# Curated triage of FlyBase gene groups (FB2026_03) into modules.
#
# Each rule names one or more FlyBase groups by symbol and gives a decision.
# `triage_groups.py` applies the rules to every group in group_index.yaml:
#
#   NEW_MODULE       the group is realized by a new module (modules/<module>.yaml)
#   EXISTING_MODULE  the group is already covered by an existing module
#   UMBRELLA         a category that only collects other groups; its children
#                    carry their own decisions
#   NOT_A_MODULE     the group is not a module (see reason codes below)
#   REGULATOR_SET    "positive/negative regulators of X" lists; the regulators
#                    are context for the pathway module, not parts of it
#
# Groups without a rule inherit from their nearest ruled ancestor: a module
# decision makes the descendant SUBSUMED into the same module, any other decision
# is inherited as is.
#
# Reason codes for NOT_A_MODULE:
#   SEQUENCE_FAMILY   proteins grouped by sequence/domain homology
#   FUNCTIONAL_CLASS  proteins grouped by a shared activity class (enzymes,
#                     transporters, receptors, transcription factors, ...)
#                     rather than by acting together
#   GENE_CLUSTER      genes grouped by genomic location
#   NONCODING_CLASS   tRNA genes and other RNA gene classes
#   SINGLE_GENE       a single-gene group cannot form a module with >= 2 parts

# ---------------------------------------------------------------- umbrellas
- groups: [CHR-MOD-C, REMOD-C, TRXG-C, CATCHR, GTF, TEFC, RABGEF-C,
    AADERMT, AAMET, CARMET, COCAVIT, ENERM, GLYCJM, LIPMET, NEUROME, NTSUB,
    PGASN, SMC-C, MKDC, OXP-AF, ER-SECIN, DYN]
  decision: UMBRELLA
  reason: Category grouping several distinct complexes or pathways; children are triaged individually.

# ------------------------------------------------- family / class umbrellas
- groups: [ENZ, PSENZ]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Enzyme classification by catalytic activity (EC-like); members do not act together.
- groups: [TMT]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Transporter and channel classification by transport mechanism and substrate.
- groups: [TM-R, RLIG]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Receptor or ligand classification; pathway membership is captured by the signaling pathway modules.
- groups: [TFS]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Transcription factor classification by DNA-binding domain.
- groups: [TRNA]
  decision: NOT_A_MODULE
  reason_code: NONCODING_CLASS
  reason: tRNA gene classes grouped by anticodon.
- groups: [IR-PSD]
  decision: NOT_A_MODULE
  reason_code: SEQUENCE_FAMILY
  reason: Pseudogene family.
- groups: [ESPL-C, HOX-C]
  decision: NOT_A_MODULE
  reason_code: GENE_CLUSTER
  reason: Genes grouped by genomic locus (gene complex), not by a shared molecular unit.
- groups: [14-3-3, 4CSP, ABC-TL, ACBP, ACE, ADAMTSL, ANX, ARID, ARP, BARA, BCL2,
    BRD-F, C1, C19, C2, C26, C48, CBD, CDA, CLECT, CNPY, COMML, CP, CUL, CYT-C,
    EPS8, FBOX, FLO, GH18, GK-L, GLYP, GOLG, HP1, IAP, IKB, IM, LARP,
    M1, M12, M13, M14, M16, M17, M19, M20, M24, M28, M3, M48, M67, MADF-BESS,
    MCO, ML, MLC-CAM, MTERF, MTN, MTX, MUCS, MYO, NOC, NTN, OBP, OBST, OSI, P24,
    PASI, PGRF, PGRP, PHLP, PRELID, PROT, RHOM-L, S1, S81, S9, SANT-MYB, SCRAM,
    SDIC, SKP1, SM-T, SP1-KLF, SPEC, SPN, SPON, SR, SVWC, SYT, TAGLN, TEP, TM2D,
    TM9SF, TRAF, TRF, TSF, TSP, UBL, WASP, WRN, YLW, TIM17RF, DNAPOL-SU, GTF-SU,
    G-SUB, NAA, LSTAU]
  decision: NOT_A_MODULE
  reason_code: SEQUENCE_FAMILY
  reason: Gene family grouped by sequence or domain homology; members do not form one complex or pathway.
