Hello! I am trying to translate a modelSEED model to a model that uses bigg ID's, I ha

mergem translate tool does not transfer new ID's to model about mergem HOT 9 CLOSED

YahyaFarooqi commented on August 16, 2024

mergem translate tool does not transfer new ID's to model

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Comments (9)

dnlobo commented on August 16, 2024

Hello,

You are using the tool correctly. Would you be able to share your modelSEED model with us so we can have a look? If so, you can email a link or the file to lobo at umbc.edu.

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YahyaFarooqi commented on August 16, 2024

Hi! Absolutely! I have sent both the models to your email.

Here is how I was checking the ID's:

import mergem
from mergem import translate, load_model, save_model, map_localization, map_metabolite_univ_id, map_reaction_univ_id, get_metabolite_properties, get_reaction_properties, update_id_mapper
    
translated_model = mergem.translate(model, trans_to_db='bigg')

translated_model.medium

{'EX_cpd08636_b': 1000.0,
 'EX_cpd11416_b': 1000.0,
 'EX_cpd11576_b': 1000.0,
 'EX_cpd04097_b': 1000.0,
 'EX_cpd00033_b': 1000.0,
 'EX_cpd00067_b': 1000.0,
 'EX_cpd01030_b': 1000.0,
 'EX_cpd01012_b': 1000.0,
 'EX_cpd00276_b': 1000.0,
 'EX_cpd00082_b': 1000.0,
 'EX_cpd00080_b': 1000.0,
 'EX_cpd00001_b': 1000.0,
...

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dnlobo commented on August 16, 2024

Thanks for sending the files. We checked them and the metabolite IDs were being translated correctly. However as you indicated, the IDs of the exchange reactions, which are based on metabolite IDs, were not translated.

We now have updated mergem to also translate the metabolite IDs in the exchange reaction IDs. Please update mergem to the latest version and it should work.

Thank you for reporting this problem.

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YahyaFarooqi commented on August 16, 2024

Hi Daniel. It looks like the new update is working for the most part, but of the ≈1000 metabolites 1/3 are not translated. Is this an expected outcome?

import mergem

from mergem import translate, load_model, save_model, map_localization, map_metabolite_univ_id, map_reaction_univ_id, get_metabolite_properties, get_reaction_properties, update_id_mapper
    
translated_model = mergem.translate(model, trans_to_db='bigg')

matching_metabolites = []

# Iterate through all metabolites in the model and check their names
for metabolite in translated_model.metabolites:
    if "cpd" in metabolite.id:
        matching_metabolites.append(metabolite)

# Get all metabolites in the model
all_metabolites = translated_model.metabolites

# Print the names of matching metabolites and count them
print("Matching Metabolites:")
for metabolite in matching_metabolites:
    print(metabolite.id, metabolite.name)

# Print the total count of matching metabolites
print(f"Total matching metabolites: {len(matching_metabolites)}")

# Print the total number of metabolites in the model
print(f"Total number of metabolites in the model: {len(all_metabolites)}")

