Pypath inputs status report

Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.

Compiled between 2025-09-16 02:22:24 and 2025-09-16 09:13:13; pypath version: 0.16.28 (from git, installed by poetry; 1546e5d )

Modules collected: 192
Modules failed to import: 3
Functions collected: 526
Functions run without error: 393
Functions returned empty value: 13
Functions skipped due to lack of arguments: 111
Functions run with error: 22

Function Started Finished Elapsed (s) Result type Result repr Result size Error Change since last time Last succeeded
pypath.inputs.abs.abs_interactions 2025-09-16 02:22:27 2025-09-16 02:22:29 1.28 list [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) 650 {} 2025-09-16 02:22:27
pypath.inputs.acsn.acsn_interactions 2025-09-16 02:22:29 2025-09-16 02:22:29 0.56 list [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) 37,725 {} 2025-09-16 02:22:29
pypath.inputs.adhesome.adhesome_annotations 2025-09-16 02:22:29 2025-09-16 02:23:46 76.92 dict {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) 239 {} 2025-09-16 02:22:29
pypath.inputs.adhesome.adhesome_interactions 2025-09-16 02:23:46 2025-09-16 02:23:47 1.07 list [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) 6,542 {} 2025-09-16 02:23:46
pypath.inputs.adrecs.adrecs_adr_ontology 2025-09-16 02:23:47 2025-09-16 02:24:04 16.66 list [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) 13,855 {} 2025-09-16 02:23:47
pypath.inputs.adrecs.adrecs_drug_adr 2025-09-16 02:24:04 2025-09-16 02:27:35 210.60 list [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) 809,346 {} 2025-09-16 02:24:04
pypath.inputs.adrecs.adrecs_drug_identifiers 2025-09-16 02:27:35 2025-09-16 02:27:38 3.83 list [AdrecsDrug(badd='BADD_D00001', drug='1,2-hexanediol', synonyms=('1,2-hexanediol',), drugbank='DB14108', pubchem_cid='94335', mesh='C119102', kegg=None, tdd=None), AdrecsDrug(badd='BADD_D00002', drug='2-hydroxy-3-phenylpropanoic acid', synonyms=('3-phenyllactate', '3-phenyllactic acid', '3-phenyllac...(truncated) 2,526 {} 2025-09-16 02:27:35
pypath.inputs.adrecs.adrecs_hierarchy 2025-09-16 02:27:38 2025-09-16 02:27:40 1.12 set {AdrecsChildParent(child=AdrecsAdr(adr_class='11.02.01.050', badd='BADD_A08879'), parent=AdrecsAdr(adr_class='11.02.01', badd='BADD_A00418')), AdrecsChildParent(child=AdrecsAdr(adr_class='17.20.02.005', badd='BADD_A00668'), parent=AdrecsAdr(adr_class='17.20.02', badd='BADD_A01841')), AdrecsChildPare...(truncated) 13,828 {} 2025-09-16 02:27:38
pypath.inputs.almen2009.almen2009_annotations 2025-09-16 02:27:40 2025-09-16 02:27:41 1.60 dict {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) 4,243 {} 2025-09-16 02:27:40
pypath.inputs.alzpathway.alzpathway_interactions 2025-09-16 02:27:41 2025-09-16 02:27:41 0.11 list [AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='O00213', genesymbol_a='APP', genesymbol_b='APBB1', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='Q8N8S7', genesymbol_a='APP', genesymbol_b='ENAH', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05...(truncated) 119 {} 2025-09-16 02:27:41
pypath.inputs.baccin2019.baccin2019_annotations 2025-09-16 02:27:41 2025-09-16 02:31:33 232.18 dict {'Q15848': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q96A54': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'Q86V24': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'P35318': {Baccin2019Annotation(ma...(truncated) 933 {} 2025-09-16 02:27:41
pypath.inputs.baccin2019.baccin2019_interactions 2025-09-16 02:31:33 2025-09-16 02:31:34 0.34 list [Baccin2019Interaction(ligand='Q15848', receptor='Q96A54', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Ramilowski2015', 'Baccin2019'}, references={'12802337'}), Baccin2019Interaction(ligand='Q15848', receptor='Q86V24', correct='Correct', ligand_location='secre...(truncated) 1,460 {} 2025-09-16 02:31:33
pypath.inputs.biogps.biogps_datasets 2025-09-16 02:31:34 2025-09-16 02:31:34 0.00 list [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) 9 {} 2025-09-16 02:31:34
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
 {} never
pypath.inputs.biogps.biogps_download_all 2025-09-16 02:31:34 2025-09-16 02:32:16 42.29 dict {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) 9 {} 2025-09-16 02:31:34
pypath.inputs.biogrid.biogrid_all_interactions 2025-09-16 02:32:17 2025-09-16 02:32:51 34.23 list [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855', experimental_system='Two-hybrid', experimental_system_type='physical', ltp=True, htp_score=None, multi_validated=True, tax_a='9606', tax_b='9606'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272', experimen...(truncated) 8,732 {'fixed': True} 2025-09-16 02:32:17
pypath.inputs.biogrid.biogrid_interactions 2025-09-16 02:32:51 2025-09-16 02:32:52 1.14 list [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) 7,462 {} 2025-09-16 02:32:51
pypath.inputs.biomart.biomart_homology 2025-09-16 02:32:52 2025-09-16 02:33:26 33.74 list [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) 303,538 {} 2025-09-16 02:32:52
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
 {} never
pypath.inputs.biomart.biomart_microarray_types 2025-09-16 02:33:26 2025-09-16 02:33:27 0.07 list [{'type': 'OLIGO', 'vendor': 'PHALANX', 'array': 'OneArray', 'description': None, 'format': 'EXPRESSION', 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'array': 'CODELINK', 'vendor': 'CODELINK', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'type': 'OLIGO', 'array': ...(truncated) 37 {} 2025-09-16 02:33:26
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
 {} never
pypath.inputs.ca1.ca1_interactions 2025-09-16 02:33:27 2025-09-16 02:33:27 0.17 list [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) 1,788 {} 2025-09-16 02:33:27
pypath.inputs.cancercellmap.ccmap_interactions 2025-09-16 02:33:27 2025-09-16 02:33:28 1.05 list [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) 47,644 {} 2025-09-16 02:33:27
pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations 2025-09-16 02:33:28 2025-09-16 02:33:36 8.40 dict {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) 216 {} 2025-09-16 02:33:28
pypath.inputs.cancerdrugsdb.cancerdrugsdb_download 2025-09-16 02:33:36 2025-09-16 02:33:36 0.00 list [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) 330 {} 2025-09-16 02:33:36
pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions 2025-09-16 02:33:36 2025-09-16 02:33:43 6.31 list [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P42336', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) 5,157 {} 2025-09-16 02:33:36
pypath.inputs.cancersea.cancersea_annotations 2025-09-16 02:33:43 2025-09-16 02:33:45 2.24 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,248 {} 2025-09-16 02:33:43
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
 {} never
pypath.inputs.cellcall.cellcall_annotations 2025-09-16 02:33:45 2025-09-16 02:33:57 11.93 dict {'Q15389': {CellcallAnnotation(role='ligand')}, 'Q02763': {CellcallAnnotation(role='receptor')}, 'O43915': {CellcallAnnotation(role='ligand')}, 'P35968': {CellcallAnnotation(role='receptor')}, 'P23582': {CellcallAnnotation(role='ligand')}, 'P20594': {CellcallAnnotation(role='receptor')}, 'P22003': {...(truncated) 460 {} 2025-09-16 02:33:45
pypath.inputs.cellcall.cellcall_download 2025-09-16 02:33:57 2025-09-16 02:33:57 0.04 list [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) 19,144 {} 2025-09-16 02:33:57
pypath.inputs.cellcall.cellcall_download_all 2025-09-16 02:33:57 2025-09-16 02:33:58 0.78 list [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) 38,645 {} 2025-09-16 02:33:57
pypath.inputs.cellcall.cellcall_interactions 2025-09-16 02:33:58 2025-09-16 02:33:58 0.11 list [CellcallInteraction(ligand_uniprot='Q15389', receptor_uniprot='Q02763', core=True), CellcallInteraction(ligand_uniprot='O43915', receptor_uniprot='P35968', core=True), CellcallInteraction(ligand_uniprot='P23582', receptor_uniprot='P20594', core=True), CellcallInteraction(ligand_uniprot='P22003', re...(truncated) 797 {} 2025-09-16 02:33:58
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2025-09-16 02:33:58 2025-09-16 02:33:59 0.66 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), Cellcellinteractions...(truncated) 3,425 {} 2025-09-16 02:33:58
pypath.inputs.cellchatdb.cellchatdb_annotations 2025-09-16 02:33:59 2025-09-16 02:34:09 10.44 dict {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P07996': {CellChatDBAnnotation(role='ligand', pathway='THBS', category='...(truncated) 1,523 {} 2025-09-16 02:33:59
pypath.inputs.cellchatdb.cellchatdb_cofactors 2025-09-16 02:34:09 2025-09-16 02:34:16 7.52 dict {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'Q13253', 'O60565', 'Q9H2X0', 'Q9H772', 'O75610', 'P41271', 'O00292', 'P12645'}, 'BMP inhibition receptor': {'Q13145'...(truncated) 32 {} 2025-09-16 02:34:09
pypath.inputs.cellchatdb.cellchatdb_complexes 2025-09-16 02:34:16 2025-09-16 02:34:23 6.40 dict {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) 330 {} 2025-09-16 02:34:16
pypath.inputs.cellchatdb.cellchatdb_download 2025-09-16 02:34:23 2025-09-16 02:34:30 7.43 dict {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) 4 {} 2025-09-16 02:34:23
pypath.inputs.cellchatdb.cellchatdb_interactions 2025-09-16 02:34:30 2025-09-16 02:34:38 7.24 list [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P07996', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) 12,424 {} 2025-09-16 02:34:30
pypath.inputs.cellinker.cellinker_annotations 2025-09-16 02:34:38 2025-09-16 02:34:38 0.46 dict {'Q16625': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, 'P55285': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'Q9P2B2': {CellinkerAnnotation(role=...(truncated) 1,919 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_complex_annotations 2025-09-16 02:34:38 2025-09-16 02:34:38 0.05 dict {Complex: COMPLEX:P13612_P26010: {CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, Complex: COMPLEX:O00238_Q13873: {CellinkerAnnotation(role='receptor', location='Membrane', t...(truncated) 134 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_complexes 2025-09-16 02:34:38 2025-09-16 02:34:38 0.00 dict {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) 143 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_complexes_raw 2025-09-16 02:34:38 2025-09-16 02:34:38 0.00 list [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) 145 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_lr_interactions 2025-09-16 02:34:38 2025-09-16 02:34:38 0.04 set {CellinkerInteraction(ligand='Q16625', receptor='Q16625', ligand_location='Membrane', receptor_location='Membrane', resources=None, pmids='32196115', type='Cell adhesion'), CellinkerInteraction(ligand='P55285', receptor='Q9P2B2', ligand_location='Membrane', receptor_location='Membrane', resources=No...(truncated) 3,810 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2025-09-16 02:34:38 2025-09-16 02:34:38 0.01 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_protein_annotations 2025-09-16 02:34:38 2025-09-16 02:34:38 0.06 dict {'Q16625': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, 'P55285': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'Q9P2B2': {CellinkerAnnotation(role=...(truncated) 1,785 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_smol_interactions 2025-09-16 02:34:38 2025-09-16 02:34:38 0.14 set {CellinkerInteraction(ligand='951', receptor='P07550', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='15102946', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5280723', receptor='Q86XQ3', ligand_location=None, receptor_location='Membrane', reso...(truncated) 314 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2025-09-16 02:34:38 2025-09-16 02:34:38 0.00 list [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) 341 {} 2025-09-16 02:34:38
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
 {} never
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2025-09-16 02:34:38 2025-09-16 02:34:39 0.20 dict {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) 358 {} 2025-09-16 02:34:38
pypath.inputs.cellphonedb.cellphonedb_complexes 2025-09-16 02:34:39 2025-09-16 02:34:39 0.02 dict {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) 358 {} 2025-09-16 02:34:39
pypath.inputs.cellphonedb.cellphonedb_interactions 2025-09-16 02:34:39 2025-09-16 02:34:39 0.49 list [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) 2,903 {} 2025-09-16 02:34:39
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2025-09-16 02:34:39 2025-09-16 02:34:39 0.02 tuple ({'O00253', 'P80162', 'P12034', 'Q8IW52', 'P52797', 'P56703', 'P04070', Complex integrin_a6b4_complex: COMPLEX:P16144_P23229, 'O95715', 'P12643', 'Q86YW7', 'Q8NFR9', 'Q9NZC2', 'P32881', 'Q9NZ94', 'Q6ZMC9', 'Q969D9', 'Q9NPF7', 'Q92673', 'Q96P56', 'Q9HC23', 'P08700', 'P01567', 'Q9NTN9', 'P22301', 'Q7Z...(truncated) 2 {} 2025-09-16 02:34:39
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2025-09-16 02:34:39 2025-09-16 02:34:39 0.02 dict {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) 1,359 {} 2025-09-16 02:34:39
pypath.inputs.celltalkdb.celltalkdb_annotations 2025-09-16 02:34:39 2025-09-16 02:34:40 0.39 dict {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='15721238'), CellTalkDBAnnotation(role='receptor', pmid='32196115')}, 'Q...(truncated) 1,598 {} 2025-09-16 02:34:39
pypath.inputs.celltalkdb.celltalkdb_download 2025-09-16 02:34:40 2025-09-16 02:34:40 0.15 list [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) 3,398 {} 2025-09-16 02:34:40
pypath.inputs.celltalkdb.celltalkdb_interactions 2025-09-16 02:34:40 2025-09-16 02:34:40 0.16 list [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) 3,398 {} 2025-09-16 02:34:40
pypath.inputs.celltypist.celltypist_annotations 2025-09-16 02:34:40 2025-09-16 02:34:40 0.27 dict {'P15391': {CelltypistAnnotation(cell_type='B cells', cell_subtype='B cells', cell_ontology='CL:0000236', marker_type='curated_marker', tissues=('Blood', 'Eye', 'Intestine', 'Kidney', 'Liver', 'Lung', 'Trachea'), datasets=('Braga et al. 2019', 'Martin et al. 2019', 'Miller et al. 2020', 'Popescu et ...(truncated) 460 {} 2025-09-16 02:34:40
pypath.inputs.clinvar.clinvar_citations 2025-09-16 02:34:40 2025-09-16 02:35:21 41.10 list [Citation(allele='1707757', variation_id='1709403', nsv='', citation_source='PubMedCentral', citation_id='4544753'), Citation(allele='1673979', variation_id='1682077', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='2919322', variation_id='2750364', nsv='', citation_sourc...(truncated) 4,182,449 {} 2025-09-16 02:34:40
