ARBA Rule Reviews Index
76 rule reviews. Includes reviews in progress; status and decisions reflect the source YAML.
Condition-set counts describe the sets recorded in each review, which may omit the full rule.
| Rule ID | Description | GO Terms | Status | Action | Parsimony | Literature | Recorded condition sets | Confidence |
|---|---|---|---|---|---|---|---|---|
| ARBA00000900 YAML |
A mega-rule with 298 condition sets attempting to annotate all E3 ubiquitin-protein ligases with EC 2.3.2.27 (ubiquitin-protein transferase activity) across bacteria, plants, animals, and viruses. The rule covers vastly different catalytic mechanisms (RING, HECT, U-box), domain architectures, and protein families. | GO:0004842 ubiquitin-protein transferase activity |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | MODERATE | 0 | 0.10 |
| ARBA00001096 YAML |
Predicts glucose-6-phosphate 1-epimerase activity (EC 5.1.3.15) based on the presence of three hierarchical InterPro domains using restrictive AND logic | COMPLETE | MODIFY | REDUNDANT | MODERATE | 1 | 0.80 | |
| ARBA00001712 YAML |
Predicts aldose 1-epimerase activity (galactose mutarotase, EC 5.1.3.3) for proteins containing aldose epimerase domains with taxonomic restrictions to Metazoa (condition set 1) or specific CATH FunFam in Eukaryota (condition set 2) | COMPLETE | MODIFY | REDUNDANT | STRONG | 2 | 0.70 | |
| ARBA00004173 YAML |
Aggregated ARBA localization rule that asserts the UniProt SUBCELLULAR LOCATION "Mitochondrion" (SL-0173) for eukaryotic proteins matching any of 1,490 OR-ed condition sets built from CATH FunFam, InterPro and PANTHER signatures. Via the UniProtKB-SubCell -> GO mapping (GO_REF:0000044) the assertion is propagated to GO:0005739 (mitochondrion) with evidence IEA / ECO:0007322. The rule currently annotates 536,854 unreviewed (TrEMBL) proteins and 0 reviewed proteins. It is not a single-family rule but an umbrella aggregating hundreds of independent branch-level classifiers of very uneven quality, ranging from canonical mitochondrial families (MIC60, TOM40, TIM/Tim10-like, cytochrome c oxidase subunits, sideroflexins) to bare single unlabeled FunFams and clade-overfitted singletons. | GO:0005739 mitochondrion |
COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 12 | 0.35 |
| ARBA00004218 YAML |
A highly problematic rule that assigns acrosome subcellular localization to 35+ unrelated protein families, including epithelial sodium channels, mitochondrial enzymes, complement proteins, and other non-sperm proteins alongside legitimate sperm components | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.10 | |
| ARBA00004725 YAML |
Rule annotating proteins involved in the de novo pyrimidine biosynthesis pathway with pathway comment "Pyrimidine metabolism; UMP biosynthesis via de novo pathway". Contains 27 condition sets covering all major enzymes: carbamoyl-phosphate synthase, aspartate carbamoyltransferase, dihydroorotase, dihydroorotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine 5-phosphate decarboxylase. | COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 0 | 0.40 | |
| ARBA00004841 YAML |
TODO: Provide a concise description of what this rule predicts and how | IN_PROGRESS | MODIFY | REDUNDANT | STRONG | 3 | 0.30 | |
| ARBA00005098 YAML |
Rule targeting ureohydrolase family proteins (arginase and agmatinase) involved in nitrogen metabolism and urea cycle, but critically lacking GO term annotations | COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 8 | 0.90 | |
| ARBA00022438 YAML |
A complex mega-rule with 86 condition sets attempting to annotate all aminopeptidases across multiple mechanistic families (M1, M24, M2, M49, S33) with only a keyword annotation. The rule spans diverse catalytic mechanisms (zinc-dependent, iron-dependent, serine proteases) and biological functions (protein degradation, methionine removal, hormone processing) without appropriate GO term annotations. | COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 0 | 0.20 | |