Matching Metabolites:
cpd01759_c0 N_Acyl_L_aspartate_c0
cpd00947_c0 LacCer_c0
cpd15746_c0 Palmitoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15755_c0 Palmitoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd11527_c0 7_methyl_trans_oct_2_enoyl_ACP_c0
cpd11528_c0 7_methyl_octanoyl_ACP_c0
cpd15736_c0 Diglucosyl_1_2_diisohexadecanoylglycerol_c0
cpd15754_c0 Isohexadecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd01949_c0 S_S_2_3_Butanediol_c0
cpd01221_c0 S_Acetoin_c0
cpd08739_c0 trans_2_Methyl_5_isopropylhexa_2_5_dienal_c0
cpd08740_c0 trans_2_Methyl_5_isopropylhexa_2_5_dienoic_acid_c0
cpd17042_c0 DNA_replication_c0
cpd11529_c0 9_methyl_3_oxo_decanoyl_ACP_c0
cpd11503_c0 6_methyl_octanoyl_ACP_c0
cpd11504_c0 8_methyl_3_oxo_decanoyl_ACP_c0
cpd15752_c0 Isopentadecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15761_c0 Isopentadecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd04097_c0 Pb_c0
cpd04097_e0 Pb_e0
cpd11540_c0 13_methyl_tetra_decanoyl_ACP_c0
cpd11541_c0 15_methyl_3_oxo_hexa_decanoyl_ACP_c0
cpd01663_c0 Chenodiol_c0
cpd15686_c0 CDP_1_2_diisopentadecanoylglycerol_c0
cpd15719_c0 Diisopentadecanoylphosphatidylglycerophosphate_c0
cpd15682_c0 1_2_diisohexadecanoyl_sn_glycerol_3_phosphate_c0
cpd15688_c0 CDP_1_2_diisohexadecanoylglycerol_c0
cpd03659_c0 GQ1_c0
cpd11543_c0 15_methyl_trans_hexa_dec_2_enoyl_ACP_c0
cpd11544_c0 15_methyl_hexa_decanoyl_ACP_c0
cpd11536_c0 11_methyl_dodecanoyl_ACP_c0
cpd11537_c0 13_methyl_3_oxo_tetra_decanoyl_ACP_c0
cpd12232_c0 Nucleoside_phosphate_c0
cpd00354_c0 NDP_c0
cpd15747_c0 Myristoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15774_c0 Myristoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd00424_c0 Cystathionine_c0
cpd11573_c0 Octodecanoyl_ACP_c0
cpd11437_c0 fa3coa_c0
cpd11502_c0 6_methyl_trans_oct_2_enoyl_ACP_c0
cpd00788_c0 N_Acetyl_beta_alanine_c0
cpd11495_c0 2_methylbutyryl_ACP_c0
cpd11514_c0 12_methyl_trans_tetra_dec_2_enoyl_ACP_c0
cpd11515_c0 12_methyl_tetra_decanoyl_ACP_c0
cpd11545_c0 isobutyryl_ACP_c0
cpd02999_c0 GD1a_c0
cpd01357_c0 R_Mandelate_c0
cpd01447_c0 Benzoylformate_c0
cpd05630_c0 Pelargonin_c0
cpd15065_c0 Pelargonidin_3_O_beta_D_glucoside_5_O_6_coumaroyl_beta_D_glucoside_c0
cpd01489_c0 beta_Alanopine_c0
cpd11549_c0 4_methyl_pentanoyl_ACP_c0
cpd11550_c0 6_methyl_3_oxo_heptanoyl_ACP_c0
cpd01407_c0 Volemulose_c0
cpd03722_c0 Sedoheptulose_1_phosphate_c0
cpd09846_c0 Cyromazine_c0
cpd09847_c0 N_Cyclopropylammeline_c0
cpd01061_c0 Geranial_c0
cpd15165_c0 Geranic_acid_c0
cpd02967_c0 N_Acetyl_beta_D_mannosaminyl_1_4_N_acetyl_D__glucosaminyldiphosphoundecaprenol_c0
cpd15679_c0 1_2_diisotetradecanoyl_sn_glycerol_3_phosphate_c0
cpd15685_c0 CDP_1_2_diisotetradecanoylglycerol_c0
cpd15687_c0 CDP_1_2_dianteisopentadecanoylglycerol_c0
cpd15720_c0 Dianteisopentadecanoylphosphatidylglycerophosphate_c0
cpd00224_c0 L_Arabinose_c0
cpd11553_c0 6_methyl_heptanoyl_ACP_c0
cpd11554_c0 8_methyl_3_oxo_nonanoyl_ACP_c0
cpd00431_c0 Sphingomyelin_c0
cpd09848_c0 N_Cyclopropylammelide_c0
cpd03962_c0 Cyanuric_acid_c0
cpd09849_c0 Cyclopropylamine_c0
cpd02264_c0 CDPparatose_c0
cpd02265_c0 CDPtyvelose_c0
cpd03963_c0 Biuret_c0
cpd11506_c0 8_methyl_trans_dec_2_enoyl_ACP_c0
cpd11507_c0 8_methyl_decanoyl_ACP_c0
cpd02298_c0 1F_beta_D_Fructosylsucrose_c0
cpd05546_c0 Cyanin_c0
cpd15088_c0 Cyanidin_3_glucoside_5_caffeoylglucoside_c0
cpd15779_c0 Isopentadecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd11568_c0 14_methyl_trans_pentadec_2_enoyl_ACP_c0
