Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2025-11-28 20:24:24 and 2025-11-29 02:54:22; pypath version: 0.16.28 (from git, installed by poetry; 0c3a98e )
| Modules collected: | 194 |
|---|---|
| Modules failed to import: | 2 |
| Functions collected: | 540 |
| Functions run without error: | 387 |
| Functions returned empty value: | 13 |
| Functions skipped due to lack of arguments: | 121 |
| Functions run with error: | 32 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2025-11-28 20:24:27 | 2025-11-28 20:24:28 | 0.44 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2025-11-28 20:24:27 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2025-11-28 20:24:28 | 2025-11-28 20:24:28 | 0.49 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2025-11-28 20:24:28 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2025-11-28 20:24:28 | 2025-11-28 20:25:22 | 53.98 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {} | 2025-11-28 20:24:28 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2025-11-28 20:25:22 | 2025-11-28 20:25:23 | 1.07 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2025-11-28 20:25:22 | |
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2025-11-28 20:25:23 | 2025-11-28 20:25:50 | 26.40 | 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 | {'fixed': True} | 2025-11-28 20:25:23 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2025-11-28 20:25:50 | 2025-11-28 20:29:27 | 217.31 | 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 | {'fixed': True} | 2025-11-28 20:25:50 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2025-11-28 20:29:27 | 2025-11-28 20:29:32 | 4.53 | 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 | {'fixed': True} | 2025-11-28 20:29:27 | |
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2025-11-28 20:29:32 | 2025-11-28 20:29:33 | 1.13 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='03.15.02.002', badd='BADD_A05108'), parent=AdrecsAdr(adr_class='03.15.02', badd='BADD_A01909')), AdrecsChildParent(child=AdrecsAdr(adr_class='11.05.17.006', badd='BADD_A04228'), parent=AdrecsAdr(adr_class='11.05.17', badd='BADD_A03875')), AdrecsChildPare...(truncated) | 13,828 | {'fixed': True} | 2025-11-28 20:29:32 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2025-11-28 20:29:33 | 2025-11-28 20:29:34 | 1.46 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,243 | {} | 2025-11-28 20:29:33 | |
| ¶ | pypath.inputs.alzpathway.alzpathway_interactions | 2025-11-28 20:29:34 | 2025-11-28 20:29:34 | 0.12 | list | [AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='O00213', genesymbol_a='APP', genesymbol_b='APBB1', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='Q8N8S7', genesymbol_a='APP', genesymbol_b='ENAH', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05...(truncated) | 119 | {} | 2025-11-28 20:29:34 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2025-11-28 20:29:34 | 2025-11-28 20:32:54 | 199.62 | dict | {'Q15848': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q96A54': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'Q86V24': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'P35318': {Baccin2019Annotation(ma...(truncated) | 933 | {} | 2025-11-28 20:29:34 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2025-11-28 20:32:54 | 2025-11-28 20:32:55 | 0.79 | list | [Baccin2019Interaction(ligand='Q15848', receptor='Q96A54', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Ramilowski2015', 'Baccin2019'}, references={'12802337'}), Baccin2019Interaction(ligand='Q15848', receptor='Q86V24', correct='Correct', ligand_location='secre...(truncated) | 1,460 | {} | 2025-11-28 20:32:54 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2025-11-28 20:32:55 | 2025-11-28 20:32:55 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2025-11-28 20:32:55 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2025-11-28 20:32:55 | 2025-11-28 20:33:33 | 37.79 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2025-11-28 20:32:55 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2025-11-28 20:33:33 | 2025-11-28 20:34:20 | 46.94 | 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) | 8,749 | {} | 2025-11-28 20:33:33 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2025-11-28 20:34:20 | 2025-11-28 20:34:21 | 1.11 | 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) | 7,478 | {} | 2025-11-28 20:34:20 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2025-11-28 20:34:21 | 2025-11-28 20:35:03 | 41.39 | list | [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) | 303,538 | {} | 2025-11-28 20:34:21 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2025-11-28 20:35:03 | 2025-11-28 20:35:03 | 0.08 | list | [{'type': 'OLIGO', 'vendor': 'PHALANX', 'array': 'OneArray', 'description': None, 'format': 'EXPRESSION', 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'array': 'CODELINK', 'vendor': 'CODELINK', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'type': 'OLIGO', 'array': ...(truncated) | 37 | {} | 2025-11-28 20:35:03 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2025-11-28 20:35:03 | 2025-11-28 20:35:04 | 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 | {} | 2025-11-28 20:35:03 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2025-11-28 20:35:04 | 2025-11-28 20:35:05 | 1.17 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2025-11-28 20:35:04 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2025-11-28 20:35:05 | 2025-11-28 20:35:13 | 7.82 | dict | {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) | 216 | {} | 2025-11-28 20:35:05 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2025-11-28 20:35:13 | 2025-11-28 20:35:13 | 0.01 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 330 | {} | 2025-11-28 20:35:13 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2025-11-28 20:35:13 | 2025-11-28 20:35:19 | 6.28 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P24385', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 5,157 | {} | 2025-11-28 20:35:13 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2025-11-28 20:35:19 | 2025-11-28 20:35:21 | 2.21 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {} | 2025-11-28 20:35:19 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2025-11-28 20:35:21 | 2025-11-28 20:35:33 | 11.64 | dict | {'P06850': {CellcallAnnotation(role='ligand')}, 'Q13324': {CellcallAnnotation(role='receptor')}, 'Q9Y219': {CellcallAnnotation(role='ligand')}, 'Q99466': {CellcallAnnotation(role='receptor')}, 'P01137': {CellcallAnnotation(role='ligand')}, 'P36897': {CellcallAnnotation(role='receptor')}, 'P13236': {...(truncated) | 460 | {} | 2025-11-28 20:35:21 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2025-11-28 20:35:33 | 2025-11-28 20:35:33 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2025-11-28 20:35:33 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2025-11-28 20:35:33 | 2025-11-28 20:35:34 | 0.79 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2025-11-28 20:35:33 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2025-11-28 20:35:34 | 2025-11-28 20:35:34 | 0.11 | list | [CellcallInteraction(ligand_uniprot='P06850', receptor_uniprot='Q13324', core=True), CellcallInteraction(ligand_uniprot='Q9Y219', receptor_uniprot='Q99466', core=True), CellcallInteraction(ligand_uniprot='P01137', receptor_uniprot='P36897', core=True), CellcallInteraction(ligand_uniprot='P13236', re...(truncated) | 797 | {} | 2025-11-28 20:35:34 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2025-11-28 20:35:34 | 2025-11-28 20:35:34 | 0.65 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinteractio...(truncated) | 3,425 | {} | 2025-11-28 20:35:34 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2025-11-28 20:35:35 | 2025-11-28 20:35:44 | 9.90 | 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='TGFb', category=...(truncated) | 1,523 | {} | 2025-11-28 20:35:35 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2025-11-28 20:35:44 | 2025-11-28 20:35:51 | 6.98 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O60565', 'Q9H772', 'Q13253', 'O00292', 'P12645', 'Q9H2X0', 'P41271', 'O75610'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 32 | {} | 2025-11-28 20:35:44 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2025-11-28 20:35:51 | 2025-11-28 20:35:58 | 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 | {} | 2025-11-28 20:35:51 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2025-11-28 20:35:58 | 2025-11-28 20:36:06 | 7.56 | dict | {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) | 4 | {} | 2025-11-28 20:35:58 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2025-11-28 20:36:06 | 2025-11-28 20:36:13 | 7.33 | 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) | 12,424 | {} | 2025-11-28 20:36:06 | |
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2025-11-28 20:36:13 | 2025-11-28 20:36:14 | 0.51 | dict | {'P23229': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'Q13443': {CellinkerAnnotation(role...(truncated) | 1,919 | {} | 2025-11-28 20:36:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.05 | dict | {Complex: COMPLEX:O00144_O75581: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:Q14028_Q8IV77: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, Complex: COMPLEX:P01857_P0CG04: {Cellinker...(truncated) | 134 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.04 | set | {CellinkerInteraction(ligand='P23229', receptor='Q13443', ligand_location='Membrane', receptor_location='Membrane', resources='HPMR', pmids='15361064;10825303', type='Cell adhesion'), CellinkerInteraction(ligand='Q96CG8', receptor='Q13467', ligand_location='ECM', receptor_location='Membrane', resour...(truncated) | 3,810 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.05 | dict | {'P23229': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'Q13443': {CellinkerAnnotation(role...(truncated) | 1,785 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.11 | set | {CellinkerInteraction(ligand='5497152', receptor='Q9HBW0', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='10727522;15177455', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='123847', receptor='O94759', ligand_location=None, receptor_location='Mem...(truncated) | 314 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.01 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.29 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 358 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2025-11-28 20:36:14 | 2025-11-28 20:36:14 | 0.02 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2025-11-28 20:36:14 | 2025-11-28 20:36:15 | 0.46 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {} | 2025-11-28 20:36:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2025-11-28 20:36:15 | 2025-11-28 20:36:15 | 0.02 | tuple | ({'Q9BY67', Complex Estradiol_byHSD17B1: COMPLEX:P14061, 'O75888', 'Q99748', 'Q9NPH3', 'P10451', 'P48066', 'O75093', Complex Calcitriol_byCYP27B1: COMPLEX:O15528, 'Q9BZD2', Complex integrin_aVb1_complex: COMPLEX:P05556_P06756, 'P01258', Complex Pregnenolone_byCYP11A1: COMPLEX:P05108_P10109_P22570_Q6...(truncated) | 2 | {} | 2025-11-28 20:36:15 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2025-11-28 20:36:15 | 2025-11-28 20:36:15 | 0.01 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,359 | {} | 2025-11-28 20:36:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2025-11-28 20:36:15 | 2025-11-28 20:36:15 | 0.46 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='26156437')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,598 | {} | 2025-11-28 20:36:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2025-11-28 20:36:15 | 2025-11-28 20:36:15 | 0.16 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2025-11-28 20:36:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2025-11-28 20:36:15 | 2025-11-28 20:36:16 | 0.16 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2025-11-28 20:36:15 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2025-11-28 20:36:16 | 2025-11-28 20:36:16 | 0.25 | dict | {'P15391': {CelltypistAnnotation(cell_type='Cycling cells', cell_subtype='Cycling B cells', cell_ontology='CL:0000236', marker_type='curated_marker', tissues=('Intestine',), datasets=('Smillie et al. 2019',)), CelltypistAnnotation(cell_type='B cells', cell_subtype='B cells', cell_ontology='CL:000023...(truncated) | 460 | {} | 2025-11-28 20:36:16 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2025-11-28 20:36:16 | 2025-11-28 20:36:56 | 39.57 | list | [Citation(allele='712224', variation_id='783586', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='78020', variation_id='67124', nsv='', citation_source='PubMed', citation_id='22581653'), Citation(allele='744328', variation_id='731543', nsv='', citation_source='PubMed', ci...(truncated) | 4,221,220 | {} | 2025-11-28 20:36:16 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2025-11-28 20:37:01 | 2025-11-28 20:46:03 | 541.96 | list | [Variant(allele='363483', type='single nucleotide variant', variant='NM_000546.6(TP53):c.733G>C (p.Gly245Arg)', entrez='7157', genesymbol='TP53', clinical_significance='Conflicting classifications of pathogenicity', review_status='criteria provided, conflicting classifications', rs='28934575', pheno...