| ARBA00022487 YAML |
Mega-rule predicting serine esterase activity (KW-0719) across 62 highly diverse condition sets covering numerous esterase, lipase, cutinase, and hydrolase families from bacteria to mammals | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.10 | |
| ARBA00022603 YAML |
ARBA rule ARBA00022603 - Comprehensive review pending rule data access. This rule requires fetching from UniProt ARBA database to determine specific condition sets and GO annotations. | GO:UNKNOWN TODO: Fetch actual GO annotation from UniProt |
IN_PROGRESS | UNDECIDED | UNDECIDED | UNDECIDED | 1 | 0.00 |
| ARBA00022670 YAML |
A catastrophically over-broad rule that annotates proteins with a generic "Protease" keyword if they contain ANY of 502 different protease-related InterPro domains. The rule uses a single massive OR-logic condition set that treats highly specific peptidases (e.g., signal peptide peptidases) the same as broad families (e.g., proteasome subunits), fundamentally violating principles of specificity in functional annotation. | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 1 | 0.05 | |
| ARBA00022679 YAML |
Catastrophically broad rule applying the "Transferase" keyword (KW-0808) to over 14 million proteins using 4,473 condition sets encompassing 1,932 unique InterPro domains and 3,730 CATH FunFam families. This represents the most extreme case of over-annotation in the ARBA system, conflating virtually all transferase activities under a single meaningless keyword. | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 1 | 0.95 | |
| ARBA00022722 YAML |
Highly problematic rule with 532 condition sets using 371 unique InterPro domains to assign only a vague "Nuclease" keyword annotation with no GO terms. This represents severe over-engineering and over-annotation of nuclease function. | COMPLETE | REMOVE | OVERLY_COMPLEX | WEAK | 0 | 0.95 | |
| ARBA00022759 YAML |
An extremely complex rule with 318 condition sets that all predict the same broad "Endonuclease" keyword annotation (KW-0255). This rule attempts to capture all types of nucleic acid cleaving enzymes through diverse combinations of InterPro domains, PANTHER families, and taxonomic restrictions, representing a clear example of rule over-engineering that conflicts with annotation best practices. | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 3 | 0.05 | |
| ARBA00022777 YAML |
Overly broad rule attempting to annotate all kinase proteins across all domains of life using 1,358 condition sets with only a keyword annotation | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 | |
| ARBA00022801 YAML |
ARBA rule predicting hydrolase activity based on 4070 condition sets - exceptionally complex rule requiring removal | COMPLETE | REMOVE | OVERLY_COMPLEX | CONTRADICTED | 4 | 0.95 | |
| ARBA00022806 YAML |
Assigns helicase keyword (KW-0347) to proteins containing helicase-related domains from multiple superfamilies including DEAD-box RNA helicases, DNA helicases, and other nucleic acid unwinding enzymes | COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 0 | 0.75 | |
| ARBA00022825 YAML |
Overly complex rule with 240 condition sets attempting to capture serine protease function, but provides only keyword annotations without GO terms | COMPLETE | REMOVE | OVERLY_COMPLEX | STRONG | 0 | 0.95 | |
| ARBA00022912 YAML |
An extremely complex mega-rule with 210 condition sets attempting to annotate all protein phosphatases across multiple mechanistic families (PTPs, PPPs, PP2C, DUSPs) with only keyword annotation. The rule spans fundamentally different catalytic mechanisms (metal-dependent, cysteine-based, dual-specificity) and lacks essential GO term annotations for enzyme function. | COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 0 | 0.90 | |
| ARBA00023002 YAML |
Extremely large rule with 2105 condition sets combining 975 InterPro domains and 1489 CATH FunFam families to annotate oxidoreductase proteins across all domains of life | COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 0 | 0.30 | |