- groups: [CSP, HSP, HOLD, HDP, SEL]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Proteins grouped by a broad activity class (structural proteins, chaperones, host-defence peptides, selenoproteins), not by acting together.
- groups: [GGA, OXA1, ALAMET]
  decision: NOT_A_MODULE
  reason_code: SINGLE_GENE
  reason: Single-gene group; a module needs at least two parts.

# --------------------------------------------------- existing modules (gene groups)
- {groups: [OXPHOS, OXPHOS-V, OXPATP], decision: EXISTING_MODULE, module: oxphos}
- {groups: [MCI-AF, MCIA], decision: EXISTING_MODULE, module: complex_i_assembly_factors}
- {groups: [MCIV-AF], decision: EXISTING_MODULE, module: complex_iv_assembly_factors}
- {groups: [PGLLO, UNAGTC], decision: EXISTING_MODULE, module: n_glycan_llo_assembly_cytoplasmic}
- {groups: [OST-C], decision: EXISTING_MODULE, module: oligosaccharyltransferase_complex}
- {groups: [GCC, GLYCLE], decision: EXISTING_MODULE, module: glycine_cleavage_system}
- {groups: [ETF, FADREG], decision: EXISTING_MODULE, module: electron_transfer_flavoprotein_system}
- {groups: [KASH], decision: EXISTING_MODULE, module: linc_complex}
- {groups: [SNARE, SNAP], decision: EXISTING_MODULE, module: snare_fusion_cycle}
- {groups: [PEX, PEXTSC, PTS], decision: EXISTING_MODULE, module: peroxisome-lifecycle}
- {groups: [BBS], decision: EXISTING_MODULE, module: bbsome}
- {groups: [PIG, PIG-CPX, GPIANB, GPI-MT-I], decision: EXISTING_MODULE, module: gpi_anchor_core_glycan_assembly}
- {groups: [GPI-GNT], decision: EXISTING_MODULE, module: gpi_anchor_glcnac_transferase}
- {groups: [GPI-TA], decision: EXISTING_MODULE, module: gpi_anchor_transamidase}
- {groups: [GPI-ET-II, GPI-ET-III], decision: EXISTING_MODULE, module: gpi_anchor_ethanolamine_phosphate}
- {groups: [DPM, DOLMAN], decision: EXISTING_MODULE, module: dolichol_phosphate_sugar_donor_supply}
- {groups: [DHDDSC, DOLPB], decision: EXISTING_MODULE, module: dolichyl_phosphate_biosynthesis}
- {groups: [GCLC, GLTHBIO], decision: EXISTING_MODULE, module: glutathione_biosynthesis}
- {groups: [MCCC, LLEUCA], decision: EXISTING_MODULE, module: leucine_catabolism}
- {groups: [MTP, FABEOXM], decision: EXISTING_MODULE, module: fatty_acid_beta_oxidation}
- {groups: [MPTS, MOBCOB], decision: EXISTING_MODULE, module: molybdenum_cofactor_biosynthesis}
- {groups: [PDSS, UBIQS], decision: EXISTING_MODULE, module: ubiquinone_biosynthesis}
- {groups: [SPTC], decision: EXISTING_MODULE, module: sphingolipid_de_novo_synthesis}
- {groups: [IDH-UC, SUCLAC, SUCLGC, OGDH-CV, TCACY], decision: EXISTING_MODULE, module: tca_cycle}
- {groups: [BCKDC, LVALCA, LILECA], decision: EXISTING_MODULE, module: branched_chain_amino_acid_catabolism}
- {groups: [OADHC], decision: EXISTING_MODULE, module: lysine_catabolism}
- {groups: [PDC-V, MPC2AC, MPC2BC, PYRCOA], decision: EXISTING_MODULE, module: pyruvate_metabolism}

# --------------------------------------------------- existing modules (metabolic pathways)
- {groups: [PPS], decision: EXISTING_MODULE, module: pentose_phosphate_pathway}
- {groups: [GLYCB], decision: EXISTING_MODULE, module: glycogen_biosynthesis}
- {groups: [GLYCO], decision: EXISTING_MODULE, module: emp_glycolysis}
- {groups: [GLUCO], decision: EXISTING_MODULE, module: gluconeogenesis}
- {groups: [GLYCC], decision: EXISTING_MODULE, module: glycogenolysis}
