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Review annotations to [aromatic compound metabolic process/ cellular/nitrogen compound metabolic process]/ heterocycle metabolic process #5148

Open ValWood opened 3 months ago

ValWood commented 3 months ago

Dear all,

The proposal has been made to obsolete

GO:0006725 cellular aromatic compound metabolic process GO:0019438 aromatic compound biosynthetic process GO:0019439 aromatic compound catabolic process No regulation terms

GO:0034641 cellular nitrogen compound metabolic process GO:0044270 cellular nitrogen compound catabolic process GO:0044271 cellular nitrogen compound biosynthetic process No regulation terms

GO:0006807 nitrogen compound metabolic process GO:0051171 regulation of nitrogen compound metabolic process GO:0051172 negative regulation of nitrogen compound metabolic process GO:0051173 positive regulation of nitrogen compound metabolic process

GO:0046483 heterocycle metabolic process GO:0018130 heterocycle biosynthetic process GO:0046700 heterocycle catabolic process No regulation terms

see https://github.com/geneontology/go-ontology/issues/27446 https://github.com/geneontology/go-ontology/issues/27445 https://github.com/geneontology/go-ontology/issues/27444 https://github.com/geneontology/go-ontology/issues/27443

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1wQT-8JPFn8JK9nyRSHDLkGmfOHh6VpVujcqTCEnxBiQ/edit#gid=0

Impacted groups: [LIST GROUPS + NUMBER OF ANNOTATIONS + ADD ASSIGNEES] 

nitrogen compound metabolic process ~4 AspGD @Antonialock~ 2 CACAO @dsiegele 6 CGD @jlewsmith ~1 EcoCyc @amandamackie~ 12 MGI @LiNiMGI ~14 UniProt @Antonialock~ 4 SGD @suzialeksander ~10 TAIR @lreiser~

regulation of nitrogen compound metabolic process ~3 TAIR @lreiser~ ~1 UniProt @Antonialock~ ~1 EcoCyc @amandamackie~ 2 MGI @LiNiMGI

positive regulation of nitrogen compound metabolic process ~3 ARUK-UCL @RLovering~ 1 PseudoCAP ? 1 SGD @suzialeksander

negative regulation of nitrogen compound metabolic process ~1 PAMGO_MGG @vanaukenk~ looks like Antonia fixed this one

cellular nitrogen compound catabolic process 3 CGD @jlewsmith 1 SGD @suzialeksander

cellular nitrogen compound biosynthetic process ~1 EcoCyc @amandamackie~

aromatic compound catabolic process ~3 BHF-UCL @RLovering~ 3 CGD @jlewsmith 3 ComplexPortal @sandraorchard 1 EcoliWiki @dsiegele ~2 RGD @gthayman~ 1 SGD @suzialeksander ~17 UniProt @Antonialock~

aromatic compound biosynthetic process ~23 UniProt @Antonialock~ 1 dictyBase @pfey03

cellular aromatic compound metabolic process 6 MGI @LiNiMGI ~3 UniProt @Antonialock~ 2 SGD @suzialeksander ~1 ZFIN @doughowe~

heterocycle metabolic process ~6 BHF-UCL @RLovering~ 1 MGI @LiNiMGI

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) [LIST IDs + ADD ASSIGNEES] 

Many of these look as though they could be assigned to more specific terms:

11 GO:0006725 interpro2go 1 GO:0006807 hamap2go 25 GO:0006807 interpro2go 1 GO:0006807 unirule2go 12 GO:0019439 hamap2go 15 GO:0019439 interpro2go 1 GO:0019439 uniprotkb_kw2go 13 GO:0019439 unirule2go

