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 2026-01-28 20:24:25 and 2026-01-29 02:32:27; pypath version: 0.16.29 (from git, installed by poetry; 0a69d5f )

Modules collected: 195
Modules failed to import: 2
Functions collected: 540
Functions run without error: 383
Functions returned empty value: 20
Functions skipped due to lack of arguments: 121
Functions run with error: 36

Function Started Finished Elapsed (s) Result type Result repr Result size Error Change since last time Last succeeded
pypath.inputs.abs.abs_interactions 2026-01-28 20:24:29 2026-01-28 20:24:30 0.43 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 {} 2026-01-28 20:24:29
pypath.inputs.acsn.acsn_interactions 2026-01-28 20:24:30 2026-01-28 20:24:30 0.51 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 {} 2026-01-28 20:24:30
pypath.inputs.adhesome.adhesome_annotations 2026-01-28 20:24:30 2026-01-28 20:25:24 53.76 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 {} 2026-01-28 20:24:30
pypath.inputs.adhesome.adhesome_interactions 2026-01-28 20:25:24 2026-01-28 20:25:25 1.16 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 {} 2026-01-28 20:25:24
pypath.inputs.adrecs.adrecs_adr_ontology 2026-01-28 20:25:25 2026-01-28 20:25:29 4.38 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 {} 2026-01-28 20:25:25
pypath.inputs.adrecs.adrecs_drug_adr 2026-01-28 20:25:29 2026-01-28 20:26:11 41.73 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 {} 2026-01-28 20:25:29
pypath.inputs.adrecs.adrecs_drug_identifiers 2026-01-28 20:26:11 2026-01-28 20:26:18 7.03 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 {} 2026-01-28 20:26:11
pypath.inputs.adrecs.adrecs_hierarchy 2026-01-28 20:26:18 2026-01-28 20:26:19 1.11 set {AdrecsChildParent(child=AdrecsAdr(adr_class='21.14.03.003', badd='BADD_A07522'), parent=AdrecsAdr(adr_class='21.14.03', badd='BADD_A02298')), AdrecsChildParent(child=AdrecsAdr(adr_class='06.05.02.008', badd='BADD_A05790'), parent=AdrecsAdr(adr_class='06.05.02', badd='BADD_A03120')), AdrecsChildPare...(truncated) 13,828 {} 2026-01-28 20:26:18
pypath.inputs.almen2009.almen2009_annotations 2026-01-28 20:26:19 2026-01-28 20:26:21 1.55 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 {} 2026-01-28 20:26:19
pypath.inputs.alzpathway.alzpathway_interactions 2026-01-28 20:26:21 2026-01-28 20:26:21 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 {} 2026-01-28 20:26:21
pypath.inputs.baccin2019.baccin2019_annotations 2026-01-28 20:26:21 2026-01-28 20:26:58 36.67 dict {} 0 {'size': -933} 2026-01-28 20:26:21
pypath.inputs.baccin2019.baccin2019_interactions 2026-01-28 20:26:58 2026-01-28 20:26:58 0.31 list [] 0 {'size': -1460} 2026-01-28 20:26:58
pypath.inputs.biogps.biogps_datasets 2026-01-28 20:26:58 2026-01-28 20:26:58 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 {} 2026-01-28 20:26:58
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
 {} never
pypath.inputs.biogps.biogps_download_all 2026-01-28 20:26:58 2026-01-28 20:27:29 30.78 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 {} 2026-01-28 20:26:58
pypath.inputs.biogrid.biogrid_all_interactions 2026-01-28 20:27:29 2026-01-28 20:28:15 45.70 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) 8,770 {'size': 21} 2026-01-28 20:27:29
pypath.inputs.biogrid.biogrid_interactions 2026-01-28 20:28:15 2026-01-28 20:28:16 1.16 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) 7,499 {'size': 21} 2026-01-28 20:28:15
pypath.inputs.biomart.biomart_homology 2026-01-28 20:28:16 2026-01-28 20:28:57 40.63 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 {} 2026-01-28 20:28:16
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
 {} never
pypath.inputs.biomart.biomart_microarray_types 2026-01-28 20:28:58 2026-01-28 20:28:58 0.06 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 {} 2026-01-28 20:28:58
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
 {} never
pypath.inputs.ca1.ca1_interactions 2026-01-28 20:28:58 2026-01-28 20:28:58 0.16 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 {} 2026-01-28 20:28:58
pypath.inputs.cancercellmap.ccmap_interactions 2026-01-28 20:28:58 2026-01-28 20:28:59 1.04 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 {} 2026-01-28 20:28:58
pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations 2026-01-28 20:28:59 2026-01-28 20:29:09 10.49 dict {'2733335': {CancerdrugsdbAnnotation(drug_label='Streptozocin', ema_approved=False, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2005, indications=('Stage 4 islet cell carcinoma',))}} 1 {'size': -215} 2026-01-28 20:28:59
pypath.inputs.cancerdrugsdb.cancerdrugsdb_download 2026-01-28 20:29:09 2026-01-28 20:29:09 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) 349 {'size': 19} 2026-01-28 20:29:09
pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions 2026-01-28 20:29:09 2026-01-28 20:29:10 1.01 list [CancerdrugsdbInteraction(drug_pubchem='2733335', drug_chembl='CHEMBL1651906', drug_drugbank='DB00428', drug_label='Streptozocin', target_uniprot='P22732', ema_approved=False, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2005, indications=('St...(truncated) 47 {'size': -5110} 2026-01-28 20:29:09
pypath.inputs.cancersea.cancersea_annotations 2026-01-28 20:29:10 2026-01-28 20:29:13 2.24 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,248 {} 2026-01-28 20:29:10
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
 {} never
pypath.inputs.cellcall.cellcall_annotations 2026-01-28 20:29:13 2026-01-28 20:29:23 10.72 dict {'P80075': {CellcallAnnotation(role='ligand')}, 'P51681': {CellcallAnnotation(role='receptor')}, 'Q8N6F1': {CellcallAnnotation(role='receptor'), CellcallAnnotation(role='ligand')}, 'P56748': {CellcallAnnotation(role='receptor')}, 'P01303': {CellcallAnnotation(role='ligand')}, 'P07550': {CellcallAnno...(truncated) 460 {} 2026-01-28 20:29:13
pypath.inputs.cellcall.cellcall_download 2026-01-28 20:29:23 2026-01-28 20:29:24 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 {} 2026-01-28 20:29:23
pypath.inputs.cellcall.cellcall_download_all 2026-01-28 20:29:24 2026-01-28 20:29:24 0.82 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 {} 2026-01-28 20:29:24
pypath.inputs.cellcall.cellcall_interactions 2026-01-28 20:29:24 2026-01-28 20:29:25 0.11 list [CellcallInteraction(ligand_uniprot='P80075', receptor_uniprot='P51681', core=True), CellcallInteraction(ligand_uniprot='Q8N6F1', receptor_uniprot='P56748', core=True), CellcallInteraction(ligand_uniprot='P01303', receptor_uniprot='P07550', core=True), CellcallInteraction(ligand_uniprot='Q9NQS3', re...(truncated) 797 {} 2026-01-28 20:29:24
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2026-01-28 20:29:25 2026-01-28 20:29:25 0.65 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinteractio...(truncated) 3,426 {'size': 1} 2026-01-28 20:29:25
pypath.inputs.cellchatdb.cellchatdb_annotations 2026-01-28 20:29:25 2026-01-28 20:29:36 10.28 dict {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='agonist', pathway='NODAL', category...(truncated) 1,530 {'size': 7} 2026-01-28 20:29:25
pypath.inputs.cellchatdb.cellchatdb_cofactors 2026-01-28 20:29:36 2026-01-28 20:29:43 7.37 dict {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'P12645', 'Q9H2X0', 'O00292', 'O75610', 'Q13253', 'Q9H772', 'O60565', 'P41271'}, 'BMP inhibition receptor': {'Q13145'...(truncated) 32 {} 2026-01-28 20:29:36
pypath.inputs.cellchatdb.cellchatdb_complexes 2026-01-28 20:29:43 2026-01-28 20:29:50 6.91 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 {} 2026-01-28 20:29:43
pypath.inputs.cellchatdb.cellchatdb_download 2026-01-28 20:29:50 2026-01-28 20:29:57 6.89 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 {} 2026-01-28 20:29:50
pypath.inputs.cellchatdb.cellchatdb_interactions 2026-01-28 20:29:57 2026-01-28 20:30:04 7.26 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='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) 12,436 {'size': 12} 2026-01-28 20:29:57
pypath.inputs.cellinker.cellinker_annotations 2026-01-28 20:30:04 2026-01-28 20:30:05 0.48 dict {'P37023': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'P27037': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor ...(truncated) 1,925 {'size': 6} 2026-01-28 20:30:04
pypath.inputs.cellinker.cellinker_complex_annotations 2026-01-28 20:30:05 2026-01-28 20:30:05 0.05 dict {Complex: COMPLEX:P16144_P23229: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='receptor', location='Membr...(truncated) 134 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_complexes 2026-01-28 20:30:05 2026-01-28 20:30:05 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 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_complexes_raw 2026-01-28 20:30:05 2026-01-28 20:30:05 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 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_lr_interactions 2026-01-28 20:30:05 2026-01-28 20:30:05 0.04 set {CellinkerInteraction(ligand='P37023', receptor='P27037', ligand_location='Membrane', receptor_location='Membrane', resources=None, pmids='30761306', type='Cell adhesion'), CellinkerInteraction(ligand='Q14790', receptor='P25445', ligand_location='Membrane', receptor_location='Membrane', resources=No...(truncated) 3,816 {'size': 6} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2026-01-28 20:30:05 2026-01-28 20:30:05 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 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_protein_annotations 2026-01-28 20:30:05 2026-01-28 20:30:05 0.06 dict {'P37023': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'P27037': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor ...(truncated) 1,791 {'size': 6} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_smol_interactions 2026-01-28 20:30:05 2026-01-28 20:30:05 0.10 set {CellinkerInteraction(ligand='5202', receptor='P21918', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='1826762', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5280884', receptor='Q9Y5Y4', ligand_location=None, receptor_location='Membrane', reso...(truncated) 314 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2026-01-28 20:30:05 2026-01-28 20:30:05 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 {} 2026-01-28 20:30:05
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
 {} never
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2026-01-28 20:30:05 2026-01-28 20:30:05 0.22 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 {} 2026-01-28 20:30:05
pypath.inputs.cellphonedb.cellphonedb_complexes 2026-01-28 20:30:05 2026-01-28 20:30:05 0.01 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 {} 2026-01-28 20:30:05
pypath.inputs.cellphonedb.cellphonedb_interactions 2026-01-28 20:30:05 2026-01-28 20:30:06 0.47 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 {} 2026-01-28 20:30:05
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2026-01-28 20:30:06 2026-01-28 20:30:06 0.03 tuple ({'P16471', 'P15018', 'Q9Y5Q6', 'Q07092', Complex Glycine_bySHMT2_and_SLC6A5: COMPLEX:P34897_Q9Y345, 'Q9NP95', 'Q8IW52', 'Q14993', 'O43300', 'P22003', 'Q9UHF0', 'P42127', 'Q05329', 'P10997', 'P01042', 'Q6PJG9', 'Q8IVG9', Complex integrin_a4b7_complex: COMPLEX:P13612_P26010, Complex ThromboxaneA2_byT...(truncated) 2 {} 2026-01-28 20:30:06
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2026-01-28 20:30:06 2026-01-28 20:30:06 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) 1,365 {'size': 6} 2026-01-28 20:30:06
pypath.inputs.celltalkdb.celltalkdb_annotations 2026-01-28 20:30:06 2026-01-28 20:30:06 0.43 dict {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='15721238'), CellTalkDBAnnotation(role='receptor', pmid='32196115')}, 'Q...(truncated) 1,599 {'size': 1} 2026-01-28 20:30:06
pypath.inputs.celltalkdb.celltalkdb_download 2026-01-28 20:30:06 2026-01-28 20:30:06 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 {} 2026-01-28 20:30:06
pypath.inputs.celltalkdb.celltalkdb_interactions 2026-01-28 20:30:06 2026-01-28 20:30:06 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 {} 2026-01-28 20:30:06
pypath.inputs.celltypist.celltypist_annotations 2026-01-28 20:30:06 2026-01-28 20:30:07 0.24 dict {'P11836': {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) 466 {'size': 6} 2026-01-28 20:30:06
pypath.inputs.clinvar.clinvar_citations 2026-01-28 20:30:07 2026-01-28 20:30:47 40.16 list [Citation(allele='1023939', variation_id='1036246', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='3767600', variation_id='3636020', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='333446', variation_id='311021', nsv='', citation_source='PubMe...(truncated) 4,285,311 {'size': 64091} 2026-01-28 20:30:07