pypath.inputs.clinvar.clinvar_raw 2025-09-16 02:35:26 2025-09-16 02:41:40 373.36 list [Variant(allele='2811439', type='single nucleotide variant', variant='NM_015443.4(KANSL1):c.749C>T (p.Pro250Leu)', entrez='284058', genesymbol='KANSL1', clinical_significance='Uncertain significance', review_status='criteria provided, single submitter', rs='2545084038', phenotype_ids=('MedGen:C36619...(truncated) 7,468,303 {} 2025-09-16 02:35:26
pypath.inputs.collectri.collectri_interactions 2025-09-16 04:04:40 2025-09-16 04:04:57 16.96 list [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) 64,990 {} 2025-09-16 04:04:40
pypath.inputs.collectri.collectri_raw 2025-09-16 04:04:57 2025-09-16 04:04:57 0.10 list [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) 43,416 {} 2025-09-16 04:04:57
pypath.inputs.compath.compath_mappings 2025-09-16 04:04:57 2025-09-16 04:04:57 0.15 list [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) 1,592 {} 2025-09-16 04:04:57
pypath.inputs.compleat.compleat_complexes 2025-09-16 04:04:57 2025-09-16 04:04:58 1.06 dict {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) 9,695 {} 2025-09-16 04:04:57
pypath.inputs.compleat.compleat_raw 2025-09-16 04:04:58 2025-09-16 04:04:58 0.05 list [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) 9,704 {} 2025-09-16 04:04:58
pypath.inputs.complexportal.complexportal_complexes 2025-09-16 04:04:58 2025-09-16 04:07:00 121.91 dict {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) 2,275 {} 2025-09-16 04:04:58
pypath.inputs.comppi.comppi_interaction_locations 2025-09-16 04:07:00 2025-09-16 04:07:16 16.36 list [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) 587,995 {} 2025-09-16 04:07:00
pypath.inputs.comppi.comppi_locations 2025-09-16 04:07:16 2025-09-16 04:07:31 14.30 dict {'A0A0R4J2E4': {ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)}, 'A0A024R0Y4': {ComppiLocation(location='nucleus', score=0.8)}, 'A0A087WWR4': {ComppiLocation(location='nucleus', score=0.8)}, 'Q08379': {ComppiLocation(location='extracellular', score=0.8),...(truncated) 22,799 {} 2025-09-16 04:07:16
pypath.inputs.connectomedb.connectomedb_annotations 2025-09-16 04:07:31 2025-09-16 04:07:31 0.35 dict {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) 1,428 {} 2025-09-16 04:07:31
pypath.inputs.connectomedb.connectomedb_interactions 2025-09-16 04:07:31 2025-09-16 04:07:31 0.01 list [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) 2,293 {} 2025-09-16 04:07:31
pypath.inputs.corum.corum_complexes 2025-09-16 04:07:31 2025-09-16 04:07:32 0.54 dict {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) 2,734 {} 2025-09-16 04:07:31
pypath.inputs.cosmic.cancer_gene_census_annotations 2025-09-16 04:07:32 2025-09-16 04:07:32 0.14 dict {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, chr_band='10q11.23', tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',), translocation_partner=(()...(truncated) 762 {} 2025-09-16 04:07:32
pypath.inputs.cosmic.cancer_gene_census_raw 2025-09-16 04:07:32 2025-09-16 04:07:32 0.00 list [{'Gene Symbol': 'A1CF', 'Name': 'APOBEC1 complementation factor', 'Entrez GeneId': '29974', 'Genome Location': '10:50799421-50885675', 'Tier': '2', 'Hallmark': '', 'Chr Band': '10q11.23', 'Somatic': 'yes', 'Germline': '', 'Tumour Types(Somatic)': 'melanoma', 'Tumour Types(Germline)': '', 'Cancer Sy...(truncated) 758 {} 2025-09-16 04:07:32
pypath.inputs.cpad.cpad_annotations 2025-09-16 04:07:32 2025-09-16 04:07:56 24.30 dict {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) 1,071 {} 2025-09-16 04:07:32
pypath.inputs.cpad.cpad_pathway_cancer 2025-09-16 04:07:56 2025-09-16 04:07:56 0.05 tuple ({'Glioma': {CpadPathwayCancer(pathway='miR-153-Nrf-2-GPx1 pathway', cancer='Glioma', pathway_category='Others', effect_on_cancer='Activating', effect_on_cancer_outcome='reduce tumorigenic capacity'), CpadPathwayCancer(pathway='SIRT3/SOD2/ROS1 pathway', cancer='Glioma', pathway_category='Others', ef...(truncated) 2 {} 2025-09-16 04:07:56
pypath.inputs.cpad.get_cpad 2025-09-16 04:07:56 2025-09-16 04:07:56 0.04 list [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) 4,709 {} 2025-09-16 04:07:56
pypath.inputs.cpdb.cpdb_interactions 2025-09-16 04:07:56 2025-09-16 04:08:03 7.23 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 531,371 {} 2025-09-16 04:07:56
pypath.inputs.cpdb.cpdb_interactions_ltp 2025-09-16 04:08:04 2025-09-16 04:08:07 2.84 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 482,222 {} 2025-09-16 04:08:04
pypath.inputs.credentials.credentials 
Not calling `pypath.inputs.credentials.credentials`, not enough arguments.
 {} never
pypath.inputs.cspa.cspa_annotations 2025-09-16 04:08:07 2025-09-16 04:08:08 0.80 dict {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) 1,449 {} 2025-09-16 04:08:07
pypath.inputs.cspa.cspa_cell_type_annotations 2025-09-16 04:08:08 2025-09-16 04:08:09 0.79 dict {'A1A5B4': {CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='SUDHL6', v...(truncated) 1,410 {} 2025-09-16 04:08:08
pypath.inputs.cspa.cspa_cell_types 2025-09-16 04:08:09 2025-09-16 04:08:09 0.40 dict {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) 47 {} 2025-09-16 04:08:09
pypath.inputs.ctdbase.ctdbase_relations 
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments.
 {} never
pypath.inputs.ctdbase.ctdbase_vocabulary 
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments.
 {} never
pypath.inputs.cytosig.cytosig_annotations 2025-09-16 04:08:09 2025-09-16 04:08:11 1.60 dict {'Q9NPC4': {CytosigAnnotation(cytokine='P08700', score=0.0802573679769995, cytokine_genesymbol='IL3', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P09603', score=0.1545099490556249, cytokine_genesymbol='MCSF', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='O95390', score=0.1075...(truncated) 4,887 {} 2025-09-16 04:08:09
pypath.inputs.cytosig.cytosig_df 2025-09-16 04:08:11 2025-09-16 04:08:11 0.03 DataFrame Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) 4,881 {} 2025-09-16 04:08:11
pypath.inputs.dbptm.dbptm_enzyme_substrate 2025-09-16 04:08:11 2025-09-16 04:08:14 3.23 list [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) 223,135 {} 2025-09-16 04:08:11
pypath.inputs.dbptm.dbptm_interactions 2025-09-16 04:08:15 2025-09-16 04:08:16 1.25 list [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) 2,071 {} 2025-09-16 04:08:15
pypath.inputs.ddinter.ddinter_drug_interactions 
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments.
 {} never
pypath.inputs.ddinter.ddinter_identifiers 
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments.
 {} never
pypath.inputs.ddinter.ddinter_interactions 2025-09-16 04:08:16 2025-09-16 04:08:52 36.00 list [DdinterInteraction(drug1_id='DDInter462', drug1_name='Dabrafenib', drug2_id='DDInter1882', drug2_name='Troleandomycin', level='Moderate'), DdinterInteraction(drug1_id='DDInter1826', drug1_name='Tolazamide', drug2_id='DDInter813', drug2_name='Gemifloxacin', level='Major'), DdinterInteraction(drug1_i...(truncated) 160,235 {} 2025-09-16 04:08:16
pypath.inputs.ddinter.ddinter_mappings 2025-09-16 04:08:52 2025-09-16 05:15:10 3,977.41 list [DdinterIdentifiers(ddinter='DDInter1072', drugbank='DB00431', chembl='CHEMBL15891', pubchem='46508542'), DdinterIdentifiers(ddinter='DDInter196', drugbank='DB00443', chembl='CHEMBL632', pubchem='46505155'), DdinterIdentifiers(ddinter='DDInter909', drugbank='DB00619', chembl='CHEMBL941', pubchem='46...(truncated) 1,939 {} 2025-09-16 04:08:52
pypath.inputs.ddinter.ddinter_n_drugs 2025-09-16 05:15:10 2025-09-16 05:15:10 0.44 int 1939 0 {} 2025-09-16 05:15:10
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2025-09-16 05:15:10 2025-09-16 05:15:10 0.14 list [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) 184 {} 2025-09-16 05:15:10
pypath.inputs.depod.depod_enzyme_substrate 2025-09-16 05:15:10 2025-09-16 05:15:11 0.40 list [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) 537 {} 2025-09-16 05:15:10
pypath.inputs.depod.depod_interactions 2025-09-16 05:15:11 2025-09-16 05:15:11 0.01 list [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) 832 {} 2025-09-16 05:15:11
pypath.inputs.dgidb.dgidb_annotations 2025-09-16 05:15:11 2025-09-16 05:15:17 6.24 dict {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='dGene'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnotation(category='TRANSCRIPTION FACTOR', source='Pharos'), DgidbAnnotation(category='TRANSCRIPTION FACTOR COMPLEX', source='GO'), DgidbAn...(truncated) 9,973 {} 2025-09-16 05:15:11
pypath.inputs.dgidb.dgidb_interactions 2025-09-16 05:15:17 2025-09-16 05:15:22 5.34 list [DgidbInteraction(genesymbol='NAIP', gene_concept_id='hgnc:7634', resource='TALC', type='inhibitor', drug_name='NULL', drug_concept_id='NULL', score='NULL', approved='NULL', anti_neoplastic='NULL', immunotherapy='NULL'), DgidbInteraction(genesymbol='CNR2', gene_concept_id='hgnc:2160', resource='TTD'...(truncated) 84,175 {} 2025-09-16 05:15:17
pypath.inputs.dip.dip_interactions 2025-09-16 05:15:22 2025-09-16 05:15:23 0.23 list [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) 2,283 {} 2025-09-16 05:15:22
pypath.inputs.dip.dip_login 
Not calling `pypath.inputs.dip.dip_login`, not enough arguments.
 {} never
pypath.inputs.diseases.diseases_general 
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments.
 {} never
pypath.inputs.diseases.experiments_filtered 2025-09-16 05:15:23 2025-09-16 05:15:23 0.46 list [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource='TIGA', source_score=27, confidence=0.865), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:535', disease='Sleep disorder', resource='TIGA'...(truncated) 30,470 {} 2025-09-16 05:15:23
pypath.inputs.diseases.experiments_full 2025-09-16 05:15:23 2025-09-16 05:15:27 3.60 list [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:150', disease='Disease of mental health', resource='TIGA', source_score=18, confidence=0.717), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resou...(truncated) 345,254 {} 2025-09-16 05:15:23
pypath.inputs.diseases.knowledge_filtered 2025-09-16 05:15:27 2025-09-16 05:15:27 0.14 list [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:1928', disease='Williams-Beuren syndrome', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Cranio...(truncated) 7,775 {} 2025-09-16 05:15:27
pypath.inputs.diseases.knowledge_full 2025-09-16 05:15:27 2025-09-16 05:15:28 0.96 list [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050177', disease='Monogenic disease', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050736', disease='Autosomal...(truncated) 98,705 {} 2025-09-16 05:15:27
pypath.inputs.diseases.textmining_filtered 2025-09-16 05:15:28 2025-09-16 05:15:28 0.12 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-09-14 05:01:35
pypath.inputs.diseases.textmining_full 2025-09-16 05:15:28 2025-09-16 05:15:28 0.08 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-09-05 04:53:51
pypath.inputs.domino.domino_ddi 2025-09-16 05:15:28 2025-09-16 05:15:31 2.87 list [<pypath.internals.intera.DomainDomain object at 0x7f03478601d0>, <pypath.internals.intera.DomainDomain object at 0x7f0347861090>, <pypath.internals.intera.DomainDomain object at 0x7f0347861c50>, <pypath.internals.intera.DomainDomain object at 0x7f0347861d50>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294 {} 2025-09-16 05:15:28
pypath.inputs.domino.domino_enzsub 2025-09-16 05:15:31 2025-09-16 05:15:32 0.63 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f03b1ba0c50>, <pypath.internals.intera.DomainDomain object at 0x7f03b1ba1bd0>, <pypath.internals.intera.DomainDomain object at 0x7f03b1ba1990>, <pypath.internals.intera.DomainDomain object at 0x7f03b1ba3110>, <pypath.internals.intera.Domain...(truncated) 2 {} 2025-09-16 05:15:31
pypath.inputs.domino.domino_interactions 2025-09-16 05:15:32 2025-09-16 05:15:32 0.36 list [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) 6,687 {} 2025-09-16 05:15:32
pypath.inputs.domino.get_domino 2025-09-16 05:15:32 2025-09-16 05:15:32 0.33 list [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) 14,539 {} 2025-09-16 05:15:32
pypath.inputs.dorothea.dorothea_full_raw 2025-09-16 05:15:32 2025-09-16 05:15:41 9.12 DataFrame tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) 1,019,220 {} 2025-09-16 05:15:32
pypath.inputs.dorothea.dorothea_interactions 2025-09-16 05:15:42 2025-09-16 05:15:55 13.88 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2025-09-16 05:15:42
pypath.inputs.dorothea.dorothea_rda_raw 2025-09-16 05:15:55 2025-09-16 05:15:57 1.89 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2025-09-16 05:15:55
pypath.inputs.dorothea.dorothea_rda_raw 2025-09-16 05:15:57 2025-09-16 05:15:59 1.34 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2025-09-16 05:15:57
pypath.inputs.dorothea.dorothea_interactions 2025-09-16 05:15:59 2025-09-16 05:16:13 13.89 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2025-09-16 05:15:59
pypath.inputs.dorothea.dorothea_old_csv 2025-09-16 05:16:13 2025-09-16 05:16:13 0.44 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
                            ~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
{} 2025-09-05 05:00:43
pypath.inputs.drugcentral.drugcentral_drugs 2025-09-16 05:16:13 2025-09-16 05:16:14 1.22 list [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) 4,099 {} 2025-09-16 05:16:13
pypath.inputs.drugcentral.drugcentral_interactions 2025-09-16 05:16:14 2025-09-16 05:16:16 1.39 list [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) 23,115 {} 2025-09-16 05:16:14
pypath.inputs.drugcentral.drugcentral_mapping 
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments.
 {} never
pypath.inputs.ebi.ebi_rest 
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments.
 {} never
pypath.inputs.elm.elm_classes 2025-09-16 05:16:16 2025-09-16 05:16:17 0.84 dict {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) 353 {} 2025-09-16 05:16:16
pypath.inputs.elm.elm_domains 2025-09-16 05:16:17 2025-09-16 05:16:17 0.30 dict {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) 604 {} 2025-09-16 05:16:17
pypath.inputs.elm.elm_instances 2025-09-16 05:16:17 2025-09-16 05:20:46 268.60 list [ELMInstance(accession='Accession', type='ELMType', identifier='ELMIdentifier', uniprot_id='ProteinName', uniprot='Primary_Acc', synonyms='Accessions', start='Start', end='End', references='References', methods='Methods', logic='InstanceLogic', pdb='PDB', organism='Organism'), ELMInstance(accession=...(truncated) 4,278 {'size': 1} 2025-09-16 05:16:17
pypath.inputs.elm.elm_interactions 2025-09-16 05:20:46 2025-09-16 05:20:46 0.09 list [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) 2,797 {} 2025-09-16 05:20:46
pypath.inputs.embopress.embopress_supplementary 
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments.
