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Adding RHEAs to catalytic activity terms with MetaCyc but no EC #28199

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sjm41 opened this issue Jun 19, 2024 · 4 comments
Closed
77 tasks done

Adding RHEAs to catalytic activity terms with MetaCyc but no EC #28199

sjm41 opened this issue Jun 19, 2024 · 4 comments
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GO-EC-RHEA xref alignment

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sjm41 commented Jun 19, 2024 •
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Spreadsheet is here: https://docs.google.com/spreadsheets/d/1eCAJAzCrdBKvEYVwW2sZw2LfNpqP8qN6eUYeIkR0m_I/edit?gid=343689728#gid=343689728

Simple cases where just need to add an exactMatch RHEA xref (and update def as necessary):

  • Add RHEA:68520 to GO:0102882 beta-acoradiene synthase activity
  • Add RHEA:68960 to GO:0102358 daphnetin-8-O-methyltransferase activity
  • Add RHEA:72871 to GO:0102585 cyanidin 3-O-[2''-O-(xylosyl)-6''-O-(p-coumaroyl) glucoside] 5-O-glucoside malonyltransferase activity
  • Add RHEA:73071 to GO:0102529 apigenin 7-O-methyltransferase activity
  • Add RHEA:73115 to GO:0102432 quercetin 7-O-methyltransferase activity
  • Add RHEA:73243 to GO:0102623 scutellarein 7-methyl ether 6-O-methyltransferase activity
  • Add RHEA:73247 to GO:0102535 ladanein 6-O-methyltransferase activity
  • Add RHEA:73251 to GO:0102625 cirsimaritin 4'-O-methyltransferase activity
  • Add RHEA:73263 to GO:0102533 genkwanin 4'-O-methyltransferase activity
  • Add RHEA:73427 to GO:0102532 genkwanin 6-hydroxylase activity
  • Add RHEA:73431 to GO:0102536 sakuranetin 6-hydroxylase activity
  • Add RHEA:73435 to GO:0102534 apigenin-7,4'-dimethyl ether 6-hydroxylase activity
  • Add RHEA:74715 to GO:0102445 3-methylquercetin 3'-O-methyltransferase activity
  • Add RHEA:74719 to GO:0102435 myricetin 7-O-methyltransferase activity
  • Add RHEA:74731 to GO:0102448 rhamnetin 4'-O-methyltransferase activity
  • Add RHEA:74735 to GO:0102441 syringetin 7-O-methyltransferase activity
  • Add RHEA:74739 to GO:0102439 3',4',5'-trimethylmyricetin 7-O-methyltransferase activity
  • Add RHEA:74743 to GO:0102449 kaempferol 3-O-methyltransferase activity
  • Add RHEA:74755 to GO:0102451 kaempferide 3-O-methyltransferase activity
  • Add RHEA:74759 to GO:0102444 isorhamnetin 3-O-methyltransferase activity
  • Add RHEA:74763 to GO:0102446 rhamnetin 3-O-methyltransferase activity
  • Add RHEA:74767 to GO:0102442 syringetin 3-O-methyltransferase activity
  • Add RHEA:74771 to GO:0102440 3',4',5'-trimethylmyricetin 3-O-methyltransferase activity
  • Add RHEA:74775 to GO:0102450 kaempferide 7-O-methyltransferase activity
  • Add RHEA:77155 to GO:0051717 inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity
  • Add RHEA:14389 to GO:0008532 N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity
  • Add RHEA:32919 to GO:0080030 methyl indole-3-acetate esterase activity
  • Add RHEA:33611 to GO:0080031 methyl salicylate esterase activity
  • Add RHEA:35815 to GO:0043793 beta-ribofuranosylaminobenzene 5'-phosphate synthase activity
  • Add RHEA:55372 to GO:0080032 methyl jasmonate esterase activity
  • Add RHEA:61732 to GO:0102377 steviol 13-O glucosyltransferase activity
  • Add RHEA:61736 to GO:0102378 steviolmonoside glucosyltransferase activity
  • Add RHEA:61744 to GO:0102379 steviolbioside glucosyltransferase activity (stevioside forming)
  • Add RHEA:61752 to GO:0102380 steviolbioside glucosyltransferase activity (rebaudioside B forming)
  • Add RHEA:61756 to GO:0102381 stevioside glucosyltransferase activity (rebaudioside A forming)
  • Add RHEA:61760 to GO:0102382 rebaudioside B glucosyltransferase activity