- {groups: [UDPGLAB], decision: EXISTING_MODULE, module: hexosamine_biosynthesis}
- {groups: [CMPNEB], decision: EXISTING_MODULE, module: sialic_acid_metabolism}
- {groups: [GALCA], decision: EXISTING_MODULE, module: galactose_leloir_pathway}
- {groups: [PAPSB], decision: EXISTING_MODULE, module: paps_sulfate_activation}
- {groups: [MALSH], decision: EXISTING_MODULE, module: malate_aspartate_shuttle}
- {groups: [GACSC], decision: EXISTING_MODULE, module: keratan_chondroitin_sulfate_lysosomal_degradation}
- {groups: [GAHSC], decision: EXISTING_MODULE, module: heparan_sulfate_lysosomal_degradation}
- {groups: [GLPSH], decision: EXISTING_MODULE, module: glycerol_phosphate_shuttle}
- {groups: [NADSAL], decision: EXISTING_MODULE, module: nad_biosynthesis_salvage}
- {groups: [HEMBS], decision: EXISTING_MODULE, module: heme_biosynthesis}
- {groups: [GLUCEB], decision: EXISTING_MODULE, module: glycosphingolipid_biosynthesis}
- {groups: [LSERBI], decision: EXISTING_MODULE, module: phosphorylated_serine_biosynthesis}
- {groups: [LCYSBI, HTSBIO], decision: EXISTING_MODULE, module: homocysteine_metabolism}
- {groups: [LMETCY], decision: EXISTING_MODULE, module: methionine_cycle}
- {groups: [LLYSCA], decision: EXISTING_MODULE, module: lysine_catabolism_saccharopine}
- {groups: [PHETYRME], decision: EXISTING_MODULE, module: tyrosine_catabolism}
- {groups: [LPROBI, LGLUBIP], decision: EXISTING_MODULE, module: proline_metabolism}
- {groups: [GLUGLNM], decision: EXISTING_MODULE, module: glutamate_glutamine_ammonia_hub}
- {groups: [KETOGENS], decision: EXISTING_MODULE, module: ketogenesis}
- {groups: [KETOLYS], decision: EXISTING_MODULE, module: ketone_body_oxidation}
- {groups: [GLTHCATA], decision: EXISTING_MODULE, module: glutathione_synthesis_gamma_glutamyl_cycle}
- {groups: [POLYBIO, POLYCAT], decision: EXISTING_MODULE, module: polyamine_metabolism}
- {groups: [TAUBIO], decision: EXISTING_MODULE, module: taurine_biosynthesis_and_transport}
- {groups: [SERMELBI], decision: EXISTING_MODULE, module: serotonin_melatonin_biosynthesis}
- {groups: [GABASH], decision: EXISTING_MODULE, module: gaba_shunt}
- {groups: [DOPABI], decision: EXISTING_MODULE, module: catecholamine_biosynthesis}
- {groups: [NOSBIO], decision: EXISTING_MODULE, module: nitric_oxide_cgmp_signaling}
- {groups: [CARSHUT], decision: EXISTING_MODULE, module: carnitine_shuttle}
- {groups: [LIPOBI], decision: EXISTING_MODULE, module: endogenous_protein_lipoylation}
- {groups: [FADFMNB], decision: EXISTING_MODULE, module: flavin_cofactor_biosynthesis}
- {groups: [FABEOXP], decision: EXISTING_MODULE, module: peroxisomal_beta_oxidation}

# --------------------------------------------------- new modules: metabolic pathways
- {groups: [GDPFUC], decision: NEW_MODULE, module: dmel_gdp_fucose_biosynthesis}
- {groups: [MANGPG], decision: NEW_MODULE, module: dmel_gdp_mannose_biosynthesis}
- {groups: [TREHB, TREHC], decision: NEW_MODULE, module: dmel_trehalose_metabolism}
- {groups: [CHIYBI, CHITCA], decision: NEW_MODULE, module: dmel_chitin_metabolism}
- {groups: [UDPGAB, UDPXYLB], decision: NEW_MODULE, module: dmel_udp_glucuronate_xylose_biosynthesis}
- {groups: [FRUCBIO], decision: NEW_MODULE, module: dmel_polyol_pathway}
- {groups: [GACSB, GAHSB, EXT1-EXT2], decision: NEW_MODULE, module: dmel_glycosaminoglycan_biosynthesis}