term file line GO:0006725 interpro2go InterPro:IPR000391 Ring-hydroxylating dioxygenase beta subunit > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR000486 Extradiol ring-cleavage dioxygenase, class I /II > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR000627 Intradiol ring-cleavage dioxygenase, C-terminal > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003430 Propane/methane/phenol/toluene hydroxylase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003454 Monooxygenase component MmoB/DmpM > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003464 Muconolactone delta-isomerase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR004183 Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR004370 4-oxalocrotonate tautomerase-like domain > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR012817 Chlorocatechol 1,2-dioxygenase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR018191 4-oxalocrotonate tautomerase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR036889 Monooxygenase component MmoB/DmpM superfamily > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006807 interpro2go InterPro:IPR001287 Nitrite reductase, copper-type > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR002639 Urease accessory protein UreF > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR002669 Urease accessory protein UreD > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003010 Carbon-nitrogen hydrolase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003168 Nitrile hydratase, beta subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003321 Cytochrome c552 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR004232 Nitrile hydratase alpha /Thiocyanate hydrolase gamma > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR004400 Urease accessory protein UreG > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR005483 Carbamoyl-phosphate synthase large subunit, CPSase domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR005848 Urease, alpha subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR006275 Carbamoyl-phosphate synthase, large subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR006982 Glutamate synthase, central-N > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008146 Glutamine synthetase, catalytic domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008147 Glutamine synthetase, N-terminal domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008221 Urease > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR010043 Bifunctional uridylyltransferase/uridylyl-removing enzyme > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR015942 Asp/Glu/hydantoin racemase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017564 Cytochrome c-type protein NrfB > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017570 Formate-dependent cytochrome c nitrite reductase, c552 subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017951 Urease alpha subunit, C-terminal > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR018141 Nitrile hydratase, alpha subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR022843 Formamidase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR036648 Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR036651 Glutamine synthetase, N-terminal domain superfamily > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR047177 Peptidase M20A > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 hamap2go HAMAP:MF_01182 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 unirule2go UniRule:UR000100881 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0019439 interpro2go InterPro:IPR003361 Acetaldehyde dehydrogenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012425 DmpG-like communication > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012690 2-oxo-hepta-4-ene-1,7-dioic acid hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012786 Protocatechuate 3,4-dioxygenase, alpha subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR015426 Acetaldehyde dehydrogenase, C-terminal > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017602 Cyclohexa-1,5-dienecarbonyl-CoA hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017624 Catechol 2,3 dioxygenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017629 4-hydroxy-2-oxovalerate aldolase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017640 Anthranilate 1,2-dioxygenase, small subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017727 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, BphD > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR020875 3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023789 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023791 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023793 2-keto-4-pentenoate hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 uniprotkb_kw2go UniProtKB-KW:KW-0058 Aromatic hydrocarbons catabolism > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01292 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01647 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01648 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01649 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01650 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01651 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01653 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01654 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01655 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01656 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01657 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01688 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083126 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083129 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083130 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083151 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083152 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083157 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083159 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083161 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083162 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083169 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000084124 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000101698 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000396796 > GO:aromatic compound catabolic process ; GO:0019439

Thanks.

ValWood commented 3 months ago

Extensions MGI MGI:MGI:88039 Apc PMID:16740478 GO:0051171 regulation of nitrogen compound metabolic process IMP MGI:MGI:3521822 PANTHER:PTHR12607 20081105 GO:0006807 NCBITaxon:10090 SGD SGD:S000002374 GDH2 PMID:6343120 GO:0004352 glutamate dehydrogenase (NAD+) activity IDA UniProtKB:P33327 PANTHER:PTHR11606 20220106 GO:0005829|GO:0006807 NCBITaxon:559292

ValWood commented 3 months ago

@tony787 for InterPro @blazaropinto for InterPro @sarach06 for InterPro @PedroRaposo for uni rule @pedruzzi for hamap @Antonialock for KW 2 GO

Note that there would be little loss of information just to move to the corresponding "X metabolic process" (will be suggested as direct replacements) But you can probably make many more specific.

gthayman commented 3 months ago

RGD done.

lreiser commented 3 months ago

GO:0006807 done GO:0051171 done TAIR done....