 {} never
pypath.inputs.embrace.embrace_annotations 2025-09-16 05:20:46 2025-09-16 05:20:52 6.68 dict {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=True)}, 'P30411': {EmbraceAnnotation(mainclass='receptor', neu...(truncated) 844 {} 2025-09-16 05:20:46
pypath.inputs.embrace.embrace_interactions 2025-09-16 05:20:52 2025-09-16 05:20:53 0.10 list [EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(ligand='O43184', receptor='P05556'), EmbraceInteraction(ligand='O43184', receptor='P31431'), EmbraceInteraction(...(truncated) 1,273 {} 2025-09-16 05:20:52
pypath.inputs.embrace.embrace_raw 2025-09-16 05:20:53 2025-09-16 05:20:53 0.09 list [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) 1,710 {} 2025-09-16 05:20:53
pypath.inputs.embrace.embrace_translated 2025-09-16 05:20:53 2025-09-16 05:20:53 0.10 list [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) 1,832 {} 2025-09-16 05:20:53
pypath.inputs.encode.encode_tf_mirna_interactions 2025-09-16 05:20:53 2025-09-16 05:20:53 0.42 list [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) 1,237 {} 2025-09-16 05:20:53
pypath.inputs.ensembl.ensembl_organisms 2025-09-16 05:20:53 2025-09-16 05:20:54 0.50 list [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) 348 {} 2025-09-16 05:20:53
pypath.inputs.eutils.esummary 
Not calling `pypath.inputs.eutils.esummary`, not enough arguments.
 {} never
pypath.inputs.exocarta.get_exocarta 2025-09-16 05:20:54 2025-09-16 05:21:41 47.83 list [ExocartaRecord(entrez='967', genesymbol='CD63', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='1803', genesymbol='DPP4', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='79574', genesymbol=...(truncated) 35,259 {} 2025-09-16 05:20:54
pypath.inputs.exocarta.get_vesiclepedia 2025-09-16 05:21:41 2025-09-16 05:24:47 185.27 list [VesiclepediaRecord(entrez='31848', genesymbol='His3.3B', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entrez='33736', genesymbol='His3.3A', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entr...(truncated) 290,197 {} 2025-09-16 05:21:41
pypath.inputs.expasy.expasy_enzyme_classes 2025-09-16 05:24:47 2025-09-16 05:24:47 0.17 list [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) 354 {} 2025-09-16 05:24:47
pypath.inputs.expasy.expasy_enzymes 2025-09-16 05:24:47 2025-09-16 05:24:49 1.73 dict {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) 8,405 {} 2025-09-16 05:24:47
pypath.inputs.genecards.genecards_datasheet 
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_soup 
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_summaries 
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments.
 {} never
pypath.inputs.go.get_go_desc 
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments.
 {} never
pypath.inputs.go.get_go_quick 2025-09-16 05:24:49 2025-09-16 05:25:41 52.80 dict {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0005743', 'GO:0045275', 'GO:0016020'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0005743', 'GO:0045259'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0005743', 'GO:0045259'}, 'A0A023I7N5': {'GO:0005743', 'GO:0016020'}, 'A0A02...(truncated) 2 {} 2025-09-16 05:24:49
pypath.inputs.go.get_goslim 2025-09-16 05:25:42 2025-09-16 05:25:43 1.27 list ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) 142 {} 2025-09-16 05:25:42
pypath.inputs.go.go_ancestors_quickgo 2025-09-16 05:25:43 2025-09-16 05:31:43 359.74 dict {'C': {'GO:0160112': {('GO:0097649', 'part_of'), ('GO:0160110', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0160111': {('GO:0097649', 'part_of'), ('GO:0160110', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:1990657': {('GO:1903958', 'is_a'), ('GO:1990658', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) 3 {} 2025-09-16 05:25:43
pypath.inputs.go.go_ancestors_goose 2025-09-16 05:31:43 2025-09-16 05:31:43 0.14 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-09-05 05:17:51
pypath.inputs.go.go_ancestors_quickgo 2025-09-16 05:31:43 2025-09-16 05:31:47 4.29 dict {'C': {'GO:0160112': {('GO:0097649', 'part_of'), ('GO:0160110', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0160111': {('GO:0097649', 'part_of'), ('GO:0160110', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:1990657': {('GO:1903958', 'is_a'), ('GO:1990658', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) 3 {} 2025-09-16 05:31:43
pypath.inputs.go.go_annotations_goa 2025-09-16 05:31:47 2025-09-16 05:31:50 2.47 dict {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005576', 'G...(truncated) 3 {} 2025-09-16 05:31:47
pypath.inputs.go.go_annotations_all 2025-09-16 05:31:50 2025-09-16 05:31:56 6.67 dict {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0016787', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0378', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) 19,697 {} 2025-09-16 05:31:50
pypath.inputs.go.go_annotations_goa 2025-09-16 05:31:59 2025-09-16 05:32:00 1.17 dict {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005576', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005576', 'G...(truncated) 3 {} 2025-09-16 05:31:59
pypath.inputs.go.go_annotations_goose 2025-09-16 05:32:00 2025-09-16 05:32:00 0.11 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/go.py", line 860, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-09-05 05:18:09
pypath.inputs.go.go_annotations_uniprot 2025-09-16 05:32:00 2025-09-16 05:32:11 11.31 dict {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0043231', 'GO:0070330'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'], 'A0A0C5B5G6': ['GO:0001649', 'GO:0003677', 'GO:0005615', ...(truncated) 19,390 {} 2025-09-16 05:32:00
pypath.inputs.go.go_descendants_quickgo 2025-09-16 05:32:11 2025-09-16 05:32:15 4.14 dict {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160112', 'part_of'), ('GO:0160111', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160280', 'part_of'), ('GO:0160279', 'part_of')}, 'GO:1990676': {(...(truncated) 3 {} 2025-09-16 05:32:11
pypath.inputs.go.go_descendants_goose 2025-09-16 05:32:15 2025-09-16 05:32:16 0.10 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/go.py", line 291, in go_descendants_goose
    anc = go_ancestors_goose(aspects = aspects)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-09-05 05:18:27
pypath.inputs.go.go_descendants_quickgo 2025-09-16 05:32:16 2025-09-16 05:32:20 4.32 dict {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160112', 'part_of'), ('GO:0160111', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160280', 'part_of'), ('GO:0160279', 'part_of')}, 'GO:1990676': {(...(truncated) 3 {} 2025-09-16 05:32:16
pypath.inputs.go.go_descendants_to_ancestors 
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments.
 {} never
pypath.inputs.go.go_terms_quickgo 2025-09-16 05:32:20 2025-09-16 05:32:24 3.63 dict {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) 3 {} 2025-09-16 05:32:20
pypath.inputs.go.go_terms_goose 2025-09-16 05:32:24 2025-09-16 05:32:24 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/go.py", line 572, in go_terms_goose
    sql_path = os.path.join(common.DATA, 'goose_terms.sql')
                            ^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
{} 2025-09-05 05:18:35
pypath.inputs.go.go_terms_quickgo 2025-09-16 05:32:24 2025-09-16 05:32:27 3.46 dict {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) 3 {} 2025-09-16 05:32:24
pypath.inputs.gpcrdb.gpcrdb_annotations 2025-09-16 05:32:27 2025-09-16 05:32:27 0.24 dict {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) 808 {} 2025-09-16 05:32:27
pypath.inputs.graphviz.graphviz_attrs 2025-09-16 05:32:27 2025-09-16 05:32:29 1.46 tuple ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) 3 {} 2025-09-16 05:32:27
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
 {} never
pypath.inputs.guide2pharma.guide2pharma_download 2025-09-16 05:32:29 2025-09-16 05:32:34 5.65 tuple ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) 2 {} 2025-09-16 05:32:29
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
 {} never
pypath.inputs.gutmgene.gutmgene_annotations 2025-09-16 05:32:34 2025-09-16 05:32:35 0.25 dict {'O95500': {GutmgeneAnnotation(gut_microbiota='Escherichia coli', gut_microbiota_ncbi_id='562', rank='species', strain='EcN, ECOR63', alteration='activation', throughput='low-throughput', associative_mode='causally', sample='T-84 cells,Caco-2 cells', experimental_method='in vitro bacterial culture,c...(truncated) 111 {} 2025-09-16 05:32:34
pypath.inputs.gutmgene.gutmgene_raw 2025-09-16 05:32:35 2025-09-16 05:32:35 0.01 list [GutmgeneRaw(index='72', pmid='31315566', gut_microbiota='Escherichia coli', gut_microbiota_ncbi_id='562', rank='species', strain='EcN, ECOR63', gene='CLDN14', gene_id='23562', alteration='activation', throughput='low-throughput', associative_mode='causally', organism='human', sample='T-84 cells,Cac...(truncated) 243 {} 2025-09-16 05:32:35
pypath.inputs.havugimana.get_havugimana 2025-09-16 05:32:35 2025-09-16 05:32:35 0.19 list [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) 622 {} 2025-09-16 05:32:35
pypath.inputs.havugimana.havugimana_complexes 2025-09-16 05:32:35 2025-09-16 05:32:35 0.03 dict {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) 622 {} 2025-09-16 05:32:35
pypath.inputs.hgnc.hgnc_genegroups 2025-09-16 05:32:35 2025-09-16 05:32:37 1.57 dict {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='Alpha-2-macroglobulin family')}, 'A8K2U0': {HGNCGeneGroupAnnotation(mainclass='Alpha-2...(truncated) 15,683 {} 2025-09-16 05:32:35
pypath.inputs.hint.hint_interactions 2025-09-16 05:32:37 2025-09-16 05:32:42 5.16 list [HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='LC'), HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='HT'), HintInteraction(id_a='A0A024R2I8', id_b='...(truncated) 88,230 {} 2025-09-16 05:32:37
pypath.inputs.hint.hint_raw 2025-09-16 05:32:42 2025-09-16 05:32:42 0.09 list [['A0A024R2I8', 'F1D8Q5', 'NR1A2', 'NR2B1', '15604093:0018:HT:binary|19211732:0018:LC:binary|7746322:0018:LC:binary|9171239:0096:LC:binary|9368056:0096:LC:binary|9415406:0047:LC:binary', '9606', 'True', 'False'], ['A0A024R2I8', 'F1D8Q7', 'NR1A2', 'NR2B3', '15604093:0018:HT:binary', '9606', 'True', '...(truncated) 163,435 {} 2025-09-16 05:32:42
pypath.inputs.hippie.hippie_interactions 2025-09-16 05:32:42 2025-09-16 05:32:53 11.11 list [HippieInteraction(id_a='Q99933', id_b='Q9UNE7', score=0.86, methods=None, references=('11676916', '15538384', '16207813', '20675402', '25036637', '26330542'), sources=None, organisms=None), HippieInteraction(id_a='O43504', id_b='Q9UHA4', score=0.83, methods=None, references=('22980980', '25561175',...(truncated) 102,409 {} 2025-09-16 05:32:42
pypath.inputs.homologene.get_homologene 2025-09-16 05:32:53 2025-09-16 05:34:09 76.21 list ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) 275,237 {} 2025-09-16 05:32:53
pypath.inputs.homologene.homologene_dict 
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments.
 {} never
pypath.inputs.homologene.homologene_uniprot_dict 
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments.
 {} never
pypath.inputs.hpmr.get_hpmr 2025-09-16 05:34:09 2025-09-16 05:34:09 0.00 dict {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) 2 {} 2025-09-16 05:34:09
pypath.inputs.hpmr.hpmr_annotations 2025-09-16 05:34:09 2025-09-16 05:34:09 0.00 dict {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) 1,141 {} 2025-09-16 05:34:09
pypath.inputs.hpmr.hpmr_complexes 2025-09-16 05:34:09 2025-09-16 05:34:09 0.00 dict {} 0 {} 2025-09-16 05:34:09
pypath.inputs.hpmr.hpmr_interactions 2025-09-16 05:34:09 2025-09-16 05:34:09 0.00 list [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) 634 {} 2025-09-16 05:34:09
pypath.inputs.hpo.hpo_annotations 2025-09-16 05:34:09 2025-09-16 05:34:14 4.25 dict {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0001903'), HpoAnnotation(entrez_ge...(truncated) 5,128 {} 2025-09-16 05:34:09
pypath.inputs.hpo.hpo_diseases 2025-09-16 05:34:14 2025-09-16 05:34:19 4.93 dict {'hpo_id': {HpoDisease(omim='database_id', name='disease_name', pmid=None, qualifier='qualifier', evidence='evidence', onset='onset', frequency='frequency', sex='sex', modifier='modifier', aspect='aspect')}, 'HP:0011097': {HpoDisease(omim='OMIM:247200', name='Miller-Dieker lissencephaly syndrome', p...(truncated) 11,421 {} 2025-09-16 05:34:14
pypath.inputs.hpo.hpo_ontology 2025-09-16 05:34:19 2025-09-16 05:34:21 2.12 dict {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) 5 {} 2025-09-16 05:34:19
pypath.inputs.hpo.hpo_terms 2025-09-16 05:34:21 2025-09-16 05:34:22 0.54 dict {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) 19,232 {} 2025-09-16 05:34:21
pypath.inputs.hprd.get_hprd 2025-09-16 05:34:22 2025-09-16 05:34:26 4.18 list [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) 86,981 {} 2025-09-16 05:34:22
pypath.inputs.hprd.hprd_enzyme_substrate 2025-09-16 05:34:26 2025-09-16 05:34:28 1.25 list [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) 4,671 {} 2025-09-16 05:34:26
pypath.inputs.hprd.hprd_interactions 2025-09-16 05:34:28 2025-09-16 05:34:29 1.24 list [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) 4,671 {} 2025-09-16 05:34:28
pypath.inputs.hprd.hprd_interactions_htp 2025-09-16 05:34:29 2025-09-16 05:34:30 1.13 list [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) 39,241 {} 2025-09-16 05:34:29
pypath.inputs.htri.htri_interactions 2025-09-16 05:34:30 2025-09-16 05:35:00 30.34 list [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) 18,630 {} 2025-09-16 05:34:30
pypath.inputs.humancellmap.humancellmap_annotations 2025-09-16 05:35:00 2025-09-16 05:35:10 9.60 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/humancellmap.py", line 43, in humancellmap_annotations
    _ = next(c.result)
        ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
{} 2025-09-09 05:19:42
pypath.inputs.humap.humap1_complexes 2025-09-16 05:35:10 2025-09-16 05:35:10 0.22 dict {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) 4,545 {} 2025-09-16 05:35:10
pypath.inputs.humap.humap2and3_complexes 2025-09-16 05:35:10 2025-09-16 05:35:13 2.29 dict {'COMPLEX:P20963_Q9NWV4_Q9UGQ2': Complex: COMPLEX:P20963_Q9NWV4_Q9UGQ2, 'COMPLEX:O94887_Q9NQ92_Q9NWB1': Complex: COMPLEX:O94887_Q9NQ92_Q9NWB1, 'COMPLEX:Q8N3D4_Q9Y3A4': Complex: COMPLEX:Q8N3D4_Q9Y3A4, 'COMPLEX:O00429_Q5T2D2': Complex: COMPLEX:O00429_Q5T2D2, 'COMPLEX:O95460_P21941_P78540_Q9H267_Q9H9C1...(truncated) 15,433 {} 2025-09-16 05:35:10
pypath.inputs.humsavar.uniprot_variants 2025-09-16 05:35:13 2025-09-16 05:35:15 2.80 dict {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs893184', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2...(truncated) 13,122 {} 2025-09-16 05:35:13
pypath.inputs.huri.hi_i_interactions 2025-09-16 05:35:15 2025-09-16 05:35:18 2.05 list [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 5,652 {} 2025-09-16 05:35:15
pypath.inputs.huri.hi_ii_interactions 2025-09-16 05:35:18 2025-09-16 05:35:26 8.76 list [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='Q8TAB5', uniprot_b='Q96F24', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 46,823 {} 2025-09-16 05:35:18
pypath.inputs.huri.hi_union_interactions 2025-09-16 05:35:26 2025-09-16 05:35:59 32.46 list [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) 227,941 {} 2025-09-16 05:35:26
pypath.inputs.huri.huri_interactions 2025-09-16 05:35:59 2025-09-16 05:36:23 24.42 list [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) 164,682 {} 2025-09-16 05:35:59
pypath.inputs.huri.lit_bm_13_interactions 2025-09-16 05:36:23 2025-09-16 05:36:24 1.07 list [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) 11,045 {} 2025-09-16 05:36:23
pypath.inputs.huri.lit_bm_17_interactions 2025-09-16 05:36:24 2025-09-16 05:36:26 1.55 list [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) 48,796 {} 2025-09-16 05:36:24
pypath.inputs.huri.lit_bm_interactions 2025-09-16 05:36:26 2025-09-16 05:36:27 1.00 list [LitBmInteraction(uniprot_a='P23511', uniprot_b='Q13952'), LitBmInteraction(uniprot_a='P23511', uniprot_b='P25208'), LitBmInteraction(uniprot_a='P43351', uniprot_b='P43351'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q92843'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q07817'), LitBmInte...(truncated) 13,535 {} 2025-09-16 05:36:26
pypath.inputs.huri.rolland_hi_ii_14 2025-09-16 05:36:27 2025-09-16 05:36:28 1.62 list [Rolland2014Interaction(entrez_a='14', entrez_b='6293', genesymbol_a='AAMP', genesymbol_b='VPS52', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='8553', genesymbol_a='AAMP', genesymbol_b='BHLHE40', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='64782', genesymbo...(truncated) 13,944 {} 2025-09-16 05:36:27
pypath.inputs.huri.vidal_hi_iii_old 
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments.