- {groups: [POGLY, POMT1-2C], decision: NEW_MODULE, module: dmel_protein_o_glycosylation}
- {groups: [PGERT, PGGOT, PGGOD, GLU2ABII], decision: NEW_MODULE, module: dmel_n_glycan_processing}
- {groups: [FESCA, CIA-SCAF, CTC, ISA, NIAUF], decision: NEW_MODULE, module: dmel_iron_sulfur_cluster_assembly}
- {groups: [LMETSA], decision: NEW_MODULE, module: dmel_methionine_salvage}
- {groups: [GLYBITH], decision: NEW_MODULE, module: dmel_glycine_biosynthesis}
- {groups: [ASPASNM], decision: NEW_MODULE, module: dmel_aspartate_asparagine_metabolism}
- {groups: [ARGMET], decision: NEW_MODULE, module: dmel_arginine_metabolism}
- {groups: [TRYCAT, OMMOBI], decision: NEW_MODULE, module: dmel_ommochrome_biosynthesis}
- {groups: [PIGMBIO, BALABIO], decision: NEW_MODULE, module: dmel_cuticle_tanning_pigmentation}
- {groups: [HYPUBIO], decision: NEW_MODULE, module: dmel_hypusine_biosynthesis}
- {groups: [HISMET], decision: NEW_MODULE, module: dmel_histamine_metabolism}
- {groups: [TYROCTBI], decision: NEW_MODULE, module: dmel_tyramine_octopamine_biosynthesis}
- {groups: [SULOXID], decision: NEW_MODULE, module: dmel_sulfide_oxidation}
- {groups: [CARLIPB], decision: NEW_MODULE, module: dmel_cardiolipin_biosynthesis_remodeling}
- {groups: [CARNIBI], decision: NEW_MODULE, module: dmel_carnitine_biosynthesis}
- {groups: [CIMALSH], decision: NEW_MODULE, module: dmel_citrate_malate_shuttle}
- {groups: [NADPHRE], decision: NEW_MODULE, module: dmel_cytosolic_nadph_regeneration}
- {groups: [MTFABIO], decision: NEW_MODULE, module: dmel_mitochondrial_fatty_acid_synthesis}

# --------------------------------------------------- new modules: signaling pathways
- {groups: [ACT-SMAD2], decision: NEW_MODULE, module: dmel_activin_signaling}
- {groups: [BMP-MAD], decision: NEW_MODULE, module: dmel_bmp_signaling}
- {groups: [CGAS-STING], decision: NEW_MODULE, module: dmel_cgas_sting_signaling}
- {groups: [EGFR-RTK], decision: NEW_MODULE, module: dmel_egfr_signaling}
- {groups: [FGFR], decision: NEW_MODULE, module: dmel_fgfr_signaling}
- {groups: [HH-SMO, HSC], decision: NEW_MODULE, module: dmel_hedgehog_signaling}
- {groups: [IMD], decision: NEW_MODULE, module: dmel_imd_signaling}
- {groups: [INS, PI3K-IA], decision: NEW_MODULE, module: dmel_insulin_like_receptor_signaling}
- {groups: [JAKSTAT], decision: NEW_MODULE, module: dmel_jak_stat_signaling}
- {groups: [NTCH, CNM], decision: NEW_MODULE, module: dmel_notch_signaling}
- {groups: [PVR-RTK], decision: NEW_MODULE, module: dmel_pvr_signaling}
- {groups: [SEVL], decision: NEW_MODULE, module: dmel_sevenless_signaling}
- {groups: [SWH, KEM], decision: NEW_MODULE, module: dmel_hippo_signaling}
- {groups: [TL-CAN, DORS], decision: NEW_MODULE, module: dmel_toll_signaling}
- {groups: [TNF], decision: NEW_MODULE, module: dmel_eiger_tnf_signaling}
- {groups: [TORS], decision: NEW_MODULE, module: dmel_torso_signaling}
- {groups: [WNT-TCF, DES, WNT-E], decision: NEW_MODULE, module: dmel_wnt_tcf_signaling}
- groups: [ACT-N, ACT-P, BMP-N, BMP-P, CGAS-STING-P, EGFR-N, EGFR-P, FGFR-N, FGFR-P,
    HH-SMON, HH-SMOP, IMD-N, IMD-P, INS-N, INS-P, JAKSTAT-N, JAKSTAT-P, NTCH-N,
    NTCH-P, PVR-N, PVR-P, SEVL-N, SEVL-P, SWH-N, SWH-P, TL-NFN, TL-NFP, TL-SPZN,
    TNF-N, TNF-P, TORS-N, TORS-P, WNT-TCFN, WNT-TCFP]
  decision: REGULATOR_SET
  reason: Genetic regulators of the pathway; context for the pathway module, not mechanistic parts.

