Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2025-09-26 02:22:23 and 2025-09-26 08:34:07; pypath version: 0.16.28 (from git, installed by poetry; 1546e5d )
| Modules collected: | 192 |
|---|---|
| Modules failed to import: | 3 |
| Functions collected: | 526 |
| Functions run without error: | 385 |
| Functions returned empty value: | 14 |
| Functions skipped due to lack of arguments: | 111 |
| Functions run with error: | 30 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2025-09-26 02:22:27 | 2025-09-26 02:22:27 | 0.43 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2025-09-26 02:22:27 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2025-09-26 02:22:27 | 2025-09-26 02:22:28 | 0.54 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2025-09-26 02:22:27 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2025-09-26 02:22:28 | 2025-09-26 02:23:27 | 59.35 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {} | 2025-09-26 02:22:28 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2025-09-26 02:23:27 | 2025-09-26 02:23:28 | 1.10 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2025-09-26 02:23:27 | |
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2025-09-26 02:23:28 | 2025-09-26 02:23:37 | 8.86 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {} | 2025-09-26 02:23:28 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2025-09-26 02:23:37 | 2025-09-26 02:24:35 | 57.47 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2025-09-26 02:23:37 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2025-09-26 02:24:35 | 2025-09-26 02:27:37 | 182.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/common.py", line 123, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-6-S_sgju-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 346, in load_workbook
reader = ExcelReader(filename, read_only, keep_vba,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-6-S_sgju-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 123, in __init__
self.archive = _validate_archive(fn)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-6-S_sgju-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 77, in _validate_archive
file_format = os.path.splitext(filename)[-1].lower()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen posixpath>", line 118, in splitext
TypeError: expected str, bytes or os.PathLike object, not NoneType
During handling of the above exception, another exception occurred:
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__20250926-022201/pypath_git/pypath/inputs/adrecs.py", line 92, in adrecs_drug_identifiers
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/adrecs.py", line 137, in _adrecs_base
contents = inputs_common.read_xls(path.outfile, cell_range = cell_range)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/common.py", line 133, in read_xls
raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: None
|
{'broke': True} | 2025-09-25 02:26:21 | |||
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2025-09-26 02:27:37 | 2025-09-26 02:27:38 | 1.10 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='02.03.04.015', badd='BADD_A04896'), parent=AdrecsAdr(adr_class='02.03.04', badd='BADD_A04559')), AdrecsChildParent(child=AdrecsAdr(adr_class='06.01.01.003', badd='BADD_A01060'), parent=AdrecsAdr(adr_class='06.01.01', badd='BADD_A03122')), AdrecsChildPare...(truncated) | 13,828 | {} | 2025-09-26 02:27:37 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2025-09-26 02:27:38 | 2025-09-26 02:27:39 | 1.18 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,243 | {} | 2025-09-26 02:27:38 | |
| ¶ | pypath.inputs.alzpathway.alzpathway_interactions | 2025-09-26 02:27:39 | 2025-09-26 02:27:39 | 0.10 | list | [AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='O00213', genesymbol_a='APP', genesymbol_b='APBB1', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='Q8N8S7', genesymbol_a='APP', genesymbol_b='ENAH', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05...(truncated) | 119 | {} | 2025-09-26 02:27:39 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2025-09-26 02:27:39 | 2025-09-26 02:31:03 | 203.74 | dict | {'Q15848': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q96A54': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'Q86V24': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'P35318': {Baccin2019Annotation(ma...(truncated) | 933 | {} | 2025-09-26 02:27:39 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2025-09-26 02:31:03 | 2025-09-26 02:31:03 | 0.33 | list | [Baccin2019Interaction(ligand='Q15848', receptor='Q96A54', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Ramilowski2015', 'Baccin2019'}, references={'12802337'}), Baccin2019Interaction(ligand='Q15848', receptor='Q86V24', correct='Correct', ligand_location='secre...(truncated) | 1,460 | {} | 2025-09-26 02:31:03 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2025-09-26 02:31:03 | 2025-09-26 02:31:03 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2025-09-26 02:31:03 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2025-09-26 02:31:03 | 2025-09-26 02:31:39 | 35.32 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2025-09-26 02:31:03 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2025-09-26 02:31:39 | 2025-09-26 02:32:13 | 34.04 | list | [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855', experimental_system='Two-hybrid', experimental_system_type='physical', ltp=True, htp_score=None, multi_validated=True, tax_a='9606', tax_b='9606'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272', experimen...(truncated) | 8,732 | {} | 2025-09-26 02:31:39 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2025-09-26 02:32:13 | 2025-09-26 02:32:14 | 1.12 | list | [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) | 7,462 | {} | 2025-09-26 02:32:13 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2025-09-26 02:32:14 | 2025-09-26 02:32:46 | 31.96 | 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 | {'size': -209762} | 2025-09-26 02:32:14 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2025-09-26 02:32:47 | 2025-09-26 02:32:47 | 0.07 | list | [{'type': 'OLIGO', 'vendor': 'PHALANX', 'array': 'OneArray', 'description': None, 'format': 'EXPRESSION', 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'array': 'CODELINK', 'vendor': 'CODELINK', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'type': 'OLIGO', 'array': ...(truncated) | 37 | {} | 2025-09-26 02:32:47 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2025-09-26 02:32:47 | 2025-09-26 02:32:47 | 0.17 | list | [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) | 1,788 | {} | 2025-09-26 02:32:47 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2025-09-26 02:32:47 | 2025-09-26 02:32:48 | 1.04 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2025-09-26 02:32:47 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2025-09-26 02:32:48 | 2025-09-26 02:32:56 | 7.51 | dict | {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) | 216 | {} | 2025-09-26 02:32:48 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2025-09-26 02:32:56 | 2025-09-26 02:32:56 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 330 | {} | 2025-09-26 02:32:56 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2025-09-26 02:32:56 | 2025-09-26 02:33:03 | 7.63 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P42336', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 5,157 | {} | 2025-09-26 02:32:56 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2025-09-26 02:33:04 | 2025-09-26 02:33:06 | 2.23 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {} | 2025-09-26 02:33:04 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2025-09-26 02:33:06 | 2025-09-26 02:33:18 | 11.90 | dict | {'P01225': {CellcallAnnotation(role='ligand')}, 'P16473': {CellcallAnnotation(role='receptor')}, 'P12644': {CellcallAnnotation(role='ligand')}, 'Q13873': {CellcallAnnotation(role='receptor')}, 'Q2I0M5': {CellcallAnnotation(role='ligand')}, 'Q9ULT6': {CellcallAnnotation(role='receptor')}, 'P14210': {...(truncated) | 460 | {} | 2025-09-26 02:33:06 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2025-09-26 02:33:18 | 2025-09-26 02:33:18 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2025-09-26 02:33:18 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2025-09-26 02:33:18 | 2025-09-26 02:33:19 | 0.81 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2025-09-26 02:33:18 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2025-09-26 02:33:19 | 2025-09-26 02:33:19 | 0.10 | list | [CellcallInteraction(ligand_uniprot='P01225', receptor_uniprot='P16473', core=True), CellcallInteraction(ligand_uniprot='P12644', receptor_uniprot='Q13873', core=True), CellcallInteraction(ligand_uniprot='Q2I0M5', receptor_uniprot='Q9ULT6', core=True), CellcallInteraction(ligand_uniprot='P14210', re...(truncated) | 797 | {} | 2025-09-26 02:33:19 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2025-09-26 02:33:19 | 2025-09-26 02:33:19 | 0.65 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='ECM'), Cellcellinteractio...(truncated) | 3,425 | {} | 2025-09-26 02:33:19 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2025-09-26 02:33:19 | 2025-09-26 02:33:29 | 9.97 | 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 | {} | 2025-09-26 02:33:19 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2025-09-26 02:33:29 | 2025-09-26 02:33:36 | 6.93 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'Q9H2X0', 'O75610', 'P12645', 'O60565', 'O00292', 'Q9H772', 'Q13253', 'P41271'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 32 | {} | 2025-09-26 02:33:29 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2025-09-26 02:33:36 | 2025-09-26 02:33:43 | 6.95 | dict | {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) | 330 | {} | 2025-09-26 02:33:36 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2025-09-26 02:33:43 | 2025-09-26 02:33:50 | 6.89 | dict | {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) | 4 | {} | 2025-09-26 02:33:43 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2025-09-26 02:33:50 | 2025-09-26 02:33:57 | 7.27 | 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 | {} | 2025-09-26 02:33:50 | |
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2025-09-26 02:33:57 | 2025-09-26 02:33:58 | 0.49 | dict | {'Q6UX41': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'O75019': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', ...(truncated) | 1,919 | {} | 2025-09-26 02:33:57 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.05 | dict | {Complex: COMPLEX:P13612_P26010: {CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, Complex: COMPLEX:P05107_P11215: {CellinkerAnnotation(role='receptor', location='Membrane', t...(truncated) | 134 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.04 | set | {CellinkerInteraction(ligand='Q6UX41', receptor='O75019', ligand_location='Membrane', receptor_location='Membrane', resources=None, pmids='32822567', type='Cell adhesion'), CellinkerInteraction(ligand='P05112', receptor='Q9HBE5', ligand_location='Secreted', receptor_location='Membrane', resources=No...(truncated) | 3,810 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.05 | dict | {'Q6UX41': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'O75019': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', ...(truncated) | 1,785 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.12 | set | {CellinkerInteraction(ligand='5311358', receptor='Q92806', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='8688080', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='51', receptor='Q96P68', ligand_location=None, receptor_location='Membrane', resour...(truncated) | 314 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.00 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2025-09-26 02:33:58 | 2025-09-26 02:33:58 | 0.22 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 358 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2025-09-26 02:33:58 | 2025-09-26 02:33:59 | 0.02 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {} | 2025-09-26 02:33:58 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2025-09-26 02:33:59 | 2025-09-26 02:33:59 | 0.49 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {} | 2025-09-26 02:33:59 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2025-09-26 02:33:59 | 2025-09-26 02:33:59 | 0.02 | tuple | ({'P0DN87', 'O14786', 'Q9NZU0', 'P14778', Complex Acetylcholine_byCHAT_and_SLC18A3: COMPLEX:P28329_Q16572, 'Q8WWG1', 'P01213', 'P01282', Complex 5-HT_byTPH1_and_SLC18A1: COMPLEX:P17752_P54219, 'P23471', 'O43508', 'Q05329', 'P48061', 'Q9UKZ4', 'Q9NPH3', 'Q9NZH7', 'Q30201', 'P48357', Complex GABA_byGA...