cpd11569_c0 14_methyl_pentadecanoyl_ACP_c0
cpd15606_c0 Gly_Tyr_c0
cpd11539_c0 13_methyl_trans_tetra_dec_2_enoyl_ACP_c0
cpd01567_c0 R_Allantoin_c0
cpd04058_c0 L_N2_2_Carboxyethylarginine_c0
cpd15731_c0 Diglucosyl_1_2_diisoheptadecanoylglycerol_c0
cpd15749_c0 Isoheptadecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15028_c0 Delphin_c0
cpd15029_c0 Delphinidin_3_glucoside_5_caffoyl_glucoside_c0
cpd11560_c0 10_methyl_trans_undec_2_enoyl_ACP_c0
cpd11561_c0 10_methyl_undecanoyl_ACP_c0
cpd11552_c0 6_methyl_trans_hept_2_enoyl_ACP_c0
cpd15730_c0 Diglucosyl_1_2_distearoylglycerol_c0
cpd15748_c0 Stearoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd11496_c0 4_methyl_3_oxo_hexanoyl_ACP_c0
cpd09790_c0 3_Methylsalicylaldehyde_c0
cpd09791_c0 3_Methylsalicylate_c0
cpd17043_c0 RNA_transcription_c0
cpd15750_c0 Anteisoheptadecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15759_c0 Anteisoheptadecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd12322_c0 1_Alkenyl_2_acylglycerol_c0
cpd12554_c0 1_Alkyl_2_acylglycerophosphoethanolamine_c0
cpd15721_c0 Diisohexadecanoylphosphatidylglycerophosphate_c0
cpd11508_c0 10_methyl_3_oxo_dodecanoyl_ACP_c0
cpd02745_c0 alpha_D_Galactosyl_diphosphoundecaprenol_c0
cpd09802_c0 2_Naphthaldehyde_c0
cpd09804_c0 2_Naphthoic_acid_c0
cpd00862_c0 alpha_D_Hexose_1_phosphate_c0
cpd02340_c0 alpha_D_Hexose_6_phosphate_c0
cpd08279_c0 1_Hydroxy_2_naphthaldehyde_c0
cpd04106_c0 S_Formylmycothiol_c0
cpd15751_c0 Isotetradecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15778_c0 Isotetradecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd02342_c0 alpha_D_Xylose_1_phosphate_c0
cpd15733_c0 Diglucosyl_1_2_diisotetradecanoylglycerol_c0
cpd04015_c0 trans_3_Chloro_2_propene_1_ol_c0
cpd04017_c0 3_Chloroallyl_aldehyde_c0
cpd02414_c0 L_2_Amino_6_oxopimelate_c0
cpd11532_c0 9_methyl_decanoyl_ACP_c0
cpd11533_c0 11_methyl_3_oxo_dodecanoyl_ACP_c0
cpd11679_c0 Secondary_alcohol_c0
cpd11733_c0 Ketone_c0
cpd15756_c0 Myristoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd09793_c0 1_Naphthaldehyde_c0
cpd09794_c0 1_Naphthoic_acid_c0
cpd04016_c0 cis_3_Chloro_2_propene_1_ol_c0
cpd15064_c0 cis_3_Chloroallyl_aldehyde_c0
cpd00907_c0 alpha_D_glucose_1_6_biphosphate_c0
cpd17041_c0 Protein_biosynthesis_c0
cpd02708_c0 cis_2_Methyl_5_isopropylhexa_2_5_dienal_c0
cpd08741_c0 cis_2_Methyl_5_isopropylhexa_2_5_dienoic_acid_c0
cpd16401_c0 4_Hydroxy_5_phenyltetrahydro_1_3_oxazin_2_one_c0
cpd16402_c0 5_Phenyl_1_3_oxazinane_2_4_dione_c0
cpd01047_c0 Apigenin_c0
cpd01043_c0 Acacetin_c0
cpd02658_c0 Nalpha_Benzyloxycarbonyl_L_leucine_c0
cpd00769_c0 N_Formyl_L_aspartate_c0
cpd11565_c0 12_methyl_tridecanoyl_ACP_c0
cpd11566_c0 14_methyl_3_oxo_pentadecanoyl_ACP_c0
cpd03657_c0 GA1_c0
cpd15681_c0 1_2_dianteisopentadecanoyl_sn_glycerol_3_phosphate_c0
cpd00838_c0 Streptomycin_6_phosphate_c0
cpd04806_c0 Aldophosphamide_c0
cpd16365_c0 Alcophosphamide_c0
cpd15773_c0 Palmitoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd18007_c0 Leachianone_G_c0
cpd18036_c0 Sophoraflavanone_G_c0
cpd15781_c0 Isohexadecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd11519_c0 14_methyl_hexa_decanoyl_ACP_c0
cpd11434_c0 fa12coa_c0
cpd11524_c0 5_methyl_hexanoyl_ACP_c0
cpd11525_c0 7_methyl_3_oxo_octanoyl_ACP_c0
cpd01859_c0 2_Naphthylmethanol_c0
cpd00195_c0 1_Alcohol_c0
cpd11616_c0 RCHO_c0
cpd15753_c0 Anteisopentadecanoyllipoteichoic_acid_n24__linked__unsubstituted_c0