# --------------------------------------------------- new modules: complexes and systems
- {groups: [GLUE], decision: NEW_MODULE, module: dmel_salivary_glue_secretion}
- {groups: [CHORN, VMP], decision: NEW_MODULE, module: dmel_eggshell_structural_proteins}
- {groups: [COL, LMN], decision: NEW_MODULE, module: dmel_basement_membrane_network}
- {groups: [FER], decision: NEW_MODULE, module: dmel_ferritin_complex}
- {groups: [LSP, LSP1], decision: NEW_MODULE, module: dmel_larval_serum_protein_hexamers}
- {groups: [ACPC], decision: NEW_MODULE, module: dmel_f_actin_capping_protein}
- {groups: [AMPK-C], decision: NEW_MODULE, module: dmel_ampk_complex}
- {groups: [AP, CLATH], decision: NEW_MODULE, module: dmel_clathrin_adaptor_coats}
- {groups: [COPI], decision: NEW_MODULE, module: dmel_copi_coat}
- {groups: [COPII], decision: NEW_MODULE, module: dmel_copii_coat}
- {groups: [APC], decision: NEW_MODULE, module: dmel_anaphase_promoting_complex}
- {groups: [RHG, APOP], decision: NEW_MODULE, module: dmel_rhg_apoptosome_caspase_activation}
- {groups: [ARPC-C], decision: NEW_MODULE, module: dmel_arp2_3_complex}
- {groups: [ATG, ATG-CPX], decision: NEW_MODULE, module: dmel_autophagosome_biogenesis}
- {groups: [ATR-ATRIP], decision: NEW_MODULE, module: dmel_atr_atrip_complex}
- {groups: [AUG], decision: NEW_MODULE, module: dmel_augmin_complex}
- {groups: [BLOC, BORC], decision: NEW_MODULE, module: dmel_bloc_borc_complexes}
- {groups: [CAF-1], decision: NEW_MODULE, module: dmel_chromatin_assembly_factor_1}
- {groups: [COG], decision: NEW_MODULE, module: dmel_cog_complex}
- {groups: [EXOC], decision: NEW_MODULE, module: dmel_exocyst}
- {groups: [GARP], decision: NEW_MODULE, module: dmel_garp_complex}
- {groups: [CBF], decision: NEW_MODULE, module: dmel_core_binding_factor}
- {groups: [CBFTF, NFY], decision: NEW_MODULE, module: dmel_nf_y_complex}
- {groups: [CCC, PF], decision: NEW_MODULE, module: dmel_cleavage_polyadenylation}
- {groups: [HCC, HPF, U7], decision: NEW_MODULE, module: dmel_histone_mrna_3prime_processing}
- {groups: [CCC-911], decision: NEW_MODULE, module: dmel_9_1_1_checkpoint_clamp}
- {groups: [CCR4-NOT], decision: NEW_MODULE, module: dmel_ccr4_not_complex}
- {groups: [CCT, HSP60-II], decision: NEW_MODULE, module: dmel_cct_chaperonin}
- {groups: [TZ, MKS, CEP290C], decision: NEW_MODULE, module: dmel_ciliary_transition_zone}
- {groups: [COMP-C, TAC1], decision: NEW_MODULE, module: dmel_compass_family_complexes}
- {groups: [GCN5], decision: NEW_MODULE, module: dmel_gcn5_acetyltransferase_complexes}
- {groups: [TIP60], decision: NEW_MODULE, module: dmel_tip60_complex}
- {groups: [MSL], decision: NEW_MODULE, module: dmel_msl_dosage_compensation_complex}
- {groups: [NURD], decision: NEW_MODULE, module: dmel_nurd_complex}
- {groups: [ENOK-C], decision: NEW_MODULE, module: dmel_enok_complex}
- {groups: [PCG-C, PCG-DNA, PRC1, PRC1-VAR, PRC2, PRC2-JJ, PHORC, PHORC-L, PR-DUB, DRAF,
    VPRC1-1, VPRC1-3-5], decision: NEW_MODULE, module: dmel_polycomb_group_complexes}
- {groups: [BRM], decision: NEW_MODULE, module: dmel_brahma_complexes}