pypath.inputs.clinvar.clinvar_raw 2026-01-28 20:30:52 2026-01-28 20:41:00 607.41 list [Variant(allele='4537811', type='single nucleotide variant', variant='NM_001042492.3(NF1):c.7870-8C>G', entrez='4763', genesymbol='NF1', clinical_significance='-', review_status='-', rs='-1', phenotype_ids=('MONDO:MONDO:0016419', 'MedGen:C0346153', 'OMIM:114480', 'Orphanet:227535'), phenotypes=('Fam...(truncated) 8,671,400 {'size': 309655} 2026-01-28 20:30:52
pypath.inputs.collectri.collectri_interactions 2026-01-28 23:01:24 2026-01-28 23:01:47 22.98 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 {} 2026-01-28 23:01:24
pypath.inputs.collectri.collectri_raw 2026-01-28 23:01:47 2026-01-28 23:01:47 0.12 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 {} 2026-01-28 23:01:47
pypath.inputs.compath.compath_mappings 2026-01-28 23:01:47 2026-01-28 23:01:48 0.59 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 {} 2026-01-28 23:01:47
pypath.inputs.compleat.compleat_complexes 2026-01-28 23:01:48 2026-01-28 23:01:52 3.84 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 {} 2026-01-28 23:01:48
pypath.inputs.compleat.compleat_raw 2026-01-28 23:01:52 2026-01-28 23:01:52 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 {} 2026-01-28 23:01:52
pypath.inputs.complexportal.complexportal_complexes 2026-01-28 23:01:52 2026-01-28 23:04:30 157.50 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) 2,343 {'size': 68} 2026-01-28 23:01:52
pypath.inputs.comppi.comppi_interaction_locations 2026-01-28 23:04:30 2026-01-28 23:04:43 13.21 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) 587,911 {'size': 170} 2026-01-28 23:04:30
pypath.inputs.comppi.comppi_locations 2026-01-28 23:04:43 2026-01-28 23:04:56 13.63 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='membrane', score=0.8), Comp...(truncated) 22,789 {'size': -8} 2026-01-28 23:04:43
pypath.inputs.connectomedb.connectomedb_annotations 2026-01-28 23:04:56 2026-01-28 23:04:57 0.39 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) 1,429 {'size': 1} 2026-01-28 23:04:56
pypath.inputs.connectomedb.connectomedb_interactions 2026-01-28 23:04:57 2026-01-28 23:04:57 0.02 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 {} 2026-01-28 23:04:57
pypath.inputs.corum.corum_complexes 2026-01-28 23:04:57 2026-01-28 23:04:58 1.36 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 {} 2026-01-28 23:04:57
pypath.inputs.cosmic.cancer_gene_census_annotations 2026-01-28 23:04:58 2026-01-28 23:04:58 0.22 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 {} 2026-01-28 23:04:58
pypath.inputs.cosmic.cancer_gene_census_raw 2026-01-28 23:04:58 2026-01-28 23:04:58 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 {} 2026-01-28 23:04:58
pypath.inputs.cpad.cpad_annotations 2026-01-28 23:04:58 2026-01-28 23:06:59 120.29 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 {} 2026-01-28 23:04:58
pypath.inputs.cpad.cpad_pathway_cancer 2026-01-28 23:06:59 2026-01-28 23:06:59 0.06 tuple ({'Glioma': {CpadPathwayCancer(pathway='Mitochondrial signaling pathway', cancer='Glioma', pathway_category='Apoptosis', effect_on_cancer='Activating', effect_on_cancer_outcome='induce brain glioma cell apoptosis and cell cycle arrest'), CpadPathwayCancer(pathway='TGF-beta signaling pathway', cancer...(truncated) 2 {} 2026-01-28 23:06:59
pypath.inputs.cpad.get_cpad 2026-01-28 23:06:59 2026-01-28 23:06:59 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 {} 2026-01-28 23:06:59
pypath.inputs.cpdb.cpdb_interactions 2026-01-28 23:06:59 2026-01-28 23:07:32 33.50 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 {} 2026-01-28 23:06:59
pypath.inputs.cpdb.cpdb_interactions_ltp 2026-01-28 23:07:33 2026-01-28 23:07:35 2.14 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 {} 2026-01-28 23:07:33
pypath.inputs.credentials.credentials 
Not calling `pypath.inputs.credentials.credentials`, not enough arguments.
 {} never
pypath.inputs.cspa.cspa_annotations 2026-01-28 23:07:35 2026-01-28 23:07:36 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 {} 2026-01-28 23:07:35
pypath.inputs.cspa.cspa_cell_type_annotations 2026-01-28 23:07:36 2026-01-28 23:07:37 1.44 dict {'A1A5B4': {CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='MedB1', v...(truncated) 1,410 {} 2026-01-28 23:07:36
pypath.inputs.cspa.cspa_cell_types 2026-01-28 23:07:37 2026-01-28 23:07:38 0.40 dict {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'P0DN37': None, 'A0A0B4J2A2': 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 {} 2026-01-28 23:07:37
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 2026-01-28 23:07:38 2026-01-28 23:07:40 2.30 dict {'Q9NPC4': {CytosigAnnotation(cytokine='P05231', score=0.0084669266516721, cytokine_genesymbol='IL6', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P09038', score=-0.0414681704910361, cytokine_genesymbol='FGF2', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='O95390', score=0.107...(truncated) 4,887 {} 2026-01-28 23:07:38
pypath.inputs.cytosig.cytosig_df 2026-01-28 23:07:40 2026-01-28 23:07:40 0.04 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 {} 2026-01-28 23:07:40
pypath.inputs.dbptm.dbptm_enzyme_substrate 2026-01-28 23:07:40 2026-01-28 23:08:03 22.09 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 {} 2026-01-28 23:07:40
pypath.inputs.dbptm.dbptm_interactions 2026-01-28 23:08:03 2026-01-28 23:08:04 1.26 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 {} 2026-01-28 23:08:03
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 2026-01-28 23:08:04 2026-01-28 23:08:58 54.14 list [DdinterInteraction(drug1_id='DDInter1074', drug1_name='Liothyronine', drug2_id='DDInter132', drug2_name='Atomoxetine', level='Unknown'), DdinterInteraction(drug1_id='DDInter1388', drug1_name='Pantoprazole', drug2_id='DDInter1815', drug2_name='Tiotropium', level='Unknown'), DdinterInteraction(drug1_...(truncated) 160,235 {} 2026-01-28 23:08:04
pypath.inputs.ddinter.ddinter_mappings 2026-01-28 23:08:59 2026-01-28 23:51:12 2,533.66 list [DdinterIdentifiers(ddinter='DDInter280', drugbank='DB08907', chembl='CHEMBL2048484', pubchem='175427146'), DdinterIdentifiers(ddinter='DDInter1827', drugbank='DB00797', chembl='CHEMBL770', pubchem='46505641'), DdinterIdentifiers(ddinter='DDInter36', drugbank='DB09043', chembl=None, pubchem='3479103...(truncated) 1,939 {} 2026-01-28 23:08:59
pypath.inputs.ddinter.ddinter_n_drugs 2026-01-28 23:51:12 2026-01-28 23:51:13 0.43 int 1939 0 {} 2026-01-28 23:51:12
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2026-01-28 23:51:13 2026-01-28 23:51:13 0.16 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 {} 2026-01-28 23:51:13
pypath.inputs.depod.depod_enzyme_substrate 2026-01-28 23:51:13 2026-01-28 23:51:13 0.41 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 {} 2026-01-28 23:51:13
pypath.inputs.depod.depod_interactions 2026-01-28 23:51:13 2026-01-28 23:51:13 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 {} 2026-01-28 23:51:13
pypath.inputs.dgidb.dgidb_annotations 2026-01-28 23:51:13 2026-01-28 23:51:21 7.61 dict {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), DgidbAnnotation(category='TRANSCRIPTION FACTOR COMPLEX', source='GO'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='GO'), DgidbA...(truncated) 9,972 {'size': -1} 2026-01-28 23:51:13
pypath.inputs.dgidb.dgidb_interactions 2026-01-28 23:51:21 2026-01-28 23:51:31 10.37 list [DgidbInteraction(genesymbol='KDM4A', gene_concept_id='hgnc:22978', resource='DTC', type='NULL', drug_name='MALEIC ACID', drug_concept_id='rxcui:1426330', score='0.059532507', approved='TRUE', anti_neoplastic='FALSE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='ERBB2', gene_concept_id='hgnc...(truncated) 84,175 {} 2026-01-28 23:51:21
pypath.inputs.dip.dip_interactions 2026-01-28 23:51:31 2026-01-28 23:51:32 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 {} 2026-01-28 23:51:31
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 2026-01-28 23:51:32 2026-01-28 23:51:32 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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:13
pypath.inputs.diseases.experiments_full 2026-01-28 23:51:32 2026-01-28 23:51:32 0.04 
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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:13
pypath.inputs.diseases.knowledge_filtered 2026-01-28 23:51:32 2026-01-28 23:51:32 0.04 
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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:15
pypath.inputs.diseases.knowledge_full 2026-01-28 23:51:32 2026-01-28 23:51:32 0.03 
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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:15
pypath.inputs.diseases.textmining_filtered 2026-01-28 23:51:32 2026-01-28 23:51:32 0.04 
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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:15
pypath.inputs.diseases.textmining_full 2026-01-28 23:51:32 2026-01-28 23:51:32 0.04 
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__20260128-202402/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
    for line in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:18:17
pypath.inputs.domino.domino_ddi 2026-01-28 23:51:32 2026-01-28 23:51:35 2.57 list [<pypath.internals.intera.DomainDomain object at 0x7f3b40694310>, <pypath.internals.intera.DomainDomain object at 0x7f3b40694810>, <pypath.internals.intera.DomainDomain object at 0x7f3b40694710>, <pypath.internals.intera.DomainDomain object at 0x7f3b406971d0>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294 {} 2026-01-28 23:51:32
pypath.inputs.domino.domino_enzsub 2026-01-28 23:51:35 2026-01-28 23:51:35 0.63 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f3d505c4210>, <pypath.internals.intera.DomainDomain object at 0x7f3d505c6590>, <pypath.internals.intera.DomainDomain object at 0x7f3d505c4bd0>, <pypath.internals.intera.DomainDomain object at 0x7f3d505c5e50>, <pypath.internals.intera.Domain...(truncated) 2 {} 2026-01-28 23:51:35
pypath.inputs.domino.domino_interactions 2026-01-28 23:51:35 2026-01-28 23:51:36 0.35 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 {} 2026-01-28 23:51:35
pypath.inputs.domino.get_domino 2026-01-28 23:51:36 2026-01-28 23:51:36 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 {} 2026-01-28 23:51:36
pypath.inputs.dorothea.dorothea_full_raw 2026-01-28 23:51:36 2026-01-28 23:51:46 9.95 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 {} 2026-01-28 23:51:36
pypath.inputs.dorothea.dorothea_interactions 2026-01-28 23:51:46 2026-01-28 23:52:00 14.15 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 {} 2026-01-28 23:51:46
pypath.inputs.dorothea.dorothea_rda_raw 2026-01-28 23:52:00 2026-01-28 23:52:02 1.85 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 {} 2026-01-28 23:52:00
pypath.inputs.dorothea.dorothea_rda_raw 2026-01-28 23:52:02 2026-01-28 23:52:04 1.36 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 {} 2026-01-28 23:52:02
pypath.inputs.dorothea.dorothea_interactions 2026-01-28 23:52:04 2026-01-28 23:52:18 14.24 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 {} 2026-01-28 23:52:04
pypath.inputs.dorothea.dorothea_old_csv 2026-01-28 23:52:18 2026-01-28 23:52:18 0.43 
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__20260128-202402/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
{} 2025-08-12 05:02:53
pypath.inputs.drugcentral.drugcentral_drugs 2026-01-28 23:52:18 2026-01-28 23:52:20 1.97 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 {} 2026-01-28 23:52:18
pypath.inputs.drugcentral.drugcentral_interactions 2026-01-28 23:52:20 2026-01-28 23:52:22 1.68 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 {} 2026-01-28 23:52:20
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 2026-01-28 23:52:22 2026-01-28 23:52:22 0.18 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 {} 2026-01-28 23:52:22
pypath.inputs.elm.elm_domains 2026-01-28 23:52:22 2026-01-28 23:52:23 0.81 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 {} 2026-01-28 23:52:22
pypath.inputs.elm.elm_instances 2026-01-28 23:52:23 2026-01-28 23:55:31 187.83 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} 2026-01-28 23:52:23
pypath.inputs.elm.elm_interactions 2026-01-28 23:55:31 2026-01-28 23:55:31 0.15 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 {} 2026-01-28 23:55:31
pypath.inputs.embopress.embopress_supplementary 
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments.