(truncated) | 8,361,745 | {} | 2025-11-28 20:37:01 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2025-11-28 22:23:44 | 2025-11-28 22:23:57 | 13.00 | list | [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) | 64,990 | {} | 2025-11-28 22:23:44 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2025-11-28 22:23:57 | 2025-11-28 22:24:00 | 3.52 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2025-11-28 22:23:57 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2025-11-28 22:24:00 | 2025-11-28 22:24:01 | 0.19 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2025-11-28 22:24:00 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2025-11-28 22:24:01 | 2025-11-28 22:24:02 | 0.93 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,695 | {} | 2025-11-28 22:24:01 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2025-11-28 22:24:02 | 2025-11-28 22:24:02 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2025-11-28 22:24:02 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2025-11-28 22:24:02 | 2025-11-28 22:26:04 | 122.48 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) | 2,275 | {} | 2025-11-28 22:24:02 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2025-11-28 22:26:04 | 2025-11-28 22:26:17 | 13.10 | 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) | 587,741 | {} | 2025-11-28 22:26:04 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2025-11-28 22:26:17 | 2025-11-28 22:26:31 | 13.39 | 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='nucleus', score=0.7), Compp...(truncated) | 22,797 | {} | 2025-11-28 22:26:17 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2025-11-28 22:26:31 | 2025-11-28 22:26:31 | 0.31 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {} | 2025-11-28 22:26:31 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2025-11-28 22:26:31 | 2025-11-28 22:26:31 | 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 | {} | 2025-11-28 22:26:31 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2025-11-28 22:26:31 | 2025-11-28 22:26:32 | 0.57 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2025-11-28 22:26:31 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2025-11-28 22:26:32 | 2025-11-28 22:26:32 | 0.17 | dict | {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, chr_band='10q11.23', tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',), translocation_partner=(()...(truncated) | 762 | {} | 2025-11-28 22:26:32 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_raw | 2025-11-28 22:26:32 | 2025-11-28 22:26:32 | 0.00 | list | [{'Gene Symbol': 'A1CF', 'Name': 'APOBEC1 complementation factor', 'Entrez GeneId': '29974', 'Genome Location': '10:50799421-50885675', 'Tier': '2', 'Hallmark': '', 'Chr Band': '10q11.23', 'Somatic': 'yes', 'Germline': '', 'Tumour Types(Somatic)': 'melanoma', 'Tumour Types(Germline)': '', 'Cancer Sy...(truncated) | 758 | {} | 2025-11-28 22:26:32 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2025-11-28 22:26:32 | 2025-11-28 22:27:11 | 39.58 |
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__20251128-202402/pypath_git/pypath/inputs/cpad.py", line 69, in cpad_annotations
mirbase = mapping.map_name(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 3552, in map_name
return mapper.map_name(
^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-pAVdo7EK-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 1979, in map_name
mapped_names = self._map_name(
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 2511, in _map_name
tbl = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 1562, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 3209, in load_mapping
reader = MapReader(param = resource, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 136, in mirbase_mature
for row in mirbase_mirna_mature(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 113, in mirbase_mirna_mature
yield from _mirbase_of_organism('mirna_mature', 1, organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 97, in _mirbase_of_organism
for row in _mirbase_table(table):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-27 23:37:18 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2025-11-28 22:27:11 | 2025-11-28 22:27:12 | 0.12 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='Fanconi anemia signaling pathway', cancer='Glioma', pathway_category='Fanconi anemia pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='increase sensitivity to TMZ and BCNU'), CpadPathwayCancer(pathway='VEGF signaling pathway', cancer='Glioma',...(truncated) | 2 | {} | 2025-11-28 22:27:11 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2025-11-28 22:27:12 | 2025-11-28 22:27:12 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2025-11-28 22:27:12 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2025-11-28 22:27:12 | 2025-11-28 22:27:21 | 9.36 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {} | 2025-11-28 22:27:12 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2025-11-28 22:27:21 | 2025-11-28 22:27:24 | 2.69 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2025-11-28 22:27:21 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2025-11-28 22:27:24 | 2025-11-28 22:27:25 | 0.63 | dict | {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) | 1,449 | {} | 2025-11-28 22:27:24 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2025-11-28 22:27:25 | 2025-11-28 22:27:26 | 0.61 | dict | {'A1A5B4': {CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='ZL55', valu...(truncated) | 1,410 | {} | 2025-11-28 22:27:25 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2025-11-28 22:27:26 | 2025-11-28 22:27:26 | 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 | {} | 2025-11-28 22:27:26 | |
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2025-11-28 22:27:26 | 2025-11-28 22:27:28 | 1.80 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P01584', score=0.2520213521212398, cytokine_genesymbol='IL1B', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='Q9GZX6', score=-0.0324696768422221, cytokine_genesymbol='IL22', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P08476', score=-0.1...(truncated) | 4,887 | {} | 2025-11-28 22:27:26 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2025-11-28 22:27:28 | 2025-11-28 22:27:28 | 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 | {} | 2025-11-28 22:27:28 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2025-11-28 22:27:28 | 2025-11-28 22:27:31 | 2.46 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2025-11-28 22:27:28 | |
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2025-11-28 22:27:31 | 2025-11-28 22:27:32 | 1.33 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2025-11-28 22:27:31 | |
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2025-11-28 22:27:32 | 2025-11-28 22:28:03 | 30.14 | list | [DdinterInteraction(drug1_id='DDInter607', drug1_name='Dulaglutide', drug2_id='DDInter678', drug2_name='Esterified estrogens', level='Moderate'), DdinterInteraction(drug1_id='DDInter1565', drug1_name='Ramipril', drug2_id='DDInter706', drug2_name='Exenatide', level='Moderate'), DdinterInteraction(dru...(truncated) | 160,235 | {} | 2025-11-28 22:27:32 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2025-11-28 22:28:03 | 2025-11-28 23:09:58 | 2,514.89 | list | [DdinterIdentifiers(ddinter='DDInter1787', drugbank=None, chembl=None, pubchem=None), DdinterIdentifiers(ddinter='DDInter1227', drugbank='DB00350', chembl='CHEMBL802', pubchem='46508344'), DdinterIdentifiers(ddinter='DDInter1128', drugbank='DB00643', chembl='CHEMBL685', pubchem='46508807'), DdinterI...(truncated) | 1,939 | {} | 2025-11-28 22:28:03 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2025-11-28 23:09:58 | 2025-11-28 23:09:58 | 0.42 | int | 1939 | 0 | {} | 2025-11-28 23:09:58 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2025-11-28 23:09:58 | 2025-11-28 23:09:58 | 0.12 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2025-11-28 23:09:58 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2025-11-28 23:09:58 | 2025-11-28 23:09:59 | 0.39 | list | [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) | 537 | {} | 2025-11-28 23:09:58 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2025-11-28 23:09:59 | 2025-11-28 23:09:59 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2025-11-28 23:09:59 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2025-11-28 23:09:59 | 2025-11-28 23:10:05 | 6.15 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='GO'), DgidbAnnotation(category='TRANSCRIPTION FACTOR', source='Pharos'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnot...(truncated) | 9,973 | {} | 2025-11-28 23:09:59 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2025-11-28 23:10:05 | 2025-11-28 23:10:11 | 6.59 | list | [DgidbInteraction(genesymbol='OPRK1', gene_concept_id='hgnc:8154', resource='TEND', type='NULL', drug_name='PROPOXYPHENE', drug_concept_id='rxcui:8785', score='0.3697723326457359', approved='TRUE', anti_neoplastic='FALSE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='POLB', gene_concept_id='...(truncated) | 84,175 | {} | 2025-11-28 23:10:05 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2025-11-28 23:10:12 | 2025-11-28 23:10:12 | 0.21 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2025-11-28 23:10:12 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2025-11-28 23:10:12 | 2025-11-28 23:10:12 | 0.32 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:11714', disease='Gestational diabetes', resource='TIGA', source_score=38, confidence=1.03), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource...(truncated) | 37,671 | {} | 2025-11-28 23:10:12 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2025-11-28 23:10:12 | 2025-11-28 23:10:14 | 1.86 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:0014667', disease='Disease of metabolism', resource='TIGA', source_score=38, confidence=1.03), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:11714', disease='Gestational diabetes'...(truncated) | 407,328 | {} | 2025-11-28 23:10:12 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2025-11-28 23:10:14 | 2025-11-28 23:10:14 | 0.14 | list | [DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Craniosynostosis', resource='UniProtKB-KW', evidence_type='CURATED', confidence=4), DiseasesInteraction(gene_id='ENSP00000003084', genesymbol='CFTR', disease_id='DOID:0111862', disease='Congenital ...(truncated) | 7,721 | {} | 2025-11-28 23:10:14 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2025-11-28 23:10:14 | 2025-11-28 23:10:15 | 0.52 | list | [DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:0080001', disease='Bone disease', resource='UniProtKB-KW', evidence_type='CURATED', confidence=4), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:0080006', disease='Bone deve...(truncated) | 97,418 | {} | 2025-11-28 23:10:14 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2025-11-28 23:10:15 | 2025-11-28 23:10:16 | 1.38 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.255, confidence=3.627, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol...(truncated) | 287,906 | {} | 2025-11-28 23:10:15 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2025-11-28 23:10:16 | 2025-11-28 23:11:08 | 51.68 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.255, confidence=3.627, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol...(truncated) | 11,401,211 | {} | 2025-11-28 23:10:16 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2025-11-28 23:11:08 | 2025-11-28 23:11:11 | 2.59 | list | [<pypath.internals.intera.DomainDomain object at 0x7f7715f50bd0>, <pypath.internals.intera.DomainDomain object at 0x7f7637b72d50>, <pypath.internals.intera.DomainDomain object at 0x7f7637b70bd0>, <pypath.internals.intera.DomainDomain object at 0x7f7637b71d10>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2025-11-28 23:11:08 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2025-11-28 23:11:11 | 2025-11-28 23:11:12 | 1.23 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f74c8d7cd50>, <pypath.internals.intera.DomainDomain object at 0x7f74c8d7cbd0>, <pypath.internals.intera.DomainDomain object at 0x7f74c8d7c910>, <pypath.internals.intera.DomainDomain object at 0x7f74c8d7cc50>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2025-11-28 23:11:11 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2025-11-28 23:11:12 | 2025-11-28 23:11:12 | 0.36 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2025-11-28 23:11:12 | |
| ¶ | pypath.inputs.domino.get_domino | 2025-11-28 23:11:12 | 2025-11-28 23:11:12 | 0.34 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2025-11-28 23:11:12 | |