| ARBA00023137 YAML |
Rule that applies UniProt keyword "Tyrosine-protein kinase" to proteins with various kinase-related InterPro domains, CATH FunFam families, and PANTHER families across diverse taxonomic groups. Contains 98 condition sets but provides no GO annotations. | COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 0 | 0.95 | |
| ARBA00023239 YAML |
Highly complex ARBA rule with 894 condition sets for detecting proteins with lyase activity based on InterPro domains, PANTHER families, and CATH FunFams across diverse taxonomic groups. Rule only assigns keyword annotation "Lyase" (KW-0456), not GO terms. Rule exceeds analysis limits due to excessive complexity, making quantitative validation impossible. | COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 0 | 0.98 | |
| ARBA00026249 YAML |
Rule predicting thioredoxin-disulfide reductase (NADPH) activity based on InterPro domains and CATH FunFam classifications. The rule uses three alternative condition sets targeting the same enzymatic function. | GO:0004791 thioredoxin-disulfide reductase (NADPH) activity |
COMPLETE | DEPRECATE | REDUNDANT | STRONG | 3 | 0.92 |
| ARBA00026302 YAML |
Massively overcomplex rule with 185 condition sets attempting to predict the broad biological process term "carbohydrate derivative biosynthetic process" (GO:1901137). The rule encompasses an extraordinarily diverse array of InterPro domains, CATH FunFams, and PANTHER families spanning multiple taxonomic groups, creating a rule of unprecedented complexity that violates all principles of parsimony. | GO:1901137 carbohydrate derivative biosynthetic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | NONE | 0 | 0.05 |
| ARBA00026372 YAML |
This rule predicts GO:0051998 (protein carboxyl O-methyltransferase activity) using 5 condition sets that identify two mechanistically distinct enzyme families: isoprenylcysteine carboxyl methyltransferases (ICMT) and protein-L-isoaspartate methyltransferases (PIMT). These enzymes share a common chemistry (methylating carboxyl groups on proteins) but differ fundamentally in substrate specificity, cellular location, biological function, and mechanism. | GO:0051998 protein carboxyl O-methyltransferase activity |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 5 | 0.95 |
| ARBA00026480 YAML |
This rule assigns GO:0010605 (negative regulation of macromolecule metabolic process) to proteins containing any of 67 different InterPro domains across 343 condition sets. The rule spans an extraordinarily broad taxonomic range including bacteria, plants, fungi, and animals. | GO:0010605 negative regulation of macromolecule metabolic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 |
| ARBA00026572 YAML |
Mega-rule with 781 condition sets applying the extremely broad GO term "nucleobase-containing compound metabolic process" to diverse protein families including DNA polymerases, tRNA synthetases, nucleotide kinases, and cofactor biosynthesis enzymes | GO:0006139 nucleobase-containing compound metabolic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.00 |
| ARBA00026647 YAML |
Mega-rule predicting GO:0010629 negative regulation of gene expression across 131 condition sets covering diverse RNA-binding proteins, chromatin modifiers, nucleases, and regulatory complexes including Dicer, PIWI, SET domain histone methyltransferases, sirtuins, pumilio repeats, and zinc finger proteins | COMPLETE | DEPRECATE | OVERLY_COMPLEX | MODERATE | 0 | 0.10 | |
| ARBA00026698 YAML |
Extremely complex rule with 26 condition sets predicting vacuolar transport (GO:0007034) based on diverse protein domains including SNARE domains, ENTH domains, Sec1-like domains, and unknown function domains. The rule attempts to capture multiple distinct vacuolar transport mechanisms under a single broad GO annotation across diverse taxonomic groups. | GO:0007034 vacuolar transport |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 6 | 0.05 |