(truncated) | 2 | {} | 2025-09-26 02:33:59 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2025-09-26 02:33:59 | 2025-09-26 02:33:59 | 0.02 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,359 | {} | 2025-09-26 02:33:59 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2025-09-26 02:33:59 | 2025-09-26 02:33:59 | 0.43 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,598 | {} | 2025-09-26 02:33:59 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2025-09-26 02:33:59 | 2025-09-26 02:34:00 | 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 | {} | 2025-09-26 02:33:59 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2025-09-26 02:34:00 | 2025-09-26 02:34:00 | 0.16 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2025-09-26 02:34:00 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2025-09-26 02:34:00 | 2025-09-26 02:34:00 | 0.25 | dict | {'P11836': {CelltypistAnnotation(cell_type='B cells', cell_subtype='Transitional B cells', cell_ontology='CL:0000818', marker_type='curated_marker', tissues=('Bone marrow',), datasets=('HCA Immune 2018',)), CelltypistAnnotation(cell_type='B cells', cell_subtype='B cells', cell_ontology='CL:0000236',...(truncated) | 460 | {} | 2025-09-26 02:34:00 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2025-09-26 02:34:00 | 2025-09-26 02:34:41 | 41.29 | list | [Citation(allele='365296', variation_id='384564', nsv='', citation_source='PubMed', citation_id='25741868'), Citation(allele='3851947', variation_id='3728616', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='916878', variation_id='928745', nsv='', citation_source='PubMed'...(truncated) | 4,183,865 | {} | 2025-09-26 02:34:00 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2025-09-26 02:34:46 | 2025-09-26 02:41:32 | 405.80 | list | [Variant(allele='681763', type='single nucleotide variant', variant='NC_012920.1(MT-CO3):m.9801G>A', entrez='4514', genesymbol='MT-CO3', clinical_significance='Benign', review_status='criteria provided, single submitter', rs='1556423726', phenotype_ids=('MONDO:MONDO:0009723', 'MedGen:C2931891', 'OMI...(truncated) | 7,476,169 | {} | 2025-09-26 02:34:46 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2025-09-26 03:58:01 | 2025-09-26 03:58:17 | 15.34 | list | [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) | 64,990 | {} | 2025-09-26 03:58:01 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2025-09-26 03:58:17 | 2025-09-26 03:58:17 | 0.16 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2025-09-26 03:58:17 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2025-09-26 03:58:17 | 2025-09-26 03:58:17 | 0.23 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2025-09-26 03:58:17 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2025-09-26 03:58:17 | 2025-09-26 03:58:18 | 1.15 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,695 | {} | 2025-09-26 03:58:17 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2025-09-26 03:58:18 | 2025-09-26 03:58:18 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2025-09-26 03:58:18 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2025-09-26 03:58:19 | 2025-09-26 04:00:19 | 120.76 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) | 2,275 | {} | 2025-09-26 03:58:19 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2025-09-26 04:00:19 | 2025-09-26 04:00:36 | 16.44 | list | [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) | 587,995 | {} | 2025-09-26 04:00:19 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2025-09-26 04:00:36 | 2025-09-26 04:00:50 | 14.10 | dict | {'A0A0R4J2E4': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.8)}, 'A0A024R0Y4': {ComppiLocation(location='nucleus', score=0.8)}, 'A0A087WWR4': {ComppiLocation(location='nucleus', score=0.8)}, 'Q08379': {ComppiLocation(location='extracellular', score=0.8),...(truncated) | 22,799 | {} | 2025-09-26 04:00:36 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2025-09-26 04:00:50 | 2025-09-26 04:00:50 | 0.33 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {} | 2025-09-26 04:00:50 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2025-09-26 04:00:50 | 2025-09-26 04:00:50 | 0.01 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2025-09-26 04:00:50 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2025-09-26 04:00:50 | 2025-09-26 04:00:51 | 0.61 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2025-09-26 04:00:50 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2025-09-26 04:00:51 | 2025-09-26 04:00:51 | 0.18 | dict | {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, chr_band='10q11.23', tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',), translocation_partner=(()...(truncated) | 762 | {} | 2025-09-26 04:00:51 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_raw | 2025-09-26 04:00:51 | 2025-09-26 04:00:51 | 0.00 | list | [{'Gene Symbol': 'A1CF', 'Name': 'APOBEC1 complementation factor', 'Entrez GeneId': '29974', 'Genome Location': '10:50799421-50885675', 'Tier': '2', 'Hallmark': '', 'Chr Band': '10q11.23', 'Somatic': 'yes', 'Germline': '', 'Tumour Types(Somatic)': 'melanoma', 'Tumour Types(Germline)': '', 'Cancer Sy...(truncated) | 758 | {} | 2025-09-26 04:00:51 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2025-09-26 04:00:51 | 2025-09-26 04:01:02 | 10.66 | dict | {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) | 1,070 | {'size': -1} | 2025-09-26 04:00:51 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2025-09-26 04:01:02 | 2025-09-26 04:01:02 | 0.10 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='PI3K-Akt signaling pathway', cancer='Glioma', pathway_category='PI3K-Akt signaling pathway', effect_on_cancer='Activating', effect_on_cancer_outcome='enhance motility'), CpadPathwayCancer(pathway='PI3K-Akt signaling pathway', cancer='Glioma', pathway_category=...(truncated) | 2 | {} | 2025-09-26 04:01:02 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2025-09-26 04:01:02 | 2025-09-26 04:01:02 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2025-09-26 04:01:02 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2025-09-26 04:01:02 | 2025-09-26 04:01:13 | 11.47 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {} | 2025-09-26 04:01:02 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2025-09-26 04:01:14 | 2025-09-26 04:01:16 | 2.74 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2025-09-26 04:01:14 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2025-09-26 04:01:17 | 2025-09-26 04:01:18 | 0.75 | dict | {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) | 1,449 | {} | 2025-09-26 04:01:17 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2025-09-26 04:01:18 | 2025-09-26 04:01:18 | 0.78 | dict | {'A1A5B4': {CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='ZL55', value...(truncated) | 1,410 | {} | 2025-09-26 04:01:18 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2025-09-26 04:01:18 | 2025-09-26 04:01:19 | 0.39 | dict | {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) | 47 | {} | 2025-09-26 04:01:18 | |
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2025-09-26 04:01:19 | 2025-09-26 04:01:20 | 1.55 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P12643', score=-0.0185015764811096, cytokine_genesymbol='BMP2', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P09038', score=-0.0414681704910361, cytokine_genesymbol='FGF2', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P01583', score=0.0...(truncated) | 4,887 | {} | 2025-09-26 04:01:19 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2025-09-26 04:01:21 | 2025-09-26 04:01:21 | 0.03 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2025-09-26 04:01:21 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2025-09-26 04:01:21 | 2025-09-26 04:01:23 | 2.90 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2025-09-26 04:01:21 | |
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2025-09-26 04:01:24 | 2025-09-26 04:01:25 | 1.22 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2025-09-26 04:01:24 | |
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2025-09-26 04:01:25 | 2025-09-26 04:01:58 | 33.23 | list | [DdinterInteraction(drug1_id='DDInter1137', drug1_name='Medroxyprogesterone acetate', drug2_id='DDInter1700', drug2_name='Somatrem', level='Moderate'), DdinterInteraction(drug1_id='DDInter197', drug1_name='Betaxolol', drug2_id='DDInter1535', drug2_name='Propantheline', level='Moderate'), DdinterInte...(truncated) | 160,235 | {} | 2025-09-26 04:01:25 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2025-09-26 04:01:59 | 2025-09-26 04:48:30 | 2,791.02 | list | [DdinterIdentifiers(ddinter='DDInter1050', drugbank='DB01210', chembl='CHEMBL1201237', pubchem='46507518'), DdinterIdentifiers(ddinter='DDInter1849', drugbank='DB00287', chembl='CHEMBL1200799', pubchem='46507637'), DdinterIdentifiers(ddinter='DDInter1677', drugbank='DB06688', chembl='CHEMBL1237024',...(truncated) | 1,939 | {} | 2025-09-26 04:01:59 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2025-09-26 04:48:30 | 2025-09-26 04:48:30 | 0.42 | int | 1939 | 0 | {} | 2025-09-26 04:48:30 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2025-09-26 04:48:30 | 2025-09-26 04:48:30 | 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 | {} | 2025-09-26 04:48:30 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2025-09-26 04:48:30 | 2025-09-26 04:48:31 | 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 | {} | 2025-09-26 04:48:30 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2025-09-26 04:48:31 | 2025-09-26 04:48:31 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2025-09-26 04:48:31 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2025-09-26 04:48:31 | 2025-09-26 04:48:36 | 5.54 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='dGene'), DgidbAnnotation(category='TRANSCRIPTION FACTOR', source='Pharos'), DgidbAnnotation(category='TRANSCRIPTION FACTOR COMPLEX', source='GO'), DgidbAnno...(truncated) | 9,973 | {} | 2025-09-26 04:48:31 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2025-09-26 04:48:36 | 2025-09-26 04:48:42 | 6.09 | list | [DgidbInteraction(genesymbol='RPS19', gene_concept_id='hgnc:10402', resource='NCI', type='NULL', drug_name='DEXAMETHASONE', drug_concept_id='rxcui:3264', score='0.1408971500063358', approved='TRUE', anti_neoplastic='TRUE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='NFE2L2', gene_concept_id...(truncated) | 84,175 | {} | 2025-09-26 04:48:36 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2025-09-26 04:48:42 | 2025-09-26 04:48:43 | 0.24 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2025-09-26 04:48:42 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2025-09-26 04:48:43 | 2025-09-26 04:48:43 | 0.45 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource='TIGA', source_score=27, confidence=0.865), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:535', disease='Sleep disorder', resource='TIGA'...(truncated) | 30,470 | {} | 2025-09-26 04:48:43 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2025-09-26 04:48:43 | 2025-09-26 04:48:47 | 3.61 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:150', disease='Disease of mental health', resource='TIGA', source_score=18, confidence=0.717), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resou...(truncated) | 345,254 | {} | 2025-09-26 04:48:43 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2025-09-26 04:48:47 | 2025-09-26 04:48:47 | 0.15 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:1928', disease='Williams-Beuren syndrome', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Cranio...(truncated) | 7,775 | {} | 2025-09-26 04:48:47 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2025-09-26 04:48:47 | 2025-09-26 04:48:48 | 0.97 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050177', disease='Monogenic disease', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050736', disease='Autosomal...(truncated) | 98,705 | {} | 2025-09-26 04:48:47 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2025-09-26 04:48:48 | 2025-09-26 04:48:53 | 5.08 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.25, confidence=3.625, 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) | 288,361 | {} | 2025-09-26 04:48:48 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2025-09-26 04:48:53 | 2025-09-26 04:54:53 | 360.53 |
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__20250926-022201/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-13 05:00:57 | |||
| ¶ | pypath.inputs.domino.domino_ddi | 2025-09-26 04:54:54 | 2025-09-26 04:54:59 | 5.81 | list | [<pypath.internals.intera.DomainDomain object at 0x7f2668628950>, <pypath.internals.intera.DomainDomain object at 0x7f273e1b7a90>, <pypath.internals.intera.DomainDomain object at 0x7f273e1b6210>, <pypath.internals.intera.DomainDomain object at 0x7f273e1b5f90>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2025-09-26 04:54:54 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2025-09-26 04:54:59 | 2025-09-26 04:55:01 | 1.16 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f26686281d0>, <pypath.internals.intera.DomainDomain object at 0x7f266862b850>, <pypath.internals.intera.DomainDomain object at 0x7f26695a0fd0>, <pypath.internals.intera.DomainDomain object at 0x7f26695a1b50>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2025-09-26 04:54:59 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2025-09-26 04:55:01 | 2025-09-26 04:55:01 | 0.36 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2025-09-26 04:55:01 | |