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2025-11-28 23:11:13 | 2025-11-28 23:11:23 | 10.19 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2025-11-28 23:11:13 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-11-28 23:11:23 | 2025-11-28 23:11:37 | 13.77 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-11-28 23:11:23 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-11-28 23:11:37 | 2025-11-28 23:11:39 | 1.93 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-11-28 23:11:37 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-11-28 23:11:39 | 2025-11-28 23:11:40 | 1.34 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-11-28 23:11:39 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-11-28 23:11:40 | 2025-11-28 23:11:54 | 14.45 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-11-28 23:11:40 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-11-28 23:11:54 | 2025-11-28 23:11:55 | 0.42 |
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__20251128-202402/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 | 2025-11-28 23:11:55 | 2025-11-28 23:11:56 | 1.00 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2025-11-28 23:11:55 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2025-11-28 23:11:56 | 2025-11-28 23:11:57 | 1.15 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2025-11-28 23:11:56 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2025-11-28 23:11:57 | 2025-11-28 23:12:11 | 14.18 | 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 | {} | 2025-11-28 23:11:57 | |
| ¶ | pypath.inputs.elm.elm_domains | 2025-11-28 23:12:11 | 2025-11-28 23:12:12 | 0.36 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2025-11-28 23:12:11 | |
| ¶ | pypath.inputs.elm.elm_instances | 2025-11-28 23:12:12 | 2025-11-28 23:12:12 | 0.18 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 4,277 | {'size': -1} | 2025-11-28 23:12:12 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2025-11-28 23:12:12 | 2025-11-28 23:12:12 | 0.13 | list | [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) | 2,797 | {} | 2025-11-28 23:12:12 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2025-11-28 23:12:12 | 2025-11-28 23:12:15 | 3.44 | dict | {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=True)}, 'P30411': {EmbraceAnnotation(mainclass='receptor', neu...(truncated) | 844 | {} | 2025-11-28 23:12:12 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2025-11-28 23:12:15 | 2025-11-28 23:12:15 | 0.10 | list | [EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(ligand='O43184', receptor='P05556'), EmbraceInteraction(ligand='O43184', receptor='P31431'), EmbraceInteraction(...(truncated) | 1,273 | {} | 2025-11-28 23:12:15 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2025-11-28 23:12:15 | 2025-11-28 23:12:16 | 0.08 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2025-11-28 23:12:15 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2025-11-28 23:12:16 | 2025-11-28 23:12:16 | 0.10 | list | [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) | 1,832 | {} | 2025-11-28 23:12:16 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2025-11-28 23:12:16 | 2025-11-28 23:12:16 | 0.40 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2025-11-28 23:12:16 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2025-11-28 23:12:16 | 2025-11-28 23:12:16 | 0.42 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 348 | {} | 2025-11-28 23:12:16 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.exocarta.get_exocarta | 2025-11-28 23:12:16 | 2025-11-28 23:12:43 | 26.48 | list | [ExocartaRecord(entrez='967', genesymbol='CD63', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='1803', genesymbol='DPP4', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='79574', genesymbol=...(truncated) | 35,259 | {} | 2025-11-28 23:12:16 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2025-11-28 23:12:43 | 2025-11-28 23:14:09 | 85.77 | list | [VesiclepediaRecord(entrez='31848', genesymbol='His3.3B', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entrez='33736', genesymbol='His3.3A', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entr...(truncated) | 290,197 | {} | 2025-11-28 23:12:43 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2025-11-28 23:14:09 | 2025-11-28 23:14:09 | 0.22 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 354 | {} | 2025-11-28 23:14:09 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2025-11-28 23:14:09 | 2025-11-28 23:14:10 | 0.82 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,405 | {} | 2025-11-28 23:14:09 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2025-11-28 23:14:10 | 2025-11-28 23:15:06 | 55.89 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0016020', 'GO:0005743', 'GO:0045275'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0005743', 'GO:0045259'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0005743', 'GO:0045259'}, 'A0A023I7N5': {'GO:0016020', 'GO:0005743'}, 'A0A02...(truncated) | 2 | {} | 2025-11-28 23:14:10 | |
| ¶ | pypath.inputs.go.get_goslim | 2025-11-28 23:15:06 | 2025-11-28 23:15:07 | 1.02 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {} | 2025-11-28 23:15:06 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-11-28 23:15:07 | 2025-11-28 23:21:08 | 361.60 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016011': {('GO:0098797', 'is_a'), ...(truncated) | 3 | {} | 2025-11-28 23:15:07 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2025-11-28 23:21:08 | 2025-11-28 23:21:09 | 0.15 |
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__20251128-202402/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 | 2025-11-28 23:21:09 | 2025-11-28 23:21:13 | 4.54 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016011': {('GO:0098797', 'is_a'), ...(truncated) | 3 | {} | 2025-11-28 23:21:09 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-11-28 23:21:13 | 2025-11-28 23:21:15 | 2.04 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737'}, '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 | {} | 2025-11-28 23:21:13 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2025-11-28 23:21:15 | 2025-11-28 23:21:21 | 5.98 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0046872', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0479', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) | 19,705 | {} | 2025-11-28 23:21:15 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-11-28 23:21:24 | 2025-11-28 23:21:25 | 1.10 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737'}, '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 | {} | 2025-11-28 23:21:24 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2025-11-28 23:21:25 | 2025-11-28 23:21:25 | 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__20251128-202402/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 | 2025-11-28 23:21:25 | 2025-11-28 23:21:36 | 11.63 | dict | {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0043231', 'GO:0070330'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'], 'A0A0C5B5G6': ['GO:0001649', 'GO:0003677', 'GO:0005615', ...(truncated) | 19,390 | {} | 2025-11-28 23:21:25 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-11-28 23:21:36 | 2025-11-28 23:21:41 | 4.29 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016013', 'part_of'), ('GO:0016014', 'part_of'), ('GO:0016011', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2025-11-28 23:21:36 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2025-11-28 23:21:41 | 2025-11-28 23:21:41 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/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__20251128-202402/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 | 2025-11-28 23:21:41 | 2025-11-28 23:21:45 | 4.48 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016013', 'part_of'), ('GO:0016014', 'part_of'), ('GO:0016011', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2025-11-28 23:21:41 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-11-28 23:21:45 | 2025-11-28 23:21:49 | 3.49 | 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 | {} | 2025-11-28 23:21:45 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2025-11-28 23:21:49 | 2025-11-28 23:21:49 | 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__20251128-202402/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 | 2025-11-28 23:21:49 | 2025-11-28 23:21:53 | 3.62 | 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 | {} | 2025-11-28 23:21:49 | |
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2025-11-28 23:21:53 | 2025-11-28 23:21:53 | 0.21 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 808 | {} | 2025-11-28 23:21:53 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2025-11-28 23:21:53 | 2025-11-28 23:21:54 | 1.30 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2025-11-28 23:21:53 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2025-11-28 23:21:54 | 2025-11-28 23:22:01 | 7.07 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {} | 2025-11-28 23:21:54 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2025-11-28 23:22:01 | 2025-11-28 23:22:01 | 0.22 | dict | {'O15263': {GutmgeneAnnotation(gut_microbiota='Lacticaseibacillus rhamnosus', gut_microbiota_ncbi_id='47715', rank='species', strain=None, alteration='inhibition', throughput='low-throughput', associative_mode='causally', sample='Caco-2 cells', experimental_method='control experiment,in vitro bacter...(truncated) | 111 | {} | 2025-11-28 23:22:01 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2025-11-28 23:22:01 | 2025-11-28 23:22:01 | 0.01 | list | [GutmgeneRaw(index='23', pmid='31732863', gut_microbiota='Lacticaseibacillus rhamnosus', gut_microbiota_ncbi_id='47715', rank='species', strain=None, gene='DEFB4A', gene_id='1673', alteration='inhibition', throughput='low-throughput', associative_mode='causally', organism='human', sample='Caco-2 cel...(truncated) | 243 | {} | 2025-11-28 23:22:01 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2025-11-28 23:22:01 | 2025-11-28 23:22:02 | 0.24 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2025-11-28 23:22:01 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2025-11-28 23:22:02 | 2025-11-28 23:22:02 | 0.03 | dict | {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) | 622 | {} | 2025-11-28 23:22:02 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2025-11-28 23:22:02 | 2025-11-28 23:22:03 | 1.55 | 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) | 15,737 | {} | 2025-11-28 23:22:02 | |
| ¶ | pypath.inputs.hint.hint_interactions | 2025-11-28 23:22:03 | 2025-11-28 23:22:10 | 6.69 | list | [HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='LC'), HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='HT'), HintInteraction(id_a='A0A024R2I8', id_b='...(truncated) | 88,230 | {} | 2025-11-28 23:22:03 | |
| ¶ | pypath.inputs.hint.hint_raw | 2025-11-28 23:22:10 | 2025-11-28 23:22:10 | 0.09 | list | [['A0A024R2I8', 'F1D8Q5', 'NR1A2', 'NR2B1', '15604093:0018:HT:binary|19211732:0018:LC:binary|7746322:0018:LC:binary|9171239:0096:LC:binary|9368056:0096:LC:binary|9415406:0047:LC:binary', '9606', 'True', 'False'], ['A0A024R2I8', 'F1D8Q7', 'NR1A2', 'NR2B3', '15604093:0018:HT:binary', '9606', 'True', '...(truncated) | 163,435 | {} | 2025-11-28 23:22:10 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2025-11-28 23:22:10 | 2025-11-28 23:22:15 | 4.49 | list | [HippieInteraction(id_a='Q9NVF7', id_b='Q9ULS5', score=0.82, methods=None, references=('28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='Q16822', id_b='P01876', score=0.82, methods=None, references=('28514442', '33961781'), sources=None, organisms=None), HippieInteracti...(truncated) | 102,409 | {} | 2025-11-28 23:22:10 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2025-11-28 23:22:15 | 2025-11-28 23:23:31 | 75.89 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2025-11-28 23:22:15 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2025-11-28 23:23:31 | 2025-11-28 23:23:31 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {} | 2025-11-28 23:23:31 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2025-11-28 23:23:31 | 2025-11-28 23:23:31 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {} | 2025-11-28 23:23:31 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2025-11-28 23:23:31 | 2025-11-28 23:23:31 | 0.00 | dict | {} | 0 | {} | 2025-11-28 23:23:31 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2025-11-28 23:23:31 | 2025-11-28 23:23:31 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {} | 2025-11-28 23:23:31 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2025-11-28 23:23:31 | 2025-11-28 23:23:32 | 1.68 | 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:0001337'), HpoAnnotation(entrez_ge...(truncated) | 5,121 | {} | 2025-11-28 23:23:31 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2025-11-28 23:23:33 | 2025-11-28 23:23:35 | 2.31 | 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='ORPHA:485421', name='MFF-related encephalopathy due to mitoc...(truncated) | 11,488 | {} | 2025-11-28 23:23:33 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2025-11-28 23:23:35 | 2025-11-28 23:23:37 | 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 | {} | 2025-11-28 23:23:35 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2025-11-28 23:23:37 | 2025-11-28 23:23:37 | 0.53 | 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) | 19,393 | {} | 2025-11-28 23:23:37 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2025-11-28 23:23:37 | 2025-11-28 23:23:41 | 3.51 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2025-11-28 23:23:37 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2025-11-28 23:23:41 | 2025-11-28 23:23:42 | 1.24 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2025-11-28 23:23:41 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2025-11-28 23:23:42 | 2025-11-28 23:23:44 | 1.77 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2025-11-28 23:23:42 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2025-11-28 23:23:44 | 2025-11-28 23:23:45 | 1.13 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2025-11-28 23:23:44 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2025-11-28 23:23:45 | 2025-11-28 23:24:15 | 30.24 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2025-11-28 23:23:45 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2025-11-28 23:24:15 | 2025-11-28 23:24:16 | 1.10 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,384 | {} | 2025-11-28 23:24:15 | |