cpd15762_c0 Anteisopentadecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd01623_c0 UDP_galactosamine_c0
cpd11546_c0 4_methyl_3_oxo_pentanoyl_ACP_c0
cpd11499_c0 4_methyl_hexanoyl_ACP_c0
cpd11500_c0 6_methyl_3_oxo_octanoyl_ACP_c0
cpd03365_c0 5_2_Formylethyl_4_6_dihydroxypicolinate_c0
cpd03366_c0 5_2_Carboxyethyl_4_6_dihydroxypicolinate_c0
cpd12064_c0 O_Acylcarnitine_c0
cpd11535_c0 11_methyl_trans_dodec_2_enoyl_ACP_c0
cpd01530_c0 Dichloromethane_c0
cpd12729_c0 Urate_3_ribonucleoside_c0
cpd15678_c0 1_2_dianteisoheptadecanoyl_sn_glycerol_3_phosphate_c0
cpd15684_c0 CDP_1_2_dianteisoheptadecanoylglycerol_c0
cpd11439_c0 fa4coa_c0
cpd06739_c0 R__plus__Citronellal_c0
cpd15166_c0 Citronellate_c0
cpd11570_c0 3_Oxooctodecanoyl_ACP_c0
cpd11435_c0 fa1coa_c0
cpd15780_c0 Anteisopentadecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd15735_c0 Diglucosyl_1_2_dianteisopentadecanoylglycerol_c0
cpd04126_c0 2_Hydroxybiphenyl_2_sulfinate_c0
cpd01642_c0 2_Biphenylol_c0
cpd15732_c0 Diglucosyl_1_2_dianteisoheptadecanoylglycerol_c0
cpd11510_c0 10_methyl_trans_dodec_2_enoyl_ACP_c0
cpd11511_c0 10_methyl_dodecanoyl_ACP_c0
cpd11712_c0 Protein_histidine_c0
cpd12508_c0 Protein_N_pros_phosphohistidine_c0
cpd14796_c0 Z_Phenylacetaldehyde_oxime_c0
cpd14795_c0 Benzyl_cyanide_c0
cpd03413_c0 L_Glutamyl_1_phosphate_c0
cpd15760_c0 Isotetradecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd02996_c0 GM2_c0
cpd03709_c0 Salicylaldehyde_c0
cpd11516_c0 14_methyl_3_oxo_hexa_decanoyl_ACP_c0
cpd11531_c0 9_methyl_trans_dec_2_enoyl_ACP_c0
cpd11432_c0 fa11coa_c0
cpd04248_c0 Chloral_hydrate_c0
cpd04661_c0 Trichloroethanol_c0
cpd12018_c0 Retinyl_ester_c0
cpd11548_c0 4_methyl_trans_pent_2_enoyl_ACP_c0
cpd01536_c0 GDP_L_galactose_c0
cpd14655_c0 L_Galactose_1_phosphate_c0
cpd11564_c0 12_methyl_trans_tridec_2_enoyl_ACP_c0
cpd12868_c0 Protein_D_serine_c0
cpd12599_c0 GM3_c0
cpd15663_c0 Prenol_45n_teichoic_acid_alanine_substituted_c0
cpd11584_c0 Ala_His_c0
cpd15734_c0 Diglucosyl_1_2_diisopentadecanoylglycerol_c0
cpd15067_c0 Delphinidin_3_O_beta_D_glucoside_5_O_6_coumaroyl_beta_D_glucoside_c0
cpd12592_c0 alpha_N_Acetylneuraminyl_2_3_beta_D_galactosyl_R_c0
cpd02972_c0 alpha_N_Acetylneuraminyl_2_8_alpha_N_acetylneuraminyl_2_3_beta_D__galactosyl_R_c0
cpd09792_c0 1_Naphthalenemethanol_c0
cpd15130_c0 Isopentenyl_ATP_c0
cpd16395_c0 2_Phenyl_1_3_propanediol_monocarbamate_c0
cpd16396_c0 3_Carbamoyl_2_phenylpropionaldehyde_c0
cpd15763_c0 Isohexadecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd02603_c0 3_Lysolecithin_c0
cpd02601_c0 2_Lysolecithin_c0
cpd11518_c0 14_methyl_trans_hexa_dec_2_enoyl_ACP_c0
cpd15758_c0 Isoheptadecanoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd15680_c0 1_2_diisopentadecanoyl_sn_glycerol_3_phosphate_c0
cpd09350_c0 N2_Acetyl_L_aminoadipyl_delta_phosphate_c0
cpd09351_c0 N2_Acetyl_L_aminoadipate_semialdehyde_c0
cpd15717_c0 Dianteisoheptadecanoylphosphatidylglycerophosphate_c0
cpd15776_c0 Isoheptadecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd01956_c0 o_Formylbenzoic_acid_c0
cpd01129_c0 Phthalate_c0
cpd11512_c0 12_methyl_3_oxo_tetra_decanoyl_ACP_c0
cpd09811_c0 4_Hydroxymethylsalicylaldehyde_c0
cpd09812_c0 4_Hydroxymethylsalicylate_c0
cpd15683_c0 CDP_1_2_diisoheptadecanoylglycerol_c0
cpd15716_c0 Diisoheptadecanoylphosphatidylglycerophosphate_c0
cpd15087_c0 Pelargonidin_3_glucoside_5_caffeoylglucoside_c0
cpd11498_c0 4_methyl_trans_hex_2_enoyl_ACP_c0
cpd11520_c0 isovaleryl_ACP_c0
cpd11521_c0 5_methyl_3_oxo_hexanoyl_ACP_c0