| ARBA00026708 YAML |
Rule predicting peroxisome organization (GO:0007031) based on multiple InterPro domains and CATH FunFam classifications across different taxonomic groups. The rule uses 10 condition sets targeting various peroxisomal proteins including peroxins and peroxisome division factors. | GO:0007031 peroxisome organization |
COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 10 | 0.45 |
| ARBA00026799 YAML |
Predicts NAD+ kinase activity (GO:0003951) for proteins containing NAD kinase domains across 6 condition sets covering bacterial, eukaryotic, and mitochondrial variants | GO:0003951 NAD+ kinase activity |
COMPLETE | ACCEPT | ACCEPTABLE | STRONG | 6 | 0.85 |
| ARBA00026991 YAML |
ARBA rule with 83 condition sets targeting diverse metabolic enzymes (glycolysis, TCA cycle, electron transport, glycogen metabolism) for broad energy metabolism annotation GO:0015980 | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.90 | |
| ARBA00027164 YAML |
Mega-rule with 51 condition sets that broadly annotates diverse RNA-associated proteins with the general GO term RNA catabolic process (GO:0006401) | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 | |
| ARBA00027169 YAML |
Annotates proteins containing Sm or Sm-like domains with GO:0120114 "Sm-like protein family complex" using 28 condition sets covering classical Sm proteins, Lsm proteins, and various spliceosomal components across different taxonomic groups | COMPLETE | DEPRECATE | OVERLY_COMPLEX | MODERATE | 0 | 0.20 | |
| ARBA00027389 YAML |
ARBA rule that predicts "cell wall biogenesis" (GO:0042546) for proteins matching any of 29 diverse condition sets spanning cell wall enzymes, polyketide synthases, protein kinases, GTPases, and other functionally unrelated families across multiple taxonomic groups | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 | |
| ARBA00027399 YAML |
Predicts serine-type peptidase activity (GO:0008236) across a highly diverse collection of 36 condition sets encompassing serine proteases from multiple functional families including blood coagulation factors, complement system proteases, digestive enzymes, proprotein convertases, and bacterial quality control proteases. | COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 0 | 0.60 | |
| ARBA00027430 YAML |
An overly complex rule with 89 condition sets that attempts to predict "alcohol metabolic process" (GO:0006066) across diverse taxonomic groups and enzyme families. The rule combines various unrelated enzyme families including cytochrome P450s, dehydrogenases, kinases, and metabolic enzymes. | GO:0006066 alcohol metabolic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.10 |
| ARBA00027624 YAML |
A highly complex rule with 304 condition sets that predicts GO:0031090 (organelle membrane) for proteins containing diverse domain families across 406 CATH FunFam domains, 68 InterPro domains, and spanning 63 taxonomic groups from genus to kingdom level. | GO:0031090 organelle membrane |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 |
| ARBA00027651 YAML |
Mega-rule attempting to annotate all phosphoprotein phosphatases with GO:0004721 (phosphoprotein phosphatase activity) using 74 diverse condition sets covering tyrosine-protein phosphatases, serine/threonine phosphatases, dual-specificity phosphatases, and related phosphatases across all domains of life | COMPLETE | DEPRECATE | OVERLY_COMPLEX | MODERATE | 0 | 0.10 | |
| ARBA00027723 YAML |
A massive rule with 1094 condition sets that attempts to annotate the entire transferase enzyme class (EC 2) using GO:0016740 (transferase activity). The rule encompasses diverse transferase families including glycosyltransferases, acetyltransferases, protein kinases, ubiquitin-conjugating enzymes, and others, but also erroneously includes non-transferase domains like PAS signaling domains. | GO:0016740 transferase activity |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 0 | 0.95 |