| ¶ | pypath.inputs.humap.humap1_complexes | 2025-11-28 23:24:16 | 2025-11-28 23:24:17 | 0.24 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,545 | {} | 2025-11-28 23:24:16 | |
| ¶ | pypath.inputs.humap.humap2and3_complexes | 2025-11-28 23:24:17 | 2025-11-28 23:24:18 | 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) | 15,429 | {} | 2025-11-28 23:24:17 | |
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2025-11-28 23:24:18 | 2025-11-28 23:24:21 | 2.53 | dict | {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2241788', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs...(truncated) | 13,122 | {} | 2025-11-28 23:24:18 | |
| ¶ | pypath.inputs.huri.hi_i_interactions | 2025-11-28 23:24:21 | 2025-11-28 23:24:22 | 1.22 |
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__20251128-202402/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 | 2025-11-28 23:24:22 | 2025-11-28 23:24:23 | 1.10 |
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__20251128-202402/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 | 2025-11-28 23:24:23 | 2025-11-28 23:24:24 | 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__20251128-202402/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 | 2025-11-28 23:24:24 | 2025-11-28 23:24:25 | 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__20251128-202402/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 | 2025-11-28 23:24:25 | 2025-11-28 23:24:27 | 1.24 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2025-11-28 23:24:25 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2025-11-28 23:24:27 | 2025-11-28 23:24:28 | 1.39 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2025-11-28 23:24:27 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2025-11-28 23:24:28 | 2025-11-28 23:24:29 | 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__20251128-202402/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 | 2025-11-28 23:24:29 | 2025-11-28 23:24:31 | 1.89 | list | [Rolland2014Interaction(entrez_a='14', entrez_b='6293', genesymbol_a='AAMP', genesymbol_b='VPS52', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='8553', genesymbol_a='AAMP', genesymbol_b='BHLHE40', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='64782', genesymbo...(truncated) | 13,944 | {} | 2025-11-28 23:24:29 | |
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2025-11-28 23:24:31 | 2025-11-28 23:24:32 | 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__20251128-202402/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 | 2025-11-28 23:24:32 | 2025-11-28 23:24:33 | 1.10 |
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__20251128-202402/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 | 2025-11-28 23:24:33 | 2025-11-28 23:24:41 | 7.81 | list | [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) | 22,184 | {} | 2025-11-28 23:24:33 | |
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2025-11-28 23:24:41 | 2025-11-28 23:24:42 | 0.34 | 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} | 2025-11-28 23:24:41 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2025-11-28 23:24:42 | 2025-11-28 23:24:42 | 0.04 | dict | {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) | 156 | {} | 2025-11-28 23:24:42 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2025-11-28 23:24:42 | 2025-11-28 23:24:42 | 0.03 | list | [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) | 1,647 | {} | 2025-11-28 23:24:42 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2025-11-28 23:24:42 | 2025-11-28 23:24:45 | 3.85 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2025-11-28 23:24:42 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2025-11-28 23:24:45 | 2025-11-28 23:24:46 | 0.46 | list | [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) | 11,470 | {} | 2025-11-28 23:24:45 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2025-11-28 23:24:46 | 2025-11-28 23:24:47 | 0.53 | NoneType | None | 0 | {} | 2025-11-28 23:24:46 | |
| ¶ | pypath.inputs.intact.intact_interactions | 2025-11-28 23:24:47 | 2025-11-28 23:26:20 | 93.85 | list | [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', i...(truncated) | 78,544 | {} | 2025-11-28 23:24:47 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2025-11-28 23:26:21 | 2025-11-28 23:26:21 | 0.59 | set | {'Q9UKX5', 'P26006', 'Q13683', 'P20702', 'P18084', 'P11215', 'P18564', 'P26012', 'Q13349', 'Q13797', 'P05106', 'P56199', 'P08648', 'P05556', 'P05107', 'P06756', 'P20701', 'P23229', 'P38570', 'P53708', 'P16144', 'P26010', 'P17301', 'P08514', 'O75578'} | 25 | {} | 2025-11-28 23:26:21 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2025-11-28 23:26:21 | 2025-11-28 23:26:22 | 1.16 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0006355', go_term_name='regulation of DNA-templated transcription'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid...(truncated) | 14,743 | {} | 2025-11-28 23:26:21 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2025-11-28 23:26:22 | 2025-11-28 23:26:23 | 0.37 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR000001', organism='9606', start='388', end='471'), InterproAnnotation(interpro_id='IPR013806', organism='9606', start='210', end='293'), InterproAnnotation(interpro_id='IPR013806', organism='9606', start='115', end='208'), Int...(truncated) | 16,611 | {} | 2025-11-28 23:26:22 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2025-11-28 23:26:23 | 2025-11-28 23:26:33 | 10.21 | 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 | {} | 2025-11-28 23:26:23 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2025-11-28 23:26:33 | 2025-11-28 23:26:34 | 0.63 | dict | {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) | 483 | {} | 2025-11-28 23:26:33 | |
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2025-11-28 23:26:34 | 2025-11-28 23:26:36 | 2.18 | dict | {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) | 86,754 | {} | 2025-11-28 23:26:34 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2025-11-28 23:26:36 | 2025-11-28 23:26:54 | 18.43 | 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 | {} | 2025-11-28 23:26:36 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2025-11-28 23:26:54 | 2025-11-28 23:26:55 | 0.63 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='growth factor'), ItalkAnnotation(mainclass='receptor', subclass='other')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {} | 2025-11-28 23:26:54 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2025-11-28 23:26:55 | 2025-11-28 23:26:55 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {} | 2025-11-28 23:26:55 | |
| ¶ | pypath.inputs.italk.italk_raw | 2025-11-28 23:26:55 | 2025-11-28 23:26:55 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2025-11-28 23:26:55 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2025-11-28 23:26:55 | 2025-11-28 23:26:57 | 1.68 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,224 | {} | 2025-11-28 23:26:55 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2025-11-28 23:26:57 | 2025-11-28 23:26:57 | 0.15 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {} | 2025-11-28 23:26:57 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2025-11-28 23:26:57 | 2025-11-28 23:45:08 | 1,091.27 | 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) | 15,233 | {} | 2025-11-28 23:26:57 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2025-11-28 23:45:08 | 2025-11-28 23:45:30 | 21.82 | set | {KeggMedicusRawInteraction(id_a='2776', id_b='5331', name_a='GNAQ', name_b='PLCB3', effect='stimulation', itype='post_translational', pw_type='variant', type_a='gene', type_b='gene', network_id='N00985'), KeggMedicusRawInteraction(id_a='6655', id_b='3265', name_a='SOS2', name_b='HRAS', effect='stimu...(truncated) | 12,946 | {} | 2025-11-28 23:45:08 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2025-11-28 23:45:30 | 2025-11-28 23:45:31 | 0.43 | dict | {'COMPLEX:Q13620_Q16531_Q9Y4B6': Complex: COMPLEX:Q13620_Q16531_Q9Y4B6, 'COMPLEX:P42336_Q92569': Complex: COMPLEX:P42336_Q92569, 'COMPLEX:Q14457_Q6ZNE5_Q8NEB9': Complex: COMPLEX:Q14457_Q6ZNE5_Q8NEB9, 'COMPLEX:P15336_P16220': Complex: COMPLEX:P15336_P16220, 'COMPLEX:P06737_P35573': Complex: COMPLEX:P...(truncated) | 528 | {} | 2025-11-28 23:45:30 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2025-11-28 23:45:31 | 2025-11-28 23:45:32 | 1.18 | list | [KeggMedicusInteraction(id_a='P50148', id_b='Q01970', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='Q07890', id_b='P01112', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,538 | {} | 2025-11-28 23:45:31 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2025-11-28 23:45:32 | 2025-11-28 23:45:44 | 12.26 | dict | {'P42574': {KeggPathway(pathway='p53 signaling pathway'), KeggPathway(pathway='Pathways of neurodegeneration - multiple diseases'), KeggPathway(pathway='Small cell lung cancer'), KeggPathway(pathway='Huntington disease'), KeggPathway(pathway='Proteoglycans in cancer'), KeggPathway(pathway='Alcoholic...(truncated) | 2,726 | {} | 2025-11-28 23:45:32 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2025-11-28 23:45:44 | 2025-11-28 23:45:45 | 0.37 | dict | {'A8K7J7': {KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Starch and...(truncated) | 813 | {} | 2025-11-28 23:45:44 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2025-11-28 23:45:45 | 2025-11-28 23:45:58 | 13.08 | tuple | ({'MAPK signaling pathway': {'P42574', 'Q12933', 'P0DPQ6', 'Q12852', 'Q12968', 'P63000', 'P80370', 'P04637', 'Q15283', 'Q13164', 'Q9UPT6', 'P0C869', 'O95382', 'P17252', 'Q9Y2U5', 'Q15628', 'Q9NRY4', 'P53041', 'Q9HC77', 'Q13387', 'Q92918', 'P35557', 'P80192', 'P48023', 'Q96KG9', 'P32248', 'Q03113', '...(truncated) | 2 | {} | 2025-11-28 23:45:45 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2025-11-28 23:45:58 | 2025-11-28 23:46:03 | 4.89 |
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__20251128-202402/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__20251128-202402/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/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__20251128-202402/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 | 2025-11-28 23:46:03 | 2025-11-28 23:46:03 | 0.31 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 503 | {} | 2025-11-28 23:46:03 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2025-11-28 23:46:03 | 2025-11-28 23:46:03 | 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 | {} | 2025-11-28 23:46:03 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2025-11-28 23:46:03 | 2025-11-28 23:46:07 | 3.51 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {} | 2025-11-28 23:46:03 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2025-11-28 23:46:07 | 2025-11-28 23:46:09 | 2.01 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {} | 2025-11-28 23:46:07 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2025-11-28 23:46:09 | 2025-11-28 23:46:10 | 0.92 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2025-11-28 23:46:09 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2025-11-28 23:46:10 | 2025-11-28 23:46:10 | 0.28 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2025-11-28 23:46:10 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2025-11-28 23:46:10 | 2025-11-28 23:46:11 | 0.61 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2025-11-28 23:46:10 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2025-11-28 23:46:11 | 2025-11-28 23:46:21 | 10.22 | list | [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) | 593 | {} | 2025-11-28 23:46:11 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2025-11-28 23:46:21 | 2025-11-28 23:46:21 | 0.02 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2025-11-28 23:46:21 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2025-11-28 23:46:21 | 2025-11-28 23:46:21 | 0.02 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2025-11-28 23:46:21 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2025-11-28 23:46:21 | 2025-11-28 23:46:22 | 1.09 | dict | {'SciTegic09271913552D': LincsCompound(lincs=None, chembl=None, chebi=None, inchi='InChI=1S/C29H24N4O4S/c1-4-27(34)31-26-16-23(12-5-18(26)2)33-28(35)14-9-21-17-30-25-13-8-20(15-24(25)29(21)33)19-6-10-22(11-7-19)32-38(3,36)37/h4-17,32H,1H2,2-3H3,(H,31,34)', inchi_key='SFMJNHNUOVADRW-UHFFFAOYSA-N', sm...