| ¶ | pypath.inputs.domino.get_domino | 2025-09-26 04:55:01 | 2025-09-26 04:55:01 | 0.35 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2025-09-26 04:55:01 | |
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2025-09-26 04:55:01 | 2025-09-26 04:55:12 | 10.50 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2025-09-26 04:55:01 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-09-26 04:55:12 | 2025-09-26 04:55:26 | 13.96 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-09-26 04:55:12 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-09-26 04:55:26 | 2025-09-26 04:55:28 | 1.88 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-09-26 04:55:26 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-09-26 04:55:28 | 2025-09-26 04:55:29 | 1.34 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-09-26 04:55:28 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-09-26 04:55:29 | 2025-09-26 04:55:43 | 13.87 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-09-26 04:55:29 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-09-26 04:55:43 | 2025-09-26 04:55:43 | 0.35 |
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__20250926-022201/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 | 2025-09-26 04:55:43 | 2025-09-26 04:55:44 | 1.08 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2025-09-26 04:55:43 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2025-09-26 04:55:44 | 2025-09-26 04:55:46 | 1.38 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2025-09-26 04:55:44 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2025-09-26 04:55:46 | 2025-09-26 04:56:01 | 15.61 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 353 | {} | 2025-09-26 04:55:46 | |
| ¶ | pypath.inputs.elm.elm_domains | 2025-09-26 04:56:01 | 2025-09-26 04:56:02 | 0.82 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2025-09-26 04:56:01 | |
| ¶ | pypath.inputs.elm.elm_instances | 2025-09-26 04:56:02 | 2025-09-26 04:56:02 | 0.12 | 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} | 2025-09-26 04:56:02 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2025-09-26 04:56:02 | 2025-09-26 04:57:37 | 94.13 | 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 | {} | 2025-09-26 04:56:02 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2025-09-26 04:57:37 | 2025-09-26 04:57:40 | 3.52 | dict | {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=True)}, 'P30411': {EmbraceAnnotation(mainclass='receptor', neu...(truncated) | 844 | {} | 2025-09-26 04:57:37 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2025-09-26 04:57:40 | 2025-09-26 04:57:40 | 0.10 | list | [EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(ligand='O43184', receptor='P05556'), EmbraceInteraction(ligand='O43184', receptor='P31431'), EmbraceInteraction(...(truncated) | 1,273 | {} | 2025-09-26 04:57:40 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2025-09-26 04:57:40 | 2025-09-26 04:57:40 | 0.09 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2025-09-26 04:57:40 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2025-09-26 04:57:40 | 2025-09-26 04:57:41 | 0.61 | list | [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) | 1,832 | {} | 2025-09-26 04:57:40 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2025-09-26 04:57:41 | 2025-09-26 04:57:41 | 0.42 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2025-09-26 04:57:41 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2025-09-26 04:57:41 | 2025-09-26 04:57:42 | 0.39 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 348 | {} | 2025-09-26 04:57:41 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.exocarta.get_exocarta | 2025-09-26 04:57:42 | 2025-09-26 04:58:45 | 63.16 | list | [ExocartaRecord(entrez='967', genesymbol='CD63', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='1803', genesymbol='DPP4', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='79574', genesymbol=...(truncated) | 35,259 | {} | 2025-09-26 04:57:42 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2025-09-26 04:58:45 | 2025-09-26 05:01:06 | 141.38 | list | [VesiclepediaRecord(entrez='31848', genesymbol='His3.3B', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entrez='33736', genesymbol='His3.3A', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entr...(truncated) | 290,197 | {} | 2025-09-26 04:58:45 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2025-09-26 05:01:06 | 2025-09-26 05:01:06 | 0.17 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 354 | {} | 2025-09-26 05:01:06 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2025-09-26 05:01:06 | 2025-09-26 05:01:08 | 1.19 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,405 | {} | 2025-09-26 05:01:06 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2025-09-26 05:01:08 | 2025-09-26 05:02:05 | 57.01 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0045275', 'GO:0005743', 'GO:0016020'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0045259', 'GO:0005743'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0045259', 'GO:0005743'}, 'A0A023I7N5': {'GO:0005743', 'GO:0016020'}, 'A0A02...(truncated) | 2 | {} | 2025-09-26 05:01:08 | |
| ¶ | pypath.inputs.go.get_goslim | 2025-09-26 05:02:05 | 2025-09-26 05:02:06 | 1.05 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 142 | {} | 2025-09-26 05:02:05 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-09-26 05:02:06 | 2025-09-26 05:09:57 | 471.58 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 341, in download_in_chunks
result = json.load(c.fileobj)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 293, in load
return loads(fp.read(),
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 41225 (char 41224)
During handling of the above exception, another exception occurred:
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__20250926-022201/pypath_git/pypath/inputs/go.py", line 233, in go_ancestors_quickgo
desc = go_descendants_quickgo(aspects = aspects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 389, in go_descendants_quickgo
desc[asp] = download_in_chunks(
^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 365, in download_in_chunks
target = taret,
^^^^^
NameError: name 'taret' is not defined
|
{'broke': True} | 2025-09-25 05:20:26 | |||
| ¶ | pypath.inputs.go.go_ancestors_goose | 2025-09-26 05:09:57 | 2025-09-26 05:09:57 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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 | 2025-09-26 05:09:57 | 2025-09-26 05:10:01 | 3.97 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 341, in download_in_chunks
result = json.load(c.fileobj)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 293, in load
return loads(fp.read(),
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 41225 (char 41224)
During handling of the above exception, another exception occurred:
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__20250926-022201/pypath_git/pypath/inputs/go.py", line 233, in go_ancestors_quickgo
desc = go_descendants_quickgo(aspects = aspects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 389, in go_descendants_quickgo
desc[asp] = download_in_chunks(
^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 365, in download_in_chunks
target = taret,
^^^^^
NameError: name 'taret' is not defined
|
{'broke': True} | 2025-09-25 05:20:26 | |||
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-09-26 05:10:01 | 2025-09-26 05:10:04 | 2.56 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2025-09-26 05:10:01 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2025-09-26 05:10:04 | 2025-09-26 05:10:10 | 6.40 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0003723', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0694', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) | 19,697 | {} | 2025-09-26 05:10:04 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-09-26 05:10:13 | 2025-09-26 05:10:14 | 1.29 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005886', 'GO:0005576', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2025-09-26 05:10:13 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2025-09-26 05:10:14 | 2025-09-26 05:10:14 | 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__20250926-022201/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 | 2025-09-26 05:10:14 | 2025-09-26 05:10:28 | 13.96 | dict | {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0043231', 'GO:0070330'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'], 'A0A0C5B5G6': ['GO:0001649', 'GO:0003677', 'GO:0005615', ...(truncated) | 19,390 | {} | 2025-09-26 05:10:14 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-09-26 05:10:28 | 2025-09-26 05:10:32 | 4.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 341, in download_in_chunks
result = json.load(c.fileobj)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 293, in load
return loads(fp.read(),
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 41225 (char 41224)
During handling of the above exception, another exception occurred:
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__20250926-022201/pypath_git/pypath/inputs/go.py", line 389, in go_descendants_quickgo
desc[asp] = download_in_chunks(
^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 365, in download_in_chunks
target = taret,
^^^^^
NameError: name 'taret' is not defined
|
{'broke': True} | 2025-09-25 05:21:00 | |||
| ¶ | pypath.inputs.go.go_descendants_goose | 2025-09-26 05:10:32 | 2025-09-26 05:10:33 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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__20250926-022201/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 | 2025-09-26 05:10:33 | 2025-09-26 05:10:37 | 4.36 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 341, in download_in_chunks
result = json.load(c.fileobj)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 293, in load
return loads(fp.read(),
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 41225 (char 41224)
During handling of the above exception, another exception occurred:
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__20250926-022201/pypath_git/pypath/inputs/go.py", line 389, in go_descendants_quickgo
desc[asp] = download_in_chunks(
^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/go.py", line 365, in download_in_chunks
target = taret,
^^^^^
NameError: name 'taret' is not defined
|
{'broke': True} | 2025-09-25 05:21:00 | |||
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-09-26 05:10:37 | 2025-09-26 05:10:40 | 3.47 | dict | {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) | 3 | {} | 2025-09-26 05:10:37 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2025-09-26 05:10:40 | 2025-09-26 05:10:40 | 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__20250926-022201/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 | 2025-09-26 05:10:40 | 2025-09-26 05:10:44 | 3.60 | dict | {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) | 3 | {} | 2025-09-26 05:10:40 | |
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2025-09-26 05:10:44 | 2025-09-26 05:10:44 | 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 | {} | 2025-09-26 05:10:44 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2025-09-26 05:10:44 | 2025-09-26 05:10:46 | 1.33 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2025-09-26 05:10:44 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2025-09-26 05:10:46 | 2025-09-26 05:10:53 | 7.20 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {} | 2025-09-26 05:10:46 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2025-09-26 05:10:53 | 2025-09-26 05:10:53 | 0.35 | dict | {'P10145': {GutmgeneAnnotation(gut_microbiota='Clostridium', gut_microbiota_ncbi_id='1485', rank='genus', strain=None, alteration='activation', throughput='low-throughput', associative_mode='correlatively', sample='fecal', experimental_method='control experiment', measurement_technique='qRT-PCR', de...(truncated) | 111 | {} | 2025-09-26 05:10:53 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2025-09-26 05:10:53 | 2025-09-26 05:10:53 | 0.01 | list | [GutmgeneRaw(index='200', pmid='37960213', gut_microbiota='Turicibacter', gut_microbiota_ncbi_id='191303', rank='genus', strain=None, gene='TNF', gene_id='7124', alteration='inhibition', throughput='low-throughput', associative_mode='correlatively', organism='human', sample='NCM460 cells', experimen...(truncated) | 243 | {} | 2025-09-26 05:10:53 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2025-09-26 05:10:53 | 2025-09-26 05:10:53 | 0.23 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2025-09-26 05:10:53 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2025-09-26 05:10:53 | 2025-09-26 05:10:53 | 0.03 | dict | {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) | 622 | {} | 2025-09-26 05:10:53 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2025-09-26 05:10:53 | 2025-09-26 05:10:55 | 1.79 | 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) | 15,691 | {} | 2025-09-26 05:10:53 | |