cpd03245_c0 Glycodeoxycholate_c0
cpd16439_c0 5_Deoxy_5_fluorocytidine_c0
cpd16329_c0 Doxifluridine_c0
cpd11556_c0 8_methyl_trans_non_2_enoyl_ACP_c0
cpd11557_c0 8_methyl_nonanoyl_ACP_c0
cpd15729_c0 Diglucosyl_1_2_dimyristoylglycerol_c0
cpd09433_c0 9_cis_Neoxanthin_c0
cpd09434_c0 9_cis_Violaxanthin_c0
cpd15131_c0 Isopentenyl_ADP_c0
cpd15666_c0 Peptidoglycan_polymer_n_1_subunits_c0
cpd15665_c0 Peptidoglycan_polymer_n_subunits_c0
cpd08238_c0 S___Citronellal_c0
cpd15066_c0 Cyanidin_3_O_beta_D_glucoside_5_O_6_coumaroyl_beta_D_glucoside_c0
cpd15728_c0 Diglucosyl_1_2_dipalmitoylglycerol_c0
cpd11558_c0 10_methyl_3_oxo_undecanoyl_ACP_c0
cpd15757_c0 Stearoyllipoteichoic_acid_n24__linked__glucose_substituted_c0
cpd15677_c0 1_2_diisoheptadecanoyl_sn_glycerol_3_phosphate_c0
cpd11572_c0 trans_Octodec_2_enoyl_ACP_c0
cpd15718_c0 Diisotetradecanoylphosphatidylglycerophosphate_c0
cpd12640_c0 GM1_c0
cpd11523_c0 5_methyl_trans_hex_2_enoyl_ACP_c0
cpd15777_c0 Anteisoheptadecanoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd11441_c0 fa6coa_c0
cpd11562_c0 12_methyl_3_oxo_tridecanoyl_ACP_c0
cpd15775_c0 Stearoyllipoteichoic_acid_n24__linked__D_alanine_substituted_c0
cpd00651_c0 D_Arabinonate_c0
cpd02386_c0 2_Dehydro_3_deoxy_D_xylonate_c0
cpd15766_c0 Stearoyllipoteichoic_acid_n24__linked__N_acetyl_D_glucosamine_c0
cpd15667_c0 glycerol_teichoic_acid_n45__linked__unsubstituted_c0
cpd15795_c0 Anteisoheptadecanoylcardiolipin_B_subtilis_c0
cpd15723_c0 Dianteisoheptadecanoylphosphatidylglycerol_c0
cpd15695_c0 Diisoheptadecanoylphosphatidylethanolamine_c0
cpd15669_c0 glycerol_teichoic_acid_n45__linked__glucose_substituted_c0
cpd15668_c0 glycerol_teichoic_acid_n45__linked__D_ala_substituted_c0
cpd15793_c0 Stearoylcardiolipin_B_subtilis_c0
cpd15768_c0 Anteisoheptadecanoyllipoteichoic_acid_n24__linked__N_acetyl_D_glucosamine_c0
cpd15767_c0 Isoheptadecanoyllipoteichoic_acid_n24__linked__N_acetyl_D_glucosamine_c0
cpd15722_c0 Diisoheptadecanoylphosphatidylglycerol_c0
cpd11416_c0 Biomass_c0
cpd11416_b Biomass_c0_b
cpd15794_c0 Isoheptadecanoylcardiolipin_B_subtilis_c0
cpd15696_c0 Dianteisoheptadecanoylphosphatidylethanolamine_c0
cpd15701_c0 1_2_Diisoheptadecanoyl_sn_glycerol_c0
cpd15740_c0 Monoglucosyl_1_2_diisoheptadecanoylglycerol_c0
cpd11534_c0 11_methyl_3_hydroxy_dodecanoyl_ACP_c0
cpd15672_c0 1_anteisoheptadecanoyl_sn_glycerol_3_phosphate_c0
cpd11517_c0 14_methyl_3_hydroxy_hexa_decanoyl_ACP_c0
cpd15689_c0 Diisoheptadecanoylphosphatidylserine_c0
cpd15702_c0 1_2_Dianteisoheptadecanoyl_sn_glycerol_c0
cpd15741_c0 Monoglucosyl_1_2_dianteisoheptadecanoylglycerol_c0
cpd15323_c0 1_Acyl_sn_glycero_3_phosphoglycerol_octadecanoyl_c0
cpd15739_c0 Monoglucosyl_1_2_distearoylglycerol_c0
cpd11530_c0 9_methyl_3_hydroxy_decanoyl_ACP_c0
cpd15690_c0 Dianteisoheptadecanoylphosphatidylserine_c0
cpd11542_c0 15_methyl_3_hydroxy_hexa_decanoyl_ACP_c0
cpd11513_c0 12_methyl_3_hydroxy_tetra_decanoyl_ACP_c0
cpd15671_c0 1_isoheptadecanoyl_sn_glycerol_3_phosphate_c0
cpd11501_c0 6_methyl_3_hydroxy_octanoyl_ACP_c0
cpd11538_c0 13_methyl_3_hydroxy_tetra_decanoyl_ACP_c0
cpd11526_c0 7_methyl_3_hydroxy_octanoyl_ACP_c0
cpd11497_c0 4_methyl_3_hydroxy_hexanoyl_ACP_c0
cpd11425_c0 2dmmq7_c0
cpd11509_c0 10_methyl_3_hydroxy_dodecanoyl_ACP_c0
cpd11505_c0 8_methyl_3_hydroxy_decanoyl_ACP_c0
cpd11522_c0 5_methyl_3_hydroxy_hexanoyl_ACP_c0
cpd15606_e0 Gly_Tyr_e0
cpd04097_b Pb_e0_b
cpd15606_b Gly_Tyr_e0_b
Total matching metabolites: 301
Total number of metabolites in the model: 1079

