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Add check for database definition cross references to also be a general cross reference #28523

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Tracked by #28763
pgaudet opened this issue Jul 17, 2024 · 10 comments · May be fixed by #29161
Open
Tracked by #28763

Add check for database definition cross references to also be a general cross reference #28523

pgaudet opened this issue Jul 17, 2024 · 10 comments · May be fixed by #29161
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pgaudet commented Jul 17, 2024 •
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(to address #28146 (comment) requested by @sjm41 )

There are many cases where the definition cross references and the general cross references don't match.

Minimally for

  • RHEA
  • EC
  • MetaCyc
  • KEGG
  • UM-BBD
  • TC

We should have a check that any def xref to these databases should ALSO be an general xref.

Thanks, Pascale
@pgaudet pgaudet added the QC label Jul 17, 2024
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sjm41 commented Jul 18, 2024

Hi @pgaudet

We should have a check that any def xref to these databases should ALSO be an general xref.

Agreed, though I think my #28146 (comment) was for a slightly different check - i.e check for terms that have the same MetaCyc/KEGG (or indeed RHEA/EC) definition xref.

But I guess your suggested check will effectively do the same thing - if we ensure that a def xref ALSO appears as a general xref, then any duplicate def xrefs will get flagged up by the existing checks for duplicate general xrefs.

So, all is probably fine!

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pgaudet commented Jul 19, 2024

Right, this is what I meant - once all def xrefs are also general xrefs then we only need to check general xrefs for duplications.

@balhoff balhoff mentioned this issue Sep 16, 2024
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pgaudet commented Nov 7, 2024

Google spreadsheet with errors:
https://docs.google.com/spreadsheets/d/1jMfBoiSRrT-Ycx6TEA9laLDLL9Tj1cFqp9V9WX3mcyk/edit?gid=0#gid=0

Def xrefs and general cross refs dont match (306 errors)

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pgaudet commented Nov 7, 2024 •
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Obsolete:

pgaudet added a commit that referenced this issue Nov 13, 2024
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fixed xef for #28523
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Merge pull request #29209 from geneontology/issue-28523-2
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fixed xef for #28523
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sjm41 commented Nov 14, 2024

Fixes cases where MetaCyc xref on def is obsolete at MetaCyc:

GO ID def xref Notes
GO:0047527 MetaCyc:1,3-DIHYDROXYBENZOATE--SERINE-LIGASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047517 MetaCyc:1,4-BETA-D-XYLAN-SYNTHASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047026 MetaCyc:1.1.1.213-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047042 MetaCyc:1.1.1.50-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050589 MetaCyc:1.14.11.19-RXN Obsolete at MetaCyc - remove from GO def.
GO:0034078 MetaCyc:125-PWY Obsolete at MetaCyc - remove from GO def.
GO:0047229 MetaCyc:2.4.1.158-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047234 MetaCyc:2.4.1.166-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047238 MetaCyc:2.4.1.175-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047244 MetaCyc:2.4.1.187-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047254 MetaCyc:2.4.1.202-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050510 MetaCyc:2.4.1.226-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047269 MetaCyc:2.4.1.70-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047276 MetaCyc:2.4.1.87-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047356 MetaCyc:2.7.8.14-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047525 MetaCyc:2'-HYDROXYDAIDZEIN-REDUCTASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047404 MetaCyc:3.2.1.56-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047573 MetaCyc:4-ACETAMIDOBUTYRATE-DEACETYLASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047468 MetaCyc:5.4.2.5-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047623 MetaCyc:ADENOSINE-PHOSPHATE-DEAMINASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047631 MetaCyc:ADP-RIBOSE-PYROPHOSPHATASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0043039 MetaCyc:Aminoacyl-tRNAs Obsolete at MetaCyc - remove from GO def.
GO:0047763 MetaCyc:CAFFEATE-O-METHYLTRANSFERASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0061681 MetaCyc:ENTNER-DOUFDOROFF-PWY-III Obsolete at MetaCyc - remove from GO def.
GO:0047895 MetaCyc:FORMALDEHYDE-DISMUTASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047930 MetaCyc:GLUCOSAMINATE-AMMONIA-LYASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050417 MetaCyc:GLUTAMINASE-ASPARAGIN-ASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047725 MetaCyc:INULOSUCRASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0048000 MetaCyc:ISOFLAVONE-3'-HYDROXYLASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0017084 MetaCyc:PROLINE-MULTI Obsolete at MetaCyc - remove from GO def.
GO:0019517 MetaCyc:PWY-901 Obsolete at MetaCyc - remove from GO def.
GO:0046499 MetaCyc:S-ADENOSYLMETHIONINAMINE Obsolete at MetaCyc - remove from GO def.
GO:0050306 MetaCyc:SUCROSE-1F-FRUCTOSYLTRANSFERASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050309 MetaCyc:SUGAR-TERMINAL-PHOSPHATASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050316 MetaCyc:T2-INDUCED-DEOXYNUCLEOTIDE-KINASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050350 MetaCyc:TRIHYDROXYSTILBENE-SYNTHASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050369 MetaCyc:TYROSINE-3-MONOOXYGENASE-KINASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0050402 MetaCyc:XYLONO-14-LACTONASE-RXN Obsolete at MetaCyc - remove from GO def.
GO:0047979 MetaCyc:HEXOSE-OXIDASE-RXN Obsolete at MetaCyc - remove from GO def. Add MetaCyc:RXN-17229, RXN-13740, RXN-13741 as narrowMatch xrefAlso, rename GO:0046562 glucose oxidase activity to beta-D-glucose oxidase activity
GO:0047792 MetaCyc:CYANOHYDRIN-BETA-GLUCOSYLTRANSFERASE-RXN Obsolete at MetaCyc - remove from GO def. Add MetaCyc:RXN-743 as dbxref
GO:0047403 MetaCyc:3.2.1.140-RXN Obsolete at MetaCyc - remove from GO def. Add MetaCyc:RXN-8731 as xref.