| ¶ | pypath.inputs.hint.hint_interactions | 2025-09-26 05:10:55 | 2025-09-26 05:11:00 | 5.04 | list | [HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='LC'), HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='HT'), HintInteraction(id_a='A0A024R2I8', id_b='...(truncated) | 88,230 | {} | 2025-09-26 05:10:55 | |
| ¶ | pypath.inputs.hint.hint_raw | 2025-09-26 05:11:00 | 2025-09-26 05:11:00 | 0.08 | list | [['A0A024R2I8', 'F1D8Q5', 'NR1A2', 'NR2B1', '15604093:0018:HT:binary|19211732:0018:LC:binary|7746322:0018:LC:binary|9171239:0096:LC:binary|9368056:0096:LC:binary|9415406:0047:LC:binary', '9606', 'True', 'False'], ['A0A024R2I8', 'F1D8Q7', 'NR1A2', 'NR2B3', '15604093:0018:HT:binary', '9606', 'True', '...(truncated) | 163,435 | {} | 2025-09-26 05:11:00 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2025-09-26 05:11:00 | 2025-09-26 05:11:12 | 11.92 | list | [HippieInteraction(id_a='Q86UZ6', id_b='Q9UMX1', score=0.82, methods=None, references=('26186194', '28514442'), sources=None, organisms=None), HippieInteraction(id_a='O14763', id_b='Q86VI4', score=0.83, methods=None, references=('26186194', '28514442', '33961781'), sources=None, organisms=None), Hip...(truncated) | 102,409 | {} | 2025-09-26 05:11:00 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2025-09-26 05:11:12 | 2025-09-26 05:12:29 | 76.22 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2025-09-26 05:11:12 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2025-09-26 05:12:29 | 2025-09-26 05:12:29 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {} | 2025-09-26 05:12:29 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2025-09-26 05:12:29 | 2025-09-26 05:12:29 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {} | 2025-09-26 05:12:29 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2025-09-26 05:12:29 | 2025-09-26 05:12:29 | 0.00 | dict | {} | 0 | {} | 2025-09-26 05:12:29 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2025-09-26 05:12:29 | 2025-09-26 05:12:29 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {} | 2025-09-26 05:12:29 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2025-09-26 05:12:29 | 2025-09-26 05:12:33 | 4.28 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0045055'), HpoAnnotation(entrez_ge...(truncated) | 5,128 | {} | 2025-09-26 05:12:29 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2025-09-26 05:12:33 | 2025-09-26 05:12:38 | 4.35 | dict | {'hpo_id': {HpoDisease(omim='database_id', name='disease_name', pmid=None, qualifier='qualifier', evidence='evidence', onset='onset', frequency='frequency', sex='sex', modifier='modifier', aspect='aspect')}, 'HP:0011097': {HpoDisease(omim='OMIM:617086', name='Encephalopathy due to defective mitochon...(truncated) | 11,421 | {} | 2025-09-26 05:12:33 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2025-09-26 05:12:38 | 2025-09-26 05:12:40 | 2.12 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2025-09-26 05:12:38 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2025-09-26 05:12:40 | 2025-09-26 05:12:41 | 0.54 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 19,232 | {} | 2025-09-26 05:12:40 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2025-09-26 05:12:41 | 2025-09-26 05:12:45 | 4.19 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2025-09-26 05:12:41 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2025-09-26 05:12:45 | 2025-09-26 05:12:47 | 1.80 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2025-09-26 05:12:45 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2025-09-26 05:12:47 | 2025-09-26 05:12:48 | 1.24 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2025-09-26 05:12:47 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2025-09-26 05:12:48 | 2025-09-26 05:12:49 | 1.14 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2025-09-26 05:12:48 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2025-09-26 05:12:49 | 2025-09-26 05:13:20 | 30.30 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2025-09-26 05:12:49 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2025-09-26 05:13:20 | 2025-09-26 05:13:29 | 9.61 |
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__20250926-022201/pypath_git/pypath/inputs/humancellmap.py", line 43, in humancellmap_annotations
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{} | 2025-08-31 05:11:31 | |||
| ¶ | pypath.inputs.humap.humap1_complexes | 2025-09-26 05:13:29 | 2025-09-26 05:13:29 | 0.18 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,545 | {} | 2025-09-26 05:13:29 | |
| ¶ | pypath.inputs.humap.humap2and3_complexes | 2025-09-26 05:13:29 | 2025-09-26 05:13:31 | 1.72 | dict | {'COMPLEX:P20963_Q9NWV4_Q9UGQ2': Complex: COMPLEX:P20963_Q9NWV4_Q9UGQ2, 'COMPLEX:O94887_Q9NQ92_Q9NWB1': Complex: COMPLEX:O94887_Q9NQ92_Q9NWB1, 'COMPLEX:Q8N3D4_Q9Y3A4': Complex: COMPLEX:Q8N3D4_Q9Y3A4, 'COMPLEX:O00429_Q5T2D2': Complex: COMPLEX:O00429_Q5T2D2, 'COMPLEX:O95460_P21941_P78540_Q9H267_Q9H9C1...(truncated) | 15,433 | {} | 2025-09-26 05:13:29 | |
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2025-09-26 05:13:31 | 2025-09-26 05:13:34 | 2.79 | 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 | {} | 2025-09-26 05:13:31 | |
| ¶ | pypath.inputs.huri.hi_i_interactions | 2025-09-26 05:13:34 | 2025-09-26 05:13:35 | 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__20250926-022201/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 | 2025-09-26 05:13:35 | 2025-09-26 05:13:36 | 1.11 |
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__20250926-022201/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 | 2025-09-26 05:13:36 | 2025-09-26 05:13:38 | 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__20250926-022201/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 | 2025-09-26 05:13:38 | 2025-09-26 05:13:39 | 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__20250926-022201/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 | 2025-09-26 05:13:39 | 2025-09-26 05:13:40 | 1.16 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2025-09-26 05:13:39 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2025-09-26 05:13:40 | 2025-09-26 05:13:41 | 1.54 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2025-09-26 05:13:40 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2025-09-26 05:13:41 | 2025-09-26 05:13:42 | 1.09 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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 | 2025-09-26 05:13:42 | 2025-09-26 05:13:45 | 2.12 | list | [Rolland2014Interaction(entrez_a='14', entrez_b='6293', genesymbol_a='AAMP', genesymbol_b='VPS52', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='8553', genesymbol_a='AAMP', genesymbol_b='BHLHE40', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='64782', genesymbo...(truncated) | 13,944 | {} | 2025-09-26 05:13:42 | |
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2025-09-26 05:13:45 | 2025-09-26 05:13:46 | 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__20250926-022201/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 | 2025-09-26 05:13:46 | 2025-09-26 05:13:47 | 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__20250926-022201/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 | 2025-09-26 05:13:47 | 2025-09-26 05:14:01 | 14.31 | list | [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) | 22,184 | {} | 2025-09-26 05:13:47 | |
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2025-09-26 05:14:01 | 2025-09-26 05:14:01 | 0.29 | dict | {Complex: COMPLEX:P01033_P14780: {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None)}, 'P01033': {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None), IcellnetAnnotation(role='ligand', family='Cell adhesion', subfamily=None, classifica...(truncated) | 1,193 | {'size': -1} | 2025-09-26 05:14:01 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2025-09-26 05:14:01 | 2025-09-26 05:14:02 | 0.04 | dict | {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) | 156 | {} | 2025-09-26 05:14:01 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2025-09-26 05:14:02 | 2025-09-26 05:14:02 | 0.03 | list | [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) | 1,647 | {} | 2025-09-26 05:14:02 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2025-09-26 05:14:02 | 2025-09-26 05:14:04 | 2.50 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2025-09-26 05:14:02 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2025-09-26 05:14:04 | 2025-09-26 05:14:05 | 0.62 | list | [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) | 11,470 | {} | 2025-09-26 05:14:04 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2025-09-26 05:14:05 | 2025-09-26 05:14:05 | 0.54 | NoneType | None | 0 | {} | 2025-09-26 05:14:05 | |
| ¶ | pypath.inputs.intact.intact_interactions | 2025-09-26 05:14:05 | 2025-09-26 05:16:37 | 151.80 | list | [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', i...(truncated) | 78,544 | {} | 2025-09-26 05:14:05 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2025-09-26 05:16:37 | 2025-09-26 05:16:38 | 0.56 | set | {'P26012', 'P53708', 'P05106', 'Q13797', 'P20702', 'P18564', 'Q13683', 'P18084', 'P06756', 'P05107', 'Q13349', 'P11215', 'O75578', 'P08648', 'P08514', 'P38570', 'P26010', 'P26006', 'P56199', 'Q9UKX5', 'P23229', 'P17301', 'P16144', 'P20701', 'P05556'} | 25 | {} | 2025-09-26 05:16:37 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2025-09-26 05:16:38 | 2025-09-26 05:16:39 | 1.31 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid receptor activity'), Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOA...(truncated) | 14,743 | {} | 2025-09-26 05:16:38 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2025-09-26 05:16:39 | 2025-09-26 05:16:40 | 0.38 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR038178', organism='9606', start='209', end='294'), InterproAnnotation(interpro_id='IPR024174', organism='9606', start='1', end='723'), InterproAnnotation(interpro_id='IPR038178', organism='9606', start='127', end='208'), Inter...(truncated) | 16,611 | {} | 2025-09-26 05:16:39 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2025-09-26 05:16:40 | 2025-09-26 05:16:52 | 12.03 | list | [InterproEntry(interpro_id='IPR000001', protein_count='20781', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 48,679 | {} | 2025-09-26 05:16:40 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2025-09-26 05:16:52 | 2025-09-26 05:16:53 | 1.00 | dict | {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) | 483 | {} | 2025-09-26 05:16:52 | |
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2025-09-26 05:16:53 | 2025-09-26 05:16:53 | 0.08 | dict | {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) | 86,754 | {} | 2025-09-26 05:16:53 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2025-09-26 05:16:53 | 2025-09-26 05:17:13 | 20.33 | list | [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', ...(truncated) | 15,834 | {} | 2025-09-26 05:16:53 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2025-09-26 05:17:13 | 2025-09-26 05:17:14 | 0.71 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {} | 2025-09-26 05:17:13 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2025-09-26 05:17:14 | 2025-09-26 05:17:14 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {} | 2025-09-26 05:17:14 | |
| ¶ | pypath.inputs.italk.italk_raw | 2025-09-26 05:17:14 | 2025-09-26 05:17:14 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2025-09-26 05:17:14 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2025-09-26 05:17:14 | 2025-09-26 05:17:18 | 4.37 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,224 | {} | 2025-09-26 05:17:14 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2025-09-26 05:17:19 | 2025-09-26 05:17:19 | 0.14 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {} | 2025-09-26 05:17:19 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2025-09-26 05:17:19 | 2025-09-26 05:31:46 | 866.91 | list | [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) | 14,739 | {} | 2025-09-26 05:17:19 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2025-09-26 05:31:46 | 2025-09-26 05:32:07 | 21.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/kegg.py", line 523, in kegg_medicus
dbget = kegg_dbget(_id)
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/kegg.py", line 719, in kegg_dbget
soup = bs4.BeautifulSoup(c.result, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-6-S_sgju-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.
|