RLovering commented 3 months ago

most of UCL's done, just waiting for new term for last 3 Ruth

pgaudet commented 3 months ago

@RLovering Is this nitric oxide signaling ?

amandamackie commented 3 months ago

EcoCyc done

Antonialock commented 3 months ago

uniprot and pamgo annotations are done, uniprot kw done

Antonialock commented 3 months ago

and aspgd

just waiting for some ntrs

doughowe commented 3 months ago

Zebrafish annotations are done Doug

From: Val Wood @.> Sent: Wednesday, March 27, 2024 7:26 AM To: geneontology/go-annotation @.> Cc: Doug Howe @.>; Mention @.> Subject: [geneontology/go-annotation] Review annotations to [aromatic compound metabolic process/ cellular/nitrogen compound metabolic process]/ heterocycle metabolic process (Issue #5148)

Dear all,

The proposal has been made to obsolete

GO:0006725 cellular aromatic compound metabolic process GO:0019438 aromatic compound biosynthetic process GO:0019439 aromatic compound catabolic process No regulation terms

GO:0034641 cellular nitrogen compound metabolic process GO:0044270 cellular nitrogen compound catabolic process GO:0044271 cellular nitrogen compound biosynthetic process No regulation terms

GO:0006807 nitrogen compound metabolic process GO:0051171 regulation of nitrogen compound metabolic process GO:0051172 negative regulation of nitrogen compound metabolic process GO:0051173 positive regulation of nitrogen compound metabolic process

GO:0046483 heterocycle metabolic process GO:0018130 heterocycle biosynthetic process GO:0046700 heterocycle catabolic process No regulation terms

see geneontology/go-ontology#27446https://github.com/geneontology/go-ontology/issues/27446 geneontology/go-ontology#27445https://github.com/geneontology/go-ontology/issues/27445 geneontology/go-ontology#27444https://github.com/geneontology/go-ontology/issues/27444 geneontology/go-ontology#27443https://github.com/geneontology/go-ontology/issues/27443

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1wQT-8JPFn8JK9nyRSHDLkGmfOHh6VpVujcqTCEnxBiQ/edit#gid=0

Impacted groups: [LIST GROUPS + NUMBER OF ANNOTATIONS + ADD ASSIGNEES]

nitrogen compound metabolic process 4 AspGD @Antonialockhttps://github.com/Antonialock 2 CACAO @dsiegelehttps://github.com/dsiegele 6 CGD @jlewsmithhttps://github.com/jlewsmith 1 EcoCyc @amandamackiehttps://github.com/amandamackie 12 MGI @LiNiMGIhttps://github.com/LiNiMGI 14 UniProt @Antonialockhttps://github.com/Antonialock 4 SGD @suzialeksanderhttps://github.com/suzialeksander 10 TAIR @lreiserhttps://github.com/lreiser

regulation of nitrogen compound metabolic process 3 TAIR @lreiserhttps://github.com/lreiser 1 UniProt @Antonialockhttps://github.com/Antonialock 1 EcoCyc @amandamackiehttps://github.com/amandamackie 2 MGI @LiNiMGIhttps://github.com/LiNiMGI

positive regulation of nitrogen compound metabolic process 3 ARUK-UCL @RLoveringhttps://github.com/RLovering 1 PseudoCAP ? 1 SGD @suzialeksanderhttps://github.com/suzialeksander

negative regulation of nitrogen compound metabolic process 1 PAMGO_MGG @vanaukenkhttps://github.com/vanaukenk

cellular nitrogen compound catabolic process 3 CGD @jlewsmithhttps://github.com/jlewsmith 1 SGD @suzialeksanderhttps://github.com/suzialeksander

cellular nitrogen compound biosynthetic process 1 EcoCyc @amandamackiehttps://github.com/amandamackie