| ARBA00027853 YAML |
Assigns GO:0006720 "isoprenoid metabolic process" to proteins matching any of 94 alternative condition sets built from InterPro entries, CATH FunFams, PANTHER families and taxon constraints. The GO term is in the right branch for most of the rule: 64 of the 94 sets identify genuine isoprenoid enzymes - terpene synthases and cyclases, the MVA and MEP precursor pathways, prenyl diphosphate synthases, carotenoid backbone and cleavage enzymes, gibberellin and ABA oxidases, named retinoid enzymes and JHAMT. Thirteen sets should be removed - twelve off-target (LDLR/LRP1, CYP2C9, CYP83B1, ADH5, ADH7, hormone-sensitive lipase, PNPLA2, phenylalanine aminomutase, bare UGT and Rossmann FunFams) plus one ALDH FunFam conjunction that appears unsatisfiable - one set is mixed and needs splitting, and sixteen cannot be audited from their identifiers. The rule's most serious defect is not biological: the 8,974 annotations it currently emits cannot be reproduced from its published condition sets. | GO:0006720 isoprenoid metabolic process |
COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 94 | 0.80 |
| ARBA00027994 YAML |
Extremely complex rule attempting to capture all chromatin remodeling activities across eukaryotes using 134 condition sets spanning ATP-dependent remodelers, histone-modifying enzymes, chromatin assembly factors, and pioneer transcription factors. | GO:0006338 chromatin remodeling |
COMPLETE | SPLIT | OVERLY_COMPLEX | MODERATE | 0 | 0.60 |
| ARBA00028131 YAML |
An extremely complex mega-rule with 41 condition sets assigning GO:0004175 (endopeptidase activity) to proteins across virtually all major endopeptidase families including aspartic proteases (pepsin family), cysteine proteases (papain/cathepsin families), serine proteases (subtilisin family), and metalloproteases (aminopeptidase family). While biologically sound, the rule represents a maintenance nightmare due to its extreme complexity and loses functional specificity by applying a single broad term to mechanistically distinct protease families. | COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 0 | Not recorded | |
| ARBA00028334 YAML |
ARBA rule that annotates proteins with "regulation of gene expression" (GO:0010468) based on presence of various InterPro domains across different taxonomic lineages. This rule contains 930 condition sets with 267 unique InterPro domains, making it extraordinarily complex and impossible to validate comprehensively. | GO:0010468 regulation of gene expression |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | NONE | 0 | 0.95 |
| ARBA00028538 YAML |
Assigns GO:0046467 to proteins matching any of 51 alternative condition sets built from 14 InterPro entries, 51 CATH FunFams and 39 taxon constraints. GO obsoleted GO:0046467 ("membrane lipid biosynthetic process") on 2025-12-09, replacing it with GO:0008610 lipid biosynthetic process, so the rule now emits no annotations at all - yet UniProt still serves it, and its last modification date of 2025-12-15 is six days after the obsoletion. The antecedents are heterogeneous: at most 26 of the 51 sets describe enzymes that build a membrane lipid, while the rest capture sphingolipid hydrolases, lipid A and GPI remodelling enzymes, GPI/dolichol-donor assembly, non-diagnostic glycosyltransferase families, and four mechanistically unrelated proteins reached through promiscuous folds (a PH-domain protein kinase, phosphoglycerate kinase, 5-aminolevulinate synthase, and a lipid-binding lipoprotein). | GO:0046467 obsolete membrane lipid biosynthetic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 51 | 0.95 |
| ARBA00028584 YAML |
Rule predicts GO:0005778 (peroxisomal membrane) localization for nine distinct protein families: fungal DysF-domain peroxins (PEX23-32), peroxisomal ABC transporters (ABCD1, ABCD3), peroxisomal import machinery (PEX13, PEX14), RING finger peroxins (PEX12), the peroxisomal solute carrier SLC25A17/PMP34, the autophagy cargo receptor NBR1, and peroxisomal 2,4-dienoyl-CoA reductase (DECR2). Each condition set uses different domain signatures with varying taxonomic restrictions. | GO:0005778 peroxisomal membrane |