(truncated) | 371 | {} | 2025-11-28 23:46:21 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2025-11-28 23:46:22 | 2025-11-28 23:46:23 | 0.69 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2025-11-28 23:46:22 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2025-11-28 23:46:23 | 2025-11-28 23:46:23 | 0.45 | list | [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) | 1,170 | {} | 2025-11-28 23:46:23 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2025-11-28 23:46:23 | 2025-11-28 23:46:24 | 1.10 | list | [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) | 1,170 | {} | 2025-11-28 23:46:23 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2025-11-28 23:46:24 | 2025-11-28 23:46:25 | 0.44 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {} | 2025-11-28 23:46:24 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2025-11-28 23:46:25 | 2025-11-28 23:46:25 | 0.39 | list | [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism=5888, pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism=9468, pmid='17175535'), LncrnadbInteraction(lncrna='G22', partner='SRP9', type='protein', o...(truncated) | 773 | {} | 2025-11-28 23:46:25 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2025-11-28 23:46:25 | 2025-11-28 23:46:57 | 31.59 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, scor...(truncated) | 9,479 | {} | 2025-11-28 23:46:25 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2025-11-28 23:46:57 | 2025-11-28 23:46:57 | 0.33 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPMR'), references=('8824219',)), LrdbAnnotation(role='receptor', cell_type=None, sources=('Fanto...(truncated) | 1,536 | {} | 2025-11-28 23:46:57 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2025-11-28 23:46:57 | 2025-11-28 23:46:57 | 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 | {} | 2025-11-28 23:46:57 | |
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2025-11-28 23:46:57 | 2025-11-28 23:46:57 | 0.17 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2025-11-28 23:46:57 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2025-11-28 23:46:57 | 2025-11-28 23:46:57 | 0.24 | dict | {'H7C4N5': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'E9PPR9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YEL2': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,501 | {} | 2025-11-28 23:46:57 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2025-11-28 23:46:57 | 2025-11-28 23:46:58 | 0.53 | dict | {} | 0 | {} | 2025-11-28 23:46:57 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2025-11-28 23:46:58 | 2025-11-28 23:47:00 | 2.03 | set | {'P56597', 'Q99584', 'Q9BY76', 'Q9UEU0', 'Q86SQ3', 'Q6IE38', 'Q99748', 'P30046', 'B3GLJ2', 'P13929', 'Q9H4A4', 'Q02763', 'Q6UW32', 'Q9Y251', 'P01569', 'P01611', 'P29120', 'O00254', 'A0A0C4DH36', 'O75173', 'Q96BH3', 'Q01344', 'Q9BRR9', 'P43652', 'Q9BRF8', 'P20742', 'O75635', 'Q8N690', 'Q6PEW0', 'Q145...(truncated) | 2,840 | {} | 2025-11-28 23:46:58 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2025-11-28 23:47:00 | 2025-11-28 23:47:00 | 0.10 | list | [MatrixdbInteraction(id_a='"chebi:""CHEBI:29105"""', id_b='uniprotkb:P05067', alt_ids_a='matrixdb:CAT_1', alt_ids_b='-', aliases_a='matrixdb:Zinc(short label)', aliases_b='"uniprotkb:""APP""(gene name)"', detection_method='"psi-mi:""MI:0004""(""affinity chromatography technology"")"', author='Bush A...(truncated) | 1,264 | {} | 2025-11-28 23:47:00 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2025-11-28 23:47:00 | 2025-11-28 23:47:00 | 0.07 | set | set() | 0 | {} | 2025-11-28 23:47:00 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2025-11-28 23:47:00 | 2025-11-28 23:47:00 | 0.06 | set | set() | 0 | {} | 2025-11-28 23:47:00 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2025-11-28 23:47:00 | 2025-11-28 23:47:01 | 1.08 | set | {'Q9BY67', 'O95500', 'Q49MI3', 'Q9HBB8', 'P25942', 'P56748', 'Q96KR4', 'Q02763', 'Q92692', 'P25940', 'Q99418', 'Q9NPY3', 'P42081', 'Q12816', 'P20702', 'Q13740', 'P42771', 'P28827', 'P12259', 'P13612', 'Q96QR6', 'Q08174', 'P01732', 'Q68D78', 'Q9UKX5', 'Q04900', 'Q13308', 'Q8TAW8', 'O60759', 'Q8WWQ8',...(truncated) | 112 | {} | 2025-11-28 23:47:00 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2025-11-28 23:47:01 | 2025-11-28 23:47:28 | 26.44 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {} | 2025-11-28 23:47:01 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2025-11-28 23:47:28 | 2025-11-28 23:47:28 | 0.11 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2025-11-28 23:47:28 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2025-11-28 23:47:28 | 2025-11-28 23:47:30 | 1.83 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2025-11-28 23:47:28 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2025-11-28 23:47:30 | 2025-11-28 23:47:31 | 0.79 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2025-11-28 23:47:30 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2025-11-28 23:47:31 | 2025-11-28 23:47:31 | 0.17 | list | [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) | 805 | {} | 2025-11-28 23:47:31 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2025-11-28 23:47:31 | 2025-11-28 23:48:01 | 30.10 |
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__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 169, in mirbase_ids
for row in mirbase_mirna_pre_mature(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 118, in mirbase_mirna_pre_mature
mirna = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 118, in <dictcomp>
mirna = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 108, in mirbase_mirna
yield from _mirbase_of_organism('mirna', 2, organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 97, in _mirbase_of_organism
for row in _mirbase_table(table):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-28 01:06:31 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2025-11-28 23:48:01 | 2025-11-28 23:48:31 | 30.01 |
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__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 136, in mirbase_mature
for row in mirbase_mirna_mature(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 113, in mirbase_mirna_mature
yield from _mirbase_of_organism('mirna_mature', 1, organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 97, in _mirbase_of_organism
for row in _mirbase_table(table):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-28 01:06:31 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2025-11-28 23:48:31 | 2025-11-28 23:48:52 | 21.48 | list | ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) | 2,693 | {} | 2025-11-28 23:48:31 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna | 2025-11-28 23:48:52 | 2025-11-28 23:48:53 | 0.76 | 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' untr...(truncated) | 39,233 | {} | 2025-11-28 23:48:52 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_mature | 2025-11-28 23:48:53 | 2025-11-28 23:48:53 | 0.02 | list | [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) | 49,168 | {} | 2025-11-28 23:48:53 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_pre_mature | 2025-11-28 23:48:53 | 2025-11-28 23:49:23 | 30.10 |
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__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 127, in mirbase_mirna_pre_mature
for row in _mirbase_table('mirna_pre_mature'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-28 01:06:31 | |||
| ¶ | pypath.inputs.mirbase.mirbase_organisms | 2025-11-28 23:49:23 | 2025-11-28 23:49:53 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 61, in mirbase_organisms
for row in _mirbase_table('mirna_species'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-28 01:06:31 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2025-11-28 23:49:53 | 2025-11-28 23:49:53 | 0.03 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,130 | {} | 2025-11-28 23:49:53 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2025-11-28 23:49:53 | 2025-11-28 23:49:53 | 0.03 | list | ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', 'MI0000081', 'MI0000082', ...(truncated) | 1,984 | {} | 2025-11-28 23:49:53 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2025-11-28 23:49:53 | 2025-11-28 23:50:23 | 30.08 |
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__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 158, in mirbase_precursor_to_mature
for row in mirbase_mirna_pre_mature(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 127, in mirbase_mirna_pre_mature
for row in _mirbase_table('mirna_pre_mature'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/mirbase.py", line 40, in _mirbase_table
for row in c.result.strip('<>/p\n')[:-3].split('<br>'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'
|
{'broke': True} | 2025-11-28 01:06:31 | |||
| ¶ | pypath.inputs.mirbase.mirbase_taxid | 2025-11-28 23:50:23 | 2025-11-28 23:50:23 | 0.00 | str | 'hsa' | 3 | {} | 2025-11-28 23:50:23 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2025-11-28 23:50:23 | 2025-11-28 23:50:24 | 0.16 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2025-11-28 23:50:23 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2025-11-28 23:50:24 | 2025-11-28 23:50:24 | 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 | {} | 2025-11-28 23:50:24 | |
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2025-11-28 23:50:24 | 2025-11-28 23:56:38 | 374.08 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=10090, target_genesymbol='Cd320', target_entrez='54219', target_organism=10090, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', data...(truncated) | 27,595 | {} | 2025-11-28 23:50:24 | |
| ¶ | 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 | 2025-11-28 23:56:38 | 2025-11-28 23:58:32 | 114.04 | 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) | 1,181,412 | {} | 2025-11-28 23:56:38 | |
| ¶ | pypath.inputs.mitab.mitab_interactions | 2025-11-28 23:58:32 | 2025-11-28 23:58:32 | 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__20251128-202402/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 | 2025-11-28 23:58:32 | 2025-11-28 23:58:39 | 6.91 | 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) | 37,967 | {} | 2025-11-28 23:58:32 | |
| ¶ | pypath.inputs.mppi.mppi_interactions | 2025-11-28 23:58:39 | 2025-11-28 23:58:39 | 0.28 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2025-11-28 23:58:39 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2025-11-28 23:58:39 | 2025-11-28 23:59:14 | 34.41 | dict | {'P43115': {MsigdbAnnotation(collection='immunesigdb', geneset='GSE17721_POLYIC_VS_CPG_4H_BMDC_UP'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE3982_EOSINOPHIL_VS_BCELL_UP'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE41978_WT_VS_ID2_KO_KLRG1_LOW_EFFECTOR_CD8_TCELL_DN'), Msig...(truncated) | 20,111 | {} | 2025-11-28 23:58:39 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2025-11-28 23:59:15 | 2025-11-28 23:59:23 | 7.81 | dict | {'MT': {'MT-TK', 'MT-TM', 'MT-RNR1', 'MT-TT', 'MT-TE', 'MT-TI', 'MT-TN', 'MT-TY', 'MT-ATP6', 'MT-RNR2', 'MT-ND4L', 'MT-TS2', 'MT-ND2', 'MT-ND5', 'MT-TL2', 'MT-TD', 'MT-ND3', 'MT-ATP8', 'MT-ND4', 'MT-ND6', 'MT-TF', 'MT-TL1', 'MT-TP', 'MT-TH', 'MT-TV', 'MT-TW', 'MT-TR', 'MT-CO2', 'MT-TQ', 'MT-CYB', 'M...(truncated) | 35,134 | {} | 2025-11-28 23:59:15 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2025-11-28 23:59:24 | 2025-11-28 23:59:24 | 0.46 | dict | {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'ACADL', 'PREB', 'ITGA7', 'GRPEL1', 'ATP5PO', 'ELMOD3', 'AK2', 'ACADS', 'APLP2', 'ELOVL6', 'SLC25A10', 'TANK', 'IMMT', 'ANGPTL4', 'ORM1', 'MYLK', 'RIOK3', 'CD151', 'ME1', 'NDUFB7', 'BCL6', 'VEGFB', 'GPHN', 'DLAT', 'SDHC', 'CYC1', 'ACLY', 'COQ9', 'BC...(truncated) | 20 | {} | 2025-11-28 23:59:24 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2025-11-28 23:59:24 | 2025-11-28 23:59:25 | 0.98 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2025-11-28 23:59:24 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2025-11-28 23:59:25 | 2025-11-28 23:59:25 | 0.15 | list | [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) | 2,171 | {} | 2025-11-28 23:59:25 | |