aromatic compound catabolic process 3 BHF-UCL @RLoveringhttps://github.com/RLovering 3 CGD @jlewsmithhttps://github.com/jlewsmith 3 ComplexPortal 1 EcoliWiki @dsiegelehttps://github.com/dsiegele 2 RGD @gthaymanhttps://github.com/gthayman 1 SGD @suzialeksanderhttps://github.com/suzialeksander 17 UniProt @Antonialockhttps://github.com/Antonialock

aromatic compound biosynthetic process 23 UniProt @Antonialockhttps://github.com/Antonialock 1 dictyBase @pfey03https://github.com/pfey03

cellular aromatic compound metabolic process 6 MGI @LiNiMGIhttps://github.com/LiNiMGI 3 UniProt @Antonialockhttps://github.com/Antonialock 2 SGD @suzialeksanderhttps://github.com/suzialeksander 1 ZFIN @doughowehttps://github.com/doughowe

heterocycle metabolic process 6 BHF-UCL @RLoveringhttps://github.com/RLovering 1 MGI @LiNiMGIhttps://github.com/LiNiMGI

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) [LIST IDs + ADD ASSIGNEES]

Many of these look as though they could be assigned to more specific terms:

11 GO:0006725 interpro2go 1 GO:0006807 hamap2go 25 GO:0006807 interpro2go 1 GO:0006807 unirule2go 12 GO:0019439 hamap2go 15 GO:0019439 interpro2go 1 GO:0019439 uniprotkb_kw2go 13 GO:0019439 unirule2go

term file line GO:0006725 interpro2go InterPro:IPR000391 Ring-hydroxylating dioxygenase beta subunit > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR000486 Extradiol ring-cleavage dioxygenase, class I /II > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR000627 Intradiol ring-cleavage dioxygenase, C-terminal > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003430 Propane/methane/phenol/toluene hydroxylase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003454 Monooxygenase component MmoB/DmpM > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR003464 Muconolactone delta-isomerase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR004183 Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR004370 4-oxalocrotonate tautomerase-like domain > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR012817 Chlorocatechol 1,2-dioxygenase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR018191 4-oxalocrotonate tautomerase > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006725 interpro2go InterPro:IPR036889 Monooxygenase component MmoB/DmpM superfamily > GO:cellular aromatic compound metabolic process ; GO:0006725 GO:0006807 interpro2go InterPro:IPR001287 Nitrite reductase, copper-type > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR002639 Urease accessory protein UreF > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR002669 Urease accessory protein UreD > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003010 Carbon-nitrogen hydrolase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003168 Nitrile hydratase, beta subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR003321 Cytochrome c552 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR004232 Nitrile hydratase alpha /Thiocyanate hydrolase gamma > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR004400 Urease accessory protein UreG > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR005483 Carbamoyl-phosphate synthase large subunit, CPSase domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR005848 Urease, alpha subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR006275 Carbamoyl-phosphate synthase, large subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR006982 Glutamate synthase, central-N > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008146 Glutamine synthetase, catalytic domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008147 Glutamine synthetase, N-terminal domain > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR008221 Urease > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR010043 Bifunctional uridylyltransferase/uridylyl-removing enzyme > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR015942 Asp/Glu/hydantoin racemase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017564 Cytochrome c-type protein NrfB > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017570 Formate-dependent cytochrome c nitrite reductase, c552 subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR017951 Urease alpha subunit, C-terminal > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR018141 Nitrile hydratase, alpha subunit > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR022843 Formamidase > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR036648 Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR036651 Glutamine synthetase, N-terminal domain superfamily > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 interpro2go InterPro:IPR047177 Peptidase M20A > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 hamap2go HAMAP:MF_01182 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0006807 unirule2go UniRule:UR000100881 > GO:nitrogen compound metabolic process ; GO:0006807 GO:0019439 interpro2go InterPro:IPR003361 Acetaldehyde dehydrogenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012425 DmpG-like communication > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012690 2-oxo-hepta-4-ene-1,7-dioic acid hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR012786 Protocatechuate 3,4-dioxygenase, alpha subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR015426 Acetaldehyde dehydrogenase, C-terminal > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017602 Cyclohexa-1,5-dienecarbonyl-CoA hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017624 Catechol 2,3 dioxygenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017629 4-hydroxy-2-oxovalerate aldolase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017640 Anthranilate 1,2-dioxygenase, small subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR017727 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, BphD > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR020875 3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023789 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023791 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 interpro2go InterPro:IPR023793 2-keto-4-pentenoate hydratase > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 uniprotkb_kw2go UniProtKB-KW:KW-0058 Aromatic hydrocarbons catabolism > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01292 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01647 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01648 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01649 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01650 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01651 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01653 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01654 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01655 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01656 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01657 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 hamap2go HAMAP:MF_01688 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083126 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083129 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083130 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083151 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083152 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083157 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083159 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083161 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083162 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000083169 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000084124 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000101698 > GO:aromatic compound catabolic process ; GO:0019439 GO:0019439 unirule2go UniRule:UR000396796 > GO:aromatic compound catabolic process ; GO:0019439