COMPLETE | MODIFY | ACCEPTABLE | STRONG | 9 | 0.80 |
| ARBA00028655 YAML |
Assigns GO:0006661 "phosphatidylinositol biosynthetic process" to proteins matching any of 25 alternative condition sets built from InterPro entries, CATH FunFams and taxon constraints. Only two of the 25 sets (CS18, CS19) identify the enzyme that actually makes phosphatidylinositol - CDP-diacylglycerol--inositol 3-phosphatidyltransferase (CDIPT/PIS, EC 2.7.8.11). The remaining 23 sets capture phosphoinositide kinases, phosphoinositide phosphatases, non-catalytic PI3K/VPS34 regulatory subunits, GPI-anchor pathway enzymes, DPM1, and two promiscuous structural folds - all of which act on, consume or are merely adjacent to PI rather than synthesising it. | GO:0006661 phosphatidylinositol biosynthetic process |
COMPLETE | SPLIT | OVERLY_COMPLEX | CONTRADICTED | 25 | 0.95 |
| ARBA00028665 YAML |
Overly complex rule with 174 condition sets attempting to annotate diverse protein classes (transcription factors, kinases, adhesion molecules, structural proteins) with the broad GO term "cell development" (GO:0048468) | COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 0 | 0.95 | |
| ARBA00028985 YAML |
A highly complex mega-rule with 357 condition sets that annotates diverse RNA-binding and RNA-processing proteins with the overly broad GO term "RNA metabolic process" (GO:0016070). The rule indiscriminately captures functionally distinct protein families including aminoacyl-tRNA synthetases, ribonucleases, RNA helicases, and RNA-binding proteins, providing minimal functional specificity. | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.05 | |
| ARBA00029057 YAML |
Overly broad ARBA rule with 89 condition sets targeting diverse protein families (metabolic enzymes, structural proteins, transport proteins, kinases) for annotation with GO:0065003 protein-containing complex assembly | COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 0 | 0.95 | |
| ARBA00035048 YAML |
Annotates diverse spliceosomal complex components including snRNPs, helicases, and associated factors across multiple taxonomic groups using 17 distinct condition sets | COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 0 | 0.60 | |
| ARBA00035068 YAML |
Assigns phosphatidylinositol-3-phosphate phosphatase activity (GO:0004438) to proteins containing myotubularin-related functional family domains, with condition set 1 targeting MTM1-related domains in Primates and condition set 2 targeting MTMR4-related domains across all Eukaryotes | COMPLETE | MODIFY | ACCEPTABLE | STRONG | 2 | 0.75 | |
| ARBA00043370 YAML |
Rule assigns GO:0140115 "export across plasma membrane" to proteins matching 12 complex condition sets covering diverse transporter families including sugar transporters, ABC transporters, MFS transporters, P-type ATPases, and antiporters across various taxonomic groups | GO:0140115 export across plasma membrane |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.90 |
| ARBA00045851 YAML |
Annotates MORN repeat-containing proteins, specifically MORN3 family members, with function involving p53 regulation through assembly of a suppression complex that tethers SIRT1 and MDM2 | COMPLETE | MODIFY | ACCEPTABLE | MODERATE | 2 | 0.40 | |
| ARBA00047230 YAML |
Predicts phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity for proteins containing myotubularin-like domains and/or specific CATH functional families, with taxonomic restrictions to Primates or Eukaryota | COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 3 | 0.65 | |
| ARBA00047239 YAML |
Rule predicts GO:0032206 (positive regulation of telomere maintenance) using 9 condition sets covering diverse protein families: TRiC chaperonin subunits, TRF2 (shelterin), ATM kinase, PARP enzymes, RTEL1 helicase, MAPK, RuvB-like helicase, and SLX4 endonuclease. The rule combines OR logic across mechanistically distinct families involved in telomere biology, but contains significant redundancy, questionable domain choices, and taxonomic errors. | GO:0032206 positive regulation of telomere maintenance |