 {} never
pypath.inputs.embrace.embrace_annotations 2026-01-28 23:55:31 2026-01-28 23:55:35 3.93 dict {} 0 {'size': -844} 2026-01-28 23:55:31
pypath.inputs.embrace.embrace_interactions 2026-01-28 23:55:35 2026-01-28 23:55:35 0.10 list [] 0 {'size': -1273} 2026-01-28 23:55:35
pypath.inputs.embrace.embrace_raw 2026-01-28 23:55:35 2026-01-28 23:55:35 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 {} 2026-01-28 23:55:35
pypath.inputs.embrace.embrace_translated 2026-01-28 23:55:35 2026-01-28 23:55:35 0.10 list [EmbraceRawRecord(ligand_symbol=None, 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=None, receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_receptor=...(truncated) 1,710 {'size': -122} 2026-01-28 23:55:35
pypath.inputs.encode.encode_tf_mirna_interactions 2026-01-28 23:55:35 2026-01-28 23:55:36 0.57 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 {} 2026-01-28 23:55:35
pypath.inputs.ensembl.ensembl_organisms 2026-01-28 23:55:36 2026-01-28 23:55:36 0.49 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 {} 2026-01-28 23:55:36
pypath.inputs.eutils.esummary 
Not calling `pypath.inputs.eutils.esummary`, not enough arguments.
 {} never
pypath.inputs.exocarta.get_exocarta 2026-01-28 23:55:36 2026-01-28 23:55:38 1.72 
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__20260128-202402/pypath_git/pypath/inputs/exocarta.py", line 96, in _get_exocarta_vesiclepedia
    _ = next(c.result)
        ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
{'broke': True} 2025-11-29 23:23:35
pypath.inputs.exocarta.get_vesiclepedia 2026-01-28 23:55:38 2026-01-28 23:55:41 2.46 
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__20260128-202402/pypath_git/pypath/inputs/exocarta.py", line 96, in _get_exocarta_vesiclepedia
    _ = next(c.result)
        ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
{'broke': True} 2025-11-29 23:23:57
pypath.inputs.expasy.expasy_enzyme_classes 2026-01-28 23:55:41 2026-01-28 23:55:41 0.08 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) 355 {'size': 1} 2026-01-28 23:55:41
pypath.inputs.expasy.expasy_enzymes 2026-01-28 23:55:41 2026-01-28 23:55:42 1.00 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) 8,441 {'size': 36} 2026-01-28 23:55:41
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 2026-01-28 23:55:42 2026-01-28 23:56:36 53.85 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 {} 2026-01-28 23:55:42
pypath.inputs.go.get_goslim 2026-01-28 23:56:36 2026-01-28 23:56:37 1.76 
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__20260128-202402/pypath_git/pypath/inputs/go.py", line 962, in get_goslim
    for l in data.split('\n'):
             ^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
{'broke': True} 2025-11-29 23:25:59
pypath.inputs.go.go_ancestors_quickgo 2026-01-28 23:56:37 2026-01-29 00:02:42 364.73 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) 3 {} 2026-01-28 23:56:37
pypath.inputs.go.go_ancestors_goose 2026-01-29 00:02:42 2026-01-29 00:02:42 0.17 
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__20260128-202402/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-08-12 05:19:26
pypath.inputs.go.go_ancestors_quickgo 2026-01-29 00:02:42 2026-01-29 00:02:47 4.69 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) 3 {} 2026-01-29 00:02:42
pypath.inputs.go.go_annotations_goa 2026-01-29 00:02:47 2026-01-29 00:02:49 2.25 dict {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6I0': {'GO:0019814', 'GO:0005576', 'G...(truncated) 3 {} 2026-01-29 00:02:47
pypath.inputs.go.go_annotations_all 2026-01-29 00:02:49 2026-01-29 00:02:56 6.22 dict {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0003723', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0694', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) 19,700 {'size': -5} 2026-01-29 00:02:49
pypath.inputs.go.go_annotations_goa 2026-01-29 00:02:58 2026-01-29 00:02:59 1.29 dict {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005576', 'GO:0005886'}, 'A0A075B6I0': {'GO:0019814', 'GO:0005576', 'G...(truncated) 3 {} 2026-01-29 00:02:58
pypath.inputs.go.go_annotations_goose 2026-01-29 00:02:59 2026-01-29 00:02:59 0.12 
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__20260128-202402/pypath_git/pypath/inputs/go.py", line 860, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-08-12 05:19:43
pypath.inputs.go.go_annotations_uniprot 2026-01-29 00:02:59 2026-01-29 00:03:10 10.42 dict {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0070330'], 'A0A096LP01': ['GO:0005739', 'GO:0005741', 'GO:0019901', 'GO:0044325'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'],...(truncated) 19,406 {'size': 16} 2026-01-29 00:02:59
pypath.inputs.go.go_descendants_quickgo 2026-01-29 00:03:10 2026-01-29 00:03:14 4.52 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) 3 {} 2026-01-29 00:03:10
pypath.inputs.go.go_descendants_goose 2026-01-29 00:03:14 2026-01-29 00:03:14 0.09 
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__20260128-202402/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__20260128-202402/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-08-12 05:19:59
pypath.inputs.go.go_descendants_quickgo 2026-01-29 00:03:14 2026-01-29 00:03:19 4.47 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) 3 {} 2026-01-29 00:03:14
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 2026-01-29 00:03:19 2026-01-29 00:03:23 3.67 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2026-01-29 00:03:19
pypath.inputs.go.go_terms_goose 2026-01-29 00:03:23 2026-01-29 00:03:23 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__20260128-202402/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'
{} 2025-08-12 05:20:07
pypath.inputs.go.go_terms_quickgo 2026-01-29 00:03:23 2026-01-29 00:03:26 3.74 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2026-01-29 00:03:23
pypath.inputs.gpcrdb.gpcrdb_annotations 2026-01-29 00:03:26 2026-01-29 00:03:27 0.22 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 {} 2026-01-29 00:03:26
pypath.inputs.graphviz.graphviz_attrs 2026-01-29 00:03:27 2026-01-29 00:03:29 2.23 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 {} 2026-01-29 00:03:27
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
 {} never
pypath.inputs.guide2pharma.guide2pharma_download 2026-01-29 00:03:29 2026-01-29 00:03:38 9.33 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 {} 2026-01-29 00:03:29
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
 {} never
pypath.inputs.gutmgene.gutmgene_annotations 2026-01-29 00:03:38 2026-01-29 00:03:39 0.30 dict {'P05112': {GutmgeneAnnotation(gut_microbiota='Lacticaseibacillus paracasei', gut_microbiota_ncbi_id='1597', rank='species', strain='JS1', alteration='inhibition', throughput='low-throughput', associative_mode='causally', sample='NHDF cells', experimental_method='in vitro bacterial culture,cell cult...(truncated) 111 {} 2026-01-29 00:03:38
pypath.inputs.gutmgene.gutmgene_raw 2026-01-29 00:03:39 2026-01-29 00:03:39 0.01 list [GutmgeneRaw(index='91', pmid='30507089', gut_microbiota='Bacteroides fragilis', gut_microbiota_ncbi_id='817', rank='species', strain='ATCC 23745', gene='IL4', gene_id='3565', alteration='activation', throughput='low-throughput', associative_mode='causally', organism='human', sample='Caco-2 cells', ...(truncated) 243 {} 2026-01-29 00:03:39
pypath.inputs.havugimana.get_havugimana 2026-01-29 00:03:39 2026-01-29 00:03:39 0.21 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 {} 2026-01-29 00:03:39
pypath.inputs.havugimana.havugimana_complexes 2026-01-29 00:03:39 2026-01-29 00:03:39 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 {} 2026-01-29 00:03:39
pypath.inputs.hgnc.hgnc_genegroups 2026-01-29 00:03:39 2026-01-29 00:03:41 2.43 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) 15,788 {'size': 51} 2026-01-29 00:03:39
pypath.inputs.hint.hint_interactions 2026-01-29 00:03:41 2026-01-29 00:04:06 24.96 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 {} 2026-01-29 00:03:41
pypath.inputs.hint.hint_raw 2026-01-29 00:04:06 2026-01-29 00:04:06 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 {} 2026-01-29 00:04:06
pypath.inputs.hippie.hippie_interactions 2026-01-29 00:04:06 2026-01-29 00:04:23 16.54 list [HippieInteraction(id_a='O00295', id_b='Q9UHR6', score=0.82, methods=None, references=('28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='Q12983', id_b='Q12983', score=0.89, methods=None, references=('10381623', '10625696', '16169070', '16189514', '25416956', '27107012',...(truncated) 102,486 {'size': 77} 2026-01-29 00:04:06
pypath.inputs.homologene.get_homologene 2026-01-29 00:04:23 2026-01-29 00:05:39 75.83 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 {} 2026-01-29 00:04:23
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 2026-01-29 00:05:39 2026-01-29 00:05:39 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 {} 2026-01-29 00:05:39
pypath.inputs.hpmr.hpmr_annotations 2026-01-29 00:05:39 2026-01-29 00:05:39 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 {} 2026-01-29 00:05:39
pypath.inputs.hpmr.hpmr_complexes 2026-01-29 00:05:39 2026-01-29 00:05:39 0.00 dict {} 0 {} 2026-01-29 00:05:39
pypath.inputs.hpmr.hpmr_interactions 2026-01-29 00:05:39 2026-01-29 00:05:39 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 {} 2026-01-29 00:05:39
pypath.inputs.hpo.hpo_annotations 2026-01-29 00:05:39 2026-01-29 00:05:42 3.37 dict {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0001264'), HpoAnnotation(entrez_ge...(truncated) 5,140 {'size': 19} 2026-01-29 00:05:39
pypath.inputs.hpo.hpo_diseases 2026-01-29 00:05:42 2026-01-29 00:05:46 4.02 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:620732', name='Neurodevelopmental disorder with hyperki...(truncated) 11,582 {'size': 94} 2026-01-29 00:05:42
pypath.inputs.hpo.hpo_ontology 2026-01-29 00:05:47 2026-01-29 00:05:48 1.26 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 {} 2026-01-29 00:05:47
pypath.inputs.hpo.hpo_terms 2026-01-29 00:05:48 2026-01-29 00:05:49 0.55 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) 19,408 {'size': 15} 2026-01-29 00:05:48
pypath.inputs.hprd.get_hprd 2026-01-29 00:05:49 2026-01-29 00:05:53 4.29 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 {} 2026-01-29 00:05:49
pypath.inputs.hprd.hprd_enzyme_substrate 2026-01-29 00:05:53 2026-01-29 00:05:55 1.29 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 {} 2026-01-29 00:05:53
pypath.inputs.hprd.hprd_interactions 2026-01-29 00:05:55 2026-01-29 00:05:56 1.26 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 {} 2026-01-29 00:05:55
pypath.inputs.hprd.hprd_interactions_htp 2026-01-29 00:05:56 2026-01-29 00:05:58 1.67 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 {} 2026-01-29 00:05:56
pypath.inputs.htri.htri_interactions 2026-01-29 00:05:58 2026-01-29 00:06:28 30.27 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 {} 2026-01-29 00:05:58
pypath.inputs.humancellmap.humancellmap_annotations 2026-01-29 00:06:28 2026-01-29 00:06:29 1.08 dict {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) 4,384 {} 2026-01-29 00:06:28
pypath.inputs.humap.humap1_complexes 2026-01-29 00:06:29 2026-01-29 00:06:29 0.23 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) 4,547 {'size': 2} 2026-01-29 00:06:29
pypath.inputs.humap.humap2and3_complexes 2026-01-29 00:06:29 2026-01-29 00:06:31 1.65 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) 15,443 {'size': 14} 2026-01-29 00:06:29
pypath.inputs.humsavar.uniprot_variants 2026-01-29 00:06:31 2026-01-29 00:06:37 5.63 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 {} 2026-01-29 00:06:31
pypath.inputs.huri.hi_i_interactions 2026-01-29 00:06:37 2026-01-29 00:06:39 1.98 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:11:38