More complicated cases:

  • GO:0004851 has wrong MetaCyc xref - should be MetaCyc:RXN-13403
  • GO:0050697: Add RHEA:67992. TCEREDCHLOR-RXN is ""1.21.99.5/1.21.99.M1"" so change parentage to match, and change name to "trichloroethene reductive dehalogenase" to match MetaCyc.
  • GO:0102734: Add RHEA:69923. Add EC:1.14.14.180 as broadMatch. Change parentage to reflect EC.
  • GO:0102137: Add RHEA:70015. Add 1.14.14.180 as broadMatch. Change parent to match EC
  • GO:0102138: Add RHEA:70019 to . Add 1.14.14.180 as broadMatch. Change parent to match EC.
  • GO:0102767: change MetaCyc xref to MetaCyc:RXN-12719
  • GO:0033799: Remove MetaCyc:RXN-13912
  • GO:0047751: Make MetaCyc:RXN-4229 and MetaCyc:CHOLESTENONE-5-ALPHA-REDUCTASE-RXN narrowMatch xrefs , add MetaCyc:1.3.99.5-RXN as exactMatch (Remove MetaCyc:RXN-4229 from obsolete GO:0102678)
  • GO:0003865: remove MetaCyc:1.3.99.5-RXN and replace with MetaCyc:RXN-13682
  • GO:0047606: Remove ACETONE-CYANHYDRIN-LYASE-RXN xref. Rename and define GO term following EC; need to move 2 children.
  • GO:0004050: Change to MetaCyc:RXN-14024
  • GO:0034317: Add RHEA:25568 & EC:2.7.1.173
  • GO:0050138: Remove MetaCyc:NICOTINATE-DEHYDROGENASE-RXN
  • GO:0008672: Change to MetaCyc:4.1.2.20-RXN
  • GO:0047562: Change to MetaCyc:RXN-11769
  • GO:0102244: Add RHEA:30695. Note RHEA:30695 is specific form of RHEA:16185, so should be child of GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
  • GO:0010326: Add RHEA:31763 & EC:2.6.1.88
  • GO:0047748: Change to MetaCyc:RXN-13690. Also fix xref: EC:1.14.15.15 line
  • GO:0052624: Add RHEA:40551 & EC:2.1.1.329. Remove MetaCyc:RXN-6723
  • GO:0106339: Add EC:2.1.1.200 as broadMatch to GO:0106339, Add RHEA:42932 as exactMatch
  • GO:0047991: Change to MetaCyc:RXN-13595
  • GO:0047880: Change MetaCyc xref to RXN-17773
  • GO:0018489: Remove MetaCyc:RXN-2
  • GO:0050040: Change to MetaCyc:RXN-19631
  • GO:0140741: Change to MetaCyc:RXN-18388
  • GO:0015625: Remove MetaCyc:ABC-9-RXN & MetaCyc:3.6.3.34-RXN
  • GO:0102014: Remove MetaCyc:ABC-18-RXN
  • GO:0140680: Change MetaCyc xref to RXN-13186
  • GO:0052773: Add RHEA:62168 and EC:3.5.1.136
  • GO:0102672: Add RHEA:63508 and EC:1.13.11.92
  • GO:0010945: Remove RHEA:75715 (obsolete at RHEA)
  • GO:0052598: Remove EC:1.4.3.22 (this should just be on the parent GO:0052597 diamine oxidase activity)
  • GO:0004574: Add RHEA:68864 as narrowMatch; make 3.2.1.10-RXN narrowMatch
  • GO:0008670: Broaden GO:0008670 def to mention both reactions associated with EC:1.3.1.34; Make RHEA:12136 and RHEA:45232 (and RXN-20995 and RXN-20994) narrowMatch ; Remove DIENOYLCOAREDUCT-RXN
  • GO:0003875: Broaden GO:0003875 def to mention both reactions associated with EC:3.2.2.19
    Make RHEA:14885 and RHEA:20784 (and MetaCyc:ADP-RIBOSYLARGININE-HYDROLASE-RXN and RXN-8732) narrowMatch
  • GO:0010283 is a combination of: MetaCyc:RXN-8678 + MetaCyc:RXN-8683, RHEA:34419 + RHEA:34427, EC:1.23.1.1 + EC:1.23.1.3 => add missing xrefs as narrowMatch
  • GO:0010284 is a combination of: MetaCyc:RXN-8679 + MetaCyc:RXN-8684, RHEA:34423 + RHEA:34431, EC:1.23.1.2 + EC:1.23.1.4 => add missing xrefs as narrowMatch