COMPLETE | MODIFY | OVERLY_COMPLEX | MODERATE | 9 | 0.35 |
| ARBA00047244 YAML |
Rule predicting amide catabolic process (GO:0043605) based on four condition sets: (1) urease domains (beta/gamma subunits and active site) across all organisms, (2) PM20D1 FunFams in Eukaryota, (3) ureide pathway hydrolases in Viridiplantae, and (4) (S)-ureidoglycine aminohydrolase in Streptophyta. The rule captures mechanistically diverse enzymes that share the common chemistry of amide bond hydrolysis but serve distinct biological functions. | GO:0043605 amide catabolic process |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | STRONG | 4 | 0.80 |
| ARBA00049204 YAML |
Rule annotates superoxide dismutase activity (EC 1.15.1.1) using 24 condition sets spanning all domains of life. While the biological target is correctly identified and universally conserved, the rule exhibits extreme complexity that exceeds manageable thresholds, making analysis and maintenance intractable. | EC:1.15.1.1 2 superoxide + 2 H(+) = H2O2 + O2 |
COMPLETE | MODIFY | OVERLY_COMPLEX | STRONG | 9 | 0.95 |
| ARBA00085337 YAML |
Predicts GO:0045454 "cell redox homeostasis" for proteins across 9 condition sets covering diverse redox-related protein families including nitric oxide synthases, thioredoxins, glutathione reductases, peroxiredoxins, and other oxidative stress response proteins with taxonomic restrictions | GO:0045454 cell redox homeostasis |
IN_PROGRESS | MODIFY | OVERLY_COMPLEX | WEAK | 9 | 0.50 |
| ARBA00085883 YAML |
Rule predicting proteoglycan catabolic process (GO:0030167) based on four condition sets: (1) beta-galactosidase in Eukaryota, (2) alpha-L-iduronidase, (3) beta-hexosaminidase in Mus, and (4) N-acetylglucosamine-6-sulfatase in Metazoa. These enzymes are lysosomal hydrolases involved in sequential degradation of glycosaminoglycan (GAG) chains that constitute proteoglycans. However, beta-galactosidase and beta-hexosaminidase are primarily known for ganglioside degradation, raising questions about annotation specificity. | GO:0030167 proteoglycan catabolic process |
COMPLETE | MODIFY | REDUNDANT | STRONG | 4 | 0.60 |
| ARBA00086620 YAML |
Rule predicts sexual sporulation resulting in cellular spore formation based on 5 condition sets containing diverse protein families (kinases, trafficking proteins, cell wall enzymes, motor proteins) across eukaryotic taxa | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 5 | 0.90 | |
| ARBA00087037 YAML |
Predicts laminin-121 trimer (GO:0005608) for proteins containing three specific CATH FunFam domains: Cadherin EGF LAG seven-pass G-type receptor (2.10.25.10:FF:000011), Laminin subunit beta 1 (2.10.25.10:FF:000065), and netrin-4 isoform X2 (2.10.25.10:FF:000333) | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 1 | 0.90 | |
| ARBA00088058 YAML |
Rule predicts GO:0051010 (microtubule plus-end binding) for proteins containing CAP-Gly domains (CLIP proteins), EB/RP family proteins, CLASP proteins, or CKAP5, in five condition sets with taxon-specific targeting across Glires, Primates, Fungi, and broader Eukaryota. | GO:0051010 microtubule plus-end binding |
COMPLETE | ACCEPT | REDUNDANT | STRONG | 5 | 0.85 |
| ARBA00088072 YAML |
Deprecated/non-existent ARBA rule allegedly applying GO:0160103 (tRNA (guanine(26)-N2/guanine(27)-N2)-dimethyltransferase activity) to TRM1/Trm1 enzymes | GO:0160103 tRNA (guanine(26)-N2/guanine(27)-N2)-dimethyltransferase activity |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 0.95 |
| ARBA00089174 YAML |
Rule predicting adaptive thermogenesis (GO:1990845) based on two alternative condition sets: PM20D1 FunFams in Eukaryota, and TRPV1 FunFams in Mus. The rule captures two mechanistically distinct pathways to thermogenic regulation. | GO:1990845 adaptive thermogenesis |