pypath.inputs.huri.hi_ii_interactions 2026-01-29 00:06:39 2026-01-29 00:06:40 1.08 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:11:40
pypath.inputs.huri.hi_union_interactions 2026-01-29 00:06:40 2026-01-29 00:06:41 1.09 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:11:49
pypath.inputs.huri.huri_interactions 2026-01-29 00:06:41 2026-01-29 00:06:42 1.09 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:12:20
pypath.inputs.huri.lit_bm_13_interactions 2026-01-29 00:06:42 2026-01-29 00:06:43 1.52 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 {} 2026-01-29 00:06:42
pypath.inputs.huri.lit_bm_17_interactions 2026-01-29 00:06:43 2026-01-29 00:06:47 3.40 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 {} 2026-01-29 00:06:43
pypath.inputs.huri.lit_bm_interactions 2026-01-29 00:06:47 2026-01-29 00:06:48 1.09 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 279, in lit_bm_interactions
    for row in c.result:
TypeError: 'NoneType' object is not iterable
{} 2025-08-31 05:12:46
pypath.inputs.huri.rolland_hi_ii_14 2026-01-29 00:06:48 2026-01-29 00:06:49 1.40 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 {} 2026-01-29 00:06:48
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 2026-01-29 00:06:49 2026-01-29 00:06:50 1.08 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:12:49
pypath.inputs.huri.yu2011_interactions 2026-01-29 00:06:50 2026-01-29 00:06:51 1.08 
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__20260128-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
    c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2025-08-31 05:12:50
pypath.inputs.i3d.get_i3d 2026-01-29 00:06:51 2026-01-29 00:07:00 8.18 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 {} 2026-01-29 00:06:51
pypath.inputs.icellnet.icellnet_annotations 2026-01-29 00:07:00 2026-01-29 00:07:00 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 {'size': 1} 2026-01-29 00:07:00
pypath.inputs.icellnet.icellnet_complexes 2026-01-29 00:07:00 2026-01-29 00:07:00 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 {} 2026-01-29 00:07:00
pypath.inputs.icellnet.icellnet_interactions 2026-01-29 00:07:00 2026-01-29 00:07:00 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 {} 2026-01-29 00:07:00
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 2026-01-29 00:07:00 2026-01-29 00:07:04 3.61 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 {} 2026-01-29 00:07:00
pypath.inputs.instruct.get_instruct 2026-01-29 00:07:04 2026-01-29 00:07:04 0.45 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 {} 2026-01-29 00:07:04
pypath.inputs.instruct.get_instruct_offsets 2026-01-29 00:07:04 2026-01-29 00:07:05 0.63 NoneType None 0 {} 2026-01-29 00:07:04
pypath.inputs.intact.intact_interactions 2026-01-29 00:07:05 2026-01-29 00:10:20 194.84 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='P49418', id_b='O43426', id_type_a='uniprot', i...(truncated) 79,206 {'size': 662} 2026-01-29 00:07:05
pypath.inputs.integrins.get_integrins 2026-01-29 00:10:20 2026-01-29 00:10:21 0.52 set {'Q13797', 'P26010', 'Q13683', 'P16144', 'P20701', 'P18084', 'P06756', 'P05107', 'P11215', 'P05106', 'P20702', 'Q13349', 'Q9UKX5', 'P08514', 'P38570', 'P18564', 'P26012', 'P53708', 'P23229', 'P26006', 'P05556', 'P08648', 'O75578', 'P17301', 'P56199'} 25 {} 2026-01-29 00:10:20
pypath.inputs.interpro.interpro2go_annotations 2026-01-29 00:10:21 2026-01-29 00:10:22 1.71 
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__20260128-202402/pypath_git/pypath/inputs/interpro.py", line 350, in interpro2go_annotations
    for r in c.result:
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-29 23:37:08
pypath.inputs.interpro.interpro_annotations 2026-01-29 00:10:22 2026-01-29 00:10:23 0.86 defaultdict defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR038178', organism='9606', start='209', end='294'), InterproAnnotation(interpro_id='IPR000001', organism='9606', start='126', end='208'), InterproAnnotation(interpro_id='IPR018056', organism='9606', start='353', end='365'), Int...(truncated) 16,611 {} 2026-01-29 00:10:22
pypath.inputs.interpro.interpro_entries 2026-01-29 00:10:23 2026-01-29 00:10:40 16.34 list [InterproEntry(interpro_id='IPR000001', protein_count='21448', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) 49,674 {} 2026-01-29 00:10:23
pypath.inputs.interpro.interpro_xrefs 
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments.
 {} never
pypath.inputs.intogen.intogen_annotations 2026-01-29 00:10:40 2026-01-29 00:10:41 1.07 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 {} 2026-01-29 00:10:40
pypath.inputs.ipi.ipi_uniprot 2026-01-29 00:10:41 2026-01-29 00:10:41 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 {} 2026-01-29 00:10:41
pypath.inputs.iptmnet.iptmnet_interactions 2026-01-29 00:10:41 2026-01-29 00:12:12 91.43 list [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) 15,834 {} 2026-01-29 00:10:41
pypath.inputs.italk.italk_annotations 2026-01-29 00:12:12 2026-01-29 00:12:13 0.66 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) 1,415 {'size': 1} 2026-01-29 00:12:12
pypath.inputs.italk.italk_interactions 2026-01-29 00:12:13 2026-01-29 00:12:13 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 {} 2026-01-29 00:12:13
pypath.inputs.italk.italk_raw 2026-01-29 00:12:13 2026-01-29 00:12:13 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 {} 2026-01-29 00:12:13
pypath.inputs.kea.kea_enzyme_substrate 2026-01-29 00:12:13 2026-01-29 00:12:15 1.74 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 {} 2026-01-29 00:12:13
pypath.inputs.kea.kea_interactions 2026-01-29 00:12:15 2026-01-29 00:12:15 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 {} 2026-01-29 00:12:15
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
 {} never
pypath.inputs.kegg.kegg_interactions 2026-01-29 00:12:15 2026-01-29 00:30:31 1,096.15 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) 15,272 {'fixed': True} 2026-01-29 00:12:15
pypath.inputs.kegg.kegg_medicus 2026-01-29 00:30:31 2026-01-29 00:30:58 26.75 set {KeggMedicusRawInteraction(id_a='C01245', id_b='C00076', name_a='D-myo-Inositol 1,4,5-trisphosphate', name_b='Calcium cation', effect='stimulation', itype='post_translational', pw_type='reference', type_a='metabolite', type_b='metabolite', network_id='N00301'), KeggMedicusRawInteraction(id_a='5291',...(truncated) 12,946 {} 2026-01-29 00:30:31
pypath.inputs.kegg.kegg_medicus_complexes 2026-01-29 00:30:58 2026-01-29 00:30:58 0.44 dict {'COMPLEX:O60583_P42568_Q8TEK3': Complex: COMPLEX:O60583_P42568_Q8TEK3, 'COMPLEX:P15918_P55895': Complex: COMPLEX:P15918_P55895, 'COMPLEX:O75694_P35658_P37198_P49792_P57740_Q12769_Q53GS7_Q5SRE5_Q7Z3B4_Q8N1F7_Q8NFH3_Q8NFH4_Q8NFH5_Q8TEM1_Q8WUM0_Q92621_Q96EE3_Q96HA1_Q99567_Q9BTX1_Q9BVL2_Q9BW27_Q9UMR2':...(truncated) 530 {'size': 2} 2026-01-29 00:30:58
pypath.inputs.kegg.kegg_medicus_interactions 2026-01-29 00:30:58 2026-01-29 00:30:59 0.37 list [KeggMedicusInteraction(id_a='P45880', id_b='P99999', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='Q07889', id_b='P01111', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) 9,539 {'size': 1} 2026-01-29 00:30:58
pypath.inputs.kegg.kegg_pathway_annotations 2026-01-29 00:30:59 2026-01-29 00:31:12 13.50 dict {'Q12852': {KeggPathway(pathway='MAPK signaling pathway')}, 'P29323': {KeggPathway(pathway='Natural killer cell mediated cytotoxicity'), KeggPathway(pathway='Cholinergic synapse'), KeggPathway(pathway='Hepatocellular carcinoma'), KeggPathway(pathway='Acute myeloid leukemia'), KeggPathway(pathway='AG...(truncated) 2,728 {'size': 2} 2026-01-29 00:30:59
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2026-01-29 00:31:12 2026-01-29 00:31:13 1.12 dict {'A8K7J7': {KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway...(truncated) 813 {} 2026-01-29 00:31:12
pypath.inputs.kegg.kegg_pathways 2026-01-29 00:31:13 2026-01-29 00:31:27 13.41 tuple ({'MAPK signaling pathway': {'Q12852', 'P29323', 'P29965', 'Q9UK32', 'P01583', 'Q8IVH8', 'Q9BQ95', 'Q13163', 'Q5STR5', 'P19419', 'Q9Y4K3', 'Q13188', 'P49407', 'P15336', 'Q99558', 'Q9NYL2', 'Q9Y2U5', 'Q92918', 'Q9Y3M2', 'Q9Y4G8', 'P45983', 'P36507', 'P18510', 'P46108', 'Q9UHA4', 'O15111', 'Q96NL6', '...(truncated) 2 {} 2026-01-29 00:31:13
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 2026-01-29 00:31:27 2026-01-29 00:31:32 4.65 
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__20260128-202402/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__20260128-202402/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
    self.load(*args)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
    self._data = {
                 ^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/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__20260128-202402/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
    return entry[0].split(':')[1]
           ~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
{} 2025-08-12 05:47:03
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 2026-01-29 00:31:32 2026-01-29 00:31:32 0.55 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 {} 2026-01-29 00:31:32
pypath.inputs.kirouac2010.kirouac2010_interactions 2026-01-29 00:31:32 2026-01-29 00:31:32 0.18 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 {} 2026-01-29 00:31:32
pypath.inputs.lambert2018.lambert2018_annotations 2026-01-29 00:31:32 2026-01-29 00:31:36 3.68 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 {} 2026-01-29 00:31:32
pypath.inputs.lambert2018.lambert2018_s1_raw 2026-01-29 00:31:36 2026-01-29 00:31:38 2.02 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 {} 2026-01-29 00:31:36
pypath.inputs.laudanna.laudanna_directions 2026-01-29 00:31:38 2026-01-29 00:31:38 0.46 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 {} 2026-01-29 00:31:38
pypath.inputs.laudanna.laudanna_effects 2026-01-29 00:31:38 2026-01-29 00:31:39 0.39 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 {} 2026-01-29 00:31:38
pypath.inputs.li2012.get_li2012 2026-01-29 00:31:39 2026-01-29 00:31:41 2.03 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 {} 2026-01-29 00:31:39
pypath.inputs.li2012.li2012_dmi 2026-01-29 00:31:41 2026-01-29 00:31:51 10.47 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 {} 2026-01-29 00:31:41
pypath.inputs.li2012.li2012_enzyme_substrate 2026-01-29 00:31:51 2026-01-29 00:31:51 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 {} 2026-01-29 00:31:51
pypath.inputs.li2012.li2012_interactions 2026-01-29 00:31:51 2026-01-29 00:31:51 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 {} 2026-01-29 00:31:51
pypath.inputs.lincs.lincs_compounds 2026-01-29 00:31:51 2026-01-29 00:31:53 1.04 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 {} 2026-01-29 00:31:51
pypath.inputs.lmpid.lmpid_dmi 2026-01-29 00:31:53 2026-01-29 00:31:53 0.66 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 {} 2026-01-29 00:31:53
pypath.inputs.lmpid.lmpid_interactions 2026-01-29 00:31:53 2026-01-29 00:31:54 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 {} 2026-01-29 00:31:53
pypath.inputs.lmpid.load_lmpid 2026-01-29 00:31:54 2026-01-29 00:31:54 0.46 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 {} 2026-01-29 00:31:54
pypath.inputs.lncdisease.lncdisease_interactions 2026-01-29 00:31:54 2026-01-29 00:31:55 0.42 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 {} 2026-01-29 00:31:54
pypath.inputs.lncrnadb.lncrnadb_interactions 2026-01-29 00:31:55 2026-01-29 00:31:56 1.05 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 {} 2026-01-29 00:31:55
pypath.inputs.locate.locate_localizations 2026-01-29 00:31:56 2026-01-29 00:32:41 45.55 dict {'P27824': {LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pm...(truncated) 9,475 {'size': -4} 2026-01-29 00:31:56