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dnlobo commented on August 16, 2024

Yes, unfortunately the modelSEED database does not include cross-references to BIGG for all their IDs. See for example the first one in your list, which only links to KEGG:

https://modelseed.org/biochem/compounds/cpd01759

The good news is that the internal dictionaries in mergem can be updated if they refresh their databases with more cross-references, but cross-references for all their metabolites probably is never going to happen.

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YahyaFarooqi commented on August 16, 2024

Ah I see. I suppose there is no alternative if I want to compare models across namespaces?

Thanks for your help!!

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dnlobo commented on August 16, 2024

Manual comparison of the missing matches would be my suggestion. In case you are not aware, you can visualize mergem results in Fluxer, which may be helpful:

https://fluxer.umbc.edu/

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YahyaFarooqi commented on August 16, 2024

I understand. Say if I had 1 curated (bigg) model, 1 bigg model reconstruction, and 1 modelSEED model reconstruction. If I were to use your tools Jaccard metric for reactions and metabolites to compare my draft reconstructions to the curated model, would the metrics be comparable, or would it be skewed towards the bigg model if the SEED mapping is not complete? Apologies if this is not the right place to ask.

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dnlobo commented on August 16, 2024

Indeed, unmapped metabolites and reactions will be counted as different between the models. You may want to have a final manual step to see if you can find any of the unmapped IDs from modelSEED in either of the BIGG models.

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mergem translate tool does not transfer new ID's to model about mergem HOT 9 CLOSED

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