sjm41 added a commit that referenced this issue Nov 14, 2024
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Removing obsolete MetaCyc xrefs as def xrefs. #28523
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Merge pull request #29228 from geneontology/issue-28523sm1
8c62acc 
Removing obsolete MetaCyc xrefs as def xrefs. #28523
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sjm41 commented Nov 14, 2024 •
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Fixing other cases where MetaCyc def xref needs to be removed:

GO ID def xref Notes
GO:0097294 MetaCyc:IMP-DEHYDROG-RXN Remove from GO def. (Already correctly on GO:0003938 MF term)
GO:0047266 MetaCyc:2.4.1.53-RXN Remove from GO def. (Associated with EC:2.4.1.70 at MetaCyc - correctly an xref on GO:0047269.)
GO:0005960 MetaCyc:GCVMULTI-CPLX Remove from GO def. (Complex entry at MetaCyc)
GO:0034079 MetaCyc:BUTANEDIOL Remove from GO def. (Compound entry at MetaCyc)
GO:0034077 MetaCyc:BUTANEDIOL Remove from GO def. (Compound entry at MetaCyc)
GO:0034078 MetaCyc:BUTANEDIOL Remove from GO def. (Compound entry at MetaCyc)
GO:0019434 MetaCyc:DIGLUCODIACETYL-DOCOSANOATE Remove from GO def. (Compound entry at MetaCyc)
GO:0006675 MetaCyc:MIPC Remove from GO def. (Compound entry at MetaCyc)
GO:0019329 MetaCyc:AMMOXID-PWY Remove from GO def. (Correctly associated with child GO term.)
GO:0019417 MetaCyc:FESULFOX-PWY Remove from GO def. (Correctly associated with child GO term.)
GO:1901790 MetaCyc:HCAMHPDEG-PWY Remove from GO def. (Correctly associated with child GO term.)
GO:0019329 MetaCyc:P303-PWY Remove from GO def. (Correctly associated with child GO term.)
GO:0019329 MetaCyc:PWY-2242 Remove from GO def. (Correctly associated with child GO term.)
GO:0033388 MetaCyc:PWY-46 Remove from GO def. (Correctly associated with child GO term.)
GO:0033331 MetaCyc:PWY-5032 Remove from GO def. (Correctly associated with child GO term.)
GO:0033383 MetaCyc:PWY-5122 Remove from GO def. (Correctly associated with child GO term.)
GO:0033329 MetaCyc:PWY-5320 Remove from GO def. (Correctly associated with child GO term.)
GO:0033302 MetaCyc:PWY-5321 Remove from GO def. (Correctly associated with child GO term.)
GO:0046494 MetaCyc:PWY-761 Remove from GO def. (Correctly associated with child GO term.)
GO:0004779 MetaCyc:SULFATE-ADENYLYLTRANS-RXN Remove from GO def. (Correctly associated with child GO term.)
GO:0004779 MetaCyc:SULFATE-ADENYLYLTRANSFERASE-ADP-RXN Remove from GO def. (Correctly associated with child GO term.)
GO:0019417 MetaCyc:SULFUROX-PWY Remove from GO def. (Correctly associated with child GO term.)
GO:0033321 MetaCyc:PWY-1186 Remove from GO def. (Correctly associated with child GO term.) Change name of the child term (GO:0033322) to "L-homomethionine..." to match MetaCyc
GO:0035446 MetaCyc:RXN1G-4 Remove from GO def. (Correctly associated with different GO term.)
GO:0019665 MetaCyc:Fermentation Remove from GO def. (Correctly associated with parent GO term.)
GO:0019662 MetaCyc:Fermentation Remove from GO def. (Correctly associated with parent GO term.)
GO:0033386 MetaCyc:PWY-5120 Remove from GO def. (single-step - correctly associated with GO:0004311 MF term.)
GO:0033385 MetaCyc:PWY-5120 Remove from GO def. (single-step - correctly associated with GO:0004311 MF term.)
GO:0033499 MetaCyc:PWY-3821 Remove from GO def. (Term already has correct xref of PWY-6317)