{'broke': True} | 2025-09-25 05:42:33 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2025-09-26 05:32:07 | 2025-09-26 05:32:45 | 38.59 | dict | {'COMPLEX:Q8IZP0_Q8WUW1_Q96F07_Q9Y2A7_Q9Y6W5': Complex: COMPLEX:Q8IZP0_Q8WUW1_Q96F07_Q9Y2A7_Q9Y6W5, 'COMPLEX:P27986_P42338': Complex: COMPLEX:P27986_P42338, 'COMPLEX:P18074_P19447_P32780_Q13888_Q13889_Q6ZYL4_Q92759': Complex: COMPLEX:P18074_P19447_P32780_Q13888_Q13889_Q6ZYL4_Q92759, 'COMPLEX:O43318_...(truncated) | 528 | {} | 2025-09-26 05:32:07 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2025-09-26 05:32:45 | 2025-09-26 05:32:46 | 0.36 | list | [KeggMedicusInteraction(id_a='P36507', id_b='Q16539', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P40225', id_b='P48357', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,538 | {} | 2025-09-26 05:32:45 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2025-09-26 05:32:46 | 2025-09-26 05:32:59 | 12.86 | dict | {'Q9Y4K3': {KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Neurotrophin signaling pathway'), KeggPathway(pathway='NF-kappa B signaling pathway'), KeggPathway(pathway='Autophagy - animal'), KeggPathway(pathway='Toll-like receptor signaling pathway'), KeggPathway(pathway='RIG-I-li...(truncated) | 2,672 | {} | 2025-09-26 05:32:46 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2025-09-26 05:32:59 | 2025-09-26 05:33:00 | 0.90 | dict | {'A8K7J7': {KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Glycolysi...(truncated) | 813 | {} | 2025-09-26 05:32:59 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2025-09-26 05:33:00 | 2025-09-26 05:33:12 | 12.92 | tuple | ({'MAPK signaling pathway': {'Q9Y4K3', 'Q13163', 'P10636', 'P14778', 'P01583', 'Q9Y6W6', 'P18848', 'Q13188', 'Q9UKG9', 'Q9UER7', 'P19438', 'P07602', 'Q03113', 'Q96KG9', 'Q9Y6R4', 'P42574', 'Q9UPT6', 'Q9HD43', 'P48023', 'P0C869', 'Q99558', 'Q7RTX0', 'P28482', 'P15976', 'P20936', 'P46734', 'P36507', '...(truncated) | 2 | {} | 2025-09-26 05:33:00 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2025-09-26 05:33:13 | 2025-09-26 05:33:16 | 3.88 |
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__20250926-022201/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__20250926-022201/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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__20250926-022201/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 | 2025-09-26 05:33:16 | 2025-09-26 05:33:17 | 0.47 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 503 | {} | 2025-09-26 05:33:16 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2025-09-26 05:33:17 | 2025-09-26 05:33:17 | 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 | {} | 2025-09-26 05:33:17 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2025-09-26 05:33:17 | 2025-09-26 05:33:21 | 3.54 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {} | 2025-09-26 05:33:17 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2025-09-26 05:33:21 | 2025-09-26 05:33:23 | 2.00 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {} | 2025-09-26 05:33:21 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2025-09-26 05:33:23 | 2025-09-26 05:33:23 | 0.39 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2025-09-26 05:33:23 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2025-09-26 05:33:23 | 2025-09-26 05:33:24 | 0.91 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2025-09-26 05:33:23 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2025-09-26 05:33:24 | 2025-09-26 05:33:25 | 0.83 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2025-09-26 05:33:24 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2025-09-26 05:33:25 | 2025-09-26 05:33:37 | 11.76 | list | [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) | 593 | {} | 2025-09-26 05:33:25 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2025-09-26 05:33:37 | 2025-09-26 05:33:37 | 0.02 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2025-09-26 05:33:37 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2025-09-26 05:33:37 | 2025-09-26 05:33:37 | 0.02 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2025-09-26 05:33:37 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2025-09-26 05:33:37 | 2025-09-26 05:34:01 | 23.84 | dict | {'<html style="height:100%"><head><META NAME="ROBOTS" CONTENT="NOINDEX, NOFOLLOW"><meta name="format-detection" content="telephone=no"><meta name="viewport" content="initial-scale=1.0"><meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"><script type="text/javascript" src="/_Incapsula_Resou...(truncated) | 372 | {'size': 1} | 2025-09-26 05:33:37 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2025-09-26 05:34:01 | 2025-09-26 05:34:01 | 0.69 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2025-09-26 05:34:01 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2025-09-26 05:34:01 | 2025-09-26 05:34:02 | 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 | {} | 2025-09-26 05:34:01 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2025-09-26 05:34:02 | 2025-09-26 05:34:02 | 0.45 | list | [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) | 1,170 | {} | 2025-09-26 05:34:02 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2025-09-26 05:34:02 | 2025-09-26 05:34:03 | 1.10 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {} | 2025-09-26 05:34:02 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2025-09-26 05:34:03 | 2025-09-26 05:34:04 | 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 | {} | 2025-09-26 05:34:03 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2025-09-26 05:34:04 | 2025-09-26 05:34:40 | 36.10 | dict | {'P27824': {LocateAnnotation(source='UniProt/SPTrEMBL', location='melanosome', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=No...(truncated) | 9,479 | {} | 2025-09-26 05:34:04 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2025-09-26 05:34:40 | 2025-09-26 05:34:40 | 0.39 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10514495',)), LrdbAnnotation(role='receptor', cell_type=None, source...(truncated) | 1,536 | {} | 2025-09-26 05:34:40 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2025-09-26 05:34:40 | 2025-09-26 05:34:40 | 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 | {} | 2025-09-26 05:34:40 | |
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2025-09-26 05:34:40 | 2025-09-26 05:34:40 | 0.23 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2025-09-26 05:34:40 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2025-09-26 05:34:40 | 2025-09-26 05:34:41 | 0.26 | dict | {'H0YF57': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C4N5': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YF18': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,501 | {} | 2025-09-26 05:34:40 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2025-09-26 05:34:41 | 2025-09-26 05:34:41 | 0.67 | dict | {} | 0 | {} | 2025-09-26 05:34:41 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2025-09-26 05:34:41 | 2025-09-26 05:34:43 | 1.43 | set | {'Q9UGI9', 'P02747', 'A0A0B4J2D9', 'Q8WWG1', 'P01011', 'Q5VTE0', 'O43508', 'P12259', 'Q9BXS0', 'Q9NS15', 'Q7Z5G4', 'P04746', 'P48357', 'Q6UXR6', 'P01588', 'P51608', 'P0C7V6', 'Q5JXM2', 'Q9Y275', 'Q7Z5A8', 'P04430', 'Q969J5', 'Q6E0U4', 'P16233', 'P68402', 'Q8N4T0', 'P10721', 'Q4G0G5', 'A0A1B0GVD1', '...(truncated) | 2,840 | {} | 2025-09-26 05:34:41 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2025-09-26 05:34:43 | 2025-09-26 05:34:43 | 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 | {} | 2025-09-26 05:34:43 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2025-09-26 05:34:43 | 2025-09-26 05:34:43 | 0.07 | set | set() | 0 | {} | 2025-09-26 05:34:43 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2025-09-26 05:34:43 | 2025-09-26 05:34:43 | 0.06 | set | set() | 0 | {} | 2025-09-26 05:34:43 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2025-09-26 05:34:43 | 2025-09-26 05:34:44 | 1.10 | set | {'P28827', 'P25940', 'Q6AZ88', 'Q5ZPR3', 'P16671', 'P12259', 'Q13449', 'Q8WWQ8', 'Q9NPY3', 'Q8TAW8', 'Q92692', 'O60759', 'Q13895', 'Q9Y4C0', 'Q9BX90', 'Q8TEW0', 'Q9NY15', 'P56856', 'Q96BL7', 'Q13308', 'Q0VAE8', 'Q04900', 'Q6MZF4', 'P78325', 'P50895', 'O75144', 'P53708', 'P42771', 'Q05084', 'Q68D78',...(truncated) | 112 | {} | 2025-09-26 05:34:43 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2025-09-26 05:34:44 | 2025-09-26 05:35:10 | 26.17 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {} | 2025-09-26 05:34:44 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2025-09-26 05:35:10 | 2025-09-26 05:35:10 | 0.14 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2025-09-26 05:35:10 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2025-09-26 05:35:10 | 2025-09-26 05:35:14 | 3.56 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2025-09-26 05:35:10 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2025-09-26 05:35:14 | 2025-09-26 05:35:14 | 0.19 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2025-09-26 05:35:14 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2025-09-26 05:35:14 | 2025-09-26 05:35:14 | 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 | {} | 2025-09-26 05:35:14 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2025-09-26 05:35:14 | 2025-09-26 05:35:15 | 0.72 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) | 2,925 | {} | 2025-09-26 05:35:14 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2025-09-26 05:35:15 | 2025-09-26 05:35:15 | 0.02 | list | [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0004481', 'hsa-let-7a-3p'), ('MIMAT0004481', 'hsa-let-7a*'), ('MIMAT0010195', 'hsa-let-7a-2-3p'), ('MIMAT0010195', 'hsa-let-7a-2*'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0004482', 'hsa-let...(truncated) | 3,299 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2025-09-26 05:35:15 | 2025-09-26 05:35:15 | 0.02 | list | ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) | 2,693 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna | 2025-09-26 05:35:15 | 2025-09-26 05:35:15 | 0.03 | list | [['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' untr...(truncated) | 39,233 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_mature | 2025-09-26 05:35:15 | 2025-09-26 05:35:15 | 0.02 | list | [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) | 49,168 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_pre_mature | 2025-09-26 05:35:15 | 2025-09-26 05:35:15 | 0.12 | list | [(['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' unt...(truncated) | 53,320 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_organisms | 2025-09-26 05:35:15 | 2025-09-26 05:35:16 | 0.97 | dict | {400682: 'aqu', 45351: 'nve', 6085: 'hma', 10224: 'sko', 7668: 'spu', 7719: 'cin', 51511: 'csa', 34765: 'odi', 7739: 'bfl', 8355: 'xla', 8364: 'xtr', 9031: 'gga', 9615: 'cfa', 13616: 'mdo', 9509: 'age', 9519: 'lla', 78454: 'sla', 9544: 'mml', 9545: 'mne', 61621: 'pbi', 9593: 'ggo', 9606: 'hsa', 9597...(truncated) | 285 | {} | 2025-09-26 05:35:15 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2025-09-26 05:35:16 | 2025-09-26 05:35:16 | 0.03 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,130 | {} | 2025-09-26 05:35:16 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2025-09-26 05:35:16 | 2025-09-26 05:35:16 | 0.03 | list | ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', 'MI0000081', 'MI0000082', ...(truncated) | 1,984 | {} | 2025-09-26 05:35:16 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2025-09-26 05:35:16 | 2025-09-26 05:35:16 | 0.08 | list | [('hsa-let-7a-1', 'hsa-let-7a-5p'), ('hsa-let-7a-1', 'hsa-let-7a'), ('hsa-let-7a-1L', 'hsa-let-7a-5p'), ('hsa-let-7a-1L', 'hsa-let-7a'), ('hsa-let-7a-1', 'hsa-let-7a-3p'), ('hsa-let-7a-1', 'hsa-let-7a*'), ('hsa-let-7a-1L', 'hsa-let-7a-3p'), ('hsa-let-7a-1L', 'hsa-let-7a*'), ('hsa-let-7a-2', 'hsa-let...(truncated) | 4,071 | {} | 2025-09-26 05:35:16 | |
| ¶ | pypath.inputs.mirbase.mirbase_taxid | 2025-09-26 05:35:16 | 2025-09-26 05:35:16 | 0.00 | str | 'hsa' | 3 | {} | 2025-09-26 05:35:16 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2025-09-26 05:35:17 | 2025-09-26 05:35:17 | 0.17 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2025-09-26 05:35:17 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2025-09-26 05:35:17 | 2025-09-26 05:35:17 | 0.41 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism=9606, target_organism=9606, pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organism=10090, target_or...(truncated) | 3,106 | {} | 2025-09-26 05:35:17 | |
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2025-09-26 05:35:17 | 2025-09-26 05:42:26 | 429.18 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=10090, target_genesymbol='Cd320', target_entrez='54219', target_organism=10090, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', data...(truncated) | 27,595 | {} | 2025-09-26 05:35:17 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2025-09-26 05:42:26 | 2025-09-26 05:42:27 | 0.24 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2025-09-26 05:42:26 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2025-09-26 05:42:27 | 2025-09-26 05:43:01 | 34.12 | dict | {'P06858': {MsigdbAnnotation(collection='immunesigdb', geneset='GSE2585_CD80_HIGH_VS_LOW_AIRE_KO_MTEC_DN'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE360_DC_VS_MAC_L_DONOVANI_DN'), MsigdbAnnotation(collection='mirna_targets_mirdb', geneset='MIR29B_3P_MIR29C_3P'), MsigdbAnnotation(collec...(truncated) | 20,111 | {} | 2025-09-26 05:42:27 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2025-09-26 05:43:02 | 2025-09-26 05:43:08 | 5.72 | dict | {'MT': {'MT-ND4', 'MT-ATP8', 'MT-ND3', 'MT-TF', 'MT-TD', 'MT-TA', 'MT-TN', 'MT-ND6', 'MT-TG', 'MT-TY', 'MT-TE', 'MT-TH', 'MT-ND1', 'MT-TP', 'MT-CO1', 'MT-ND2', 'MT-TC', 'MT-TK', 'MT-TQ', 'MT-TV', 'MT-RNR2', 'MT-TS2', 'MT-TL1', 'MT-TR', 'MT-ND4L', 'MT-CO2', 'MT-CYB', 'MT-TS1', 'MT-ATP6', 'MT-TI', 'MT...(truncated) | 35,134 | {} | 2025-09-26 05:43:02 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2025-09-26 05:43:08 | 2025-09-26 05:43:09 | 0.42 | dict | {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'IMMT', 'MGST3', 'PLIN2', 'CD36', 'CYP4B1', 'ESRRA', 'ANGPTL4', 'DNAJB9', 'STOM', 'GPD2', 'SSPN', 'ME1', 'NDUFS3', 'GPAM', 'RNF11', 'ESYT1', 'UBC', 'ALDOA', 'DHRS7B', 'CYC1', 'LIPE', 'ACAA2', 'JAGN1', 'BCL6', 'DLD', 'PHYH', 'MDH2', 'PIM3', 'DHRS7', ...(truncated) | 20 | {} | 2025-09-26 05:43:08 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2025-09-26 05:43:09 | 2025-09-26 05:43:10 | 0.49 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2025-09-26 05:43:09 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2025-09-26 05:43:10 | 2025-09-26 05:43:10 | 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 | {'fixed': True} | 2025-09-26 05:43:10 | |