pypath.inputs.lrdb.lrdb_annotations 2026-01-29 00:32:41 2026-01-29 00:32:42 0.32 dict {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Reactome',), references=()), LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD'), re...(truncated) 1,542 {'size': 6} 2026-01-29 00:32:41
pypath.inputs.lrdb.lrdb_interactions 2026-01-29 00:32:42 2026-01-29 00:32:42 0.03 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 {} 2026-01-29 00:32:42
pypath.inputs.macrophage.macrophage_interactions 2026-01-29 00:32:42 2026-01-29 00:32:42 0.32 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 {} 2026-01-29 00:32:42
pypath.inputs.matrisome.matrisome_annotations 2026-01-29 00:32:42 2026-01-29 00:32:42 0.28 dict {'H0YDN0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C524': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C5S3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 2,500 {'size': -1} 2026-01-29 00:32:42
pypath.inputs.matrixdb.matrixdb_annotations 2026-01-29 00:32:42 2026-01-29 00:32:43 0.78 dict {} 0 {} 2026-01-29 00:32:42
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2026-01-29 00:32:43 2026-01-29 00:32:44 1.43 set {'Q9UKQ2', 'P15018', 'Q8WXW3', 'Q07092', 'Q9Y5Q6', 'P14735', 'A6NJW4', 'P08217', 'Q9H2P0', 'P02814', 'P07339', 'Q14993', 'O43300', 'Q8IWL1', 'Q9Y625', 'P10997', 'Q12904', 'Q8IVG9', 'P08949', 'P41159', 'B2RUY7', 'Q96P20', 'O75882', 'Q96QH8', 'Q5VTE0', 'Q04721', 'O75015', 'P22303', 'Q99466', 'Q9Y240',...(truncated) 2,847 {'size': 7} 2026-01-29 00:32:43
pypath.inputs.matrixdb.matrixdb_interactions 2026-01-29 00:32:44 2026-01-29 00:32:44 0.11 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 {} 2026-01-29 00:32:44
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2026-01-29 00:32:45 2026-01-29 00:32:45 0.07 set set() 0 {} 2026-01-29 00:32:45
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2026-01-29 00:32:45 2026-01-29 00:32:45 0.07 set set() 0 {} 2026-01-29 00:32:45
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2026-01-29 00:32:45 2026-01-29 00:32:46 0.95 set {'P56748', 'Q96KR4', 'O43854', 'P20702', 'Q9NPY3', 'Q13449', 'O15394', 'Q68D78', 'P13612', 'O95297', 'Q9NY15', 'P53708', 'P16150', 'P22105', 'P42081', 'P25942', 'P11215', 'Q49MI3', 'O94856', 'Q59H14', 'Q02763', 'Q5ZPR3', 'Q4G160', 'Q9Y5B2', 'P18827', 'Q9BY67', 'Q13797', 'Q9NZ94', 'Q8WWQ8', 'Q15223',...(truncated) 112 {} 2026-01-29 00:32:45
pypath.inputs.membranome.membranome_annotations 2026-01-29 00:32:46 2026-01-29 00:33:20 34.10 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 {} 2026-01-29 00:32:46
pypath.inputs.mimp.get_kinase_class 2026-01-29 00:33:20 2026-01-29 00:33:20 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 {} 2026-01-29 00:33:20
pypath.inputs.mimp.mimp_enzyme_substrate 2026-01-29 00:33:20 2026-01-29 00:33:23 3.08 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 {} 2026-01-29 00:33:20
pypath.inputs.mimp.mimp_interactions 2026-01-29 00:33:23 2026-01-29 00:33:23 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 {} 2026-01-29 00:33:23
pypath.inputs.mir2disease.mir2disease_interactions 2026-01-29 00:33:23 2026-01-29 00:33:23 0.18 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 {} 2026-01-29 00:33:23
pypath.inputs.mirbase.mirbase_ids 2026-01-29 00:33:23 2026-01-29 00:33:24 0.73 list [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) 2,925 {} 2026-01-29 00:33:23
pypath.inputs.mirbase.mirbase_mature 2026-01-29 00:33:24 2026-01-29 00:33:24 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_mature_all 2026-01-29 00:33:24 2026-01-29 00:33:24 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_mirna 2026-01-29 00:33:24 2026-01-29 00:33:24 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_mirna_mature 2026-01-29 00:33:24 2026-01-29 00:33:24 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_mirna_pre_mature 2026-01-29 00:33:24 2026-01-29 00:33:24 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_organisms 2026-01-29 00:33:24 2026-01-29 00:33:25 0.16 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 {} 2026-01-29 00:33:24
pypath.inputs.mirbase.mirbase_precursor 2026-01-29 00:33:25 2026-01-29 00:33:25 0.05 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 {} 2026-01-29 00:33:25
pypath.inputs.mirbase.mirbase_precursor_all 2026-01-29 00:33:25 2026-01-29 00:33:25 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 {} 2026-01-29 00:33:25
pypath.inputs.mirbase.mirbase_precursor_to_mature 2026-01-29 00:33:25 2026-01-29 00:33:25 0.09 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 {} 2026-01-29 00:33:25
pypath.inputs.mirbase.mirbase_taxid 2026-01-29 00:33:25 2026-01-29 00:33:25 0.00 str 'hsa' 3 {} 2026-01-29 00:33:25
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2026-01-29 00:33:25 2026-01-29 00:33:25 0.17 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 {} 2026-01-29 00:33:25
pypath.inputs.mirecords.mirecords_interactions 2026-01-29 00:33:25 2026-01-29 00:33:25 0.39 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 {} 2026-01-29 00:33:25
pypath.inputs.mirtarbase.mirtarbase_interactions 2026-01-29 00:33:25 2026-01-29 00:39:39 373.78 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 {} 2026-01-29 00:33:25
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.mitab.mitab_intact 2026-01-29 00:39:39 2026-01-29 00:42:32 173.32 list ['#ID(s) interactor A\tID(s) interactor B\tAlt. ID(s) interactor A\tAlt. ID(s) interactor B\tAlias(es) interactor A\tAlias(es) interactor B\tInteraction detection method(s)\tPublication 1st author(s)\tPublication Identifier(s)\tTaxid interactor A\tTaxid interactor B\tInteraction type(s)\tSource data...(truncated) 1,240,728 {'size': 59316} 2026-01-29 00:39:39
pypath.inputs.mitab.mitab_interactions 2026-01-29 00:42:32 2026-01-29 00:42:32 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__20260128-202402/pypath_git/pypath/inputs/mitab.py", line 438, in mitab_interactions
    raise ValueError("Must specify 'resource'")
ValueError: Must specify 'resource'
{} 2025-11-18 23:16:47
pypath.inputs.mitab.mitab_parse_aliases 
Not calling `pypath.inputs.mitab.mitab_parse_aliases`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_confidence 
Not calling `pypath.inputs.mitab.mitab_parse_confidence`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_features 
Not calling `pypath.inputs.mitab.mitab_parse_features`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_identifier 
Not calling `pypath.inputs.mitab.mitab_parse_identifier`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_identifiers 
Not calling `pypath.inputs.mitab.mitab_parse_identifiers`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_mi_term 
Not calling `pypath.inputs.mitab.mitab_parse_mi_term`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_mi_terms 
Not calling `pypath.inputs.mitab.mitab_parse_mi_terms`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_parameters 
Not calling `pypath.inputs.mitab.mitab_parse_parameters`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_pubmeds 
Not calling `pypath.inputs.mitab.mitab_parse_pubmeds`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_parse_taxid 
Not calling `pypath.inputs.mitab.mitab_parse_taxid`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_signor 2026-01-29 00:42:32 2026-01-29 00:42:43 10.97 list ['\ufeff#ID(s) interactor A\tID(s) interactor B\tAlt. ID(s) interactor A\tAlt. ID(s) interactor B\tAlias(es) interactor A\tAlias(es) interactor B\tInteraction detection method(s)\tPublication 1st author(s)\tPublication Identifier(s)\tTaxid interactor A\tTaxid interactor B\tInteraction type(s)\tSourc...(truncated) 38,323 {'size': 356} 2026-01-29 00:42:32
pypath.inputs.mppi.mppi_interactions 2026-01-29 00:42:43 2026-01-29 00:42:44 0.26 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 {} 2026-01-29 00:42:43
pypath.inputs.msigdb.msigdb_annotations 2026-01-29 00:42:44 2026-01-29 00:43:23 38.93 dict {'Q16873': {MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='LIU_VAV3_PROSTATE_CARCINOGENESIS_UP'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='NAKAJIMA_MAST_CELL'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE17721_LPS_VS_GARDIQUIM...(truncated) 20,120 {'size': 9} 2026-01-29 00:42:44
pypath.inputs.msigdb.msigdb_download 2026-01-29 00:43:24 2026-01-29 00:43:41 16.37 dict {'MT': {'MT-CO1', 'MT-TA', 'MT-TL2', 'MT-TQ', 'MT-ATP6', 'MT-CYB', 'MT-TW', 'MT-TH', 'MT-TK', 'MT-ND4L', 'MT-TN', 'MT-ND4', 'MT-ND1', 'MT-ND5', 'MT-CO3', 'MT-TG', 'MT-TC', 'MT-TR', 'MT-TT', 'MT-TS1', 'MT-ND3', 'MT-ND2', 'MT-TY', 'MT-TI', 'MT-TF', 'MT-ATP8', 'MT-TM', 'MT-RNR1', 'MT-TV', 'MT-ND6', 'MT...(truncated) 35,134 {} 2026-01-29 00:43:24
pypath.inputs.msigdb.msigdb_download_collections 2026-01-29 00:43:41 2026-01-29 00:43:41 0.45 dict {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'ACAA2', 'SOD1', 'ECHS1', 'ACADL', 'CPT2', 'LPCAT3', 'SAMM50', 'SLC1A5', 'LEP', 'IMMT', 'DBT', 'ANGPT1', 'PFKFB3', 'CYP4B1', 'BCL2L13', 'SOWAHC', 'PEX14', 'PPARG', 'RETSAT', 'GPAT4', 'BCL6', 'COQ5', 'COL15A1', 'CAVIN2', 'MGST3', 'UQCRQ', 'TOB1', 'LP...(truncated) 20 {} 2026-01-29 00:43:41
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2026-01-29 00:43:42 2026-01-29 00:43:42 0.44 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 {} 2026-01-29 00:43:42
pypath.inputs.negatome.negatome_interactions 2026-01-29 00:43:42 2026-01-29 00:43:42 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 {} 2026-01-29 00:43:42
pypath.inputs.netbiol.arn_interactions 2026-01-29 00:43:42 2026-01-29 00:43:42 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 {} 2026-01-29 00:43:42
pypath.inputs.netbiol.nrf2ome_interactions 2026-01-29 00:43:42 2026-01-29 00:43:43 0.11 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 {} 2026-01-29 00:43:42
pypath.inputs.netpath.netpath_interactions 2026-01-29 00:43:43 2026-01-29 00:43:44 1.97 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 {} 2026-01-29 00:43:43
pypath.inputs.netpath.netpath_names 2026-01-29 00:43:45 2026-01-29 00:43:45 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 {} 2026-01-29 00:43:45
pypath.inputs.netpath.netpath_pathway_annotations 2026-01-29 00:43:45 2026-01-29 00:43:45 0.50 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='B cell receptor (B...(truncated) 1,870 {} 2026-01-29 00:43:45
pypath.inputs.offsides.offsides_side_effects 2026-01-29 00:43:45 2026-01-29 00:45:03 77.69 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 {} 2026-01-29 00:43:45
pypath.inputs.oma.oma_orthologs 2026-01-29 00:45:03 2026-01-29 00:45:03 0.05 list [] 0 {'size': -22374} 2026-01-29 00:45:03
pypath.inputs.oma.oma_table 2026-01-29 00:45:03 2026-01-29 00:45:03 0.04 defaultdict defaultdict(<class 'set'>, {}) 0 {'size': -17895} 2026-01-29 00:45:03
pypath.inputs.ontology.listof_ontologies 2026-01-29 00:45:03 2026-01-29 00:45:03 0.39 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 {'size': -3} 2026-01-29 00:45:03
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
 {} never
pypath.inputs.opentargets.opentargets_adverse_reactions 2026-01-29 00:45:03 2026-01-29 00:45:25 21.48 list [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) 112,928 {} 2026-01-29 00:45:03
pypath.inputs.opentargets.opentargets_baseline_expression 2026-01-29 00:45:25 2026-01-29 00:47:23 118.18 list [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) 43,791 {} 2026-01-29 00:45:25
pypath.inputs.opentargets.opentargets_direct_score 2026-01-29 00:47:23 2026-01-29 00:48:20 57.31 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 {} 2026-01-29 00:47:23
pypath.inputs.opentargets.opentargets_general 
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments.