Thanks.

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RLovering commented 2 months ago

Hi Pascale

I don't think this is related to NO signaling. There seem to be a lot of articles https://pubmed.ncbi.nlm.nih.gov/?term=reactive+nitrogen+ifn&sort=pubdate suggesting that acute inflammatory responses often involve the production of reactive oxygen and nitrogen species by innate immune cells, particularly macrophages. See figure 1A in https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.123.323223 where NO is converted to RNS (Reactive nitrogen species) which then leads to apoptosis. Or see https://www.researchgate.net/publication/347180751_The_Relationship_Between_Reactive_Oxygen_Species_and_Endothelial_Cell_Metabolism FIGURE 3 | Reactive nitrogen species (RNS). Inflammatory cells are a prominent source of nitric oxide and, when in excess, RNS are formed by combining NO with ROS, especially with superoxide. Examples of RNS include peroxynitrite, nitrogen dioxide, and 3-nitrotyrosine, which have inhibitory effects on DNA repair enzymes,cytochrome c oxidase, and mitochondrial biogenesis.

I guess I could just use the positively regulates qualifier with the reactive nitrogen metabolism term instead?

Best

Ruth

PedroRaposo commented 1 month ago

Hi @pedruzzi, would it be possible to follow the mentioned changed in the following rules, as they are HAMAP rules?

On GO:0019439 (aromatic compound catabolic process): UR000083126 UR000083129 UR000083130 UR000083151 UR000083152 UR000083157 UR000083159 UR000083161 UR000083162 UR000083169 UR000084124 UR000101698 UR000101698

On GO:0006807 (nitrogen compound metabolic process) UR000100881

But on UR000396796 [pertaining to GO:0019439 (aromatic compound catabolic process)] this a PIR rule so I will ask them to look at this.

blazaropinto commented 1 month ago

Hi Val, Thanks for tagging us. I've been checking a few entries in the InterPro live database and they seem to be already ok, we take care about obsolete GO terms just before any release and probably in InterPro 100.0 (which is about to be publicly released, probably next week) most of that, if not all, is already corrected. We can try and filter any error out after this. Best, Beatriz

pedruzzi commented 1 month ago

Hi @pedruzzi, would it be possible to follow the mentioned changed in the following rules, as they are HAMAP rules?

On GO:0019439 (aromatic compound catabolic process): UR000083126 UR000083129 UR000083130 UR000083151 UR000083152 UR000083157 UR000083159 UR000083161 UR000083162 UR000083169 UR000084124 UR000101698 UR000101698

On GO:0006807 (nitrogen compound metabolic process) UR000100881

But on UR000396796 [pertaining to GO:0019439 (aromatic compound catabolic process)] this a PIR rule so I will ask them to look at this.

HAMAP rules fixed. UniRules should be updated upon next reload.