| ¶ | pypath.inputs.netbiol.arn_interactions | 2025-09-26 05:43:10 | 2025-09-26 05:43:10 | 0.12 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2025-09-26 05:43:10 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2025-09-26 05:43:10 | 2025-09-26 05:43:10 | 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 | {} | 2025-09-26 05:43:10 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2025-09-26 05:43:10 | 2025-09-26 05:43:12 | 2.19 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2025-09-26 05:43:10 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2025-09-26 05:43:12 | 2025-09-26 05:43:12 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2025-09-26 05:43:12 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2025-09-26 05:43:12 | 2025-09-26 05:43:12 | 0.14 | 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='Inhibitor of diffe...(truncated) | 1,870 | {} | 2025-09-26 05:43:12 | |
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2025-09-26 05:43:12 | 2025-09-26 05:43:37 | 24.27 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2025-09-26 05:43:12 | |
| ¶ | pypath.inputs.oma.oma_orthologs | 2025-09-26 05:43:37 | 2025-09-26 05:45:43 | 126.52 | list | [OmaOrthology(a=OmaGene(id='BBS7_HUMAN', oma_group=1350148, hog='HOG:E0804196.8a', taxon=9606, chr='4', start=121825860, end=121870313, strand=-1, main_isoform=True), b=OmaGene(id='BBS7_MOUSE', oma_group=1350148, hog='HOG:E0804196', taxon=10090, chr='3', start=36627638, end=36667434, strand=-1, main...(truncated) | 22,374 | {} | 2025-09-26 05:43:37 | |
| ¶ | pypath.inputs.oma.oma_table | 2025-09-26 05:45:43 | 2025-09-26 05:45:51 | 8.21 | defaultdict | defaultdict(<class 'set'>, {'BBS7_HUMAN': {'BBS7_MOUSE'}, 'COBL_HUMAN': {'COBL_MOUSE'}, 'SLIK5_HUMAN': {'SLIK5_MOUSE'}, 'UB2E1_HUMAN': {'UB2E1_MOUSE'}, 'CD80_HUMAN': {'CD80_MOUSE'}, 'WDR97_HUMAN': {'A0A140LHH9'}, 'TCP4_HUMAN': {'TCP4_MOUSE'}, 'BPL1_HUMAN': {'Q920N2'}, 'IGS21_HUMAN': {'IGS21_MOUSE'},...(truncated) | 17,895 | {} | 2025-09-26 05:45:43 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2025-09-26 05:45:51 | 2025-09-26 05:45:52 | 0.49 | 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) | 273 | {'size': -1} | 2025-09-26 05:45:51 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2025-09-26 05:45:52 | 2025-09-26 05:46:38 | 45.79 | 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} | 2025-09-26 05:45:52 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2025-09-26 05:46:38 | 2025-09-26 05:50:50 | 252.35 | 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 | {'fixed': True} | 2025-09-26 05:46:38 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2025-09-26 05:50:50 | 2025-09-26 05:53:54 | 184.19 | 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 | {'fixed': True} | 2025-09-26 05:50:50 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2025-09-26 05:53:54 | 2025-09-26 05:57:16 | 202.02 | 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 | {'fixed': True} | 2025-09-26 05:53:54 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2025-09-26 05:57:16 | 2025-09-26 05:57:34 | 17.60 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 88 | {} | 2025-09-26 05:57:16 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2025-09-26 05:57:34 | 2025-09-26 05:58:05 | 31.29 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {} | 2025-09-26 05:57:34 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2025-09-26 05:58:05 | 2025-09-26 05:58:09 | 4.09 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 2,219,572 | {} | 2025-09-26 05:58:05 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2025-09-26 05:58:09 | 2025-09-26 05:58:13 | 3.71 | defaultdict | defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=False, cell_type='Enterocytes', organ='GI tract', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=0.0, mouse_sensitivity=0.00331126, human_specificity=0.00439422, mouse_specifici...(truncated) | 4,492 | {} | 2025-09-26 05:58:09 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2025-09-26 05:58:13 | 2025-09-26 05:58:13 | 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 | {} | 2025-09-26 05:58:13 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2025-09-26 05:58:13 | 2025-09-26 05:58:13 | 0.00 | list | [] | 0 | {} | 2025-09-26 05:58:13 | |
| ¶ | 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 | 2025-09-26 05:58:13 | 2025-09-26 05:58:38 | 25.01 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='controls-expression-of', id_b='A2M', resource='pid'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b=...(truncated) | 2,524,906 | {} | 2025-09-26 05:58:13 | |
| ¶ | 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 | 2025-09-26 05:58:40 | 2025-09-26 05:58:40 | 0.21 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2025-09-26 05:58:40 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2025-09-26 05:58:40 | 2025-09-26 05:58:47 | 7.29 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2025-09-26 05:58:40 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2025-09-26 05:58:50 | 2025-09-26 05:58:59 | 8.42 | 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) | 49,290 | {} | 2025-09-26 05:58:50 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2025-09-26 05:58:59 | 2025-09-26 05:59:04 | 5.19 | tuple | ({'P02185': {('2w6w', 'X-ray', 1.99), ('2mgc', 'X-ray', 1.9), ('1ofk', 'X-ray', 1.8), ('1iop', 'X-ray', 1.9), ('2zt4', 'X-ray', 1.21), ('1mbc', 'X-ray', 1.5), ('1dtm', 'X-ray', 2.13), ('8f9i', 'X-ray', 1.8), ('1mym', 'X-ray', 1.7), ('7spe', 'X-ray', 1.7), ('3u3e', 'X-ray', 1.21), ('104m', 'X-ray', 1...(truncated) | 2 | {} | 2025-09-26 05:58:59 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2025-09-26 05:59:04 | 2025-09-26 05:59:05 | 0.53 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2025-09-26 05:59:04 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2025-09-26 05:59:05 | 2025-09-26 06:10:07 | 661.79 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2025-09-26 05:59:05 | |
| ¶ | pypath.inputs.pfam.pfam_names | 2025-09-26 06:10:07 | 2025-09-26 06:10:08 | 1.17 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2025-09-26 06:10:07 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2025-09-26 06:10:08 | 2025-09-26 06:10:12 | 3.95 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) | 2 | {} | 2025-09-26 06:10:08 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2025-09-26 06:10:13 | 2025-09-26 06:19:08 | 534.99 | tuple | ({}, {}) | 2 | {} | 2025-09-26 06:10:13 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2025-09-26 06:19:08 | 2025-09-26 06:34:41 | 933.39 | tuple | ({}, {}) | 2 | {} | 2025-09-26 06:19:08 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2025-09-26 06:34:41 | 2025-09-26 06:37:07 | 145.67 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:34:41 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2025-09-26 06:37:08 | 2025-09-26 06:37:12 | 4.05 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:37:08 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2025-09-26 06:37:13 | 2025-09-26 06:37:16 | 3.58 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:37:13 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2025-09-26 06:37:17 | 2025-09-26 06:37:20 | 3.25 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:37:17 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2025-09-26 06:37:21 | 2025-09-26 06:37:24 | 2.75 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:37:21 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2025-09-26 06:37:25 | 2025-09-26 06:38:27 | 62.30 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2025-09-26 06:37:25 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2025-09-26 06:38:27 | 2025-09-26 06:38:30 | 3.16 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-09-26 06:38:27 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2025-09-26 06:38:31 | 2025-09-26 06:38:32 | 0.44 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2025-09-26 06:38:31 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2025-09-26 06:38:32 | 2025-09-26 06:38:36 | 4.24 | dict | {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) | 264 | {} | 2025-09-26 06:38:32 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2025-09-26 06:38:36 | 2025-09-26 06:38:43 | 6.98 |
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__20250926-022201/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-6-S_sgju-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 | 2025-09-26 06:38:43 | 2025-09-26 06:38:52 | 9.00 |
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__20250926-022201/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__20250926-022201/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-6-S_sgju-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 | 2025-09-26 06:38:52 | 2025-09-26 06:39:01 | 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__20250926-022201/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-6-S_sgju-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 | 2025-09-26 06:39:01 | 2025-09-26 06:39:02 | 1.32 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2025-09-26 06:39:01 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2025-09-26 06:39:02 | 2025-09-26 06:39:02 | 0.02 | list | [['STK17A', 'SP100'], ['RPS6KA4', 'NFATC4'], ['TYK2', 'EIF2AK2'], ['BMPR2', 'MTA1'], ['PAK4', 'LUC7L2'], ['PRKCA', 'PSEN1'], ['RPS6KA2', 'CRK'], ['CDK9', 'CHEK2'], ['RIPK2', 'CRK'], ['CDK5', 'ZHX1'], ['DYRK4', 'YWHAH'], ['PRKCA', 'INSR'], ['CDK5', 'XRCC1'], ['BLK', 'FCGR2B'], ['PTK6', 'RUVBL2'], ['S...(truncated) | 1,821 | {} | 2025-09-26 06:39:02 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2025-09-26 06:39:02 | 2025-09-26 06:39:03 | 0.22 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2025-09-26 06:39:02 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.31 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 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 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2025-09-26 06:39:03 | 2025-09-26 06:39:03 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) | 4,790 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2025-09-26 06:39:03 | 2025-09-26 06:39:08 | 5.19 | dict | {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) | 198,635 | {} | 2025-09-26 06:39:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2025-09-26 06:39:09 | 2025-09-26 06:39:22 | 13.06 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {} | 2025-09-26 06:39:09 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2025-09-26 06:39:22 | 2025-09-26 06:39:23 | 0.52 | 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 | {} | 2025-09-26 06:39:22 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2025-09-26 06:39:23 | 2025-09-26 06:40:49 | 85.90 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21209006', '21148409', '28052875', '24876223'}, 'isoforms': {1}, 'process': {''}, 'function': {'protein degradation', 'ubiquitination', 'protein stabilization', 'intracellular localization', 'phosphorylation'}...(truncated) | 3,621 | {} | 2025-09-26 06:39:23 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2025-09-26 06:40:49 | 2025-09-26 06:41:15 | 26.31 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2025-09-26 06:40:49 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2025-09-26 06:41:15 | 2025-09-26 06:41:16 | 0.45 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 394,059 | {} | 2025-09-26 06:41:15 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2025-09-26 06:41:16 | 2025-09-26 06:42:21 | 65.10 | dict | {'P35250': {ProgenyAnnotation(pathway='Androgen', weight=-1.28437624907, p_value=0.121273439673), ProgenyAnnotation(pathway='TNFa', weight=-0.12499324201483122, p_value=0.8334557980340556), ProgenyAnnotation(pathway='JAK-STAT', weight=0.0012188579040493524, p_value=0.998388257483376), ProgenyAnnotat...(truncated) | 18,582 | {} | 2025-09-26 06:41:16 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2025-09-26 06:42:21 | 2025-09-26 06:43:27 | 65.81 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2025-09-26 06:42:21 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2025-09-26 06:43:27 | 2025-09-26 06:43:32 | 4.93 | dict | {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) | 2 | {} | 2025-09-26 06:43:27 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2025-09-26 06:43:33 | 2025-09-26 06:43:43 | 9.61 | dict | {'O43657': {ProtainatlasAnnotation(organ='Bone marrow', tissue='Bone marrow', cell_type='hematopoietic 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), ProtainatlasAnnotatio...(truncated) | 15,045 | {} | 2025-09-26 06:43:33 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2025-09-26 06:43:45 | 2025-09-26 06:43:45 | 0.34 | list | [ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interac...(truncated) | 46,472 | {} | 2025-09-26 06:43:45 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2025-09-26 06:43:45 | 2025-09-26 06:43:45 | 0.29 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,590 | {} | 2025-09-26 06:43:45 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2025-09-26 06:43:45 | 2025-09-26 06:43:47 | 1.11 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Cytosol', status='main', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', reliability='Approved', m...(truncated) | 13,336 | {} | 2025-09-26 06:43:45 | |