- {groups: [ISWI], decision: NEW_MODULE, module: dmel_iswi_complexes}
- {groups: [INO80], decision: NEW_MODULE, module: dmel_ino80_complex}
- {groups: [SWR1], decision: NEW_MODULE, module: dmel_swr1_domino_complex}
- {groups: [ELBA], decision: NEW_MODULE, module: dmel_elba_boundary_complex}
- {groups: [RDC, PICTS], decision: NEW_MODULE, module: dmel_pirna_nuclear_complexes}
- {groups: [CLNK-C12], decision: NEW_MODULE, module: dmel_cyclin_k_cdk12_complex}
- {groups: [CLPXP], decision: NEW_MODULE, module: dmel_mitochondrial_clpxp}
- {groups: [ORC, MCM2-7, DDK, CMG, GINS], decision: NEW_MODULE, module: dmel_replication_origin_licensing_activation}
- {groups: [COP9-C], decision: NEW_MODULE, module: dmel_cop9_signalosome}
- {groups: [CPC], decision: NEW_MODULE, module: dmel_chromosomal_passenger_complex}
- {groups: [CRAC], decision: NEW_MODULE, module: dmel_crac_channel_complex}
- {groups: [PAR, CRBC, SCRIBC], decision: NEW_MODULE, module: dmel_epithelial_polarity_complexes}
- {groups: [DGC, SCG, SYN, DYS-REL], decision: NEW_MODULE, module: dmel_dystrophin_glycoprotein_complex}
- {groups: [DNAPOL], decision: NEW_MODULE, module: dmel_dna_polymerase_complexes}
- {groups: [DPH1-DPH2], decision: NEW_MODULE, module: dmel_diphthamide_dph1_dph2_complex}
- {groups: [DYNA-C, DYNC, DYNC-IC, DYN-LIC, DYN-LC], decision: NEW_MODULE, module: dmel_cytoplasmic_dynein_dynactin}
- {groups: [DYNA, DYN-IAD, DYN-OAD, DYNA-IC, DYNIA-IC, DYNOA-IC], decision: NEW_MODULE, module: dmel_axonemal_dynein_arms}
- {groups: [ECUP], decision: NEW_MODULE, module: dmel_eif4e_cup_complex}
- {groups: [ELG1-C], decision: NEW_MODULE, module: dmel_elg1_rfc_like_complex}
- {groups: [ELP], decision: NEW_MODULE, module: dmel_elongator_complex}
- {groups: [EMPC], decision: NEW_MODULE, module: dmel_er_membrane_protein_complex}
- {groups: [SRP, SRPR], decision: NEW_MODULE, module: dmel_srp_cotranslational_targeting}
- {groups: [SEC-PF, SEC-T, SEC61TC, SEC62-63, SEC-TRAP], decision: NEW_MODULE, module: dmel_sec61_translocon}
- {groups: [SPC], decision: NEW_MODULE, module: dmel_signal_peptidase_complex}
- {groups: [ESCRT], decision: NEW_MODULE, module: dmel_escrt_machinery}
- {groups: [FUSF], decision: NEW_MODULE, module: dmel_fused_smurf_complex}
- {groups: [G-TUC], decision: NEW_MODULE, module: dmel_gamma_tubulin_complexes}
- {groups: [GATCAB], decision: NEW_MODULE, module: dmel_glutamyl_trna_amidotransferase}
- {groups: [GBP3MC], decision: NEW_MODULE, module: dmel_gtpbp3_mto1_complex}
- {groups: [GSC], decision: NEW_MODULE, module: dmel_gamma_secretase_complex}
- {groups: [TFIIA, TFIID, TFIIE, TFIIF, TFIIH, CAK-XPD, T-TAF], decision: NEW_MODULE, module: dmel_rnapii_general_transcription_factors}
- {groups: [DSIF, ELO, FACT, LEC, NELF, P-TEFB, PAF1C, PAF1C-T, SEC, 7SKRNP], decision: NEW_MODULE, module: dmel_rnapii_elongation_complexes}
- {groups: [THO-C, TREX, TREX-2, NXF], decision: NEW_MODULE, module: dmel_mrna_nuclear_export}
- {groups: [MTV, HHTC], decision: NEW_MODULE, module: dmel_terminin_telomere_capping}
- {groups: [HIF], decision: NEW_MODULE, module: dmel_hif_complex}