 {} never
pypath.inputs.huri.yang2016_interactions 2025-09-16 05:36:28 2025-09-16 05:36:30 1.27 list [HuriInteraction(uniprot_a='A0A0S2Z436', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriIntera...(truncated) 2,880 {} 2025-09-16 05:36:28
pypath.inputs.huri.yu2011_interactions 2025-09-16 05:36:30 2025-09-16 05:36:32 2.25 list [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) 7,331 {} 2025-09-16 05:36:30
pypath.inputs.i3d.get_i3d 2025-09-16 05:36:32 2025-09-16 05:36:44 11.80 list [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) 22,184 {} 2025-09-16 05:36:32
pypath.inputs.icellnet.icellnet_annotations 2025-09-16 05:36:44 2025-09-16 05:36:44 0.29 dict {Complex: COMPLEX:P01033_P14780: {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None)}, 'P01033': {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None), IcellnetAnnotation(role='ligand', family='Cell adhesion', subfamily=None, classifica...(truncated) 1,194 {} 2025-09-16 05:36:44
pypath.inputs.icellnet.icellnet_complexes 2025-09-16 05:36:44 2025-09-16 05:36:44 0.04 dict {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) 156 {} 2025-09-16 05:36:44
pypath.inputs.icellnet.icellnet_interactions 2025-09-16 05:36:44 2025-09-16 05:36:44 0.03 list [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) 1,647 {} 2025-09-16 05:36:44
pypath.inputs.ielm.get_ielm 
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments.
 {} never
pypath.inputs.ielm.get_ielm_huge 
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments.
 {} never
pypath.inputs.innatedb.innatedb_interactions 2025-09-16 05:36:44 2025-09-16 05:36:46 1.97 list [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) 19,036 {} 2025-09-16 05:36:44
pypath.inputs.instruct.get_instruct 2025-09-16 05:36:46 2025-09-16 05:36:47 0.52 list [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) 11,470 {} 2025-09-16 05:36:46
pypath.inputs.instruct.get_instruct_offsets 2025-09-16 05:36:47 2025-09-16 05:36:47 0.63 NoneType None 0 {} 2025-09-16 05:36:47
pypath.inputs.intact.intact_interactions 2025-09-16 05:36:47 2025-09-16 05:39:21 153.33 list [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', i...(truncated) 78,544 {} 2025-09-16 05:36:47
pypath.inputs.integrins.get_integrins 2025-09-16 05:39:21 2025-09-16 05:39:22 0.57 set {'Q13349', 'P53708', 'Q13797', 'P16144', 'P23229', 'P26010', 'P05556', 'P05107', 'P08648', 'P20702', 'P20701', 'P26006', 'P11215', 'P26012', 'P18564', 'P38570', 'P18084', 'P05106', 'P17301', 'Q9UKX5', 'P08514', 'O75578', 'P06756', 'Q13683', 'P56199'} 25 {} 2025-09-16 05:39:21
pypath.inputs.interpro.interpro2go_annotations 2025-09-16 05:39:22 2025-09-16 05:39:24 2.07 defaultdict defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid receptor activity'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0008270', go_term_name='zinc ion binding'), Int...(truncated) 14,743 {} 2025-09-16 05:39:22
pypath.inputs.interpro.interpro_annotations 2025-09-16 05:39:24 2025-09-16 05:39:24 0.38 defaultdict defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR003609', organism='9606', start='37', end='123'), InterproAnnotation(interpro_id='IPR038178', organism='9606', start='127', end='208'), InterproAnnotation(interpro_id='IPR018056', organism='9606', start='176', end='189'), Inte...(truncated) 16,611 {} 2025-09-16 05:39:24
pypath.inputs.interpro.interpro_entries 2025-09-16 05:39:24 2025-09-16 05:39:36 11.65 list [InterproEntry(interpro_id='IPR000001', protein_count='20781', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) 48,679 {} 2025-09-16 05:39:24
pypath.inputs.interpro.interpro_xrefs 
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments.
 {} never
pypath.inputs.intogen.intogen_annotations 2025-09-16 05:39:36 2025-09-16 05:39:37 0.99 dict {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) 483 {} 2025-09-16 05:39:36
pypath.inputs.ipi.ipi_uniprot 2025-09-16 05:39:37 2025-09-16 05:39:37 0.08 dict {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) 86,754 {} 2025-09-16 05:39:37
pypath.inputs.iptmnet.iptmnet_interactions 2025-09-16 05:39:37 2025-09-16 05:39:58 20.55 list [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', ...(truncated) 15,834 {} 2025-09-16 05:39:37
pypath.inputs.italk.italk_annotations 2025-09-16 05:39:58 2025-09-16 05:39:58 0.75 dict {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='growth factor'), ItalkAnnotation(mainclass='receptor', subclass='other')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) 1,414 {} 2025-09-16 05:39:58
pypath.inputs.italk.italk_interactions 2025-09-16 05:39:58 2025-09-16 05:39:58 0.02 list [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) 2,706 {} 2025-09-16 05:39:58
pypath.inputs.italk.italk_raw 2025-09-16 05:39:58 2025-09-16 05:39:58 0.01 DataFrame Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) 2,649 {} 2025-09-16 05:39:58
pypath.inputs.kea.kea_enzyme_substrate 2025-09-16 05:39:58 2025-09-16 05:40:00 1.88 list [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) 35,224 {} 2025-09-16 05:39:58
pypath.inputs.kea.kea_interactions 2025-09-16 05:40:00 2025-09-16 05:40:00 0.15 list [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) 35,224 {} 2025-09-16 05:40:00
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
 {} never
pypath.inputs.kegg.kegg_interactions 2025-09-16 05:40:01 2025-09-16 05:54:29 868.14 list [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) 14,739 {} 2025-09-16 05:40:01
pypath.inputs.kegg.kegg_medicus 2025-09-16 05:54:29 2025-09-16 05:54:56 27.03 set {KeggMedicusRawInteraction(id_a='K21660', id_b='578', name_a='(vBCL2) vBCL2; KSHV apoptosis regulator BCL2 homolog', name_b='BAK1', effect='inhibition', itype='post_translational', pw_type='pathogen', type_a='perturbant', type_b='gene', network_id='N00164'), KeggMedicusRawInteraction(id_a='4067', i...(truncated) 12,946 {} 2025-09-16 05:54:29
pypath.inputs.kegg.kegg_medicus_complexes 2025-09-16 05:54:56 2025-09-16 05:54:56 0.47 dict {'COMPLEX:A8MT69_Q8IYD8_Q8N2Z9_Q92547_Q9BTP7': Complex: COMPLEX:A8MT69_Q8IYD8_Q8N2Z9_Q92547_Q9BTP7, 'COMPLEX:P36896_Q13705': Complex: COMPLEX:P36896_Q13705, 'COMPLEX:O15488_P13807': Complex: COMPLEX:O15488_P13807, 'COMPLEX:Q12933_Q15628': Complex: COMPLEX:Q12933_Q15628, 'COMPLEX:P54274_Q15554_Q96AP0...(truncated) 528 {} 2025-09-16 05:54:56
pypath.inputs.kegg.kegg_medicus_interactions 2025-09-16 05:54:56 2025-09-16 05:54:57 0.37 list [KeggMedicusInteraction(id_a='P07948', id_b='P42336', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P0DP24', id_b='P48454', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) 9,538 {} 2025-09-16 05:54:56
pypath.inputs.kegg.kegg_pathway_annotations 2025-09-16 05:54:57 2025-09-16 05:55:10 13.27 dict {'Q9NYJ8': {KeggPathway(pathway='Toll-like receptor signaling pathway'), KeggPathway(pathway='MAPK signaling pathway')}, 'Q9Y3M2': {KeggPathway(pathway='Parathyroid hormone synthesis, secretion and action'), KeggPathway(pathway='Chemokine signaling pathway'), KeggPathway(pathway='Chemical carcinogen...(truncated) 2,672 {} 2025-09-16 05:54:57
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2025-09-16 05:55:10 2025-09-16 05:55:10 0.36 dict {'A8K7J7': {KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathwa...(truncated) 813 {} 2025-09-16 05:55:10
pypath.inputs.kegg.kegg_pathways 2025-09-16 05:55:10 2025-09-16 05:55:23 13.06 tuple ({'MAPK signaling pathway': {'Q9NYJ8', 'Q9Y3M2', 'Q9NYB0', 'P17535', 'P45985', 'P19838', 'Q96NL6', 'P21359', 'P16949', 'P35813', 'P15056', 'P22736', 'Q15750', 'O43318', 'O95257', 'P17980', 'Q16584', 'P62834', 'Q9BQ95', 'P15976', 'Q12933', 'O15111', 'P07333', 'O75676', 'P32248', 'P28482', 'O95819', '...(truncated) 2 {} 2025-09-16 05:55:10
pypath.inputs.kegg_api. 
Not calling `pypath.inputs.kegg_api.`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_drug 
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_gene 
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_pathway 
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_disease 
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_drug 2025-09-16 05:55:23 2025-09-16 05:55:27 3.73 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
    entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
                         ^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
    self.load(*args)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
    self._data = {
                 ^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
    self.proc_key(entry[0]): self.proc_value(entry[1])
    ^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
    return entry[0].split(':')[1]
           ~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
{} 2025-09-05 05:41:41
pypath.inputs.kegg_api.drug_to_gene 
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_pathway 
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_disease 
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_drug 
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_pathway 
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_drug_to_chebi 
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid 
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_gene_to_uniprot 
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_disease 
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_drug 
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_gene 
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments.