| ¶ | pypath.inputs.netbiol.arn_interactions | 2025-11-28 23:59:25 | 2025-11-28 23:59:26 | 0.10 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2025-11-28 23:59:25 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2025-11-28 23:59:26 | 2025-11-28 23:59:26 | 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 | {} | 2025-11-28 23:59:26 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2025-11-28 23:59:26 | 2025-11-28 23:59:27 | 1.44 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2025-11-28 23:59:26 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2025-11-28 23:59:27 | 2025-11-28 23:59:27 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2025-11-28 23:59:27 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2025-11-28 23:59:27 | 2025-11-28 23:59:27 | 0.13 | dict | {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Hedgehog'), Netpat...(truncated) | 1,870 | {} | 2025-11-28 23:59:27 | |
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2025-11-28 23:59:27 | 2025-11-28 23:59:55 | 27.99 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2025-11-28 23:59:27 | |
| ¶ | pypath.inputs.oma.oma_orthologs | 2025-11-28 23:59:55 | 2025-11-29 00:01:49 | 113.58 | list | [OmaOrthology(a=OmaGene(id='NUFP1_HUMAN', oma_group=1070227, hog='HOG:E0801468.10sgp.7266b.5816c', taxon=9606, chr='13', start=44941206, end=44989436, strand=-1, main_isoform=True), b=OmaGene(id='NUFP1_MOUSE', oma_group=1070227, hog='HOG:E0801468.10sgp.7266b', taxon=10090, chr='14', start=76348373, ...(truncated) | 22,374 | {} | 2025-11-28 23:59:55 | |
| ¶ | pypath.inputs.oma.oma_table | 2025-11-29 00:01:49 | 2025-11-29 00:01:58 | 8.83 | defaultdict | defaultdict(<class 'set'>, {'NUFP1_HUMAN': {'NUFP1_MOUSE'}, 'RU2B_HUMAN': {'RU2B_MOUSE'}, 'BAP1_HUMAN': {'BAP1_MOUSE'}, 'A0A075B7D0': {'A0A0G2JGK2', 'A0A075B5W6', 'A0A075B5T4', 'A0A0A6YXC3', 'A0A075B5Y5', 'A0A0B4J1M0', 'A0A075B674', 'A0A0A6YXA5', 'A0A075B5V2', 'A0A075B5W5', 'A0A075B5W9', 'A0A075B5R7...(truncated) | 17,895 | {} | 2025-11-29 00:01:49 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2025-11-29 00:01:58 | 2025-11-29 00:01:58 | 0.54 | 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) | 277 | {} | 2025-11-29 00:01:58 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2025-11-29 00:01:58 | 2025-11-29 00:02:25 | 26.92 | 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 | {'fixed': True} | 2025-11-29 00:01:58 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2025-11-29 00:02:25 | 2025-11-29 00:04:02 | 96.81 | 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 | {} | 2025-11-29 00:02:25 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2025-11-29 00:04:02 | 2025-11-29 00:05:07 | 65.07 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {} | 2025-11-29 00:04:02 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2025-11-29 00:05:07 | 2025-11-29 00:06:33 | 85.75 | 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 | {} | 2025-11-29 00:05:07 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2025-11-29 00:06:33 | 2025-11-29 00:06:49 | 16.13 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 88 | {} | 2025-11-29 00:06:33 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2025-11-29 00:06:49 | 2025-11-29 00:07:05 | 16.02 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {} | 2025-11-29 00:06:49 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2025-11-29 00:07:05 | 2025-11-29 00:07:09 | 3.87 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 2,219,572 | {} | 2025-11-29 00:07:05 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2025-11-29 00:07:09 | 2025-11-29 00:07:13 | 3.63 | defaultdict | defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=False, cell_type='Enterocytes', organ='GI tract', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=0.0, mouse_sensitivity=0.00331126, human_specificity=0.00439422, mouse_specifici...(truncated) | 4,492 | {} | 2025-11-29 00:07:09 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2025-11-29 00:07:13 | 2025-11-29 00:07:13 | 0.03 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2025-11-29 00:07:13 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2025-11-29 00:07:13 | 2025-11-29 00:07:13 | 0.00 | list | [] | 0 | {} | 2025-11-29 00:07:13 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2025-11-29 00:07:13 | 2025-11-29 00:07:35 | 22.52 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='controls-expression-of', id_b='A2M', resource='pid'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b=...(truncated) | 2,524,906 | {} | 2025-11-29 00:07:13 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2025-11-29 00:07:37 | 2025-11-29 00:07:37 | 0.27 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2025-11-29 00:07:37 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2025-11-29 00:07:37 | 2025-11-29 00:07:44 | 6.97 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2025-11-29 00:07:37 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2025-11-29 00:07:47 | 2025-11-29 00:07:56 | 8.28 | dict | {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) | 49,179 | {} | 2025-11-29 00:07:47 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2025-11-29 00:07:56 | 2025-11-29 00:08:00 | 4.43 | tuple | ({'P02185': {('5ile', 'X-ray', 1.77), ('1yoh', 'X-ray', 1.65), ('2ekt', 'X-ray', 1.1), ('4nxc', 'X-ray', 1.55), ('6z4t', 'X-ray', 1.23), ('7a44', 'X-ray', 1.75), ('1duk', 'X-ray', 2.13), ('2mgk', 'X-ray', 2.0), ('6n03', 'X-ray', 2.1), ('104m', 'X-ray', 1.71), ('2mye', 'X-ray', 1.68), ('1vxc', 'X-ray...(truncated) | 2 | {} | 2025-11-29 00:07:56 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2025-11-29 00:08:01 | 2025-11-29 00:08:01 | 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 | {} | 2025-11-29 00:08:01 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2025-11-29 00:08:01 | 2025-11-29 00:19:41 | 700.14 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2025-11-29 00:08:01 | |
| ¶ | pypath.inputs.pfam.pfam_names | 2025-11-29 00:19:41 | 2025-11-29 00:19:43 | 1.20 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2025-11-29 00:19:41 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2025-11-29 00:19:43 | 2025-11-29 00:19:47 | 4.06 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) | 2 | {} | 2025-11-29 00:19:43 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2025-11-29 00:19:47 | 2025-11-29 00:26:02 | 374.69 | tuple | ({}, {}) | 2 | {'fixed': True} | 2025-11-29 00:19:47 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2025-11-29 00:26:02 | 2025-11-29 00:41:28 | 925.79 | tuple | ({}, {}) | 2 | {} | 2025-11-29 00:26:02 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2025-11-29 00:41:28 | 2025-11-29 00:43:46 | 138.04 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:41:28 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2025-11-29 00:43:47 | 2025-11-29 00:43:50 | 3.53 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:43:47 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2025-11-29 00:43:51 | 2025-11-29 00:43:55 | 3.82 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:43:51 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2025-11-29 00:43:56 | 2025-11-29 00:43:59 | 2.86 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:43:56 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2025-11-29 00:44:00 | 2025-11-29 00:44:03 | 3.67 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:44:00 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2025-11-29 00:44:04 | 2025-11-29 00:45:04 | 59.51 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2025-11-29 00:44:04 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2025-11-29 00:45:04 | 2025-11-29 00:45:07 | 2.94 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-11-29 00:45:04 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2025-11-29 00:45:08 | 2025-11-29 00:45:08 | 0.42 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2025-11-29 00:45:08 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2025-11-29 00:45:08 | 2025-11-29 00:45:13 | 4.25 | dict | {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) | 264 | {} | 2025-11-29 00:45:08 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2025-11-29 00:45:13 | 2025-11-29 00:45:22 | 9.81 |
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__20251128-202402/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
n for d, n in iteritems(data)
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-pAVdo7EK-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2025-08-31 06:30:34 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2025-11-29 00:45:22 | 2025-11-29 00:45:31 | 9.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/phosphoelm.py", line 101, in phosphoelm_interactions
data = phosphoelm_enzyme_substrate(ltp_only = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
n for d, n in iteritems(data)
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-pAVdo7EK-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2025-08-31 06:30:36 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2025-11-29 00:45:31 | 2025-11-29 00:45:40 | 9.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/phosphoelm.py", line 121, in phosphoelm_kinases
soup = bs4.BeautifulSoup(data, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-pAVdo7EK-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{} | 2025-08-31 06:30:37 | |||
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2025-11-29 00:45:40 | 2025-11-29 00:45:42 | 1.24 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2025-11-29 00:45:40 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.02 | list | [['FGFR1', 'DDX6'], ['TESK2', 'RPS6KA2'], ['PAK1', 'HNRPK'], ['MAPK8', 'ATF7'], ['CSNK2A1', 'IGF2R'], ['MAPK8', 'HTATIP'], ['STK11', 'KIAA0999'], ['NEK3', 'METTL3'], ['WEE1', 'TSC22D4'], ['BTK', 'WAS'], ['PLK1', 'ANAPC7'], ['NEK4', 'MTA1'], ['CLK2', 'TRIM28'], ['MAP2K4', 'EIF4A2'], ['CSNK2A1', 'HNRN...(truncated) | 1,821 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.22 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.30 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 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 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2025-11-29 00:45:42 | 2025-11-29 00:45:42 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) | 4,790 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2025-11-29 00:45:42 | 2025-11-29 00:45:47 | 5.00 | dict | {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,635 | {} | 2025-11-29 00:45:42 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2025-11-29 00:45:48 | 2025-11-29 00:46:01 | 13.25 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {} | 2025-11-29 00:45:48 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2025-11-29 00:46:01 | 2025-11-29 00:46:02 | 0.40 | 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 | {} | 2025-11-29 00:46:01 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2025-11-29 00:46:02 | 2025-11-29 00:47:24 | 81.73 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'28052875', '21209006', '24876223', '21148409'}, 'isoforms': {1}, 'process': {''}, 'function': {'phosphorylation', 'protein stabilization', 'intracellular localization', 'ubiquitination', 'protein degradation'}...(truncated) | 3,621 | {} | 2025-11-29 00:46:02 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2025-11-29 00:47:24 | 2025-11-29 00:47:50 | 26.25 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2025-11-29 00:47:24 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2025-11-29 00:47:50 | 2025-11-29 00:47:50 | 0.46 | 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 | {} | 2025-11-29 00:47:50 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2025-11-29 00:47:51 | 2025-11-29 00:48:56 | 65.81 | dict | {'P35250': {ProgenyAnnotation(pathway='VEGF', weight=-0.15684553639501156, p_value=0.8477560090795286), ProgenyAnnotation(pathway='Hypoxia', weight=-2.049501418649251, p_value=0.0007040310639538167), ProgenyAnnotation(pathway='MAPK', weight=2.277341180050157, p_value=3.324844332731664e-11), ProgenyA...(truncated) | 18,582 | {} | 2025-11-29 00:47:51 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2025-11-29 00:48:57 | 2025-11-29 00:50:03 | 66.37 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2025-11-29 00:48:57 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2025-11-29 00:50:03 | 2025-11-29 00:50:08 | 4.47 | dict | {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) | 2 | {} | 2025-11-29 00:50:03 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2025-11-29 00:50:09 | 2025-11-29 00:50:20 | 10.78 | dict | {'O43657': {ProtainatlasAnnotation(organ='Lymph node', tissue='Lymph node', cell_type='non-germinal center cells', level='Not detected', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnot...(truncated) | 15,055 | {} | 2025-11-29 00:50:09 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2025-11-29 00:50:22 | 2025-11-29 00:50:23 | 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 | {} | 2025-11-29 00:50:22 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2025-11-29 00:50:23 | 2025-11-29 00:50:23 | 0.26 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,590 | {} | 2025-11-29 00:50:23 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2025-11-29 00:50:23 | 2025-11-29 00:50:23 | 0.49 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='main', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', reliability='Appro...(truncated) | 13,404 | {} | 2025-11-29 00:50:23 | |