COMPLETE | MODIFY | REDUNDANT | STRONG | 2 | 0.85 |
| ARBA00089175 YAML |
This rule predicts GO:1990849 (vacuolar localization) for eukaryotic proteins containing two specific CATH FunFam domains: 1.20.58.900:FF:000013 and 2.30.29.30:FF:000315, both associated with pleckstrin homology domain-containing family M member 1 (PLEKHM1). The rule targets the eukaryotic domain (NCBITaxon:2759). | GO:1990849 vacuolar localization |
COMPLETE | ACCEPT | ACCEPTABLE | STRONG | 1 | 0.80 |
| ARBA00089176 YAML |
This rule predicts GO:1990840 (response to lectin) for primate proteins using two distinct condition sets. Condition set 1 requires non-specific serine/threonine protein kinase domains (FunFams 1.10.510.10:FF:000011 and 3.30.200.20:FF:000069) in Primates (NCBITaxon:9443). Condition set 2 requires E1A binding protein p300 domains (FunFams 1.10.246.20:FF:000001 and 1.20.1020.10:FF:000001) in Catarrhini (NCBITaxon:9526, Old World monkeys and apes). | GO:1990840 response to lectin |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 2 | 0.25 |
| ARBA00089180 YAML |
Rule predicts GO:1990858 "cellular response to lectin" based on two disjoint condition sets: (1) two serine/threonine protein kinase domains in Primates, and (2) two E1A binding protein p300 acetyltransferase domains in Catarrhini (Old World primates). Analysis reveals complete disjunction between condition sets (Jaccard=0.0), complete redundancy within condition set 2 (Jaccard=1.0), and very low coverage of the predicted GO term (3-40% containment, 3-4% Jaccard for all domain-GO pairs). | GO:1990858 cellular response to lectin |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 2 | 0.95 |
| ARBA00089391 YAML |
ARBA00089391 predicts spermidine transmembrane transport (GO:1903711) for fungal proteins containing either MFS multidrug transporter domains (in Taphrinomycotina) or urea active transporter domains (in all Fungi). The rule combines taxonomic restrictions with functionally distinct transporter families. | GO:1903711 spermidine transmembrane transport |
COMPLETE | DEPRECATE | OVERLY_COMPLEX | WEAK | 2 | 0.15 |
| ARBA00089395 YAML |
Predicts spermine transmembrane transport function for proteins containing CATH FunFam 1.20.1250.20:FF:000011 domain in Taphrinomycotina fungi | COMPLETE | DEPRECATE | PARSIMONIOUS | WEAK | 1 | 0.10 | |
| ARBA00090047 YAML |
This rule annotates proteins containing the SepA cytokinesis protein domain (CATH FunFam 1.20.58.2220:FF:000006) in Taphrinomycotina fungi with the highly specific GO term GO:1904498 (protein localization to mitotic actomyosin contractile ring). The rule targets a well-characterized cytokinesis regulator but applies an extremely specific localization annotation that requires strong experimental validation. | COMPLETE | MODIFY | PARSIMONIOUS | MODERATE | 1 | 0.70 | |
| ARBA00090252 YAML |
Rule annotates ribosomal protein components (L40, L10a) in fungi with nuclear export of ribosomal large subunit. Contains two condition sets targeting ubiquitin-ribosomal protein fusions and ribosomal proteins in fungal taxa. | COMPLETE | DEPRECATE | REDUNDANT | CONTRADICTED | 2 | 1.00 | |
| ARBA00090718 YAML |
Rule assigns (S)-2-hydroxyglutarate dehydrogenase activity (GO:0047545) to proteins containing CATH FunFam 3.40.50.720:FF:000041 (D-3-phosphoglycerate dehydrogenase domain) | COMPLETE | DEPRECATE | PARSIMONIOUS | CONTRADICTED | 1 | 0.90 | |
| ARBA00092121 YAML |
Annotates fungal proteins in CATH FunFam 3.10.20.30:FF:000003 (Developmentally-regulated GTP-binding protein 1) with GO:1903833 (positive regulation of cellular response to amino acid starvation). Currently covers 0 proteins. | COMPLETE | DEPRECATE | ACCEPTABLE | NONE | 1 | 0.95 | |
| ARBA00095398 YAML |
Deprecated ARBA rule that inappropriately annotated ribosomal protein L12.1/L12A with ribophagy function | COMPLETE | DEPRECATE | OVERLY_COMPLEX | CONTRADICTED | 0 | 1.00 |
Generated from cached review YAML by just rules-index.