 {} never
pypath.inputs.kinasedotcom.kinasedotcom_annotations 2025-09-16 05:55:27 2025-09-16 05:55:28 0.45 dict {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) 503 {} 2025-09-16 05:55:27
pypath.inputs.kirouac2010.kirouac2010_interactions 2025-09-16 05:55:28 2025-09-16 05:55:28 0.16 list [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) 267 {} 2025-09-16 05:55:28
pypath.inputs.lambert2018.lambert2018_annotations 2025-09-16 05:55:28 2025-09-16 05:55:31 2.80 dict {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) 2,760 {} 2025-09-16 05:55:28
pypath.inputs.lambert2018.lambert2018_s1_raw 2025-09-16 05:55:31 2025-09-16 05:55:33 2.81 list [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) 2,765 {} 2025-09-16 05:55:31
pypath.inputs.laudanna.laudanna_directions 2025-09-16 05:55:33 2025-09-16 05:55:34 0.43 list [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) 77,555 {} 2025-09-16 05:55:33
pypath.inputs.laudanna.laudanna_effects 2025-09-16 05:55:34 2025-09-16 05:55:34 0.36 list [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) 63,438 {} 2025-09-16 05:55:34
pypath.inputs.li2012.get_li2012 2025-09-16 05:55:34 2025-09-16 05:55:35 0.81 list [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) 583 {} 2025-09-16 05:55:34
pypath.inputs.li2012.li2012_dmi 2025-09-16 05:55:35 2025-09-16 05:55:47 12.03 list [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) 593 {} 2025-09-16 05:55:35
pypath.inputs.li2012.li2012_enzyme_substrate 2025-09-16 05:55:47 2025-09-16 05:55:47 0.02 list [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) 349 {} 2025-09-16 05:55:47
pypath.inputs.li2012.li2012_interactions 2025-09-16 05:55:47 2025-09-16 05:55:47 0.02 list [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) 503 {} 2025-09-16 05:55:47
pypath.inputs.lincs.lincs_compounds 2025-09-16 05:55:47 2025-09-16 05:55:49 1.36 dict {'SciTegic09271913552D': LincsCompound(lincs=None, chembl=None, chebi=None, inchi='InChI=1S/C29H24N4O4S/c1-4-27(34)31-26-16-23(12-5-18(26)2)33-28(35)14-9-21-17-30-25-13-8-20(15-24(25)29(21)33)19-6-10-22(11-7-19)32-38(3,36)37/h4-17,32H,1H2,2-3H3,(H,31,34)', inchi_key='SFMJNHNUOVADRW-UHFFFAOYSA-N', sm...(truncated) 371 {} 2025-09-16 05:55:47
pypath.inputs.lmpid.lmpid_dmi 2025-09-16 05:55:49 2025-09-16 05:55:49 0.69 list [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) 1,170 {} 2025-09-16 05:55:49
pypath.inputs.lmpid.lmpid_interactions 2025-09-16 05:55:49 2025-09-16 05:55:50 0.46 list [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) 1,170 {} 2025-09-16 05:55:49
pypath.inputs.lmpid.load_lmpid 2025-09-16 05:55:50 2025-09-16 05:55:50 0.45 list [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) 1,170 {} 2025-09-16 05:55:50
pypath.inputs.lncdisease.lncdisease_interactions 2025-09-16 05:55:50 2025-09-16 05:55:51 0.44 list [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) 478 {} 2025-09-16 05:55:50
pypath.inputs.lncrnadb.lncrnadb_interactions 2025-09-16 05:55:51 2025-09-16 05:55:51 0.38 list [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism=5888, pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism=9468, pmid='17175535'), LncrnadbInteraction(lncrna='G22', partner='SRP9', type='protein', o...(truncated) 773 {} 2025-09-16 05:55:51
pypath.inputs.locate.locate_localizations 2025-09-16 05:55:51 2025-09-16 05:56:27 36.26 dict {'P27824': {LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='lysosomes', cls='typeI', pmid=None, score=None), Loc...(truncated) 9,479 {} 2025-09-16 05:55:51
pypath.inputs.lrdb.lrdb_annotations 2025-09-16 05:56:27 2025-09-16 05:56:28 0.42 dict {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD'), references=('12212791', '75')), LrdbAnnotation(role='receptor', cell_type=None, sources=(...(truncated) 1,536 {} 2025-09-16 05:56:27
pypath.inputs.lrdb.lrdb_interactions 2025-09-16 05:56:28 2025-09-16 05:56:28 0.57 list [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) 3,251 {} 2025-09-16 05:56:28
pypath.inputs.macrophage.macrophage_interactions 2025-09-16 05:56:28 2025-09-16 05:56:28 0.24 list [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) 4,516 {} 2025-09-16 05:56:28
pypath.inputs.matrisome.matrisome_annotations 2025-09-16 05:56:28 2025-09-16 05:56:29 0.30 dict {'D3YTG3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C4S3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C5S3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 2,501 {} 2025-09-16 05:56:28
pypath.inputs.matrixdb.matrixdb_annotations 2025-09-16 05:56:29 2025-09-16 05:56:30 0.78 dict {} 0 {} 2025-09-16 05:56:29
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2025-09-16 05:56:30 2025-09-16 05:56:31 1.44 set {'O60565', 'P80162', 'P12034', 'P12724', 'Q8IUH2', 'P24347', 'Q9Y5X9', 'P00441', 'Q92982', 'Q8WWQ2', 'P60709', 'P05413', 'Q9Y2Y6', 'P0CJ72', 'Q6UDR6', 'O14727', 'Q9Y5I3', 'Q8TAV5', 'P0DPK4', 'Q92673', 'Q8TCZ2', 'Q9HC23', 'Q9Y5I2', 'Q5R387', 'Q16819', 'Q17RR3', 'P11226', 'Q9GZN4', 'Q8N729', 'P10323',...(truncated) 2,840 {} 2025-09-16 05:56:30
pypath.inputs.matrixdb.matrixdb_interactions 2025-09-16 05:56:31 2025-09-16 05:56:31 0.12 list [MatrixdbInteraction(id_a='"chebi:""CHEBI:29105"""', id_b='uniprotkb:P05067', alt_ids_a='matrixdb:CAT_1', alt_ids_b='-', aliases_a='matrixdb:Zinc(short label)', aliases_b='"uniprotkb:""APP""(gene name)"', detection_method='"psi-mi:""MI:0004""(""affinity chromatography technology"")"', author='Bush A...(truncated) 1,264 {} 2025-09-16 05:56:31
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2025-09-16 05:56:31 2025-09-16 05:56:31 0.07 set set() 0 {} 2025-09-16 05:56:31
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2025-09-16 05:56:31 2025-09-16 05:56:31 0.06 set set() 0 {} 2025-09-16 05:56:31
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2025-09-16 05:56:31 2025-09-16 05:56:32 1.17 set {'Q9BYD3', 'P16144', 'Q6MZM7', 'Q9Y624', 'Q9HBB8', 'Q08174', 'Q86SJ6', 'P05107', 'Q9NZ94', 'Q6MZK0', 'Q9HDB5', 'Q14956', 'O60759', 'O75144', 'Q9BRX2', 'Q0VAE8', 'Q9NY15', 'Q8N726', 'Q86WK7', 'Q05084', 'O95297', 'Q12860', 'Q9BX67', 'P34741', 'Q15223', 'P18827', 'Q13895', 'O95500', 'Q96FX9', 'Q13308',...(truncated) 112 {} 2025-09-16 05:56:31
pypath.inputs.membranome.membranome_annotations 2025-09-16 05:56:32 2025-09-16 05:56:57 24.59 list [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) 2,419 {} 2025-09-16 05:56:32
pypath.inputs.mimp.get_kinase_class 2025-09-16 05:56:57 2025-09-16 05:56:57 0.13 dict {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) 4 {} 2025-09-16 05:56:57
pypath.inputs.mimp.mimp_enzyme_substrate 2025-09-16 05:56:57 2025-09-16 05:57:01 3.57 list [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) 17,030 {} 2025-09-16 05:56:57
pypath.inputs.mimp.mimp_interactions 2025-09-16 05:57:01 2025-09-16 05:57:01 0.19 list [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) 17,030 {} 2025-09-16 05:57:01
pypath.inputs.mir2disease.mir2disease_interactions 2025-09-16 05:57:01 2025-09-16 05:57:01 0.15 list [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) 805 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_ids 2025-09-16 05:57:01 2025-09-16 05:57:01 0.18 list [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) 2,925 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_mature 2025-09-16 05:57:01 2025-09-16 05:57:01 0.02 list [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0004481', 'hsa-let-7a-3p'), ('MIMAT0004481', 'hsa-let-7a*'), ('MIMAT0010195', 'hsa-let-7a-2-3p'), ('MIMAT0010195', 'hsa-let-7a-2*'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0004482', 'hsa-let...(truncated) 3,299 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_mature_all 2025-09-16 05:57:01 2025-09-16 05:57:01 0.02 list ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) 2,693 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_mirna 2025-09-16 05:57:01 2025-09-16 05:57:01 0.03 list [['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3&#x27; untr...(truncated) 39,233 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_mirna_mature 2025-09-16 05:57:01 2025-09-16 05:57:01 0.02 list [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) 49,168 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_mirna_pre_mature 2025-09-16 05:57:01 2025-09-16 05:57:02 0.12 list [(['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3&#x27; unt...(truncated) 53,320 {} 2025-09-16 05:57:01
pypath.inputs.mirbase.mirbase_organisms 2025-09-16 05:57:02 2025-09-16 05:59:03 121.21 dict {400682: 'aqu', 45351: 'nve', 6085: 'hma', 10224: 'sko', 7668: 'spu', 7719: 'cin', 51511: 'csa', 34765: 'odi', 7739: 'bfl', 8355: 'xla', 8364: 'xtr', 9031: 'gga', 9615: 'cfa', 13616: 'mdo', 9509: 'age', 9519: 'lla', 78454: 'sla', 9544: 'mml', 9545: 'mne', 61621: 'pbi', 9593: 'ggo', 9606: 'hsa', 9597...(truncated) 285 {} 2025-09-16 05:57:02
pypath.inputs.mirbase.mirbase_precursor 2025-09-16 05:59:03 2025-09-16 05:59:03 0.03 list [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) 2,130 {} 2025-09-16 05:59:03
pypath.inputs.mirbase.mirbase_precursor_all 2025-09-16 05:59:03 2025-09-16 05:59:03 0.03 list ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', 'MI0000081', 'MI0000082', ...(truncated) 1,984 {} 2025-09-16 05:59:03
pypath.inputs.mirbase.mirbase_precursor_to_mature 2025-09-16 05:59:03 2025-09-16 05:59:03 0.08 list [('hsa-let-7a-1', 'hsa-let-7a-5p'), ('hsa-let-7a-1', 'hsa-let-7a'), ('hsa-let-7a-1L', 'hsa-let-7a-5p'), ('hsa-let-7a-1L', 'hsa-let-7a'), ('hsa-let-7a-1', 'hsa-let-7a-3p'), ('hsa-let-7a-1', 'hsa-let-7a*'), ('hsa-let-7a-1L', 'hsa-let-7a-3p'), ('hsa-let-7a-1L', 'hsa-let-7a*'), ('hsa-let-7a-2', 'hsa-let...(truncated) 4,071 {} 2025-09-16 05:59:03
pypath.inputs.mirbase.mirbase_taxid 2025-09-16 05:59:03 2025-09-16 05:59:03 0.00 str 'hsa' 3 {} 2025-09-16 05:59:03
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2025-09-16 05:59:03 2025-09-16 05:59:03 0.16 list [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) 462 {} 2025-09-16 05:59:03
pypath.inputs.mirecords.mirecords_interactions 2025-09-16 05:59:03 2025-09-16 05:59:04 0.96 list [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism=9606, target_organism=9606, pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organism=10090, target_or...(truncated) 3,106 {} 2025-09-16 05:59:03
pypath.inputs.mirtarbase.mirtarbase_interactions 2025-09-16 05:59:04 2025-09-16 06:05:16 371.95 list [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=10090, target_genesymbol='Cd320', target_entrez='54219', target_organism=10090, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', data...(truncated) 27,595 {} 2025-09-16 05:59:04
pypath.inputs.mitab.mitab_field_list 
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_field_uniprot 
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments.
 {} never
pypath.inputs.mppi.mppi_interactions 2025-09-16 06:05:16 2025-09-16 06:05:16 0.25 list [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) 777 {} 2025-09-16 06:05:16
pypath.inputs.msigdb.msigdb_annotations 2025-09-16 06:05:16 2025-09-16 06:05:50 34.06 dict {'P10176': {MsigdbAnnotation(collection='tf_targets_legacy', geneset='TGACCTY_ERR1_Q2'), MsigdbAnnotation(collection='cancer_modules', geneset='MODULE_307'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE27786_CD4_TCELL_VS_NEUTROPHIL_DN'), MsigdbAnnotation(collection='cell_type_signatures',...(truncated) 20,111 {} 2025-09-16 06:05:16
pypath.inputs.msigdb.msigdb_download 2025-09-16 06:05:52 2025-09-16 06:05:58 5.81 dict {'MT': {'MT-TR', 'MT-ND4', 'MT-TY', 'MT-ND4L', 'MT-TI', 'MT-TL1', 'MT-ND2', 'MT-CYB', 'MT-ND3', 'MT-TA', 'MT-TF', 'MT-TH', 'MT-TM', 'MT-RNR2', 'MT-ND1', 'MT-TL2', 'MT-TS1', 'MT-TW', 'MT-TN', 'MT-TT', 'MT-RNR1', 'MT-TP', 'MT-TS2', 'MT-CO2', 'MT-TK', 'MT-ATP8', 'MT-ND6', 'MT-TG', 'MT-CO1', 'MT-TC', 'M...(truncated) 35,134 {} 2025-09-16 06:05:52
pypath.inputs.msigdb.msigdb_download_collections 2025-09-16 06:05:58 2025-09-16 06:05:59 0.45 dict {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'ENPP2', 'CAVIN1', 'MIGA2', 'RREB1', 'SNCG', 'REEP5', 'SUCLG1', 'ATP5PO', 'UCP2', 'MTCH2', 'ARL4A', 'CIDEA', 'PFKL', 'UBC', 'ACLY', 'IMMT', 'LIFR', 'SLC5A6', 'NKIRAS1', 'LPL', 'ATP1B3', 'CYC1', 'LEP', 'GADD45A', 'MCCC1', 'SCARB1', 'ANGPT1', 'SPARCL1...(truncated) 20 {} 2025-09-16 06:05:58
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2025-09-16 06:05:59 2025-09-16 06:05:59 0.40 list [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) 7,305 {} 2025-09-16 06:05:59
pypath.inputs.negatome.negatome_interactions 2025-09-16 06:05:59 2025-09-16 06:05:59 0.15 list [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) 2,171 {} 2025-09-16 06:05:59
pypath.inputs.netbiol.arn_interactions 2025-09-16 06:05:59 2025-09-16 06:06:00 0.11 list [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) 95 {} 2025-09-16 06:05:59
pypath.inputs.netbiol.nrf2ome_interactions 2025-09-16 06:06:00 2025-09-16 06:06:00 0.12 list [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) 109 {} 2025-09-16 06:06:00
pypath.inputs.netpath.netpath_interactions 2025-09-16 06:06:00 2025-09-16 06:06:02 2.04 list [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) 7,555 {} 2025-09-16 06:06:00
pypath.inputs.netpath.netpath_names 2025-09-16 06:06:02 2025-09-16 06:06:02 0.01 dict {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) 35 {} 2025-09-16 06:06:02
pypath.inputs.netpath.netpath_pathway_annotations 2025-09-16 06:06:02 2025-09-16 06:06:02 0.13 dict {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Alpha6 Beta4 Integ...(truncated) 1,870 {} 2025-09-16 06:06:02
pypath.inputs.offsides.offsides_side_effects 2025-09-16 06:06:02 2025-09-16 06:06:27 24.97 list [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) 3,206,558 {} 2025-09-16 06:06:02
pypath.inputs.oma.oma_orthologs 2025-09-16 06:06:27 2025-09-16 06:08:17 109.94 list [OmaOrthology(a=OmaGene(id='MILR1_HUMAN', oma_group=1075509, hog='HOG:E0732066', taxon=9606, chr='17', start=64449169, end=64467617, strand=1, main_isoform=True), b=OmaGene(id='MILR1_MOUSE', oma_group=1100017, hog='HOG:E0719661.1b', taxon=10090, chr='11', start=106642110, end=106657831, strand=1, ma...(truncated) 22,374 {} 2025-09-16 06:06:27
pypath.inputs.oma.oma_table 2025-09-16 06:08:17 2025-09-16 06:08:25 8.28 defaultdict defaultdict(<class 'set'>, {'MILR1_HUMAN': {'MILR1_MOUSE'}, 'SYT1_HUMAN': {'SYT1_MOUSE'}, 'NDUB1_HUMAN': {'NDUB1_MOUSE'}, 'TVAM2_HUMAN': {'A0A075B654', 'A0A075B622', 'Q5R1F6', 'A0A075B642', 'Q5R1I8', 'A0A075B6D8', 'A0A075B614', 'A0A075B652', 'A0A075B5Z7'}, 'H4_HUMAN': {'H4_MOUSE'}, 'NPY1R_HUMAN': {'...(truncated) 17,895 {} 2025-09-16 06:08:17
pypath.inputs.ontology.listof_ontologies 2025-09-16 06:08:25 2025-09-16 06:08:26 0.44 dict {'ado': "Alzheimer's Disease Ontology (ADO)", 'afpo': 'African Population Ontology', 'agro': 'Agronomy Ontology', 'aism': 'Ontology for the Anatomy of the Insect SkeletoMuscular system', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'apo': 'Ascomycete Phenotype Ontology (APO)', 'apo...(truncated) 274 {} 2025-09-16 06:08:25
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
 {} never
pypath.inputs.opentargets.opentargets_adverse_reactions 2025-09-16 06:08:26 2025-09-16 06:08:52 26.37 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/opentargets.py", line 131, in _opentargets_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-09-15 05:38:37
pypath.inputs.opentargets.opentargets_baseline_expression 2025-09-16 06:08:52 2025-09-16 06:08:54 2.08 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/opentargets.py", line 124, in _opentargets_general
    json_files = repart.findall(c.result)
                 ^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: expected string or bytes-like object, got 'NoneType'
{'broke': True} 2025-09-15 05:38:57
pypath.inputs.opentargets.opentargets_direct_score 2025-09-16 06:08:54 2025-09-16 06:12:30 215.98 list [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) 2,146,271 {} 2025-09-16 06:08:54
pypath.inputs.opentargets.opentargets_general 
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments.