 {} never
pypath.inputs.opentargets.opentargets_indirect_score 2026-01-29 00:48:20 2026-01-29 00:51:41 200.31 list [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) 6,960,486 {} 2026-01-29 00:48:20
pypath.inputs.opm.opm_annotations 2026-01-29 00:51:41 2026-01-29 00:51:56 15.71 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 {} 2026-01-29 00:51:41
pypath.inputs.oreganno.oreganno_interactions 2026-01-29 00:51:56 2026-01-29 00:52:23 26.99 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 {} 2026-01-29 00:51:56
pypath.inputs.oreganno.oreganno_raw 2026-01-29 00:52:23 2026-01-29 00:52:27 3.98 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 {} 2026-01-29 00:52:23
pypath.inputs.panglaodb.panglaodb_annotations 2026-01-29 00:52:27 2026-01-29 00:52:31 3.83 defaultdict defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=True, cell_type='Acinar cells', organ='Pancreas', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=1.0, mouse_sensitivity=0.957143, human_specificity=0.000628931, mouse_specificit...(truncated) 4,491 {'size': -1} 2026-01-29 00:52:27
pypath.inputs.panglaodb.panglaodb_raw 2026-01-29 00:52:31 2026-01-29 00:52:31 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 {} 2026-01-29 00:52:31
pypath.inputs.pathophenodb.disease_pathogen_interactions 2026-01-29 00:52:31 2026-01-29 00:52:31 0.00 list [] 0 {} 2026-01-29 00:52:31
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 2026-01-29 00:52:31 2026-01-29 00:53:28 56.70 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 {} 2026-01-29 00:52:31
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 2026-01-29 00:53:30 2026-01-29 00:53:30 0.26 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 {} 2026-01-29 00:53:30
pypath.inputs.pdb.pdb_chains 2026-01-29 00:53:30 2026-01-29 00:53:37 7.48 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 {} 2026-01-29 00:53:30
pypath.inputs.pdb.pdb_complexes 2026-01-29 00:53:40 2026-01-29 00:53:49 8.78 dict {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:Q4E2L0': Complex: COMPLEX:Q4E2L0, 'COMPLEX:Q13UJ9': Complex: COMPLEX:Q13UJ9, 'COMPLEX:Q5NHB4': Complex: COMPLEX:Q5NHB4, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963...(truncated) 49,750 {'size': 571} 2026-01-29 00:53:40
pypath.inputs.pdb.pdb_uniprot 2026-01-29 00:53:49 2026-01-29 00:53:55 5.34 tuple ({'P02185': {('6z4t', 'X-ray', 1.23), ('2mb5', 'Neutron', 1.8), ('1a6m', 'X-ray', 1.0), ('2mgl', 'X-ray', 2.0), ('5jom', 'X-ray', 1.9), ('2mgf', 'X-ray', 1.8), ('8esu', 'X-ray', 1.04), ('4of9', 'X-ray', 1.24), ('2blh', 'X-ray', 1.77), ('1mym', 'X-ray', 1.7), ('1j3f', 'X-ray', 1.45), ('1do1', 'X-ray'...(truncated) 2 {} 2026-01-29 00:53:49
pypath.inputs.pdzbase.pdzbase_interactions 2026-01-29 00:53:55 2026-01-29 00:53:56 0.57 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 {} 2026-01-29 00:53:55
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
 {} never
pypath.inputs.pepcyber.pepcyber_interactions 2026-01-29 00:53:56 2026-01-29 01:05:32 696.36 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 {} 2026-01-29 00:53:56
pypath.inputs.pfam.pfam_names 2026-01-29 01:05:32 2026-01-29 01:05:33 0.99 tuple ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'Pro_isomerase': {'PF00160'}, 'Pkinase': {'PF00069'}, 'RS_preATP-grasp-like': {'PF22660'}, 'ATP-grasp': {'PF02222'}, 'PurK_C': {'PF17769'}, 'Aldedh': {'PF00171'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'P...(truncated) 2 {} 2026-01-29 01:05:32
pypath.inputs.pfam.pfam_pdb 2026-01-29 01:05:33 2026-01-29 01:05:36 3.24 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 {} 2026-01-29 01:05:33
pypath.inputs.pfam.pfam_regions 2026-01-29 01:05:37 2026-01-29 01:14:17 520.26 tuple ({}, {}) 2 {} 2026-01-29 01:05:37
pypath.inputs.pfam.pfam_uniprot 2026-01-29 01:14:17 2026-01-29 01:29:43 925.83 tuple ({}, {}) 2 {} 2026-01-29 01:14:17
pypath.inputs.pharos.pharos_diseases 2026-01-29 01:29:43 2026-01-29 01:44:26 883.35 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 {} 2026-01-29 01:29:43
pypath.inputs.pharos.pharos_expression 2026-01-29 01:44:27 2026-01-29 01:44:32 4.20 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 {} 2026-01-29 01:44:27
pypath.inputs.pharos.pharos_general 
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments.
 {} never
pypath.inputs.pharos.pharos_gtex 2026-01-29 01:44:32 2026-01-29 01:44:37 4.36 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 {} 2026-01-29 01:44:32
pypath.inputs.pharos.pharos_ligands 2026-01-29 01:44:38 2026-01-29 01:44:41 2.99 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 {} 2026-01-29 01:44:38
pypath.inputs.pharos.pharos_orthologs 2026-01-29 01:44:42 2026-01-29 01:44:45 3.16 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 {} 2026-01-29 01:44:42
pypath.inputs.pharos.pharos_targets 2026-01-29 01:44:46 2026-01-29 01:51:20 394.10 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 {} 2026-01-29 01:44:46
pypath.inputs.pharos.pharos_xrefs 2026-01-29 01:51:20 2026-01-29 01:51:23 3.23 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 {} 2026-01-29 01:51:20
pypath.inputs.phobius.phobius_annotations 2026-01-29 01:51:24 2026-01-29 01:51:25 0.65 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 {} 2026-01-29 01:51:24
pypath.inputs.phosphatome.phosphatome_annotations 2026-01-29 01:51:25 2026-01-29 01:51:32 7.01 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 {} 2026-01-29 01:51:25
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2026-01-29 01:51:32 2026-01-29 01:51:34 2.85 list [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) 2,426 {'fixed': True} 2026-01-29 01:51:32
pypath.inputs.phosphoelm.phosphoelm_interactions 2026-01-29 01:51:34 2026-01-29 01:51:35 0.41 list [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) 2,426 {'fixed': True} 2026-01-29 01:51:34
pypath.inputs.phosphoelm.phosphoelm_kinases 2026-01-29 01:51:35 2026-01-29 01:51:35 0.10 dict {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) 247 {'fixed': True} 2026-01-29 01:51:35
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2026-01-29 01:51:35 2026-01-29 01:51:37 2.12 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 {} 2026-01-29 01:51:35
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2026-01-29 01:51:37 2026-01-29 01:51:37 0.02 list [['CDK5', 'IRF3'], ['AURKB', 'PPP1R13L'], ['CSNK2A1', 'VTN'], ['RPS6KB1', 'MDM2'], ['CDK4', 'CSDC2'], ['CDK4', 'NCL'], ['PRKAA2', 'ZMYM3'], ['LYN', 'CSNK2A1'], ['MAPK1', 'NCOA1'], ['RAF1', 'EIF4B'], ['RPS6KA5', 'PPP2R5D'], ['BMPR1A', 'ZAP70'], ['CSNK2A1', 'ZHX1'], ['PLK1', 'TPT1'], ['EPHA3', 'ZAP70'...(truncated) 1,821 {} 2026-01-29 01:51:37
pypath.inputs.phosphopoint.phosphopoint_directions 2026-01-29 01:51:37 2026-01-29 01:51:37 0.24 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 {} 2026-01-29 01:51:37
pypath.inputs.phosphopoint.phosphopoint_interactions 2026-01-29 01:51:37 2026-01-29 01:51:37 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 {} 2026-01-29 01:51:37
pypath.inputs.phosphosite.phosphosite_directions 2026-01-29 01:51:37 2026-01-29 01:51:37 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 {} 2026-01-29 01:51:37
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2026-01-29 01:51:37 2026-01-29 01:51:38 0.44 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 {} 2026-01-29 01:51:37
pypath.inputs.phosphosite.phosphosite_interactions 2026-01-29 01:51:38 2026-01-29 01:51:38 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 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_interactions_all 2026-01-29 01:51:38 2026-01-29 01:51:38 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) 9,164 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_interactions_curated 2026-01-29 01:51:38 2026-01-29 01:51:38 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 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_interactions_new 2026-01-29 01:51:38 2026-01-29 01:51:38 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 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_interactions_noref 2026-01-29 01:51:38 2026-01-29 01:51:38 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 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2026-01-29 01:51:38 2026-01-29 01:52:02 23.96 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 {} 2026-01-29 01:51:38
pypath.inputs.phosphosite.phosphosite_ptms 2026-01-29 01:52:02 2026-01-29 01:52:16 13.18 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 {} 2026-01-29 01:52:02
pypath.inputs.phosphosite.phosphosite_regsites 2026-01-29 01:52:16 2026-01-29 01:52:17 0.76 dict {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'phosphorylation', 'protein degradation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) 5,435 {} 2026-01-29 01:52:16
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2026-01-29 01:52:17 2026-01-29 01:53:21 64.76 dict {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21209006', '21148409', '24876223', '28052875'}, 'isoforms': {1}, 'process': {''}, 'function': {'phosphorylation', 'ubiquitination', 'protein degradation', 'intracellular localization', 'protein stabilization'}...(truncated) 3,621 {} 2026-01-29 01:52:17
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 2026-01-29 01:53:22 2026-01-29 01:54:11 49.66 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> 0 {} 2026-01-29 01:53:22
pypath.inputs.pro.pro_mapping 2026-01-29 01:54:11 2026-01-29 01:54:12 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) 395,915 {} 2026-01-29 01:54:11
pypath.inputs.progeny.progeny_annotations 2026-01-29 01:54:12 2026-01-29 01:55:19 67.27 dict {'P35250': {ProgenyAnnotation(pathway='NFkB', weight=-0.4099507693295503, p_value=0.37172804911595947), ProgenyAnnotation(pathway='TNFa', weight=-0.12499324201483122, p_value=0.8334557980340556), ProgenyAnnotation(pathway='JAK-STAT', weight=0.0012188579040493524, p_value=0.998388257483376), ProgenyA...(truncated) 18,581 {'size': -1} 2026-01-29 01:54:12
pypath.inputs.progeny.progeny_raw 2026-01-29 01:55:20 2026-01-29 01:56:27 67.77 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 {} 2026-01-29 01:55:20
pypath.inputs.proteinatlas.get_proteinatlas 2026-01-29 01:56:27 2026-01-29 01:56:33 5.52 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 {} 2026-01-29 01:56:27
pypath.inputs.proteinatlas.proteinatlas_annotations 2026-01-29 01:56:34 2026-01-29 01:56:45 10.90 dict {'O43657': {ProtainatlasAnnotation(organ='Oral mucosa', tissue='Oral mucosa', cell_type='squamous epithelial 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), ProtainatlasAnnotatio...(truncated) 15,058 {'size': 3} 2026-01-29 01:56:34
pypath.inputs.proteinatlas.proteinatlas_interactions 2026-01-29 01:56:47 2026-01-29 01:56:47 0.40 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) 47,188 {} 2026-01-29 01:56:47
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2026-01-29 01:56:47 2026-01-29 01:56:48 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) 2,591 {'size': 1} 2026-01-29 01:56:47
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2026-01-29 01:56:48 2026-01-29 01:56:48 0.52 dict {'O43657': {ProteinatlasSubcellularAnnotation(location='Nucleoli fibrillar center', status='approved', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cytosol', status='main', reliability='A...(truncated) 13,407 {'size': 3} 2026-01-29 01:56:48
pypath.inputs.proteins.variants 2026-01-29 01:56:48 2026-01-29 02:03:29 401.05 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) 29,523 {'size': -818} 2026-01-29 01:56:48
pypath.inputs.protmapper.get_protmapper 2026-01-29 02:03:30 2026-01-29 02:03:31 1.36 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 {} 2026-01-29 02:03:30
pypath.inputs.protmapper.protmapper_enzyme_substrate 2026-01-29 02:03:32 2026-01-29 02:03:33 1.18 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 {} 2026-01-29 02:03:32
pypath.inputs.protmapper.protmapper_interactions 
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments.