| ¶ | pypath.inputs.proteins.variants | 2025-11-29 00:50:24 | 2025-11-29 00:56:34 | 370.71 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 30,341 | {} | 2025-11-29 00:50:24 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2025-11-29 00:56:35 | 2025-11-29 00:56:36 | 1.08 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q05513', 'CTRL_GENE_NAME': 'PRKCZ', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P27448', 'TARGET_GENE_NAME': 'MARK3', 'TARGET_RES': 'T', 'TARGET_POS': '564', 'SOURCES': 'psp,signor', 'BELIEF': '1'}, {'ID': '1', 'CTRL_NS': 'UP', 'CTRL_ID': 'P41743', 'CTRL_GEN...(truncated) | 2 | {} | 2025-11-29 00:56:35 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2025-11-29 00:56:36 | 2025-11-29 00:56:37 | 0.95 | list | [{'kinase': 'Q05513', 'resaa': 'T', 'resnum': 564, 'references': {'15084291'}, 'substrate': 'P27448', 'databases': {'PhosphoSite', 'SIGNOR'}}, {'kinase': 'P41743', 'resaa': 'T', 'resnum': 564, 'references': set(), 'substrate': 'P27448', 'databases': {'PhosphoSite'}}, {'kinase': 'Q9NRM7', 'resaa': 'S...(truncated) | 31,263 | {} | 2025-11-29 00:56:36 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.psimi.psimi_ontology | 2025-11-29 00:56:37 | 2025-11-29 00:56:37 | 0.30 | 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) | 1,652 | {} | 2025-11-29 00:56:37 | |
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2025-11-29 00:56:37 | 2025-11-29 00:56:38 | 0.34 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2025-11-29 00:56:37 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2025-11-29 00:56:38 | 2025-11-29 00:56:47 | 9.69 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), Ramil...(truncated) | 18,879 | {} | 2025-11-29 00:56:38 | |
| ¶ | pypath.inputs.reaction.acsn_biopax | 2025-11-29 00:56:48 | 2025-11-29 00:56:48 | 0.59 | NoneType | None | 0 | {} | 2025-11-29 00:56:48 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2025-11-29 00:56:48 | 2025-11-29 00:56:48 | 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 | {} | 2025-11-29 00:56:48 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2025-11-29 00:56:48 | 2025-11-29 00:56:49 | 0.36 |
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__20251128-202402/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/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 | 2025-11-29 00:56:49 | 2025-11-29 00:56:56 | 7.51 | dict | {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) | 178 | {} | 2025-11-29 00:56:49 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2025-11-29 00:56:56 | 2025-11-29 00:56:58 | 2.24 | NoneType | None | 0 | {} | 2025-11-29 00:56:56 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2025-11-29 00:56:58 | 2025-11-29 00:57:21 | 22.51 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2025-11-29 00:56:58 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2025-11-29 00:57:21 | 2025-11-29 01:04:01 | 399.59 | 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 94 on 9/8/25, 6:26 PM using JSBML version 1.5.</p> </annotati...(truncated) | 2,825 | {} | 2025-11-29 00:57:21 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2025-11-29 01:04:22 | 2025-11-29 01:04:24 | 1.77 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/cache/9c...(truncated) | 2,825 | {} | 2025-11-29 01:04:22 | |
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2025-11-29 01:04:24 | 2025-11-29 01:04:25 | 0.79 | 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) | 23,259 | {} | 2025-11-29 01:04:24 | |
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2025-11-29 01:04:25 | 2025-11-29 01:04:31 | 6.21 |
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__20251128-202402/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 | 2025-11-29 01:04:31 | 2025-11-29 01:04:31 | 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__20251128-202402/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 | 2025-11-29 01:04:31 | 2025-11-29 01:04:32 | 1.10 |
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__20251128-202402/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 | 2025-11-29 01:04:32 | 2025-11-29 01:04:47 | 14.84 |
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__20251128-202402/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 | 2025-11-29 01:04:47 | 2025-11-29 01:05:09 | 22.47 | list | [{'Reaction identifier': 'RHEA:21252', 'Equation': '(S)-2-hydroxyglutarate + A = 2-oxoglutarate + AH2', 'ChEBI name': '(S)-2-hydroxyglutarate;A;2-oxoglutarate;AH2', 'ChEBI identifier': 'CHEBI:16782;CHEBI:13193;CHEBI:16810;CHEBI:17499', 'EC number': 'EC:1.1.99.2', 'Enzymes': '4258', 'Gene Ontology': ...(truncated) | 17,783 | {} | 2025-11-29 01:04:47 | |
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2025-11-29 01:05:09 | 2025-11-29 01:05:27 | 17.80 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human'), ScconnectAnnota...(truncated) | 3,285 | {} | 2025-11-29 01:05:09 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2025-11-29 01:05:27 | 2025-11-29 01:05:27 | 0.03 | set | {Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:O15263, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:O75462_Q9UBD9, Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01562, Complex: CO...(truncated) | 17 | {} | 2025-11-29 01:05:27 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2025-11-29 01:05:27 | 2025-11-29 01:09:57 | 269.34 | list | [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) | 1,766 | {} | 2025-11-29 01:05:27 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2025-11-29 01:09:57 | 2025-11-29 01:09:57 | 0.14 | dict | {'CID106918182': {SiderDrug(name='strontium', atc='M05BX03')}, 'CID100004896': {SiderDrug(name='prednisolone', atc=None)}, 'CID100005939': {SiderDrug(name='biguanide', atc=None)}, 'CID104369359': {SiderDrug(name='sitagliptin', atc='A10BH01')}, 'CID100005238': {SiderDrug(name='sodium', atc='V09FX04')...(truncated) | 1,430 | {} | 2025-11-29 01:09:57 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2025-11-29 01:09:57 | 2025-11-29 01:09:57 | 0.27 | list | [SiderSideeffectMeddra(cid='C0233472', meddra_id='10054196', side_effect_name='Affect lability'), SiderSideeffectMeddra(cid='C1863751', meddra_id='10070939', side_effect_name='Wound healing normal'), SiderSideeffectMeddra(cid='C3544189', meddra_id='10073301', side_effect_name='Exposure via contamina...(truncated) | 20,307 | {} | 2025-11-29 01:09:57 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2025-11-29 01:09:57 | 2025-11-29 01:09:58 | 0.84 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0009806', umls_concept_in_meddra='C0009806', side_effect='Constipation', frequency='3%'), SiderSideeffetFrequency(umls_concept_on_label='C0019080', umls_concept_in_meddra='C0019080', side_effect='Haemorrhage', frequency='2%'), SiderSi...(truncated) | 968 | {} | 2025-11-29 01:09:57 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2025-11-29 01:09:58 | 2025-11-29 01:09:59 | 0.82 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0035455', umls_concept_in_meddra='C0035455', side_effect='Rhinitis'), SiderSideeffect(umls_concept_on_label='C0015230', umls_concept_in_meddra='C0015230', side_effect='Rash'), SiderSideeffect(umls_concept_on_label='C0000737', umls_concept_in_...(truncated) | 1,430 | {} | 2025-11-29 01:09:58 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2025-11-29 01:09:59 | 2025-11-29 01:10:01 | 1.81 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathw...(truncated) | 2 | {} | 2025-11-29 01:09:59 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2025-11-29 01:10:01 | 2025-11-29 01:10:01 | 0.39 | dict | {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 785 | {} | 2025-11-29 01:10:01 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2025-11-29 01:10:01 | 2025-11-29 01:10:02 | 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 | {} | 2025-11-29 01:10:01 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2025-11-29 01:10:02 | 2025-11-29 01:10:02 | 0.41 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate i...(truncated) | 839 | {} | 2025-11-29 01:10:02 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2025-11-29 01:10:02 | 2025-11-29 01:10:03 | 0.86 | 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) | 4,891 | {} | 2025-11-29 01:10:02 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2025-11-29 01:10:03 | 2025-11-29 01:10:06 | 2.99 | list | [{'typ': 'phosphorylation', 'resnum': 571, 'instance': 'RDTYSDRSGSSSPDS', 'substrate': 'P17812', 'start': 564, 'end': 578, 'kinase': 'P49841', 'resaa': 'S', 'motif': 'RDTYSDRSGSSSPDS', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'17681942'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) | 13,469 | {} | 2025-11-29 01:10:03 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2025-11-29 01:10:06 | 2025-11-29 01:10:06 | 0.57 | list | [SignorInteraction(source='Q969X5', target='Q9Y282', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates quantity by stabilization', mechanism='binding', ncbi_tax_id='9606', pubmeds='15308636', direct=True, ptm_type='binding', ptm_residue='', ...(truncated) | 96,074 | {} | 2025-11-29 01:10:06 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2025-11-29 01:10:07 | 2025-11-29 01:10:27 | 20.67 | dict | {'P24385': {SignorPathway(pathway='Tenascin-C in PDAC'), SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q96FE7': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P40763': {SignorPathway(pathway='SARS-CoV CYTOKINE STORM'), SignorPathway(pathway='EBV infection'), SignorPathway(pathway='LIF in P...(truncated) | 787 | {} | 2025-11-29 01:10:07 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2025-11-29 01:10:27 | 2025-11-29 01:10:27 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 91 | {} | 2025-11-29 01:10:27 | |
| ¶ | pypath.inputs.slc.slc_annotation | 2025-11-29 01:10:27 | 2025-11-29 01:10:28 | 0.26 | list | [SlcAnnotation(Entrez_ID=56172, Ensembl_ID='ENSG00000154122', HGNC_symbol='ANKH', Substrate_class='Orphan', Substrates='', Substrates_PMID='', Coupled_ions='Unknown', Coupled_ions_PMID='', Transport_mechanism='Unknown', Transport_system_PMID='', Subcellular_localization='Unknown', Subcellular_locali...(truncated) | 446 | {} | 2025-11-29 01:10:27 | |
| ¶ | pypath.inputs.slc.slc_chebi_mapping | 2025-11-29 01:10:28 | 2025-11-29 01:10:28 | 0.17 | list | [SlcChebiMapping(Substrate_name_annotation='17-beta-glucuronosyl estradiol', chebi_id='CHEBI:791', chebi_term='17beta-estradiol 17-glucosiduronic acid', synonym='3-hydroxyestra-1,3,5(10)-trien-17beta-yl beta-D-glucopyranosiduronic acid', description='A steroid glucosiduronic acid that consists of 17...(truncated) | 382 | {} | 2025-11-29 01:10:28 | |
| ¶ | pypath.inputs.slc.slc_interactions | 2025-11-29 01:10:28 | 2025-11-29 01:10:28 | 0.10 | list | [SlcInteraction(transporter=SlcTransporter(uniprot='Q9Y5Y0', genesymbol='FLVCR1', entrez=28982, ensg='ENSG00000162769'), substrate=SlcSubstrate(slc_name='Heme', chebi='CHEBI:30413', label='heme', synonyms=['heme', 'hemes']), role='substrate', pmids='15369674', localization='Plasma membrane', transpo...(truncated) | 1,288 | {} | 2025-11-29 01:10:28 | |
| ¶ | pypath.inputs.slc.slc_localization_annotations | 2025-11-29 01:10:28 | 2025-11-29 01:10:28 | 0.06 | dict | {'Q9HCJ1': {SlcLocalization(localization='Unknown', pmids=None)}, 'Q13286': {SlcLocalization(localization='Endosome; Lysosome', pmids='15471887;22261744')}, 'Q96SL1': {SlcLocalization(localization='Lysosome', pmids='21692750')}, 'Q9Y5Y0': {SlcLocalization(localization='Plasma membrane', pmids='18815...(truncated) | 447 | {} | 2025-11-29 01:10:28 | |
| ¶ | pypath.inputs.slc.slc_substrate_ontology | 2025-11-29 01:10:28 | 2025-11-29 01:10:29 | 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 | {} | 2025-11-29 01:10:28 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2025-11-29 01:10:29 | 2025-11-29 01:12:49 | 140.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/spike.py", line 197, in spike_complexes
interactions = spike_interactions(min_confidence = min_confidence)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/spike.py", line 50, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2025-11-27 01:52:51 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2025-11-29 01:12:49 | 2025-11-29 01:14:22 | 93.46 |
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__20251128-202402/pypath_git/pypath/inputs/spike.py", line 50, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2025-11-27 01:52:59 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2025-11-29 01:14:22 | 2025-11-29 01:15:14 | 52.34 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2025-11-29 01:14:22 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2025-11-29 01:15:14 | 2025-11-29 01:16:26 | 71.60 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2025-11-29 01:15:14 | |