 {} never
pypath.inputs.opentargets.opentargets_indirect_score 2025-09-16 06:12:30 2025-09-16 06:15:32 182.16 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/opentargets.py", line 131, in _opentargets_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-09-15 05:43:21
pypath.inputs.opm.opm_annotations 2025-09-16 06:15:32 2025-09-16 06:15:51 18.32 dict {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) 88 {} 2025-09-16 06:15:32
pypath.inputs.oreganno.oreganno_interactions 2025-09-16 06:15:51 2025-09-16 06:16:22 31.56 list [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) 5,903 {} 2025-09-16 06:15:51
pypath.inputs.oreganno.oreganno_raw 2025-09-16 06:16:22 2025-09-16 06:16:26 3.97 list [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) 2,219,572 {} 2025-09-16 06:16:22
pypath.inputs.panglaodb.panglaodb_annotations 2025-09-16 06:16:26 2025-09-16 06:16:29 3.20 defaultdict defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=False, cell_type='Enterocytes', organ='GI tract', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=0.0, mouse_sensitivity=0.00331126, human_specificity=0.00439422, mouse_specifici...(truncated) 4,492 {} 2025-09-16 06:16:26
pypath.inputs.panglaodb.panglaodb_raw 2025-09-16 06:16:29 2025-09-16 06:16:29 0.04 list [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) 8,286 {} 2025-09-16 06:16:29
pypath.inputs.pathophenodb.disease_pathogen_interactions 2025-09-16 06:16:29 2025-09-16 06:16:29 0.00 list [] 0 {} 2025-09-16 06:16:29
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons.pathwaycommons_interactions 2025-09-16 06:16:29 2025-09-16 06:16:55 25.85 list [PathwayCommonsInteraction(id_a='A1BG', interaction_type='controls-expression-of', id_b='A2M', resource='pid'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b=...(truncated) 2,524,906 {} 2025-09-16 06:16:29
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pazar.pazar_interactions 2025-09-16 06:16:57 2025-09-16 06:16:57 0.25 list [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) 16,386 {} 2025-09-16 06:16:57
pypath.inputs.pdb.pdb_chains 2025-09-16 06:16:57 2025-09-16 06:17:04 6.63 tuple ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) 2 {} 2025-09-16 06:16:57
pypath.inputs.pdb.pdb_complexes 2025-09-16 06:17:07 2025-09-16 06:17:15 8.43 dict {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) 49,170 {} 2025-09-16 06:17:07
pypath.inputs.pdb.pdb_uniprot 2025-09-16 06:17:15 2025-09-16 06:17:24 8.47 tuple ({'P02185': {('1mln', 'X-ray', 2.0), ('8xbj', 'X-ray', 1.55), ('1lue', 'X-ray', 1.7), ('2zso', 'X-ray', 1.21), ('1bz6', 'X-ray', 1.2), ('8eko', 'X-ray', 1.34), ('5oja', 'X-ray', 1.35), ('5ojb', 'X-ray', 1.54), ('1myz', 'X-ray', 1.6), ('1cp0', 'X-ray', 2.0), ('6mv0', 'X-ray', 1.97), ('1ltw', 'X-ray',...(truncated) 2 {} 2025-09-16 06:17:15
pypath.inputs.pdzbase.pdzbase_interactions 2025-09-16 06:17:24 2025-09-16 06:17:25 1.11 list [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) 339 {} 2025-09-16 06:17:24
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
 {} never
pypath.inputs.pepcyber.pepcyber_interactions 2025-09-16 06:17:25 2025-09-16 06:28:19 653.59 list [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) 5,590 {} 2025-09-16 06:17:25
pypath.inputs.pfam.pfam_names 2025-09-16 06:28:19 2025-09-16 06:28:20 1.17 tuple ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) 2 {} 2025-09-16 06:28:19
pypath.inputs.pfam.pfam_pdb 2025-09-16 06:28:20 2025-09-16 06:28:24 4.12 tuple ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) 2 {} 2025-09-16 06:28:20
pypath.inputs.pfam.pfam_regions 2025-09-16 06:28:25 2025-09-16 06:37:28 543.01 tuple ({}, {}) 2 {} 2025-09-16 06:28:25
pypath.inputs.pfam.pfam_uniprot 2025-09-16 06:37:28 2025-09-16 06:52:53 925.35 tuple ({}, {}) 2 {} 2025-09-16 06:37:28
pypath.inputs.pharos.pharos_diseases 2025-09-16 06:52:53 2025-09-16 07:03:08 614.11 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 06:52:53
pypath.inputs.pharos.pharos_expression 2025-09-16 07:03:08 2025-09-16 07:03:12 3.67 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 07:03:08
pypath.inputs.pharos.pharos_general 
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments.
 {} never
pypath.inputs.pharos.pharos_gtex 2025-09-16 07:03:13 2025-09-16 07:03:16 3.33 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 07:03:13
pypath.inputs.pharos.pharos_ligands 2025-09-16 07:03:17 2025-09-16 07:03:20 2.90 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 07:03:17
pypath.inputs.pharos.pharos_orthologs 2025-09-16 07:03:21 2025-09-16 07:03:24 3.32 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 07:03:21
pypath.inputs.pharos.pharos_targets 2025-09-16 07:03:25 2025-09-16 07:08:48 323.03 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) 20,412 {} 2025-09-16 07:03:25
pypath.inputs.pharos.pharos_xrefs 2025-09-16 07:08:48 2025-09-16 07:08:52 3.22 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2025-09-16 07:08:48
pypath.inputs.phobius.phobius_annotations 2025-09-16 07:08:52 2025-09-16 07:08:53 0.42 dict {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) 20,350 {} 2025-09-16 07:08:52
pypath.inputs.phosphatome.phosphatome_annotations 2025-09-16 07:08:53 2025-09-16 07:08:57 4.29 dict {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) 264 {} 2025-09-16 07:08:53
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2025-09-16 07:08:57 2025-09-16 07:09:06 9.05 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
    n for d, n in iteritems(data)
                  ^^^^^^^^^^^^^^^
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-HmNuT9VC-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
    func = obj.items
           ^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
{} 2025-09-14 06:47:54
pypath.inputs.phosphoelm.phosphoelm_interactions 2025-09-16 07:09:06 2025-09-16 07:09:15 9.01 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/phosphoelm.py", line 101, in phosphoelm_interactions
    data = phosphoelm_enzyme_substrate(ltp_only = True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
    n for d, n in iteritems(data)
                  ^^^^^^^^^^^^^^^
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-HmNuT9VC-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
    func = obj.items
           ^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
{} 2025-09-14 06:47:56
pypath.inputs.phosphoelm.phosphoelm_kinases 2025-09-16 07:09:15 2025-09-16 07:09:24 9.02 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/phosphoelm.py", line 121, in phosphoelm_kinases
    soup = bs4.BeautifulSoup(data, 'html.parser')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-HmNuT9VC-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
    raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
{} 2025-09-14 06:47:56
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2025-09-16 07:09:24 2025-09-16 07:09:26 1.98 list [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) 4,417 {} 2025-09-16 07:09:24
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2025-09-16 07:09:26 2025-09-16 07:09:26 0.02 list [['CDK7', 'CRY1'], ['MAPK1', 'TSC2'], ['RPS6KA5', 'CAMKK1'], ['CDK4', 'NCL'], ['ILK', 'PPP1R14B'], ['BUB1', 'PPP2R5D'], ['MAPK8', 'RPA1'], ['PRKACA', 'EIF4ENIF1'], ['MAPK9', 'SOX10'], ['TESK2', 'TRIM24'], ['BTK', 'RAD51'], ['PDPK1', 'PDLIM5'], ['NEK2', 'ZYX'], ['RAF1', 'EIF4H'], ['PIM1', 'EIF4B'], [...(truncated) 1,821 {} 2025-09-16 07:09:26
pypath.inputs.phosphopoint.phosphopoint_directions 2025-09-16 07:09:26 2025-09-16 07:09:26 0.22 list [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) 9,269 {} 2025-09-16 07:09:26
pypath.inputs.phosphopoint.phosphopoint_interactions 2025-09-16 07:09:26 2025-09-16 07:09:26 0.01 list [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) 9,269 {} 2025-09-16 07:09:26
pypath.inputs.phosphosite.phosphosite_directions 2025-09-16 07:09:27 2025-09-16 07:09:27 0.01 list [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) 9,094 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2025-09-16 07:09:27 2025-09-16 07:09:27 0.32 list [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) 13,459 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_interactions 2025-09-16 07:09:27 2025-09-16 07:09:27 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) 2 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_interactions_all 2025-09-16 07:09:27 2025-09-16 07:09:27 0.01 list [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) 9,164 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_interactions_curated 2025-09-16 07:09:27 2025-09-16 07:09:27 0.00 list [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) 4,374 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_interactions_new 2025-09-16 07:09:27 2025-09-16 07:09:27 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) 2 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_interactions_noref 2025-09-16 07:09:27 2025-09-16 07:09:27 0.00 list [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) 4,790 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2025-09-16 07:09:27 2025-09-16 07:09:32 5.13 dict {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) 198,635 {} 2025-09-16 07:09:27
pypath.inputs.phosphosite.phosphosite_ptms 2025-09-16 07:09:33 2025-09-16 07:09:46 13.20 list [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) 239,789 {} 2025-09-16 07:09:33
pypath.inputs.phosphosite.phosphosite_regsites 2025-09-16 07:09:46 2025-09-16 07:09:47 0.49 dict {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'protein degradation', 'phosphorylation', 'intracellular localization'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) 5,435 {} 2025-09-16 07:09:46
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2025-09-16 07:09:47 2025-09-16 07:10:55 68.13 dict {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'28052875', '21148409', '21209006', '24876223'}, 'isoforms': {1}, 'process': {''}, 'function': {'ubiquitination', 'protein degradation', 'phosphorylation', 'intracellular localization', 'protein stabilization'}...(truncated) 3,621 {} 2025-09-16 07:09:47
pypath.inputs.phosphosite.regsites_tab 
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_bonds 
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_interfaces 
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments.
 {} never
pypath.inputs.pro.get_pro 2025-09-16 07:10:55 2025-09-16 07:11:28 33.24 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> 0 {} 2025-09-16 07:10:55
pypath.inputs.pro.pro_mapping 2025-09-16 07:11:28 2025-09-16 07:11:29 0.47 list [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) 394,059 {} 2025-09-16 07:11:28
pypath.inputs.progeny.progeny_annotations 2025-09-16 07:11:29 2025-09-16 07:12:36 66.94 dict {'P35250': {ProgenyAnnotation(pathway='Estrogen', weight=2.40982404059, p_value=0.0238138596584), ProgenyAnnotation(pathway='EGFR', weight=1.4706466171905381, p_value=0.0016552751715941223), ProgenyAnnotation(pathway='MAPK', weight=2.277341180050157, p_value=3.324844332731664e-11), ProgenyAnnotation...(truncated) 18,582 {} 2025-09-16 07:11:29
pypath.inputs.progeny.progeny_raw 2025-09-16 07:12:36 2025-09-16 07:13:44 68.35 DataFrame gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) 274,143 {} 2025-09-16 07:12:36
pypath.inputs.proteinatlas.get_proteinatlas 2025-09-16 07:13:44 2025-09-16 07:13:50 5.04 dict {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) 2 {} 2025-09-16 07:13:44
pypath.inputs.proteinatlas.proteinatlas_annotations 2025-09-16 07:13:51 2025-09-16 07:14:02 10.79 dict {'O43657': {ProtainatlasAnnotation(organ='Gallbladder', tissue='Gallbladder', cell_type='glandular cells', level='Medium', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotation(organ='K...(truncated) 15,045 {} 2025-09-16 07:13:51
pypath.inputs.proteinatlas.proteinatlas_interactions 2025-09-16 07:14:04 2025-09-16 07:14:04 0.34 list [ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interac...(truncated) 46,472 {} 2025-09-16 07:14:04
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2025-09-16 07:14:04 2025-09-16 07:14:04 0.30 dict {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) 2,590 {} 2025-09-16 07:14:04
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2025-09-16 07:14:04 2025-09-16 07:14:05 0.55 dict {'O43657': {ProteinatlasSubcellularAnnotation(location='Nucleoli fibrillar center', status='additional', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cytosol', status='main', reliability=...(truncated) 13,336 {} 2025-09-16 07:14:04
pypath.inputs.proteins.variants 2025-09-16 07:14:05 2025-09-16 07:21:12 426.89 list [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) 30,452 {} 2025-09-16 07:14:05
pypath.inputs.protmapper.get_protmapper 2025-09-16 07:21:12 2025-09-16 07:21:14 1.50 tuple ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q05513', 'CTRL_GENE_NAME': 'PRKCZ', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P27448', 'TARGET_GENE_NAME': 'MARK3', 'TARGET_RES': 'T', 'TARGET_POS': '564', 'SOURCES': 'psp,signor', 'BELIEF': '1'}, {'ID': '1', 'CTRL_NS': 'UP', 'CTRL_ID': 'P41743', 'CTRL_GEN...(truncated) 2 {} 2025-09-16 07:21:12
pypath.inputs.protmapper.protmapper_enzyme_substrate 2025-09-16 07:21:14 2025-09-16 07:21:15 0.98 list [{'kinase': 'Q05513', 'resaa': 'T', 'resnum': 564, 'references': {'15084291'}, 'substrate': 'P27448', 'databases': {'SIGNOR', 'PhosphoSite'}}, {'kinase': 'P41743', 'resaa': 'T', 'resnum': 564, 'references': set(), 'substrate': 'P27448', 'databases': {'PhosphoSite'}}, {'kinase': 'Q9NRM7', 'resaa': 'S...(truncated) 31,263 {} 2025-09-16 07:21:14
pypath.inputs.protmapper.protmapper_interactions 
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments.
 {} never
pypath.inputs.pubchem.pubchem_mapping 
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pmid 
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pubmeds 
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments.
 {} never
pypath.inputs.pubmed.only_pmids 
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments.
 {} never
pypath.inputs.pubmed.open_pubmed 
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_dict 
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_list 
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments.