- {groups: [IFT], decision: NEW_MODULE, module: dmel_intraflagellar_transport}
- {groups: [INT, INTAC], decision: NEW_MODULE, module: dmel_integrator_complex}
- {groups: [IRM-CAM], decision: NEW_MODULE, module: dmel_irm_myoblast_adhesion}
- {groups: [KMN], decision: NEW_MODULE, module: dmel_kmn_network}
- {groups: [KPC], decision: NEW_MODULE, module: dmel_kpc_ubiquitin_ligase}
- {groups: [SEA, LAMTOR, RAG, TSC1-2C], decision: NEW_MODULE, module: dmel_torc1_nutrient_sensing}
- {groups: [TOR], decision: NEW_MODULE, module: dmel_tor_complexes}
- {groups: [LKB1C], decision: NEW_MODULE, module: dmel_lkb1_strad_mo25_complex}
- {groups: [MCU-CPXS], decision: NEW_MODULE, module: dmel_mitochondrial_calcium_uniporter}
- {groups: [MPT, TIMM23, MDRS, MPP, IMP], decision: NEW_MODULE, module: dmel_mitochondrial_protein_import}
- {groups: [MCII-AF, MCIII-AF, MCR-AF, MCV-AF], decision: NEW_MODULE, module: dmel_respiratory_complex_assembly_factors}
- {groups: [MEDC], decision: NEW_MODULE, module: dmel_mediator_complex}
- {groups: [METWD], decision: NEW_MODULE, module: dmel_mettl1_wuho_methyltransferase}
- {groups: [MICOS], decision: NEW_MODULE, module: dmel_micos_complex}
- {groups: [MITDEG], decision: NEW_MODULE, module: dmel_mitochondrial_degradosome}
- {groups: [MRN], decision: NEW_MODULE, module: dmel_mrn_complex}
- {groups: [MT-REP], decision: NEW_MODULE, module: dmel_mitochondrial_dna_replisome}
- {groups: [MTC], decision: NEW_MODULE, module: dmel_m6a_methyltransferase_complex}
- {groups: [MUVB, MUVB-C], decision: NEW_MODULE, module: dmel_muvb_complexes}
- {groups: [NACS], decision: NEW_MODULE, module: dmel_nascent_polypeptide_associated_complex}
- {groups: [NAT-CPX], decision: NEW_MODULE, module: dmel_n_terminal_acetyltransferase_complexes}
- {groups: [NALCN, NALCN-CH], decision: NEW_MODULE, module: dmel_nalcn_channel_complex}
- {groups: [NEXT, RNAEXO], decision: NEW_MODULE, module: dmel_rna_exosome}
- {groups: [NPC], decision: NEW_MODULE, module: dmel_nuclear_pore_complex}
- {groups: [PFDN], decision: NEW_MODULE, module: dmel_prefoldin}
- {groups: [PP2A], decision: NEW_MODULE, module: dmel_pp2a_holoenzymes}
- {groups: [PTWP], decision: NEW_MODULE, module: dmel_ptw_pp1_complexes}
- {groups: [PSM, PSM-V], decision: NEW_MODULE, module: dmel_proteasome}
- {groups: [TRAPP], decision: NEW_MODULE, module: dmel_trapp_complexes}
- {groups: [MCC], decision: NEW_MODULE, module: dmel_mon1_ccz1_complex}
- {groups: [RETRO], decision: NEW_MODULE, module: dmel_retromer}
- {groups: [RIC], decision: NEW_MODULE, module: dmel_raps_insc_complex}
- {groups: [RLC, miRISC], decision: NEW_MODULE, module: dmel_risc_loading_complexes}
- {groups: [RNAP], decision: NEW_MODULE, module: dmel_nuclear_rna_polymerases}
- {groups: [RNASEP, RNASEMRP], decision: NEW_MODULE, module: dmel_rnase_p_mrp}
- {groups: [RNRC], decision: NEW_MODULE, module: dmel_ribonucleotide_reductase}
- {groups: [CRP], decision: NEW_MODULE, module: dmel_cytoplasmic_ribosome}
- {groups: [MRP], decision: NEW_MODULE, module: dmel_mitochondrial_ribosome}