 {} never
pypath.inputs.psimi.psimi_ontology 2026-01-29 02:03:33 2026-01-29 02:03:33 0.24 list [PsimiRecord(id='MI:0000', name='molecular interaction', definition='Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.', definition_refs='[PMID:14755292]', parent_ids=None, parent_names=None, synonyms='mi', alt_ids=None), PsimiReco...(truncated) 1,653 {'size': 1} 2026-01-29 02:03:33
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 2026-01-29 02:03:33 2026-01-29 02:03:33 0.33 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 {} 2026-01-29 02:03:33
pypath.inputs.ramilowski2015.ramilowski_locations 2026-01-29 02:03:33 2026-01-29 02:03:43 9.61 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='Consensus', tmh=0, note=None, long_note=None), Ram...(truncated) 18,879 {} 2026-01-29 02:03:33
pypath.inputs.reaction.acsn_biopax 2026-01-29 02:03:43 2026-01-29 02:03:44 0.33 NoneType None 0 {} 2026-01-29 02:03:43
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
 {} never
pypath.inputs.reaction.get_acsn_effects 2026-01-29 02:03:44 2026-01-29 02:03:44 0.08 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 {} 2026-01-29 02:03:44
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 2026-01-29 02:03:44 2026-01-29 02:03:44 0.33 
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__20260128-202402/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
    rea.load_all()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
    self.load_wikipathways()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
    len(biopaxes.result),
    ^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
{} 2025-08-12 06:52:15
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
 {} never
pypath.inputs.reaction.panther_biopax 2026-01-29 02:03:44 2026-01-29 02:03:50 5.81 dict {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) 178 {} 2026-01-29 02:03:44
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.pid_biopax 2026-01-29 02:03:50 2026-01-29 02:03:52 2.29 NoneType None 0 {} 2026-01-29 02:03:50
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 2026-01-29 02:03:52 2026-01-29 02:05:19 86.53 TextIOWrapper <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> 0 {} 2026-01-29 02:03:52
pypath.inputs.reaction.reactome_bs 2026-01-29 02:05:19 2026-01-29 02:12:37 438.52 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 95 on 11/25/25, 4:17 AM using JSBML version 1.5.</p> </annota...(truncated) 2,848 {'size': 23} 2026-01-29 02:05:19
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_sbml 2026-01-29 02:13:00 2026-01-29 02:13:02 1.86 dict {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/cache/9c...(truncated) 2,848 {'size': 23} 2026-01-29 02:13:00
pypath.inputs.reactome.pathway_hierarchy 2026-01-29 02:13:02 2026-01-29 02:13:03 1.00 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) 23,403 {'size': 144} 2026-01-29 02:13:02
pypath.inputs.reactome.reactome_raw 
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments.
 {} never
pypath.inputs.reactome_old.reactome_chebis 2026-01-29 02:13:03 2026-01-29 02:13:14 10.72 
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__20260128-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-08-12 07:00:10
pypath.inputs.reactome_old.reactome_pathway_relations 2026-01-29 02:13:14 2026-01-29 02:13:14 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__20260128-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-08-12 07:00:23
pypath.inputs.reactome_old.reactome_pathways 2026-01-29 02:13:14 2026-01-29 02:13:15 1.21 
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__20260128-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-08-12 07:00:23
pypath.inputs.reactome_old.reactome_uniprots 2026-01-29 02:13:15 2026-01-29 02:13:50 35.41 
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__20260128-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
    record = collections.namedtuple('Reactome', fields)
                                                ^^^^^^
NameError: name 'fields' is not defined
{} 2025-08-12 07:00:24
pypath.inputs.rhea.rhea_gui 2026-01-29 02:13:50 2026-01-29 02:14:00 9.39 list [{'Reaction identifier': 'RHEA:10000', 'Equation': 'pentanamide + H2O = pentanoate + NH4(+)', 'ChEBI name': 'pentanamide;water;valerate;ammonium', 'ChEBI identifier': 'CHEBI:16459;CHEBI:15377;CHEBI:31011;CHEBI:28938', 'EC number': 'EC:3.5.1.50', 'Enzymes': '0', 'Gene Ontology': 'GO:0050168 pentanami...(truncated) 18,343 {'size': 560} 2026-01-29 02:13:50
pypath.inputs.rhea.rhea_raw 
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments.
 {} never
pypath.inputs.scconnect.scconnect_annotations 2026-01-29 02:14:00 2026-01-29 02:14:17 17.29 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) 3,290 {'size': 5} 2026-01-29 02:14:00
pypath.inputs.scconnect.scconnect_complexes 2026-01-29 02:14:17 2026-01-29 02:14:17 0.02 set {Complex: COMPLEX:P0DML2_P0DML3, Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:O15263, Complex: COMPLEX:Q16552_Q96PD4, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:O75462_Q9UBD9, Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01215_P0DN86, Comp...(truncated) 17 {} 2026-01-29 02:14:17
pypath.inputs.scconnect.scconnect_interactions 2026-01-29 02:14:17 2026-01-29 02:17:36 198.66 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) 1,784 {'size': 18} 2026-01-29 02:14:17
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
 {} never
pypath.inputs.sider.sider_drug_names 2026-01-29 02:17:36 2026-01-29 02:17:36 0.15 dict {'CID100002520': {SiderDrug(name='verapamil', atc='C08DA01')}, 'CID104630253': {SiderDrug(name='alclometasone', atc='D07AB10'), SiderDrug(name='alclometasone', atc='S01BA10')}, 'CID100004428': {SiderDrug(name='naltrexone', atc='N07BB04')}, 'CID100444013': {SiderDrug(name='gadoversetamide', atc='V08C...(truncated) 1,430 {} 2026-01-29 02:17:36
pypath.inputs.sider.sider_meddra_side_effects 2026-01-29 02:17:36 2026-01-29 02:17:36 0.35 list [SiderSideeffectMeddra(cid='C0341465', meddra_id='10049566', side_effect_name='Cytomegalovirus pancreatitis'), SiderSideeffectMeddra(cid='C2747794', meddra_id='10069689', side_effect_name='Spinal column injury'), SiderSideeffectMeddra(cid='C1168036', meddra_id='10060043', side_effect_name='Head circ...(truncated) 20,307 {} 2026-01-29 02:17:36
pypath.inputs.sider.sider_side_effect_frequencies 2026-01-29 02:17:36 2026-01-29 02:17:38 1.48 dict {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0013395', umls_concept_in_meddra='C0013395', side_effect='Dyspepsia', frequency='9%'), SiderSideeffetFrequency(umls_concept_on_label='C0020461', umls_concept_in_meddra='C0020461', side_effect='Hyperkalaemia', frequency='6%'), SiderSid...(truncated) 968 {} 2026-01-29 02:17:36
pypath.inputs.sider.sider_side_effects 2026-01-29 02:17:38 2026-01-29 02:17:39 0.80 dict {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0151736', umls_concept_in_meddra='C3263723', side_effect='Injury'), SiderSideeffect(umls_concept_on_label='C0035078', umls_concept_in_meddra='C0035078', side_effect='Renal failure'), SiderSideeffect(umls_concept_on_label='C0030554', umls_conc...(truncated) 1,430 {} 2026-01-29 02:17:38
pypath.inputs.signalink.signalink_annotations 2026-01-29 02:17:39 2026-01-29 02:17:40 1.13 dict {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='Toll-like receptor'), Signalin...(truncated) 2 {} 2026-01-29 02:17:39
pypath.inputs.signalink.signalink_function_annotations 2026-01-29 02:17:40 2026-01-29 02:17:40 0.40 dict {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) 786 {'size': 1} 2026-01-29 02:17:40
pypath.inputs.signalink.signalink_interactions 2026-01-29 02:17:40 2026-01-29 02:17:41 0.39 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 {} 2026-01-29 02:17:40
pypath.inputs.signalink.signalink_pathway_annotations 2026-01-29 02:17:41 2026-01-29 02:17:42 1.02 dict {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pat...(truncated) 840 {'size': 1} 2026-01-29 02:17:41
pypath.inputs.signor.signor_complexes 2026-01-29 02:17:42 2026-01-29 02:17:42 0.66 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) 4,894 {'size': 3} 2026-01-29 02:17:42
pypath.inputs.signor.signor_enzyme_substrate 2026-01-29 02:17:42 2026-01-29 02:17:46 3.24 list [{'typ': 'phosphorylation', 'resnum': 183, 'instance': 'PTQQYAKSLPVSVPV', 'substrate': 'Q96B36', 'start': 176, 'end': 190, 'kinase': 'P42345', 'resaa': 'S', 'motif': 'PTQQYAKSLPVSVPV', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'17517883'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) 13,473 {'size': 4} 2026-01-29 02:17:42
pypath.inputs.signor.signor_interactions 2026-01-29 02:17:46 2026-01-29 02:17:46 0.57 list [SignorInteraction(source='P81133', target=Complex AHR-ARNT: COMPLEX:P27540_P35869, source_isoform=None, target_isoform=None, source_type='protein', target_type='complex', effect='down-regulates activity', mechanism='binding', ncbi_tax_id='-1', pubmeds='9020169', direct=True, ptm_type='binding', ptm...(truncated) 96,536 {'size': 462} 2026-01-29 02:17:46
pypath.inputs.signor.signor_pathway_annotations 2026-01-29 02:17:46 2026-01-29 02:18:12 25.12 dict {'Q06609': {SignorPathway(pathway='Cell cycle: G2/M phase transition'), SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q13191': {SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='EGFR Signaling')}, 'P01116': {SignorPathway(pathway='Thyroid cancer'), SignorPathway(pathway='C...(truncated) 804 {'size': 17} 2026-01-29 02:17:46
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
 {} never
pypath.inputs.signor.signor_protein_families 2026-01-29 02:18:12 2026-01-29 02:18:12 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 {} 2026-01-29 02:18:12
pypath.inputs.slc.slc_annotation 2026-01-29 02:18:12 2026-01-29 02:18:13 1.10 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 {} 2026-01-29 02:18:12
pypath.inputs.slc.slc_chebi_mapping 2026-01-29 02:18:13 2026-01-29 02:18:13 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 {} 2026-01-29 02:18:13
pypath.inputs.slc.slc_interactions 2026-01-29 02:18:13 2026-01-29 02:18:13 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 {} 2026-01-29 02:18:13
pypath.inputs.slc.slc_localization_annotations 2026-01-29 02:18:13 2026-01-29 02:18:13 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) 446 {'size': -1} 2026-01-29 02:18:13
pypath.inputs.slc.slc_substrate_ontology 2026-01-29 02:18:13 2026-01-29 02:18:14 0.64 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 {} 2026-01-29 02:18:13
pypath.inputs.spike.spike_complexes 2026-01-29 02:18:14 2026-01-29 02:18:19 5.36 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 {} 2026-01-29 02:18:14
pypath.inputs.spike.spike_interactions 2026-01-29 02:18:19 2026-01-29 02:18:22 2.59 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 {} 2026-01-29 02:18:19
pypath.inputs.stitch.stitch_actions_interactions 2026-01-29 02:18:22 2026-01-29 02:18:22 0.10 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 928, in test_input
    size = i + 1
           ^
UnboundLocalError: cannot access local variable 'i' where it is not associated with a value
{'broke': True} 2025-11-30 01:20:11
pypath.inputs.stitch.stitch_links_interactions 2026-01-29 02:18:22 2026-01-29 02:18:22 0.12 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 928, in test_input
    size = i + 1
           ^
UnboundLocalError: cannot access local variable 'i' where it is not associated with a value
{'broke': True} 2025-11-30 01:21:02
pypath.inputs.string.string_effects 2026-01-29 02:18:22 2026-01-29 02:18:30 8.16 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 {} 2026-01-29 02:18:22
pypath.inputs.string.string_links_interactions 2026-01-29 02:18:31 2026-01-29 02:19:04 32.81 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 {} 2026-01-29 02:18:31
pypath.inputs.string.string_physical_interactions 2026-01-29 02:19:04 2026-01-29 02:19:05 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 {} 2026-01-29 02:19:04
pypath.inputs.string.string_species 2026-01-29 02:19:05 2026-01-29 02:19:05 0.20 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 {} 2026-01-29 02:19:05
pypath.inputs.surfaceome.surfaceome_annotations 2026-01-29 02:19:05 2026-01-29 02:19:08 2.18 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', {'TMEM30', 'Unknown_function'}), '...(truncated) 2,844 {} 2026-01-29 02:19:05