 {} never
pypath.inputs.ramilowski2015.ramilowski_interactions 2025-09-16 07:21:15 2025-09-16 07:21:16 0.41 list [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) 1,894 {} 2025-09-16 07:21:15
pypath.inputs.ramilowski2015.ramilowski_locations 2025-09-16 07:21:16 2025-09-16 07:21:24 8.66 dict {'P04217': {RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), Ramil...(truncated) 18,879 {} 2025-09-16 07:21:16
pypath.inputs.reaction.acsn_biopax 2025-09-16 07:21:24 2025-09-16 07:21:25 0.33 NoneType None 0 {} 2025-09-16 07:21:24
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
 {} never
pypath.inputs.reaction.get_acsn_effects 2025-09-16 07:21:25 2025-09-16 07:21:25 0.69 list [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) 37,288 {} 2025-09-16 07:21:25
pypath.inputs.reaction.get_controls 
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.get_interactions 
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.get_reactions 2025-09-16 07:21:25 2025-09-16 07:21:26 0.31 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
    rea.load_all()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
    self.load_wikipathways()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
    len(biopaxes.result),
    ^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
{} 2025-09-05 06:55:41
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
 {} never
pypath.inputs.reaction.panther_biopax 2025-09-16 07:21:26 2025-09-16 07:21:32 6.29 dict {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) 178 {} 2025-09-16 07:21:26
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.pid_biopax 2025-09-16 07:21:32 2025-09-16 07:21:34 1.84 NoneType None 0 {} 2025-09-16 07:21:32
pypath.inputs.reaction.pid_interactions 
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.process_complex 
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments.
 {} never
pypath.inputs.reaction.process_controls 
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.process_reactions 
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactions_biopax 
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_biopax 2025-09-16 07:21:34 2025-09-16 07:21:55 21.58 TextIOWrapper <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> 0 {} 2025-09-16 07:21:34
pypath.inputs.reaction.reactome_bs 2025-09-16 07:21:55 2025-09-16 07:28:31 395.66 list [('R-HSA-1059683', <?xml version="1.0" encoding="utf-8"?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 93 on 6/13/25, 9:16 PM using JSBML version 1.5.</p> </annotat...(truncated) 2,803 {} 2025-09-16 07:21:55
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_sbml 2025-09-16 07:28:54 2025-09-16 07:28:56 1.82 dict {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/cache/9c...(truncated) 2,803 {} 2025-09-16 07:28:54
pypath.inputs.reactome.pathway_hierarchy 2025-09-16 07:28:56 2025-09-16 07:28:57 0.82 list [{'parent': 'R-BTA-109581', 'child': 'R-BTA-109606'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-169911'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-5357769'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-75153'}, {'parent': 'R-BTA-109582', 'child': 'R-BTA-140877'}, {'parent': 'R-BTA-109582', 'child'...(truncated) 23,019 {} 2025-09-16 07:28:56
pypath.inputs.reactome.reactome_raw 
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments.
 {} never
pypath.inputs.reactome_old.reactome_chebis 2025-09-16 07:28:57 2025-09-16 07:29:02 5.74 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-09-05 07:03:10
pypath.inputs.reactome_old.reactome_pathway_relations 2025-09-16 07:29:02 2025-09-16 07:29:02 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-09-05 07:03:15
pypath.inputs.reactome_old.reactome_pathways 2025-09-16 07:29:02 2025-09-16 07:29:03 0.97 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-09-05 07:03:15
pypath.inputs.reactome_old.reactome_uniprots 2025-09-16 07:29:03 2025-09-16 07:29:18 14.98 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-09-05 07:03:16
pypath.inputs.rhea.rhea_gui 2025-09-16 07:29:18 2025-09-16 07:29:36 17.83 list [{'Reaction identifier': 'RHEA:21252', 'Equation': '(S)-2-hydroxyglutarate + A = 2-oxoglutarate + AH2', 'ChEBI name': '(S)-2-hydroxyglutarate;A;2-oxoglutarate;AH2', 'ChEBI identifier': 'CHEBI:16782;CHEBI:13193;CHEBI:16810;CHEBI:17499', 'EC number': 'EC:1.1.99.2', 'Enzymes': '4258', 'Gene Ontology': ...(truncated) 17,783 {} 2025-09-16 07:29:18
pypath.inputs.rhea.rhea_raw 
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments.
 {} never
pypath.inputs.scconnect.scconnect_annotations 2025-09-16 07:29:36 2025-09-16 07:29:38 1.72 dict {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human'), ScconnectAnnota...(truncated) 3,285 {} 2025-09-16 07:29:36
pypath.inputs.scconnect.scconnect_complexes 2025-09-16 07:29:38 2025-09-16 07:29:38 0.02 set {Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:P01215_P01225, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P29459_P29460, Comp...(truncated) 17 {} 2025-09-16 07:29:38
pypath.inputs.scconnect.scconnect_interactions 2025-09-16 07:29:38 2025-09-16 07:34:42 304.25 list [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) 1,766 {} 2025-09-16 07:29:38
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
 {} never
pypath.inputs.sider.sider_drug_names 2025-09-16 07:34:42 2025-09-16 07:34:42 0.10 dict {'CID100002391': {SiderDrug(name='bisacodyl', atc='A06AB02'), SiderDrug(name='bisacodyl', atc='A06AG02')}, 'CID100062959': {SiderDrug(name='trovafloxacin', atc='J01MA13')}, 'CID100002881': {SiderDrug(name='sodium', atc='R03BC01'), SiderDrug(name='sodium', atc='D11AH03'), SiderDrug(name='sodium', atc...(truncated) 1,430 {} 2025-09-16 07:34:42
pypath.inputs.sider.sider_meddra_side_effects 2025-09-16 07:34:42 2025-09-16 07:34:43 0.28 list [SiderSideeffectMeddra(cid='C1697946', meddra_id='10065177', side_effect_name='Otitis media viral'), SiderSideeffectMeddra(cid='C3665767', meddra_id='10073628', side_effect_name='Instillation site vesicles'), SiderSideeffectMeddra(cid='C0919837', meddra_id='10050935', side_effect_name='Megakaryocyte...(truncated) 20,307 {} 2025-09-16 07:34:42
pypath.inputs.sider.sider_side_effect_frequencies 2025-09-16 07:34:43 2025-09-16 07:34:57 14.95 dict {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C1510472', umls_concept_in_meddra='C1510472', side_effect='Drug dependence', frequency='6%'), SiderSideeffetFrequency(umls_concept_on_label='C0013378', umls_concept_in_meddra='C0013378', side_effect='Dysgeusia', frequency='3%'), SiderS...(truncated) 968 {} 2025-09-16 07:34:43
pypath.inputs.sider.sider_side_effects 2025-09-16 07:34:58 2025-09-16 07:34:58 0.86 dict {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0013395', umls_concept_in_meddra='C0013395', side_effect='Dyspepsia'), SiderSideeffect(umls_concept_on_label='C0151735', umls_concept_in_meddra='C0151735', side_effect='Injection site reaction'), SiderSideeffect(umls_concept_on_label='C151047...(truncated) 1,430 {} 2025-09-16 07:34:58
pypath.inputs.signalink.signalink_annotations 2025-09-16 07:34:59 2025-09-16 07:35:00 1.34 dict {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase'), Signal...(truncated) 2 {} 2025-09-16 07:34:59
pypath.inputs.signalink.signalink_function_annotations 2025-09-16 07:35:00 2025-09-16 07:35:01 1.01 dict {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) 785 {} 2025-09-16 07:35:00
pypath.inputs.signalink.signalink_interactions 2025-09-16 07:35:01 2025-09-16 07:35:01 0.41 list [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) 1,939 {} 2025-09-16 07:35:01
pypath.inputs.signalink.signalink_pathway_annotations 2025-09-16 07:35:01 2025-09-16 07:35:02 0.43 dict {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(p...(truncated) 839 {} 2025-09-16 07:35:01
pypath.inputs.signor.signor_complexes 2025-09-16 07:35:02 2025-09-16 07:35:03 0.77 dict {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) 4,890 {} 2025-09-16 07:35:02
pypath.inputs.signor.signor_enzyme_substrate 2025-09-16 07:35:03 2025-09-16 07:35:06 3.67 list [{'typ': 'phosphorylation', 'resnum': 1644, 'instance': 'SPTSPSYSPTSPSYS', 'substrate': 'P24928', 'start': 1637, 'end': 1651, 'kinase': 'Q14004', 'resaa': 'S', 'motif': 'SPTSPSYSPTSPSYS', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'32917631'}}, {'typ': 'phosphorylation', 'resn...(truncated) 13,391 {} 2025-09-16 07:35:03
pypath.inputs.signor.signor_interactions 2025-09-16 07:35:06 2025-09-16 07:35:07 1.19 list [SignorInteraction(source='Q15722', target='Q03113', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates activity', mechanism='binding', ncbi_tax_id='9606', pubmeds='31160049', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), Si...(truncated) 95,631 {'size': 31} 2025-09-16 07:35:06
pypath.inputs.signor.signor_pathway_annotations 2025-09-16 07:35:08 2025-09-16 07:35:27 19.39 dict {'Q16611': {SignorPathway(pathway='Malignant Melanoma'), SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='Non-small-cell lung cancer (NSCLC)')}, 'P01116': {SignorPathway(pathway='Noonan syndrome'), SignorPathway(pathway='LIF in PDAC'), SignorPathway(pathway='COVID-19 Causal Ne...(truncated) 775 {} 2025-09-16 07:35:08
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
 {} never
pypath.inputs.signor.signor_protein_families 2025-09-16 07:35:27 2025-09-16 07:35:27 0.00 dict {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) 91 {} 2025-09-16 07:35:27
pypath.inputs.slc.slc_annotation 2025-09-16 07:35:27 2025-09-16 07:35:27 0.25 list [SlcAnnotation(Entrez_ID=56172, Ensembl_ID='ENSG00000154122', HGNC_symbol='ANKH', Substrate_class='Orphan', Substrates='', Substrates_PMID='', Coupled_ions='Unknown', Coupled_ions_PMID='', Transport_mechanism='Unknown', Transport_system_PMID='', Subcellular_localization='Unknown', Subcellular_locali...(truncated) 446 {} 2025-09-16 07:35:27
pypath.inputs.slc.slc_chebi_mapping 2025-09-16 07:35:27 2025-09-16 07:35:28 0.17 list [SlcChebiMapping(Substrate_name_annotation='17-beta-glucuronosyl estradiol', chebi_id='CHEBI:791', chebi_term='17beta-estradiol 17-glucosiduronic acid', synonym='3-hydroxyestra-1,3,5(10)-trien-17beta-yl beta-D-glucopyranosiduronic acid', description='A steroid glucosiduronic acid that consists of 17...(truncated) 382 {} 2025-09-16 07:35:27
pypath.inputs.slc.slc_interactions 2025-09-16 07:35:28 2025-09-16 07:35:28 0.10 list [SlcInteraction(transporter=SlcTransporter(uniprot='Q9Y5Y0', genesymbol='FLVCR1', entrez=28982, ensg='ENSG00000162769'), substrate=SlcSubstrate(slc_name='Heme', chebi='CHEBI:30413', label='heme', synonyms=['heme', 'hemes']), role='substrate', pmids='15369674', localization='Plasma membrane', transpo...(truncated) 1,288 {} 2025-09-16 07:35:28
pypath.inputs.slc.slc_localization_annotations 2025-09-16 07:35:28 2025-09-16 07:35:28 0.06 dict {'Q9HCJ1': {SlcLocalization(localization='Unknown', pmids=None)}, 'Q13286': {SlcLocalization(localization='Endosome; Lysosome', pmids='15471887;22261744')}, 'Q96SL1': {SlcLocalization(localization='Lysosome', pmids='21692750')}, 'Q9Y5Y0': {SlcLocalization(localization='Plasma membrane', pmids='18815...(truncated) 447 {} 2025-09-16 07:35:28
pypath.inputs.slc.slc_substrate_ontology 2025-09-16 07:35:28 2025-09-16 07:35:29 0.95 list [SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='heme', ChEBI_ID='CHEBI:30413', ChEBI_subontology='chemical entity'), SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='cyclic tetrapyrrole', ChEB...(truncated) 24,810 {} 2025-09-16 07:35:28
pypath.inputs.spike.spike_complexes 2025-09-16 07:35:29 2025-09-16 07:35:39 10.36 dict {'COMPLEX:P67775_Q15172_Q15257': Complex PP2A: COMPLEX:P67775_Q15172_Q15257, 'COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478': Complex AMPK: COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478, 'COMPLEX:P67870_P68400': Complex CK2: COMPLEX:P67870_P68400, 'COMPLEX:P05412_P15336': Compl...(truncated) 154 {} 2025-09-16 07:35:29
pypath.inputs.spike.spike_interactions 2025-09-16 07:35:39 2025-09-16 07:35:41 1.96 list [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) 8,903 {} 2025-09-16 07:35:39
pypath.inputs.stitch.stitch_actions_interactions 2025-09-16 07:35:41 2025-09-16 07:36:47 66.07 list [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) 21,773,491 {} 2025-09-16 07:35:41
pypath.inputs.stitch.stitch_links_interactions 2025-09-16 07:36:47 2025-09-16 07:38:05 77.74 list [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) 150,645 {} 2025-09-16 07:36:47
pypath.inputs.string.string_effects 2025-09-16 07:38:05 2025-09-16 07:38:14 8.78 list [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) 2,250,122 {} 2025-09-16 07:38:05
pypath.inputs.string.string_links_interactions 2025-09-16 07:38:15 2025-09-16 07:38:47 32.13 list [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) 201,712 {} 2025-09-16 07:38:15
pypath.inputs.string.string_physical_interactions 2025-09-16 07:38:47 2025-09-16 07:38:48 1.16 list [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) 89,862 {} 2025-09-16 07:38:47
pypath.inputs.string.string_species 2025-09-16 07:38:48 2025-09-16 07:38:48 0.19 dict {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) 12,535 {} 2025-09-16 07:38:48
pypath.inputs.surfaceome.surfaceome_annotations 2025-09-16 07:38:48 2025-09-16 07:38:51 2.44 dict {'A0AV02': (0.8363, 'Transporters', {'SLC12', 'APC', 'SLC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC5', 'APC', 'SLC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) 2,844 {} 2025-09-16 07:38:48
pypath.inputs.switches_elm.get_switches_elm 2025-09-16 07:38:51 2025-09-16 07:38:55 4.58 list [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) 839 {} 2025-09-16 07:38:51