- {groups: [RP], decision: UMBRELLA, reason: Cytoplasmic and mitochondrial ribosomes are separate modules.}
- {groups: [RZZ], decision: NEW_MODULE, module: dmel_rzz_complex}
- {groups: [SCF-SLMB], decision: NEW_MODULE, module: dmel_scf_slimb_ubiquitin_ligase}
- {groups: [SEPT-C], decision: NEW_MODULE, module: dmel_septin_complexes}
- {groups: [COHSN, COHSN-C2M-SA, COHSN-SOLO-SUNN], decision: NEW_MODULE, module: dmel_cohesin_complexes}
- {groups: [COND], decision: NEW_MODULE, module: dmel_condensin_complexes}
- {groups: [SMC5-6-T, SMC5-6-V], decision: NEW_MODULE, module: dmel_smc5_6_complex}
- {groups: [SMN-CPX, GEM], decision: NEW_MODULE, module: dmel_smn_complex}
- {groups: [SNURPS, SPL-C, SM-ALL, U2AF], decision: NEW_MODULE, module: dmel_spliceosome}
- {groups: [SRNPS], decision: NEW_MODULE, module: dmel_small_nucleolar_rnps}
- {groups: [SREBP-SCAP], decision: NEW_MODULE, module: dmel_srebp_scap_complex}
- {groups: [STRIPAK], decision: NEW_MODULE, module: dmel_stripak_complex}
- {groups: [TCTC], decision: NEW_MODULE, module: dmel_threonylcarbamoyl_transferase_complex}
- {groups: [TDRD3-TOP3B], decision: NEW_MODULE, module: dmel_tdrd3_top3b_complex}
- {groups: [TGTC], decision: NEW_MODULE, module: dmel_trna_guanine_transglycosylase}
- {groups: [TPN-C], decision: NEW_MODULE, module: dmel_troponin_complex}
- {groups: [TRFC], decision: NEW_MODULE, module: dmel_erf1_erf3_termination_complex}
- {groups: [USP46-C], decision: NEW_MODULE, module: dmel_usp46_deubiquitinase_complex}
- {groups: [VCB], decision: NEW_MODULE, module: dmel_vcb_ubiquitin_ligase}
- {groups: [VPS-C], decision: NEW_MODULE, module: dmel_hops_corvet_tethering}
- {groups: [WASH-C], decision: NEW_MODULE, module: dmel_wash_complex}
- {groups: [WRC], decision: NEW_MODULE, module: dmel_wave_regulatory_complex}
- {groups: [VHA], decision: NEW_MODULE, module: dmel_vacuolar_atpase}
- {groups: [TLNF], decision: NOT_A_MODULE, reason_code: FUNCTIONAL_CLASS,
   reason: Translation factors grouped by stage of translation; they act as separate factors, not one complex.}
- groups: [RAS-SF-GAP, RAS-SF-GEF]
  decision: NOT_A_MODULE
  reason_code: FUNCTIONAL_CLASS
  reason: Small-GTPase regulators grouped by activity (GAP or GEF) and target GTPase family.
- {groups: [STON], decision: NOT_A_MODULE, reason_code: SEQUENCE_FAMILY, reason: Stonin gene family.}
- {groups: [DYN-HC, DYN-IC, MC-AF], decision: UMBRELLA, reason: Subunit-type or assembly-factor category; children are triaged individually.}
- {groups: [TRAPP-CAT], decision: NEW_MODULE, module: dmel_trapp_complexes}
- {groups: [RAGGEF], decision: NEW_MODULE, module: dmel_torc1_nutrient_sensing}
- {groups: [MCI, MCI-U, MCI-T], decision: EXISTING_MODULE, module: mitochondrial_complex_i_core}
- {groups: [MCII-SDH, MCII-U, MCII-T], decision: EXISTING_MODULE, module: mitochondrial_complex_ii}
- {groups: [MCIII, MCIII-U, MCIII-T], decision: EXISTING_MODULE, module: mitochondrial_complex_iii}
- {groups: [MCIV, MCIV-U, MCIV-T], decision: EXISTING_MODULE, module: mitochondrial_complex_iv}
- {groups: [MCV, MCV-U, MCV-T], decision: EXISTING_MODULE, module: mitochondrial_complex_v}