| ¶ | pypath.inputs.proteins.variants | 2025-09-26 06:43:47 | 2025-09-26 06:43:47 | 0.27 | list | [] | 0 | {'size': -30452} | 2025-09-26 06:43:47 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2025-09-26 06:43:47 | 2025-09-26 06:43:48 | 1.29 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q05513', 'CTRL_GENE_NAME': 'PRKCZ', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P27448', 'TARGET_GENE_NAME': 'MARK3', 'TARGET_RES': 'T', 'TARGET_POS': '564', 'SOURCES': 'psp,signor', 'BELIEF': '1'}, {'ID': '1', 'CTRL_NS': 'UP', 'CTRL_ID': 'P41743', 'CTRL_GEN...(truncated) | 2 | {} | 2025-09-26 06:43:47 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2025-09-26 06:43:49 | 2025-09-26 06:43:49 | 0.80 | 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 | {} | 2025-09-26 06:43:49 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2025-09-26 06:43:50 | 2025-09-26 06:43:50 | 0.37 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2025-09-26 06:43:50 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2025-09-26 06:43:50 | 2025-09-26 06:43:55 | 5.21 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), Ramil...(truncated) | 18,879 | {} | 2025-09-26 06:43:50 | |
| ¶ | pypath.inputs.reaction.acsn_biopax | 2025-09-26 06:43:55 | 2025-09-26 06:43:56 | 0.36 | NoneType | None | 0 | {} | 2025-09-26 06:43:55 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2025-09-26 06:43:56 | 2025-09-26 06:43:56 | 0.11 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2025-09-26 06:43:56 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2025-09-26 06:43:56 | 2025-09-26 06:43:56 | 0.34 |
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__20250926-022201/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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 | 2025-09-26 06:43:56 | 2025-09-26 06:44:03 | 6.60 | dict | {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) | 178 | {} | 2025-09-26 06:43:56 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2025-09-26 06:44:03 | 2025-09-26 06:44:05 | 2.03 | NoneType | None | 0 | {} | 2025-09-26 06:44:03 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2025-09-26 06:44:05 | 2025-09-26 06:44:27 | 22.35 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2025-09-26 06:44:05 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2025-09-26 06:44:27 | 2025-09-26 06:50:59 | 392.38 | 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 | {'size': 1694} | 2025-09-26 06:44:27 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2025-09-26 06:51:21 | 2025-09-26 06:51:23 | 1.86 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/cache/9c...(truncated) | 2,825 | {'size': 1694} | 2025-09-26 06:51:21 | |
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2025-09-26 06:51:23 | 2025-09-26 06:51:24 | 0.82 | list | [{'parent': 'R-BTA-109581', 'child': 'R-BTA-109606'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-169911'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-5357769'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-75153'}, {'parent': 'R-BTA-109582', 'child': 'R-BTA-140877'}, {'parent': 'R-BTA-109582', 'child'...(truncated) | 23,259 | {} | 2025-09-26 06:51:23 | |
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2025-09-26 06:51:24 | 2025-09-26 06:51:30 | 6.08 |
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__20250926-022201/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 | 2025-09-26 06:51:30 | 2025-09-26 06:51:30 | 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__20250926-022201/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 | 2025-09-26 06:51:30 | 2025-09-26 06:51:31 | 1.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250926-022201/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 | 2025-09-26 06:51:31 | 2025-09-26 06:51:46 | 14.94 |
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__20250926-022201/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 | 2025-09-26 06:51:46 | 2025-09-26 06:51:56 | 10.18 | list | [{'Reaction identifier': 'RHEA:21252', 'Equation': '(S)-2-hydroxyglutarate + A = 2-oxoglutarate + AH2', 'ChEBI name': '(S)-2-hydroxyglutarate;A;2-oxoglutarate;AH2', 'ChEBI identifier': 'CHEBI:16782;CHEBI:13193;CHEBI:16810;CHEBI:17499', 'EC number': 'EC:1.1.99.2', 'Enzymes': '4258', 'Gene Ontology': ...(truncated) | 17,783 | {} | 2025-09-26 06:51:46 | |
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2025-09-26 06:51:56 | 2025-09-26 06:52:12 | 15.60 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human'), ScconnectAnnota...(truncated) | 3,285 | {} | 2025-09-26 06:51:56 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2025-09-26 06:52:12 | 2025-09-26 06:52:12 | 0.02 | set | {Complex: COMPLEX:P29459_P29460, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P01562, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:O15263, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P01215_P01225, Complex: COMPLEX:P...(truncated) | 17 | {} | 2025-09-26 06:52:12 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2025-09-26 06:52:12 | 2025-09-26 06:57:03 | 291.38 | list | [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) | 1,766 | {} | 2025-09-26 06:52:12 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2025-09-26 06:57:03 | 2025-09-26 06:57:03 | 0.12 | dict | {'CID100022318': {SiderDrug(name='gold', atc='M01CB01')}, 'CID100005576': {SiderDrug(name='trimethadione', atc='N03AC02')}, 'CID100004197': {SiderDrug(name='milrinone', atc='C01CE02')}, 'CID100003706': {SiderDrug(name='indinavir', atc='J05AE02')}, 'CID100055480': {SiderDrug(name='milnacipran', atc='...(truncated) | 1,430 | {} | 2025-09-26 06:57:03 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2025-09-26 06:57:03 | 2025-09-26 06:57:04 | 0.28 | list | [SiderSideeffectMeddra(cid='C1142317', meddra_id='10058386', side_effect_name='Bursal operation'), SiderSideeffectMeddra(cid='C0019061', meddra_id='10018932', side_effect_name='Haemolytic uraemic syndrome'), SiderSideeffectMeddra(cid='C0024894', meddra_id='10006262', side_effect_name='Breast inflamm...(truncated) | 20,307 | {} | 2025-09-26 06:57:03 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2025-09-26 06:57:04 | 2025-09-26 06:57:05 | 1.54 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0010200', umls_concept_in_meddra='C0010200', side_effect='Cough', frequency='10%'), SiderSideeffetFrequency(umls_concept_on_label='C0043096', umls_concept_in_meddra='C0043096', side_effect='Weight decreased', frequency='5%'), SiderSid...(truncated) | 968 | {} | 2025-09-26 06:57:04 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2025-09-26 06:57:05 | 2025-09-26 06:57:06 | 0.87 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0042029', umls_concept_in_meddra='C0042029', side_effect='Urinary tract infection'), SiderSideeffect(umls_concept_on_label='C0002871', umls_concept_in_meddra='C0002871', side_effect='Anaemia'), SiderSideeffect(umls_concept_on_label='C0151735'...(truncated) | 1,430 | {} | 2025-09-26 06:57:05 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2025-09-26 06:57:06 | 2025-09-26 06:57:08 | 1.30 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate immune pathways'), Signalin...(truncated) | 2 | {} | 2025-09-26 06:57:06 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2025-09-26 06:57:08 | 2025-09-26 06:57:08 | 0.39 | dict | {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 785 | {} | 2025-09-26 06:57:08 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2025-09-26 06:57:08 | 2025-09-26 06:57:09 | 0.95 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2025-09-26 06:57:08 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2025-09-26 06:57:09 | 2025-09-26 06:57:09 | 0.38 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pat...(truncated) | 839 | {} | 2025-09-26 06:57:09 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2025-09-26 06:57:09 | 2025-09-26 06:57:10 | 0.67 | dict | {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) | 4,890 | {} | 2025-09-26 06:57:09 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2025-09-26 06:57:10 | 2025-09-26 06:57:14 | 3.66 | list | [{'typ': 'phosphorylation', 'resnum': 282, 'instance': 'RGKEGPGTPTRSSVI', 'substrate': 'Q05516', 'start': 275, 'end': 289, 'kinase': 'P24941', 'resaa': 'T', 'motif': 'RGKEGPGTPTRSSVI', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'18246121'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) | 13,391 | {} | 2025-09-26 06:57:10 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2025-09-26 06:57:14 | 2025-09-26 06:57:14 | 0.55 | list | [SignorInteraction(source='P24941', target='Q05516', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates', mechanism='phosphorylation', ncbi_tax_id='9606', pubmeds='18246121', direct=True, ptm_type='phosphorylation', ptm_residue='Thr282', pt...(truncated) | 95,631 | {} | 2025-09-26 06:57:14 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2025-09-26 06:57:14 | 2025-09-26 06:57:34 | 19.57 | dict | {'Q13363': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P01116': {SignorPathway(pathway='LIF in PDAC'), SignorPathway(pathway='GPCR_CRC'), SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='SARS-CoV MAPK PERTURBATION'), SignorPathway(pathway='Thyroid cancer'), SignorPathw...(truncated) | 775 | {} | 2025-09-26 06:57:14 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2025-09-26 06:57:34 | 2025-09-26 06:57:34 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 91 | {} | 2025-09-26 06:57:34 | |
| ¶ | pypath.inputs.slc.slc_annotation | 2025-09-26 06:57:34 | 2025-09-26 06:57:34 | 0.28 | list | [SlcAnnotation(Entrez_ID=56172, Ensembl_ID='ENSG00000154122', HGNC_symbol='ANKH', Substrate_class='Orphan', Substrates='', Substrates_PMID='', Coupled_ions='Unknown', Coupled_ions_PMID='', Transport_mechanism='Unknown', Transport_system_PMID='', Subcellular_localization='Unknown', Subcellular_locali...(truncated) | 446 | {} | 2025-09-26 06:57:34 | |
| ¶ | pypath.inputs.slc.slc_chebi_mapping | 2025-09-26 06:57:34 | 2025-09-26 06:57:34 | 0.16 | list | [SlcChebiMapping(Substrate_name_annotation='17-beta-glucuronosyl estradiol', chebi_id='CHEBI:791', chebi_term='17beta-estradiol 17-glucosiduronic acid', synonym='3-hydroxyestra-1,3,5(10)-trien-17beta-yl beta-D-glucopyranosiduronic acid', description='A steroid glucosiduronic acid that consists of 17...(truncated) | 382 | {} | 2025-09-26 06:57:34 | |
| ¶ | pypath.inputs.slc.slc_interactions | 2025-09-26 06:57:34 | 2025-09-26 06:57:35 | 0.10 | list | [SlcInteraction(transporter=SlcTransporter(uniprot='Q9Y5Y0', genesymbol='FLVCR1', entrez=28982, ensg='ENSG00000162769'), substrate=SlcSubstrate(slc_name='Heme', chebi='CHEBI:30413', label='heme', synonyms=['heme', 'hemes']), role='substrate', pmids='15369674', localization='Plasma membrane', transpo...(truncated) | 1,288 | {} | 2025-09-26 06:57:34 | |
| ¶ | pypath.inputs.slc.slc_localization_annotations | 2025-09-26 06:57:35 | 2025-09-26 06:57:35 | 0.06 | dict | {'Q9HCJ1': {SlcLocalization(localization='Unknown', pmids=None)}, 'Q13286': {SlcLocalization(localization='Endosome; Lysosome', pmids='15471887;22261744')}, 'Q96SL1': {SlcLocalization(localization='Lysosome', pmids='21692750')}, 'Q9Y5Y0': {SlcLocalization(localization='Plasma membrane', pmids='18815...(truncated) | 447 | {} | 2025-09-26 06:57:35 | |
| ¶ | pypath.inputs.slc.slc_substrate_ontology | 2025-09-26 06:57:35 | 2025-09-26 06:57:36 | 1.23 | list | [SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='heme', ChEBI_ID='CHEBI:30413', ChEBI_subontology='chemical entity'), SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='cyclic tetrapyrrole', ChEB...(truncated) | 24,810 | {} | 2025-09-26 06:57:35 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2025-09-26 06:57:36 | 2025-09-26 06:57:45 | 9.16 | dict | {'COMPLEX:P67775_Q15172_Q15257': Complex PP2A: COMPLEX:P67775_Q15172_Q15257, 'COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478': Complex AMPK: COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478, 'COMPLEX:P67870_P68400': Complex CK2: COMPLEX:P67870_P68400, 'COMPLEX:P05412_P15336': Compl...(truncated) | 154 | {} | 2025-09-26 06:57:36 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2025-09-26 06:57:45 | 2025-09-26 06:57:47 | 2.51 | list | [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) | 8,903 | {} | 2025-09-26 06:57:45 | |