  • GO:0043793: Add RHEA:48556 & RHEA:35815 as narrowMatch; add EC:2.4.2.54 as exact match and change GO term to match EC (including comment)
  • NTR for 'fatty acid CoA ligase' grouping term, mapped to RHEA:38883 & BUTYRATE--COA-LIGASE-RXN
  • GO:0004051: make EC:1.13.11.34 = RHEA:32307 exactMatch; RHEA:17961, RHEA:17485, ARACHIDONATE-5-LIPOXYGENASE-RXN & RXN-8647 should be narrowMatch, add comment saying 'multistep reaction'
  • GO:0000823: make MetaCyc xref exactMatch, change RHEA xref to RHEA:17717 (exactMatch), remove EC:2.7.1.151
@sjm41 sjm41 self-assigned this Jun 19, 2024
@sjm41 sjm41 added this to To do in GO-EC-RHEA xref alignment via automation Jun 19, 2024
sjm41 added a commit that referenced this issue Jun 19, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing simple cases. #28199
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sjm41 added a commit that referenced this issue Jun 19, 2024
@sjm41
Merge pull request #28200 from geneontology/issue-28199a
f09ea47 
Has MetaCyc, lacks RHEA - fixing simple cases. #28199
sjm41 added a commit that referenced this issue Jun 19, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing complicated cases. #28199
30b0db1
sjm41 added a commit that referenced this issue Jun 19, 2024
@sjm41
Merge pull request #28202 from geneontology/issue-28199b
69f8761 
Has MetaCyc, lacks RHEA - fixing complicated cases. #28199
sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more simple cases. #28199
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sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more simple cases. #28199
05ca879
sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more simple cases. #28199
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sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more complicated cases. #28199
b618689
sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more complicated cases. #28199
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sjm41 commented Jun 20, 2024 •
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id: GO:0045486
name: naringenin 3-dioxygenase activity
namespace: molecular_function
def: "Catalysis of the reaction: naringenin + 2-oxoglutarate + O2 = dihydrokaempferol + succinate + CO2." [EC:1.14.11.9]
synonym: "(2S)-flavanone 3-hydroxylase activity" RELATED [EC:1.14.11.9]
synonym: "flavanone 3-beta-hydroxylase activity" RELATED [EC:1.14.11.9]
synonym: "flavanone 3-dioxygenase activity" RELATED [EC:1.14.11.9]
synonym: "flavanone 3-hydroxylase activity" RELATED [EC:1.14.11.9]
synonym: "flavanone 3beta-hydroxylase activity" RELATED [EC:1.14.11.9]
synonym: "flavanone synthase I activity" RELATED [EC:1.14.11.9]
synonym: "flavanone,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.11.9]
synonym: "naringenin 3-hydroxylase activity" RELATED [EC:1.14.11.9]
synonym: "naringenin,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating) activity" RELATED [EC:1.14.11.9]
xref: EC:1.14.11.9
xref: MetaCyc:NARINGENIN-3-DIOXYGENASE-RXN
xref: RHEA:18621
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity

EC:1.14.11.9/RHEA:18621 is for the more general reaction:
flavanone 3-dioxygenase
2-oxoglutarate + a (2S)-flavan-4-one + O2 <=> a (2R,3R)-dihydroflavonol + CO2 + succinate

  • change GO name and def to match EC/RHEA
  • Change MetaCyc to 1.14.11.9-RXN

sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Has MetaCyc, lacks RHEA - fixing more complicated cases. #28199
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@sjm41 sjm41 closed this as completed in ea7792a Jun 20, 2024
sjm41 added a commit that referenced this issue Jun 20, 2024
@sjm41
Merge pull request #28218 from geneontology/issue-28199e
db97259 
Has MetaCyc, lacks RHEA - fixing final cases. Fixes #28199
GO-EC-RHEA xref alignment automation moved this from To do to Done Jun 20, 2024
@sjm41 sjm41 mentioned this issue Jun 20, 2024
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sjm41 commented Jun 25, 2024

Need to remove H+ from these reaction defs to match RHEA:

[Term]
id: GO:0102533
name: genkwanin 4'-O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: genkwanin + S-adenosyl-L-methionine = apigenin 4',7-dimethyl ether + S-adenosyl-L-homocysteine + H+." [RHEA:73263]
xref: MetaCyc:RXN-14750 {source="skos:exactMatch"}
xref: RHEA:73263 {source="skos:exactMatch"}
is_a: GO:0008168 ! methyltransferase activity
property_value: term_tracker_item "#28199" xsd:anyURI

[Term]
id: GO:0102439
name: 3',4',5'-trimethylmyricetin 7-O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3',4',5'-O-trimethylmyricetin + S-adenosyl-L-methionine = 7,3',4',5'-O-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [RHEA:74739]
xref: MetaCyc:RXN-13916 {source="skos:exactMatch"}
xref: RHEA:74739 {source="skos:exactMatch"}
is_a: GO:0008168 ! methyltransferase activity
property_value: term_tracker_item "#28199" xsd:anyURI

id: GO:0102440
name: 3',4',5'-trimethylmyricetin 3-O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3',4',5'-O-trimethylmyricetin + S-adenosyl-L-methionine = 3,3',4',5'-O-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [RHEA:74771]
xref: MetaCyc:RXN-13918 {source="skos:exactMatch"}
xref: RHEA:74771 {source="skos:exactMatch"}
is_a: GO:0008168 ! methyltransferase activity
property_value: term_tracker_item "#28199" xsd:anyURI

@sjm41 sjm41 reopened this Jun 25, 2024
GO-EC-RHEA xref alignment automation moved this from Done to In progress Jun 25, 2024
@sjm41 sjm41 closed this as completed in 62ce2b8 Jun 25, 2024
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Merge pull request #28281 from geneontology/issue-28199a
ee13535 
Fixed defs. Fixes #28199
GO-EC-RHEA xref alignment automation moved this from In progress to Done Jun 25, 2024
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sjm41 commented Jun 25, 2024 •
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After checking with RHEA:

  • add RHEA:30003 to GO:0047270
  • add RHEA:30015 to GO:0008919
  • change RHEA on GO:0033230 from RHEA:32795 to RHEA:29783
  • GO:0008718 - MetaCyc:RXN-11193 and EC:1.4.5.1 are narrowMatch, RHEA:18125 is exactMatch
  • GO:0102624 - add RHEA:73239 and improve def
  • GO:0102447 - add RHEA:73271 and improve def
  • GO:0010945 - make RHEA:50044, RHEA:64988, MetaCyc:RXN-10811 narrowMatch