sjm41 added a commit that referenced this issue Nov 14, 2024
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Removing incorrect MetaCyc xrefs as def xrefs. #28523
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Merge pull request #29230 from geneontology/issue-28523sm2
445dd04 
Removing incorrect MetaCyc xrefs as def xrefs. #28523
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sjm41 commented Nov 14, 2024 •
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Fixing cases where MetaCyc xref in def needs to be added as dbxref:

GO ID def xref Notes
GO:1901794 MetaCyc:PWY0-1277 Add as broadMatch xref
GO:1901791 MetaCyc:HCAMHPDEG-PWY Add as broadMatch xref.
GO:1901782 MetaCyc:PWY-5273 Add as dbxref
GO:1901815 MetaCyc:PWY-5288 Add as dbxref
GO:1901812 MetaCyc:PWY-5943 Add as dbxref
GO:1901827 MetaCyc:PWY-5944 Add as dbxref
GO:1901830 MetaCyc:PWY-6288 Add as dbxref
GO:0090638 MetaCyc:PWY-6825 Add as dbxref
GO:1901780 MetaCyc:PWY-6915 Add as dbxref
GO:1901774 MetaCyc:PWY-6955 Add as dbxref
GO:1901802 MetaCyc:PWY-6992 Add as dbxref
GO:1901158 MetaCyc:PWY-7016 Add as dbxref
GO:0090640 MetaCyc:PWY-7470 Add as dbxref
GO:1990055 MetaCyc:RXN-8990 Add as dbxref
GO:1901833 MetaCyc:PWY-6809 Add as dbxref (and rename/redefine/change LD to match current MetaCyc "neoxanthin biosynthesis")
GO:1901866 MetaCyc:PWY-5174 Add as dbxref (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:1901809 MetaCyc:PWY-5174 Add as dbxref (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:0019287 MetaCyc:PWY-922 Add as dbxref, and remove from GO:0010142
GO:0033389 MetaCyc:PWY-40 Add as dbxref & tweak LD.
GO:0033390 MetaCyc:PWY-43 Add as dbxref & tweak LD.
GO:1901824 MetaCyc:PWY-5946 Add as dbxref. Also need to redefine/rename/change LD to reflect MetaCyc ("alpha carotene")
GO:0033387 MetaCyc:PWY-46 Add as dbxref. Also need to redefine/rename/change LD to reflect MetaCyc ("from arginine, via ornithine")
GO:0006601 MetaCyc:GLYCGREAT-PWY Add as dbxref. Remove from GO:0019463 and obsolete that term (no annotations)
GO:1901788 MetaCyc:PWY-1361 Add as narrow dbxref
GO:1901788 MetaCyc:P321-PWY Add as narrow dbxref, remove from GO:0018874
GO:1901788 MetaCyc:CENTBENZCOA-PWY Add as narrow dbxref, remove from GO:0018875
GO:0008153 MetaCyc:PWY-6543 Add as narrowMatch dbxref (and rename to match MetaCyc - "4-aminobenzoate biosynthesis"Also add PWY-8276 and PWY-8281 as narrowMatch.
GO:0019664 MetaCyc:FERMENTATION-PWY Add this as dbxref, remove from GO:0006113
GO:0006113 MetaCyc:Fermentation Add this as dbxref, remove MetaCyc:FERMENTATION-PWY

sjm41 added a commit that referenced this issue Nov 15, 2024
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Adding MetaCyc def xrefs as db xrefs. #28523
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sjm41 commented Nov 15, 2024

Fixing remaining MetaCyc xref issues:

GO ID def xref Notes
GO:0090439 MetaCyc:RXN-12183 Change def xref to MetaCyc:RXN-16407
GO:0006601 MetaCyc:PWY-6158 One-step reaction - add as relatedMatch on GO:0004111 (MF)
GO:0052776 MetaCyc:PWY-6855 PWY-6855 is "chitin degradation I (archaea)" and is currently a narrowMatch xref on GO:0006032 chitin catabolic process. So, make GO:0052776 a child of GO:0006032 and edit xrefs as appropriate. Also need to redefine/rename/change LD of GO:0052776 to match current PWY-6855 description.
GO:1901864 MetaCyc:PWY-5174 Remove from GO def (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:1901865 MetaCyc:PWY-5174 Remove from GO def (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:1901807 MetaCyc:PWY-5174 Remove from GO def (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:1901808 MetaCyc:PWY-5174 Remove from GO def (PWY-5174 = capsanthin and capsorubin biosynthesis, so should be broadMatch on just GO:1901866 capsorubin biosynthetic process and GO:1901809 capsanthin biosynthetic process)
GO:0033359 MetaCyc:DAPLYSINESYN-PWY- Remove trailing hyphen

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Adding MetaCyc def xrefs as db xrefs. #28523
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Merge pull request #29235 from geneontology/issue-28523sm3
91035f7 
Adding MetaCyc def xrefs as db xrefs. #28523
sjm41 added a commit that referenced this issue Nov 15, 2024
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Fixing MetaCyc def xrefs as db xrefs. #28523
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sjm41 added a commit that referenced this issue Nov 15, 2024
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Fixing MetaCyc def xrefs as db xrefs. #28523
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sjm41 added a commit that referenced this issue Nov 15, 2024
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Merge pull request #29239 from geneontology/issue-28523sm4
5ee566f 
Fixing MetaCyc def xrefs as db xrefs. #28523
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sjm41 commented Nov 15, 2024

GO:0140859 | RHEA:35811 |
RHEA:35811 is a specific reaction, remove from def xref and replace with current dbxref RHEA:35407

sjm41 added a commit that referenced this issue Nov 15, 2024
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Fixing RHEA:35811 def xref. #28523
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Merge pull request #29240 from geneontology/issue-28523sm5
286b008 
Fixing RHEA:35811 def xref. #28523
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sjm41 commented Nov 15, 2024

Fixing UM-BBD def xrefs:

GO ID def xref Notes
GO:0008695 UM-BBD_enzymeID:e0307 Replace current UM-BBD dbxref with this one.
GO:0009390 UM-BBD_enzymeID:r0207 This is a complex - replace with PMID:21357619 and PMID:3280546
GO:0018901 UM-BBD_pathwayID:2,4d Remove UM-BBD xrefs from this term and move to catabolic child (GO:0046300) - dbxref should be '2,4-d'
GO:0019490 UM-BBD_pathwayID:abs Add as dbref; replace def xref with MetaCyc:2ASDEG-PWY. Remove UM-BBD_pathwayID:abs from parent GO:0018868
GO:0019381 UM-BBD_pathwayID:atr Add as dbref; replace def xref with MetaCyc:PWY-5724. Remove UM-BBD_pathwayID:atr from parent GO:0018873
GO:0019383 UM-BBD_pathwayID:cam Add as dbref; replace def xref with MetaCyc:P601-PWY. Remove UM-BBD_pathwayID:cam from parent GO:0018882
GO:0018983 UM-BBD_pathwayID:car Replace this def xref with dbxref of UM-BBD_pathwayID:pao
GO:0042201 UM-BBD_pathwayID:cpm Remove from def - already correctly a def xref & dbxref on child.
GO:0042199 UM-BBD_pathwayID:cya Remove from def - already correctly a def xref & dbxref on child.
GO:0019497 UM-BBD_pathwayID:ghch Add as narrowMatch dbxref
GO:0019497 UM-BBD_pathwayID:hch Add as narrowMatch dbxref
GO:0042212 UM-BBD_pathwayID:mcr Remove from def - already correctly a dbxref on child.
GO:0019339 UM-BBD_pathwayID:pthn Add as dbref; replace def xref with MetaCyc:PARATHION-DEGRADATION-PWY Remove UM-BBD_pathwayID:pthn from parent GO:0018952
GO:0018970 UM-BBD_pathwayID:tol Remove this def xref and add as def xref and dbxref on GO:0042203 toluene catabolic process
GO:0019119 UM-BBD_reactionID:r0496 Add as narrowMatch dbxref
GO:0019118 UM-BBD_reactionID:r0535 Add as narrowMatch dbxref
GO:0019118 UM-BBD_reactionID:r0536 Add as narrowMatch dbxref
GO:0019119 UM-BBD_reactionID:r0560 Add as narrowMatch dbxref
GO:0018594 UM-BBD_reactionID:r0615 Add as dbxref
GO:0018591 UM-BBD_reactionID:r1023 Add as dbxref
GO:0018755 UM-BBD_reactionID:r1414 Add as dbxref

sjm41 added a commit that referenced this issue Nov 15, 2024
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Fixing UM-BBD def xrefs. #28523
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Fixing UM-BBD def xrefs. #28523
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Add check for definition xrefs that are not also term xrefs geneontology/go-ontology
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