| ¶ | pypath.inputs.string.string_effects | 2025-11-29 01:16:26 | 2025-11-29 01:16:34 | 7.95 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2025-11-29 01:16:26 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2025-11-29 01:16:35 | 2025-11-29 01:17:00 | 24.59 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {} | 2025-11-29 01:16:35 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2025-11-29 01:17:00 | 2025-11-29 01:17:01 | 1.20 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2025-11-29 01:17:00 | |
| ¶ | pypath.inputs.string.string_species | 2025-11-29 01:17:01 | 2025-11-29 01:17:01 | 0.14 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2025-11-29 01:17:01 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2025-11-29 01:17:01 | 2025-11-29 01:17:07 | 5.37 | dict | {'A0AV02': (0.8363, 'Transporters', {'SLC', 'SLC12', 'APC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC', 'SLC5', 'APC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,844 | {} | 2025-11-29 01:17:01 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2025-11-29 01:17:07 | 2025-11-29 01:17:11 | 4.24 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2025-11-29 01:17:07 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2025-11-29 01:17:11 | 2025-11-29 01:17:11 | 0.56 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False)}, 'Q16613': {Talklr...(truncated) | 1,344 | {} | 2025-11-29 01:17:11 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2025-11-29 01:17:11 | 2025-11-29 01:17:11 | 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 | {} | 2025-11-29 01:17:11 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2025-11-29 01:17:11 | 2025-11-29 01:17:11 | 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 | {} | 2025-11-29 01:17:11 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2025-11-29 01:17:12 | 2025-11-29 01:17:17 | 5.03 |
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__20251128-202402/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 | 2025-11-29 01:17:17 | 2025-11-29 01:17:17 | 0.03 | dict | {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) | 24,317 | {} | 2025-11-29 01:17:17 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2025-11-29 01:17:17 | 2025-11-29 01:17:17 | 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) | 2,122 | {} | 2025-11-29 01:17:17 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2025-11-29 01:17:17 | 2025-11-29 01:17:17 | 0.20 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,871 | {} | 2025-11-29 01:17:17 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2025-11-29 01:17:17 | 2025-11-29 01:17:21 | 4.26 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2025-11-29 01:17:17 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2025-11-29 01:17:21 | 2025-11-29 01:17:42 | 21.14 | set | {ThreedcomplexContact(pdb='2nps_1', uniprot_1='O70480', uniprot_2='G3V7P1', chain_1='A', chain_2='B', n_residues=31.0, length_1=63, length_2=68, domain_s1=('58038',), domain_p1=('PF00957.16',), domain_s2=('58038',), domain_p2=('PF05739.14',), ident=False, homo=True), ThreedcomplexContact(pdb='4esv_2...(truncated) | 258,351 | {} | 2025-11-29 01:17:21 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2025-11-29 01:17:43 | 2025-11-29 01:21:07 | 203.75 | list | [<pypath.internals.intera.DomainDomain object at 0x7f73ed6ed410>, <pypath.internals.intera.DomainDomain object at 0x7f75d352cfd0>, <pypath.internals.intera.DomainDomain object at 0x7f7463b31990>, <pypath.internals.intera.DomainDomain object at 0x7f74f400a950>, <pypath.internals.intera.DomainDomain o...(truncated) | 521,949 | {} | 2025-11-29 01:17:43 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2025-11-29 01:21:08 | 2025-11-29 01:21:16 | 8.52 | dict | {'2nps_1': {('G3V7P1', 'O70480'): 31.0, ('O43752', 'Q9JI51'): 28.5, ('O70480', 'Q9JI51'): 6.5, ('G3V7P1', 'Q9JI51'): 29.5, ('G3V7P1', 'O43752'): 7.0, ('O43752', 'O70480'): 27.0}, '4esv_2': {('Q9X4C9', 'Q9X4C9'): 33.5}, '2fwp_1': {('Q2QJL3', 'Q2QJL3'): 11.5}, '3mo2_5': {('Q9H9B1', 'Q9H9B1'): 22.5}, '...(truncated) | 80,605 | {} | 2025-11-29 01:21:08 | |
| ¶ | pypath.inputs.threedid.get_3did | 2025-11-29 01:21:16 | 2025-11-29 02:30:46 | 4,169.32 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7f76b41e9d50>, <pypath.internals.intera.DomainDomain object at 0x7f7716af5190>, <pypath.internals.intera.DomainDomain object at 0x7f772d89ddd0>, <pypath.internals.intera.DomainDomain object at 0x7f76a7ab9b90>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2025-11-29 01:21:16 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2025-11-29 02:30:46 | 2025-11-29 02:46:37 | 951.35 | dict | {} | 0 | {} | 2025-11-29 02:30:46 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2025-11-29 02:46:37 | 2025-11-29 02:46:57 | 19.35 | dict | {'P18825': {TopdbAnnotation(membrane='Cell membrane', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell membrane', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='E...(truncated) | 2,027 | {} | 2025-11-29 02:46:37 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2025-11-29 02:46:57 | 2025-11-29 02:46:57 | 0.11 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2025-11-29 02:46:57 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2025-11-29 02:46:57 | 2025-11-29 02:46:57 | 0.00 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2025-11-29 02:46:57 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2025-11-29 02:46:57 | 2025-11-29 02:46:57 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;11983166;12601176', 'Fluorescence probe labeling;Patch clamp;Fusion protein-pull down ...(truncated) | 359 | {} | 2025-11-29 02:46:57 | |
| ¶ | pypath.inputs.trip.trip_process | 2025-11-29 02:46:57 | 2025-11-29 02:46:57 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2025-11-29 02:46:57 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2025-11-29 02:46:57 | 2025-11-29 02:47:01 | 4.45 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-11-29 02:46:57 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2025-11-29 02:47:01 | 2025-11-29 02:47:01 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-11-29 02:47:01 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2025-11-29 02:47:01 | 2025-11-29 02:47:05 | 3.47 | list | [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) | 7,057 | {} | 2025-11-29 02:47:01 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2025-11-29 02:47:05 | 2025-11-29 02:52:27 | 322.76 |
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__20251128-202402/pypath_git/pypath/inputs/offsides.py", line 80, in _sides_base
yield record(**{
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251128-202402/pypath_git/pypath/inputs/offsides.py", line 81, in <dictcomp>
f: line[i].strip(' "')
~~~~^^^
IndexError: list index out of range
|
{} | 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 | 2025-11-29 02:52:28 | 2025-11-29 02:52:28 | 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 | {} | 2025-11-29 02:52:28 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2025-11-29 02:52:28 | 2025-11-29 02:52:28 | 0.00 | dict | {1: 'ChEMBL', 2: 'DrugBank', 3: 'PDBe', 4: 'Guide to Pharmacology', 5: 'PubChem: Drugs of the Future ', 6: 'KEGG Ligand', 7: 'ChEBI', 8: 'NIH Clinical Collection', 9: 'ZINC', 10: 'eMolecules', 12: 'Atlas', 14: 'FDA SRS', 15: 'SureChEMBL', 17: 'PharmGKB', 18: 'Human Metabolome Database', 20: 'Selleck...(truncated) | 41 | {} | 2025-11-29 02:52:28 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2025-11-29 02:52:28 | 2025-11-29 02:52:28 | 0.52 | 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) | 72,370 | {} | 2025-11-29 02:52:28 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2025-11-29 02:52:28 | 2025-11-29 02:52:38 | 9.97 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0AV02': {UniprotFamily(family='SLC12A transporter', subfamily=None)}, 'A0AV96': {UniprotFam...(truncated) | 14,485 | {} | 2025-11-29 02:52:28 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2025-11-29 02:52:38 | 2025-11-29 02:52:48 | 9.46 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Heme'), UniprotKeyword(keyword='Iron'), UniprotKey...(truncated) | 20,420 | {} | 2025-11-29 02:52:38 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2025-11-29 02:52:48 | 2025-11-29 02:52:48 | 0.08 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,837 | {} | 2025-11-29 02:52:48 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2025-11-29 02:52:48 | 2025-11-29 02:52:49 | 1.61 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'H8ZM71': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Pinus grandis', 'Abies grandis', '...(truncated) | 558,858 | {} | 2025-11-29 02:52:48 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2025-11-29 02:52:50 | 2025-11-29 02:53:01 | 10.99 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Plasma', level='undefined'), UniprotTissue(tissue='Skeletal muscle', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Myeloid dendritic cells', level='undefined'), UniprotTissue(ti...(truncated) | 10,169 | {} | 2025-11-29 02:52:50 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2025-11-29 02:53:01 | 2025-11-29 02:53:45 | 43.77 | dict | {'A0A087X1C5': {UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', ...(truncated) | 5,244 | {} | 2025-11-29 02:53:01 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2025-11-29 02:53:45 | 2025-11-29 02:53:45 | 0.01 | set | {'O94818', 'Q8IWF2', 'B3GLJ2', 'Q16186', 'Q9UM01', 'P48449', 'Q2M1V0', 'Q9NVR7', 'P15622', 'Q9NRD9', 'Q6NTF7', 'Q8NG84', 'Q8NE01', 'P0DKV0', 'Q86WC4', 'P86481', 'Q9NWC5', 'A0A494C071', 'Q6NUN0', 'Q9Y673', 'Q8TE54', 'Q86XJ1', 'Q8N3F9', 'Q96KK5', 'Q92823', 'Q8NGX8', 'O94887', 'P13727', 'Q9H0F7', 'P481...(truncated) | 20,420 | {} | 2025-11-29 02:53:45 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2025-11-29 02:53:45 | 2025-11-29 02:54:15 | 30.68 | set | {'A0A343GLQ5', 'A0A023I8L7', 'A0A6B7HG42', 'Q209I4', 'X5D8U0', 'L8EA76', 'D6RJF7', 'D6R9U8', 'A0A0P0H5M6', 'Q32P42', 'G3D6H1', 'A0A0A7CAY8', 'S6CPZ0', 'A0A5K1TTC0', 'M0R3B3', 'Q6ZPB9', 'C9K092', 'Q8IZH9', 'A0A5H2UIV7', 'A0A0M7BFM3', 'A0A5H2UEA6', 'B4DPJ8', 'A0A0A7C3M0', 'J3QRS7', 'S6B303', 'A0A343JT...(truncated) | 184,808 | {} | 2025-11-29 02:53:45 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2025-11-29 02:54:15 | 2025-11-29 02:54:15 | 0.00 | set | {'A0A343GLQ5', 'A0A023I8L7', 'A0A6B7HG42', 'Q209I4', 'X5D8U0', 'L8EA76', 'D6RJF7', 'D6R9U8', 'A0A0P0H5M6', 'Q32P42', 'G3D6H1', 'A0A0A7CAY8', 'S6CPZ0', 'A0A5K1TTC0', 'M0R3B3', 'Q6ZPB9', 'C9K092', 'Q8IZH9', 'P48449', 'A0A5H2UIV7', 'Q9NVR7', 'A0A0M7BFM3', 'A0A5H2UEA6', 'P15622', 'B4DPJ8', 'A0A0A7C3M0',...(truncated) | 205,228 | {} | 2025-11-29 02:54:15 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2025-11-29 02:54:15 | 2025-11-29 02:54:15 | 0.00 | set | {'A0A343GLQ5', 'A0A023I8L7', 'A0A6B7HG42', 'Q209I4', 'X5D8U0', 'L8EA76', 'D6RJF7', 'D6R9U8', 'A0A0P0H5M6', 'Q32P42', 'G3D6H1', 'A0A0A7CAY8', 'S6CPZ0', 'A0A5K1TTC0', 'M0R3B3', 'Q6ZPB9', 'C9K092', 'Q8IZH9', 'P48449', 'A0A5H2UIV7', 'Q9NVR7', 'A0A0M7BFM3', 'A0A5H2UEA6', 'P15622', 'B4DPJ8', 'A0A0A7C3M0',...(truncated) | 205,228 | {} | 2025-11-29 02:54:15 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2025-11-29 02:54:15 | 2025-11-29 02:54:15 | 0.05 | NoneType | None | 0 | {} | 2025-11-29 02:54:15 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2025-11-29 02:54:15 | 2025-11-29 02:54:16 | 0.10 | set | {('GuidetoPHARMACOLOGY', 'UniProtKB-Swiss-Prot'), ('FlyBase', 'UniProtKB-Swiss-Prot'), ('UniProtKB_AC-ID', 'DrugBank'), ('STRING', 'UniProtKB-Swiss-Prot'), ('UniProtKB', 'VEuPathDB'), ('PIR', 'UniProtKB'), ('UniProtKB_AC-ID', 'FlyBase'), ('UniProtKB-Swiss-Prot', 'UniRef100'), ('DrugBank', 'UniProtKB...(truncated) | 481 | {} | 2025-11-29 02:54:15 | |
| ¶ | pypath.inputs.wang.cui_interactions | 2025-11-29 02:54:16 | 2025-11-29 02:54:16 | 0.30 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2025-11-29 02:54:16 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2025-11-29 02:54:16 | 2025-11-29 02:54:16 | 0.60 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2025-11-29 02:54:16 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2025-11-29 02:54:17 | 2025-11-29 02:54:21 | 4.22 | dict | {'NA': {WangAnnotation(function='Messenger', location='Cytosol'), WangAnnotation(function='DNA', location='Nucleus'), WangAnnotation(function='Ligand', location='Extracellular'), WangAnnotation(function='Adapter', location='Ribosomes'), WangAnnotation(function='Adapter', location='Cytosol'), WangAnn...(truncated) | 1,547 | {} | 2025-11-29 02:54:17 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2025-11-29 02:54:21 | 2025-11-29 02:54:22 | 0.86 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2025-11-29 02:54:21 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2025-11-29 02:54:22 | 2025-11-29 02:54:22 | 0.35 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {} | 2025-11-29 02:54:22 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2025-11-29 02:54:22 | 2025-11-29 02:54:22 | 0.10 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {} | 2025-11-29 02:54:22 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2025-11-29 02:54:22 | 2025-11-29 02:54:22 | 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 | {} | 2025-11-29 02:54:22 |
The OmniPath Team • Saez Lab • 2025-11-29