@sjm41 sjm41 reopened this Jun 25, 2024
GO-EC-RHEA xref alignment automation moved this from Done to In progress Jun 25, 2024
@sjm41 sjm41 closed this as completed in 97322a4 Jun 25, 2024
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Merge pull request #28282 from geneontology/issue-28199b
4911dc6 
Added RHEAs. Fixes #28199
GO-EC-RHEA xref alignment automation moved this from In progress to Done Jun 25, 2024
@sjm41 sjm41 reopened this Jun 25, 2024
GO-EC-RHEA xref alignment automation moved this from Done to In progress Jun 25, 2024
@sjm41 sjm41 closed this as completed in edbec1d Jun 25, 2024
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Merge pull request #28284 from geneontology/issue-28199c
341f8c7 
Added RHEAs. Fixes #28199
GO-EC-RHEA xref alignment automation moved this from In progress to Done Jun 25, 2024
@sjm41 sjm41 reopened this Jun 25, 2024
GO-EC-RHEA xref alignment automation moved this from Done to In progress Jun 25, 2024
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Fixing glycosylceramidase terms. #28199
309b87d
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Merge pull request #28291 from geneontology/issue-28199c
4587bff 
Fixing glycosylceramidase terms. #28199
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Adding RHEA xrefs etc. #28199
72dcd6d
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Adding RHEA xrefs etc. #28199
27ac28f
sjm41 added a commit that referenced this issue Jun 25, 2024
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Merge pull request #28296 from geneontology/issue-28199d
49b13db 
Adding RHEA xrefs etc. #28199
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sjm41 commented Jun 25, 2024 •
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id: GO:0050550
name: pinene synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: geranyl diphosphate = pinene + diphosphate. This reaction can produce both alpha-pinene and beta-pinene." [PMID:21385377, PMID:23679205]
synonym: "(-)-(1S,5S)-pinene synthase activity" NARROW [EC:4.2.3.120]
synonym: "alpha-pinene synthase activity" NARROW [EC:4.2.3.119]
synonym: "beta-geraniolene synthase activity" RELATED [EC:4.2.3.120]
synonym: "beta-pinene synthase activity" NARROW [EC:4.2.3.120]
xref: EC:4.2.3.119 {source="skos:narrowMatch"}
xref: EC:4.2.3.120 {source="skos:narrowMatch"}
xref: MetaCyc:RXN-5106 {source="skos:narrowMatch"}
xref: MetaCyc:RXN-5107 {source="skos:narrowMatch"}
xref: RHEA:25488 {source="skos:narrowMatch"}
xref: RHEA:25496 {xref="skos:narrowMatch"}
is_a: GO:0010333 ! terpene synthase activity
property_value: term_tracker_item "#26207" xsd:anyURI

  • Add additional xrefs as narrowMatch: EC:4.2.3.121 = RHEA:32575 = RXN-8563, EC:4.2.3.122 = RHEA:32579 = RXN-8564
  • Also, modify def to indicate all forms that are covered by this single GO term.
  • fix {xref="skos:narrowMatch"} line

sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Adding xrefs to pinene synthase activity. Fixes #28199
40cf6d5
sjm41 added a commit that referenced this issue Jun 25, 2024
@sjm41
Adding xrefs to pinene synthase activity. Fixes #28199
08a547b
@sjm41 sjm41 closed this as completed in 792257d Jun 25, 2024
GO-EC-RHEA xref alignment automation moved this from In progress to Done Jun 25, 2024
@sjm41 sjm41 reopened this Jun 28, 2024
GO-EC-RHEA xref alignment automation moved this from Done to In progress Jun 28, 2024
sjm41 added a commit that referenced this issue Jun 28, 2024
@sjm41
Fixing GO:0043793 xrefs. #28199
bb93772
sjm41 added a commit that referenced this issue Jun 28, 2024
@sjm41
Merge pull request #28352 from geneontology/issue-28199-1
bfa7887 
Fixing GO:0043793 xrefs. #28199
@sjm41 sjm41 closed this as completed Jun 28, 2024
GO-EC-RHEA xref alignment automation moved this from In progress to Done Jun 28, 2024
@sjm41 sjm41 mentioned this issue Jul 16, 2024
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