pypath.inputs.switches_elm.get_switches_elm 2026-01-29 02:19:08 2026-01-29 02:19:11 2.90 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 {} 2026-01-29 02:19:08
pypath.inputs.talklr.talklr_annotations 2026-01-29 02:19:11 2026-01-29 02:19:11 0.53 dict {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False)}, 'Q16613': {Talklr...(truncated) 1,345 {'size': 1} 2026-01-29 02:19:11
pypath.inputs.talklr.talklr_interactions 2026-01-29 02:19:11 2026-01-29 02:19:11 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 {} 2026-01-29 02:19:11
pypath.inputs.talklr.talklr_raw 2026-01-29 02:19:11 2026-01-29 02:19:11 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 {} 2026-01-29 02:19:11
pypath.inputs.tcdb.tcdb_annotations 2026-01-29 02:19:11 2026-01-29 02:19:16 5.13 
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__20260128-202402/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
{} 2025-08-13 07:12:59
pypath.inputs.tcdb.tcdb_classes 2026-01-29 02:19:16 2026-01-29 02:19:16 0.04 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) 24,364 {'size': 42} 2026-01-29 02:19:16
pypath.inputs.tcdb.tcdb_families 2026-01-29 02:19:16 2026-01-29 02:19:16 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) 2,146 {'size': 24} 2026-01-29 02:19:16
pypath.inputs.tfcensus.tfcensus_annotations 2026-01-29 02:19:16 2026-01-29 02:19:27 10.34 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) 1,873 {'size': 2} 2026-01-29 02:19:16
pypath.inputs.threedcomplex.threedcomplex_chains 2026-01-29 02:19:27 2026-01-29 02:19:31 4.29 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 {} 2026-01-29 02:19:27
pypath.inputs.threedcomplex.threedcomplex_contacts 2026-01-29 02:19:31 2026-01-29 02:19:53 22.22 set {ThreedcomplexContact(pdb='4mpy_2', uniprot_1='A0A0H2X0S3', uniprot_2='A0A0H2X0S3', chain_1='F', chain_2='E', n_residues=77.0, length_1=497, length_2=500, domain_s1=('53720',), domain_p1=('PF00171.17',), domain_s2=('53720',), domain_p2=('PF00171.17',), ident=True, homo=True), ThreedcomplexContact(pd...(truncated) 258,351 {} 2026-01-29 02:19:31
pypath.inputs.threedcomplex.threedcomplex_ddi 2026-01-29 02:19:54 2026-01-29 02:23:20 206.19 list [<pypath.internals.intera.DomainDomain object at 0x7f3dc9065550>, <pypath.internals.intera.DomainDomain object at 0x7f3dc9067790>, <pypath.internals.intera.DomainDomain object at 0x7f3dc9065650>, <pypath.internals.intera.DomainDomain object at 0x7f3dc9065110>, <pypath.internals.intera.DomainDomain o...(truncated) 521,949 {} 2026-01-29 02:19:54
pypath.inputs.threedcomplex.threedcomplex_nresidues 2026-01-29 02:23:21 2026-01-29 02:23:31 9.60 dict {'4mpy_2': {('A0A0H2X0S3', 'A0A0H2X0S3'): 13.0}, '4g1f_7': {('P27487', 'P27487'): 5.5}, '4gam_2': {('P18798', 'P22869'): 5.5, ('P11987', 'P18798'): 28.0, ('P18798', 'P18798'): 34.0, ('P18797', 'P18798'): 3.5, ('P18797', 'P22869'): 51.5, ('P22869', 'P22869'): 11.5, ('P11987', 'P22869'): 38.5}, '3hov_...(truncated) 80,605 {} 2026-01-29 02:23:21
pypath.inputs.threedid.get_3did 2026-01-29 02:23:31 2026-01-29 02:23:31 0.04 NoneType None 0 {'size': -2, 'type': {'previous': 'tuple', 'current': 'NoneType'}} 2026-01-29 02:23:31
pypath.inputs.threedid.get_3did_ddi 2026-01-29 02:23:31 2026-01-29 02:23:31 0.03 NoneType None 0 {'type': {'previous': 'dict', 'current': 'NoneType'}} 2026-01-29 02:23:31
pypath.inputs.topdb.topdb_annotations 2026-01-29 02:23:31 2026-01-29 02:24:24 53.54 dict {'P18825': {TopdbAnnotation(membrane='Cell membrane', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='Extracellular', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='C...(truncated) 2,025 {'size': -2} 2026-01-29 02:23:31
pypath.inputs.transmir.transmir_interactions 2026-01-29 02:24:25 2026-01-29 02:24:25 0.07 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 {} 2026-01-29 02:24:25
pypath.inputs.trip.take_a_trip 2026-01-29 02:24:25 2026-01-29 02:24:25 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 {} 2026-01-29 02:24:25
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 2026-01-29 02:24:25 2026-01-29 02:24:25 0.01 list [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;11983166;12601176', 'Patch clamp;Fusion protein-pull down assay;Fluorescence probe lab...(truncated) 359 {} 2026-01-29 02:24:25
pypath.inputs.trip.trip_process 2026-01-29 02:24:25 2026-01-29 02:24:25 0.00 dict {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'HEK293', 'Rat aortic vascular smooth muscle cell', 'Porcine coronary artery', 'Rat vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) 359 {} 2026-01-29 02:24:25
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
 {} never
pypath.inputs.trrust.trrust_human 2026-01-29 02:24:25 2026-01-29 02:24:27 2.69 
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__20260128-202402/pypath_git/pypath/inputs/trrust.py", line 87, in trrust_human
    return trrust_interactions('human')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
    interactions = [TrrustInteraction(line) for line in c.result]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-30 02:48:04
pypath.inputs.trrust.trrust_interactions 2026-01-29 02:24:27 2026-01-29 02:24:29 1.81 
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__20260128-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
    interactions = [TrrustInteraction(line) for line in c.result]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-30 02:48:08
pypath.inputs.trrust.trrust_mouse 2026-01-29 02:24:29 2026-01-29 02:24:31 1.82 
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__20260128-202402/pypath_git/pypath/inputs/trrust.py", line 92, in trrust_mouse
    return trrust_interactions('mouse')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260128-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
    interactions = [TrrustInteraction(line) for line in c.result]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
{'broke': True} 2025-11-30 02:48:09
pypath.inputs.twosides.twosides_interactions 2026-01-29 02:24:31 2026-01-29 02:30:31 360.25 
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__20260128-202402/pypath_git/pypath/inputs/offsides.py", line 70, in _sides_base
    _ = next(c.result)
        ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
{} 2025-11-27 03:32:08
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_info 2026-01-29 02:30:31 2026-01-29 02:30:31 0.00 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 {} 2026-01-29 02:30:31
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_sources 2026-01-29 02:30:31 2026-01-29 02:30:31 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 {} 2026-01-29 02:30:31
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
 {} never
pypath.inputs.uniprot.get_uniprot_sec 2026-01-29 02:30:31 2026-01-29 02:30:32 0.70 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) 72,409 {'size': 39} 2026-01-29 02:30:31
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 2026-01-29 02:30:32 2026-01-29 02:30:41 9.42 dict {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A096LP01': {UniprotFamily(family='SMIM26', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0A8I5KQE6': {UniprotFamily(...(truncated) 14,503 {'size': 18} 2026-01-29 02:30:32
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 2026-01-29 02:30:41 2026-01-29 02:30:50 8.61 dict {'A0A087X1C5': {UniprotKeyword(keyword='Heme'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Mitochondrion'), UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='...(truncated) 20,431 {'size': 11} 2026-01-29 02:30:41
pypath.inputs.uniprot.uniprot_locations 
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2026-01-29 02:30:50 2026-01-29 02:30:50 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 {} 2026-01-29 02:30:50
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 2026-01-29 02:30:50 2026-01-29 02:30:52 1.40 dict {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Balsam fir', 'Pinus balsamea'}, 'H8ZM71': {'Abies balsamea', 'Balsam fir', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies grandis', 'Grand fir', 'Pinu...(truncated) 559,781 {'size': 923} 2026-01-29 02:30:50
pypath.inputs.uniprot.uniprot_tissues 2026-01-29 02:30:52 2026-01-29 02:31:02 10.36 dict {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A096LP01': {UniprotTissue(tissue='Kidney', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tis...(truncated) 10,185 {'size': 16} 2026-01-29 02:30:52
pypath.inputs.uniprot.uniprot_topology 2026-01-29 02:31:02 2026-01-29 02:31:45 42.88 dict {'A0A087X1C5': {UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Transmembrane...(truncated) 5,253 {'size': 9} 2026-01-29 02:31:02
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot_db.all_swissprots 2026-01-29 02:31:45 2026-01-29 02:31:45 0.00 set {'Q8N4V2', 'Q8NGH6', 'P08217', 'Q96I51', 'Q92564', 'P10997', 'Q68CQ4', 'Q9BYJ4', 'Q9BV81', 'Q7Z5J8', 'Q8N4Z0', 'Q8NB49', 'O95715', 'Q14943', 'Q8NB78', 'A0A0K0K1C0', 'P87889', 'Q6ZN17', 'Q01201', 'Q9BV86', 'Q86WN1', 'P51955', 'Q9P1U1', 'P0CG47', 'Q16568', 'Q52LD8', 'Q5JTW2', 'P02753', 'Q96HH6', 'Q9P2...(truncated) 20,431 {'size': 11} 2026-01-29 02:31:45
pypath.inputs.uniprot_db.all_trembls 2026-01-29 02:31:45 2026-01-29 02:32:21 35.14 set {'K7P519', 'A0A1U9X938', 'H3BRZ6', 'Q5JQP3', 'A0A8A0T5S1', 'A7E2D6', 'A0A2I4PZM2', 'Q8N618', 'U5LKH9', 'A0A5C2GTR6', 'G0Z8B7', 'B3KNH2', 'G1EMQ5', 'A0A994J4E5', 'A0A386IRN0', 'A0A5H2UZP6', 'C9JMQ7', 'G1EMZ3', 'A0A5A4LIA5', 'G8FPZ9', 'D6MLF8', 'L7PG08', 'Q8SP62', 'B8ZZY7', 'A1A525', 'H0YN33', 'A0A8I5...(truncated) 184,724 {'size': -84} 2026-01-29 02:31:45
pypath.inputs.uniprot_db.all_uniprots 2026-01-29 02:32:21 2026-01-29 02:32:21 0.00 set {'K7P519', 'A0A1U9X938', 'H3BRZ6', 'Q5JQP3', 'A0A8A0T5S1', 'A7E2D6', 'A0A2I4PZM2', 'P08217', 'Q8N618', 'Q96I51', 'A0A5C2GTR6', 'G0Z8B7', 'B3KNH2', 'G1EMQ5', 'A0A994J4E5', 'A0A386IRN0', 'A0A5H2UZP6', 'C9JMQ7', 'G1EMZ3', 'A0A5A4LIA5', 'G8FPZ9', 'D6MLF8', 'L7PG08', 'Q8SP62', 'B8ZZY7', 'A1A525', 'H0YN33...(truncated) 205,155 {'size': -73} 2026-01-29 02:32:21
pypath.inputs.uniprot_db.get_db 2026-01-29 02:32:21 2026-01-29 02:32:21 0.00 set {'K7P519', 'A0A1U9X938', 'H3BRZ6', 'Q5JQP3', 'A0A8A0T5S1', 'A7E2D6', 'A0A2I4PZM2', 'P08217', 'Q8N618', 'Q96I51', 'A0A5C2GTR6', 'G0Z8B7', 'B3KNH2', 'G1EMQ5', 'A0A994J4E5', 'A0A386IRN0', 'A0A5H2UZP6', 'C9JMQ7', 'G1EMZ3', 'A0A5A4LIA5', 'G8FPZ9', 'D6MLF8', 'L7PG08', 'Q8SP62', 'B8ZZY7', 'A1A525', 'H0YN33...(truncated) 205,155 {'size': -73} 2026-01-29 02:32:21
pypath.inputs.uniprot_db.init_db 2026-01-29 02:32:21 2026-01-29 02:32:21 0.05 NoneType None 0 {} 2026-01-29 02:32:21
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 2026-01-29 02:32:21 2026-01-29 02:32:21 0.04 set {('Ensembl_Genomes_Protein', 'UniProtKB'), ('dictyBase', 'UniProtKB-Swiss-Prot'), ('UniProtKB_AC-ID', 'SGD'), ('UniProtKB', 'EchoBASE'), ('UniProtKB-Swiss-Prot', 'RGD'), ('GenomeRNAi', 'UniProtKB'), ('UniRef100', 'UniProtKB'), ('UniProtKB_AC-ID', 'GuidetoPHARMACOLOGY'), ('UniProtKB_AC-ID', 'Ensembl_...(truncated) 475 {'size': -6} 2026-01-29 02:32:21
pypath.inputs.wang.cui_interactions 2026-01-29 02:32:21 2026-01-29 02:32:21 0.47 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 {} 2026-01-29 02:32:21
pypath.inputs.wang.hsn_interactions 2026-01-29 02:32:21 2026-01-29 02:32:22 0.45 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 {} 2026-01-29 02:32:21
pypath.inputs.wang.wang_annotations 2026-01-29 02:32:22 2026-01-29 02:32:27 4.88 dict {'NA': {WangAnnotation(function='Lipid', location='Cytosol'), WangAnnotation(function='Peptide', location='Ribosomes'), WangAnnotation(function='DNA', location='Nucleus'), WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='RNA', location='Ribosomes'), WangAnnotation(func...(truncated) 1,547 {} 2026-01-29 02:32:22
pypath.inputs.wang.wang_interactions 2026-01-29 02:32:27 2026-01-29 02:32:27 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 {} 2026-01-29 02:32:27
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2026-01-29 02:32:27 2026-01-29 02:32:27 0.29 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 {} 2026-01-29 02:32:27
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2026-01-29 02:32:27 2026-01-29 02:32:27 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 {} 2026-01-29 02:32:27
pypath.inputs.zhong2015.zhong2015_annotations 2026-01-29 02:32:27 2026-01-29 02:32:27 0.16 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 {} 2026-01-29 02:32:27

The OmniPath Team • Saez Lab • 2026-01-29