pypath.inputs.talklr.talklr_annotations 2025-09-16 07:38:55 2025-09-16 07:38:56 0.55 dict {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) 1,344 {} 2025-09-16 07:38:55
pypath.inputs.talklr.talklr_interactions 2025-09-16 07:38:56 2025-09-16 07:38:56 0.04 list [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) 2,422 {} 2025-09-16 07:38:56
pypath.inputs.talklr.talklr_raw 2025-09-16 07:38:56 2025-09-16 07:38:56 0.03 DataFrame Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) 2,422 {} 2025-09-16 07:38:56
pypath.inputs.tcdb.tcdb_annotations 2025-09-16 07:38:56 2025-09-16 07:39:01 4.99 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
    value = fun(*_args, **_kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/tcdb/__init__.py", line 95, in tcdb_annotations
    for ac, (tc, family) in iteritems(classes):
                            ^^^^^^^^^
NameError: name 'iteritems' is not defined
{} 2025-09-05 07:10:53
pypath.inputs.tcdb.tcdb_classes 2025-09-16 07:39:01 2025-09-16 07:39:01 0.03 dict {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) 24,296 {} 2025-09-16 07:39:01
pypath.inputs.tcdb.tcdb_families 2025-09-16 07:39:01 2025-09-16 07:39:01 0.01 dict {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) 2,110 {'size': 2} 2025-09-16 07:39:01
pypath.inputs.tfcensus.tfcensus_annotations 2025-09-16 07:39:01 2025-09-16 07:39:01 0.16 dict {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) 1,871 {} 2025-09-16 07:39:01
pypath.inputs.threedcomplex.threedcomplex_chains 2025-09-16 07:39:01 2025-09-16 07:39:05 3.58 dict {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) 174,325 {} 2025-09-16 07:39:01
pypath.inputs.threedcomplex.threedcomplex_contacts 2025-09-16 07:39:05 2025-09-16 07:39:27 21.74 set {ThreedcomplexContact(pdb='3pcn_1', uniprot_1='P00437', uniprot_2='P00436', chain_1='P', chain_2='B', n_residues=4.5, length_1=233, length_2=200, domain_s1=('49482',), domain_p1=('PF12391.3', 'PF00775.16'), domain_s2=('49482',), domain_p2=('PF00775.16',), ident=False, homo=True), ThreedcomplexContac...(truncated) 259,377 {} 2025-09-16 07:39:05
pypath.inputs.threedcomplex.threedcomplex_ddi 2025-09-16 07:39:28 2025-09-16 07:42:35 187.25 list [<pypath.internals.intera.DomainDomain object at 0x7f05849dfbd0>, <pypath.internals.intera.DomainDomain object at 0x7f05849df9d0>, <pypath.internals.intera.DomainDomain object at 0x7f05849df5d0>, <pypath.internals.intera.DomainDomain object at 0x7f05849df3d0>, <pypath.internals.intera.DomainDomain o...(truncated) 524,087 {} 2025-09-16 07:39:28
pypath.inputs.threedcomplex.threedcomplex_nresidues 2025-09-16 07:42:36 2025-09-16 07:42:46 10.39 dict {'3pcn_1': {('P00436', 'P00437'): 3.0, ('P00437', 'P00437'): 30.0, ('P00436', 'P00436'): 2.5}, '4gyp_1': {('P0AES2', 'Q46915'): 13.5, ('P0AES2', 'P0AES2'): 30.0, ('Q46915', 'Q46915'): 28.5}, '4std_1': {('P56221', 'P56221'): 22.5}, '2yfi_1': {('P37334', 'P37334'): 31.5, ('P37333', 'P37334'): 35.5, ('...(truncated) 80,996 {} 2025-09-16 07:42:36
pypath.inputs.threedid.get_3did 2025-09-16 07:42:46 2025-09-16 08:49:01 3,975.07 tuple ([<pypath.internals.intera.DomainDomain object at 0x7f056639bdd0>, <pypath.internals.intera.DomainDomain object at 0x7f04869ebb10>, <pypath.internals.intera.DomainDomain object at 0x7f040ad1bf10>, <pypath.internals.intera.DomainDomain object at 0x7f048640a0d0>, <pypath.internals.intera.DomainDomain ...(truncated) 2 {} 2025-09-16 07:42:46
pypath.inputs.threedid.get_3did_ddi 2025-09-16 08:49:01 2025-09-16 09:04:52 950.13 dict {} 0 {} 2025-09-16 08:49:01
pypath.inputs.topdb.topdb_annotations 2025-09-16 09:04:52 2025-09-16 09:05:31 39.39 dict {'P18825': {TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Extracellular', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell membrane', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cyto...(truncated) 2,027 {} 2025-09-16 09:04:52
pypath.inputs.transmir.transmir_interactions 2025-09-16 09:05:31 2025-09-16 09:05:31 0.12 list [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) 2,678 {} 2025-09-16 09:05:31
pypath.inputs.trip.take_a_trip 2025-09-16 09:05:31 2025-09-16 09:05:31 0.00 dict {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) 5 {} 2025-09-16 09:05:31
pypath.inputs.trip.trip_find_uniprot 
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_get_uniprot 
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_interactions 2025-09-16 09:05:31 2025-09-16 09:05:31 0.01 list [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;12601176;11983166', 'Patch clamp;Calcium measurement;Fusion protein-pull down assay;Fl...(truncated) 359 {} 2025-09-16 09:05:31
pypath.inputs.trip.trip_process 2025-09-16 09:05:31 2025-09-16 09:05:31 0.01 dict {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'Rat vascular smooth muscle cell', 'Porcine coronary artery', 'Rat aortic vascular smooth muscle cell', 'HEK293'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) 359 {} 2025-09-16 09:05:31
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
 {} never
pypath.inputs.trrust.trrust_human 2025-09-16 09:05:31 2025-09-16 09:05:35 3.63 list [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) 9,396 {} 2025-09-16 09:05:31
pypath.inputs.trrust.trrust_interactions 2025-09-16 09:05:35 2025-09-16 09:05:35 0.01 list [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) 9,396 {} 2025-09-16 09:05:35
pypath.inputs.trrust.trrust_mouse 2025-09-16 09:05:35 2025-09-16 09:05:38 2.92 list [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) 7,057 {} 2025-09-16 09:05:35
pypath.inputs.twosides.twosides_interactions 2025-09-16 09:05:38 2025-09-16 09:11:11 332.75 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/offsides.py", line 80, in _sides_base
    yield record(**{
                   ^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250916-022202/pypath_git/pypath/inputs/offsides.py", line 81, in <dictcomp>
    f: line[i].strip(' "')
       ~~~~^^^
IndexError: list index out of range
{'broke': True} 2025-09-15 08:22:37
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_info 2025-09-16 09:11:11 2025-09-16 09:11:11 0.01 list [UnichemSource(number=1, label='ChEMBL', name='chembl', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='2024-12-11'), UnichemSource(number=2, label='DrugBank', name='drugbank', description='A database that com...(truncated) 41 {} 2025-09-16 09:11:11
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_sources 2025-09-16 09:11:11 2025-09-16 09:11:11 0.00 dict {1: 'ChEMBL', 2: 'DrugBank', 3: 'PDBe', 4: 'Guide to Pharmacology', 5: 'PubChem: Drugs of the Future ', 6: 'KEGG Ligand', 7: 'ChEBI', 8: 'NIH Clinical Collection', 9: 'ZINC', 10: 'eMolecules', 12: 'Atlas', 14: 'FDA SRS', 15: 'SureChEMBL', 17: 'PharmGKB', 18: 'Human Metabolome Database', 20: 'Selleck...(truncated) 41 {} 2025-09-16 09:11:11
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
 {} never
pypath.inputs.uniprot.get_uniprot_sec 2025-09-16 09:11:11 2025-09-16 09:11:11 0.58 list [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ13', 'K7EN86'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZ66', 'K7EQ86'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZK0', 'A0A024QZP7'], ['A0A024Q...(truncated) 72,358 {} 2025-09-16 09:11:11
pypath.inputs.uniprot.protein_datasheet 
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.query_builder 
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_data 
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_families 2025-09-16 09:11:11 2025-09-16 09:11:23 11.51 dict {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0AV02': {UniprotFamily(family='SLC12A transporter', subfamily=None)}, 'A0AV96': {UniprotFam...(truncated) 14,485 {} 2025-09-16 09:11:11
pypath.inputs.uniprot.uniprot_history 
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_history_recent_datasheet 
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_keywords 2025-09-16 09:11:23 2025-09-16 09:11:33 10.63 dict {'A0A087X1C5': {UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Mitochondrion'), UniprotKeyword(keyword='Transmembrane'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Transmembrane helix'),...(truncated) 20,420 {} 2025-09-16 09:11:23
pypath.inputs.uniprot.uniprot_locations 
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2025-09-16 09:11:33 2025-09-16 09:11:34 0.08 dict {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) 27,837 {} 2025-09-16 09:11:33
pypath.inputs.uniprot.uniprot_preprocess 
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_query 
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_recent_version 
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_taxonomy 2025-09-16 09:11:34 2025-09-16 09:11:35 1.64 dict {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'H8ZM71': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'Q9MV51': {'Momi fir', 'Abies firma'}, 'O81086': {'Pinus grandis', 'Abies grandis', '...(truncated) 558,858 {} 2025-09-16 09:11:34
pypath.inputs.uniprot.uniprot_tissues 2025-09-16 09:11:36 2025-09-16 09:11:48 12.04 dict {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Myeloid dendritic cells', level='undefined'), UniprotTissue(ti...(truncated) 10,169 {} 2025-09-16 09:11:36
pypath.inputs.uniprot.uniprot_topology 2025-09-16 09:11:48 2025-09-16 09:12:35 47.23 dict {'A0A087X1C5': {UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', ...(truncated) 5,244 {} 2025-09-16 09:11:48
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot_db.all_swissprots 2025-09-16 09:12:35 2025-09-16 09:12:35 0.01 set {'O60565', 'P05538', 'Q6P2H8', 'Q6QHC5', 'P35712', 'Q9Y5I3', 'P28749', 'Q9UBS8', 'P04629', 'O60431', 'O95297', 'O43526', 'Q10469', 'Q4VC31', 'Q9UDY6', 'Q86XN8', 'Q17RM4', 'Q9NPI1', 'Q8N1B4', 'P12235', 'Q58FG0', 'Q96J86', 'Q16825', 'Q6IQ20', 'Q9BTC8', 'Q9Y4K4', 'Q8NGG2', 'Q8TEB9', 'Q14246', 'Q9H7P9',...(truncated) 20,420 {} 2025-09-16 09:12:35
pypath.inputs.uniprot_db.all_trembls 2025-09-16 09:12:35 2025-09-16 09:13:07 31.70 set {'A0A7G2CXH1', 'C9JE69', 'A0A7I2V3W7', 'Q8TAQ1', 'A0A7S5EUN7', 'B7Z1P5', 'A0A0A0MR54', 'A8K5T7', 'B4DIG6', 'G1ENJ7', 'A0A0A0MTL8', 'D2DKN6', 'A2I832', 'C6L831', 'D3VVG9', 'A0A385JFK9', 'G3V5K4', 'A1DVN4', 'A0A2K4XGT9', 'B2R7Y8', 'A0A343KKG5', 'Q5U0C3', 'B4DF21', 'B3KXA5', 'F6UGA0', 'B4DF68', 'A0A1S6...(truncated) 184,785 {} 2025-09-16 09:12:35
pypath.inputs.uniprot_db.all_uniprots 2025-09-16 09:13:07 2025-09-16 09:13:07 0.00 set {'A0A7G2CXH1', 'C9JE69', 'A0A7I2V3W7', 'Q8TAQ1', 'Q6P2H8', 'A0A7S5EUN7', 'B7Z1P5', 'A0A0A0MR54', 'A8K5T7', 'B4DIG6', 'G1ENJ7', 'A0A0A0MTL8', 'D2DKN6', 'A2I832', 'C6L831', 'D3VVG9', 'A0A385JFK9', 'G3V5K4', 'A1DVN4', 'A0A2K4XGT9', 'B2R7Y8', 'A0A343KKG5', 'Q5U0C3', 'P04629', 'B4DF21', 'B3KXA5', 'F6UGA0...(truncated) 205,205 {} 2025-09-16 09:13:07
pypath.inputs.uniprot_db.get_db 2025-09-16 09:13:07 2025-09-16 09:13:07 0.00 set {'A0A7G2CXH1', 'C9JE69', 'A0A7I2V3W7', 'Q8TAQ1', 'Q6P2H8', 'A0A7S5EUN7', 'B7Z1P5', 'A0A0A0MR54', 'A8K5T7', 'B4DIG6', 'G1ENJ7', 'A0A0A0MTL8', 'D2DKN6', 'A2I832', 'C6L831', 'D3VVG9', 'A0A385JFK9', 'G3V5K4', 'A1DVN4', 'A0A2K4XGT9', 'B2R7Y8', 'A0A343KKG5', 'Q5U0C3', 'P04629', 'B4DF21', 'B3KXA5', 'F6UGA0...(truncated) 205,205 {} 2025-09-16 09:13:07
pypath.inputs.uniprot_db.init_db 2025-09-16 09:13:07 2025-09-16 09:13:07 0.05 NoneType None 0 {} 2025-09-16 09:13:07
pypath.inputs.uniprot_db.is_swissprot 
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments.
 {} never
pypath.inputs.uniprot_db.is_trembl 
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments.
 {} never
pypath.inputs.uniprot_db.is_uniprot 
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot_idmapping.idtypes 2025-09-16 09:13:07 2025-09-16 09:13:07 0.05 set {('UniProtKB', 'TCDB'), ('UniProtKB_AC-ID', 'Ensembl_Genomes_Transcript'), ('Orphanet', 'UniProtKB'), ('UniProtKB', 'WBParaSite'), ('BioGRID', 'UniProtKB-Swiss-Prot'), ('UniProtKB_AC-ID', 'PIR'), ('MaizeGDB', 'UniProtKB-Swiss-Prot'), ('FlyBase', 'UniProtKB'), ('UniProtKB_AC-ID', 'RefSeq_Protein'), (...(truncated) 481 {} 2025-09-16 09:13:07
pypath.inputs.wang.cui_interactions 2025-09-16 09:13:07 2025-09-16 09:13:07 0.30 list [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) 5,089 {} 2025-09-16 09:13:07
pypath.inputs.wang.hsn_interactions 2025-09-16 09:13:07 2025-09-16 09:13:08 0.61 list [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) 62,937 {} 2025-09-16 09:13:07
pypath.inputs.wang.wang_annotations 2025-09-16 09:13:08 2025-09-16 09:13:13 4.79 dict {'NA': {WangAnnotation(function='Adapter', location='Ribosomes'), WangAnnotation(function='Ion', location='Cytosol'), WangAnnotation(function='Ribosome', location='Ribosomes'), WangAnnotation(function='RNA', location='Ribosomes'), WangAnnotation(function='Messenger', location='Cytosol'), WangAnnotat...(truncated) 1,547 {} 2025-09-16 09:13:08
pypath.inputs.wang.wang_interactions 2025-09-16 09:13:13 2025-09-16 09:13:13 0.14 list [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) 62,937 {} 2025-09-16 09:13:13
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2025-09-16 09:13:13 2025-09-16 09:13:13 0.31 list [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) 483 {} 2025-09-16 09:13:13
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2025-09-16 09:13:13 2025-09-16 09:13:13 0.10 list [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) 495 {} 2025-09-16 09:13:13
pypath.inputs.zhong2015.zhong2015_annotations 2025-09-16 09:13:13 2025-09-16 09:13:13 0.17 dict {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) 466 {} 2025-09-16 09:13:13

The OmniPath Team • Saez Lab • 2025-09-16