 patchoulene synthase activity
  • GO:0102385 patchoulol synthase activity
  • GO:0050467 pentalenene synthase activity
  • GO:0102907 sesquisabinene synthase activity
  • GO:0102304 sesquithujene synthase activity
  • GO:0045482 trichodiene synthase activity
  • GO:0102905 valencene synthase activity
  • GO:0102412 valerena-4,7(11)-diene synthase activity
  • GO:0034003 vetispiradiene synthase activity

Need to

  1. Check that the term is valid: it should not capture a specific substrate (ie have a 'more general form of the reaction'), unless that specific form has enzymes specific for them. If the term is not valid, obsolete. Otherwise:
  2. Make sure that there is a single EC and a single RHEA that corresponds to the reaction
  3. Update definition to match RHEA's
  4. Add RHEA as def xref, and remove other database xrefs
  5. Add xref types for EC and RHEA
@pgaudet pgaudet added the enzymes label Sep 4, 2024
@deustp01
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deustp01 commented Sep 4, 2024

@cmungall In an ideal world where ChEBI had an ontology structure that provided a complete accounting of stereochemical and ionization state variants of each chemical, properly aligned with RHEA's expert determination pf the physiologically relevant form of the chemical, problems like this one would auto-resolve and GO could simply inherit the result?

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