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2025-09-26 06:57:48 | 2025-09-26 06:58:53 | 65.57 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2025-09-26 06:57:48 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2025-09-26 06:58:53 | 2025-09-26 07:00:12 | 78.79 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2025-09-26 06:58:53 | |
| ¶ | pypath.inputs.string.string_effects | 2025-09-26 07:00:12 | 2025-09-26 07:00:20 | 7.81 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2025-09-26 07:00:12 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2025-09-26 07:00:21 | 2025-09-26 07:00:54 | 33.25 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {} | 2025-09-26 07:00:21 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2025-09-26 07:00:54 | 2025-09-26 07:00:55 | 1.16 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2025-09-26 07:00:54 | |
| ¶ | pypath.inputs.string.string_species | 2025-09-26 07:00:55 | 2025-09-26 07:00:56 | 0.17 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2025-09-26 07:00:55 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2025-09-26 07:00:56 | 2025-09-26 07:00:58 | 2.44 | dict | {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC', 'SLC12'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC', 'SLC5'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'TMEM30', 'Unknown_function'}), '...(truncated) | 2,844 | {} | 2025-09-26 07:00:56 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2025-09-26 07:00:58 | 2025-09-26 07:01:07 | 8.84 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2025-09-26 07:00:58 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2025-09-26 07:01:07 | 2025-09-26 07:01:07 | 0.48 | 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 | {} | 2025-09-26 07:01:07 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2025-09-26 07:01:07 | 2025-09-26 07:01:07 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2025-09-26 07:01:07 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2025-09-26 07:01:07 | 2025-09-26 07:01:07 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2025-09-26 07:01:07 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2025-09-26 07:01:07 | 2025-09-26 07:01:12 | 4.95 |
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__20250926-022201/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 | 2025-09-26 07:01:12 | 2025-09-26 07:01:12 | 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) | 24,298 | {} | 2025-09-26 07:01:12 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2025-09-26 07:01:12 | 2025-09-26 07:01:12 | 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) | 2,118 | {} | 2025-09-26 07:01:12 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2025-09-26 07:01:12 | 2025-09-26 07:01:13 | 0.21 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,871 | {} | 2025-09-26 07:01:12 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2025-09-26 07:01:13 | 2025-09-26 07:01:16 | 3.82 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2025-09-26 07:01:13 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2025-09-26 07:01:17 | 2025-09-26 07:01:37 | 20.85 | set | {ThreedcomplexContact(pdb='1x81_1', uniprot_1='Q04631', uniprot_2='Q02293', chain_1='A', chain_2='B', n_residues=63.0, length_1=315, length_2=397, domain_s1=('48439',), domain_p1=('PF01239.17', 'PF01239.17', 'PF01239.17', 'PF01239.17', 'PF01239.17'), domain_s2=('48239',), domain_p2=('PF13249.1', 'PF...(truncated) | 259,376 | {} | 2025-09-26 07:01:17 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2025-09-26 07:01:38 | 2025-09-26 07:04:47 | 188.31 | list | [<pypath.internals.intera.DomainDomain object at 0x7f272133f890>, <pypath.internals.intera.DomainDomain object at 0x7f272133f690>, <pypath.internals.intera.DomainDomain object at 0x7f272133f3d0>, <pypath.internals.intera.DomainDomain object at 0x7f272133f050>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,086 | {} | 2025-09-26 07:01:38 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2025-09-26 07:04:47 | 2025-09-26 07:04:56 | 9.13 | dict | {'1x81_1': {('Q02293', 'Q04631'): 63.0}, '1b9l_1': {('P0AC19', 'P0AC19'): 2.0}, '4no8_1': {('P32379', 'P40303'): 27.0, ('P23639', 'P25451'): 10.5, ('P22141', 'P22141'): 16.0, ('P30657', 'P38624'): 11.5, ('P21242', 'P21243'): 28.0, ('P23724', 'P40302'): 5.5, ('P21242', 'P23638'): 2.0, ('P21243', 'P23...(truncated) | 80,995 | {} | 2025-09-26 07:04:47 | |
| ¶ | pypath.inputs.threedid.get_3did | 2025-09-26 07:04:57 | 2025-09-26 08:11:48 | 4,011.34 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7f2753152dd0>, <pypath.internals.intera.DomainDomain object at 0x7f274d3c6a10>, <pypath.internals.intera.DomainDomain object at 0x7f275375c990>, <pypath.internals.intera.DomainDomain object at 0x7f274f068c90>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2025-09-26 07:04:57 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2025-09-26 08:11:48 | 2025-09-26 08:27:44 | 956.10 | dict | {} | 0 | {} | 2025-09-26 08:11:48 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2025-09-26 08:27:44 | 2025-09-26 08:28:26 | 42.08 | dict | {'P18825': {TopdbAnnotation(membrane='Cell membrane', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell membrane', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Ex...(truncated) | 2,027 | {} | 2025-09-26 08:27:44 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2025-09-26 08:28:26 | 2025-09-26 08:28:26 | 0.05 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2025-09-26 08:28:26 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2025-09-26 08:28:26 | 2025-09-26 08:28:26 | 0.00 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2025-09-26 08:28:26 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2025-09-26 08:28:26 | 2025-09-26 08:28:26 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;11290752;12601176', 'Fluorescence probe labeling;Calcium measurement;Patch clamp;Fusio...(truncated) | 359 | {} | 2025-09-26 08:28:26 | |
| ¶ | pypath.inputs.trip.trip_process | 2025-09-26 08:28:26 | 2025-09-26 08:28:26 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Rat vascular smooth muscle cell', 'Rat aortic vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2025-09-26 08:28:26 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2025-09-26 08:28:26 | 2025-09-26 08:28:30 | 3.31 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-09-26 08:28:26 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2025-09-26 08:28:30 | 2025-09-26 08:28:30 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-09-26 08:28:30 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2025-09-26 08:28:30 | 2025-09-26 08:28:33 | 2.97 | list | [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) | 7,057 | {} | 2025-09-26 08:28:30 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2025-09-26 08:28:33 | 2025-09-26 08:32:11 | 217.88 | list | [TwosidesInteraction(drug1_rxnorm='10355', drug1='Temazepam', drug2_rxnorm='136411', drug2='sildenafil', condition_meddra='10003239', condition='Arthralgia', prr='2.91667', pee_error='0.421275', mean_reporting_frequency='0.0448718'), TwosidesInteraction(drug1_rxnorm='1808', drug1='Bumetanide', drug2...(truncated) | 42,920,391 | {} | 2025-09-26 08:28:33 | |
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2025-09-26 08:32:11 | 2025-09-26 08:32:11 | 0.01 | list | [UnichemSource(number=1, label='ChEMBL', name='chembl', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='2024-12-11'), UnichemSource(number=2, label='DrugBank', name='drugbank', description='A database that com...(truncated) | 41 | {} | 2025-09-26 08:32:11 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2025-09-26 08:32:11 | 2025-09-26 08:32:11 | 0.00 | dict | {1: 'ChEMBL', 2: 'DrugBank', 3: 'PDBe', 4: 'Guide to Pharmacology', 5: 'PubChem: Drugs of the Future ', 6: 'KEGG Ligand', 7: 'ChEBI', 8: 'NIH Clinical Collection', 9: 'ZINC', 10: 'eMolecules', 12: 'Atlas', 14: 'FDA SRS', 15: 'SureChEMBL', 17: 'PharmGKB', 18: 'Human Metabolome Database', 20: 'Selleck...(truncated) | 41 | {} | 2025-09-26 08:32:11 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2025-09-26 08:32:11 | 2025-09-26 08:32:11 | 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) | 72,358 | {} | 2025-09-26 08:32:11 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2025-09-26 08:32:11 | 2025-09-26 08:32:22 | 10.86 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0AV02': {UniprotFamily(family='SLC12A transporter', subfamily=None)}, 'A0AV96': {UniprotFam...(truncated) | 14,485 | {} | 2025-09-26 08:32:11 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2025-09-26 08:32:22 | 2025-09-26 08:32:33 | 10.51 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Heme'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Reference proteome'), UniprotKeywor...(truncated) | 20,420 | {} | 2025-09-26 08:32:22 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2025-09-26 08:32:33 | 2025-09-26 08:32:33 | 0.08 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,837 | {} | 2025-09-26 08:32:33 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2025-09-26 08:32:33 | 2025-09-26 08:32:34 | 1.25 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'H8ZM71': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies grandis', 'Pinus grandis', '...(truncated) | 558,858 | {} | 2025-09-26 08:32:33 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2025-09-26 08:32:34 | 2025-09-26 08:32:46 | 11.47 | 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 | {} | 2025-09-26 08:32:34 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2025-09-26 08:32:46 | 2025-09-26 08:33:32 | 45.75 | dict | {'A0A087X1C5': {UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Cytoplasmic',...(truncated) | 5,244 | {} | 2025-09-26 08:32:46 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2025-09-26 08:33:32 | 2025-09-26 08:33:32 | 0.00 | set | {'P02747', 'O15119', 'Q8N0S2', 'Q9C019', 'Q16763', 'P53778', 'Q9Y2E4', 'O75052', 'Q9H8S5', 'Q7Z5G4', 'Q8WVM8', 'Q6ZUF6', 'Q8IYF3', 'Q9H8H0', 'Q53RT3', 'P21579', 'O00268', 'Q15018', 'Q6T423', 'Q9Y5U9', 'Q8NFP7', 'Q5TGY1', 'P10827', 'J3KSC0', 'P15391', 'Q9Y561', 'Q6EMB2', 'Q8TBK2', 'Q8IVG9', 'Q8WV19',...(truncated) | 20,420 | {} | 2025-09-26 08:33:32 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2025-09-26 08:33:32 | 2025-09-26 08:34:01 | 29.05 | set | {'A0A8V8TLS2', 'C8CHA8', 'A0A8J8YUH5', 'A0A087WYT3', 'Q59F56', 'G3V3X1', 'A6H900', 'A0A6S7YTP9', 'E9KY01', 'A0A126LAZ9', 'A0A7S5BYM5', 'A0A890VUG8', 'E9PC71', 'A0A7S5C0W9', 'D4HPJ2', 'X6RL83', 'B9A6L1', 'H7C327', 'A0A143FYP3', 'B3GQE5', 'A0A5C2GQ18', 'A8WBZ2', 'H7C570', 'J3QRG4', 'A0A7P0TAF3', 'G3V3...(truncated) | 184,785 | {} | 2025-09-26 08:33:32 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2025-09-26 08:34:01 | 2025-09-26 08:34:01 | 0.00 | set | {'A0A8V8TLS2', 'C8CHA8', 'O15119', 'A0A8J8YUH5', 'A0A087WYT3', 'Q59F56', 'G3V3X1', 'A6H900', 'A0A6S7YTP9', 'E9KY01', 'A0A126LAZ9', 'A0A7S5BYM5', 'A0A890VUG8', 'E9PC71', 'A0A7S5C0W9', 'D4HPJ2', 'X6RL83', 'B9A6L1', 'H7C327', 'A0A143FYP3', 'B3GQE5', 'A0A5C2GQ18', 'A8WBZ2', 'H7C570', 'J3QRG4', 'A0A7P0TA...(truncated) | 205,205 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2025-09-26 08:34:01 | 2025-09-26 08:34:01 | 0.00 | set | {'A0A8V8TLS2', 'C8CHA8', 'O15119', 'A0A8J8YUH5', 'A0A087WYT3', 'Q59F56', 'G3V3X1', 'A6H900', 'A0A6S7YTP9', 'E9KY01', 'A0A126LAZ9', 'A0A7S5BYM5', 'A0A890VUG8', 'E9PC71', 'A0A7S5C0W9', 'D4HPJ2', 'X6RL83', 'B9A6L1', 'H7C327', 'A0A143FYP3', 'B3GQE5', 'A0A5C2GQ18', 'A8WBZ2', 'H7C570', 'J3QRG4', 'A0A7P0TA...(truncated) | 205,205 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2025-09-26 08:34:01 | 2025-09-26 08:34:01 | 0.05 | NoneType | None | 0 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2025-09-26 08:34:01 | 2025-09-26 08:34:01 | 0.10 | set | {('UniProtKB-Swiss-Prot', 'ChiTaRS'), ('Araport', 'UniProtKB-Swiss-Prot'), ('Gene_Name', 'UniProtKB'), ('UniProtKB-Swiss-Prot', 'WormBase_Protein'), ('UniProtKB', 'Reactome'), ('WormBase_Transcript', 'UniProtKB-Swiss-Prot'), ('PeroxiBase', 'UniProtKB-Swiss-Prot'), ('Ensembl_Transcript', 'UniProtKB')...(truncated) | 481 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.wang.cui_interactions | 2025-09-26 08:34:01 | 2025-09-26 08:34:01 | 0.29 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2025-09-26 08:34:01 | 2025-09-26 08:34:02 | 0.42 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2025-09-26 08:34:01 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2025-09-26 08:34:02 | 2025-09-26 08:34:06 | 4.16 | dict | {'NA': {WangAnnotation(function='Ribosome', location='Ribosomes'), WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='Adapter', location='Ribosomes'), WangAnnotation(function='Adapter', location='Cytosol'), WangAnnotation(function='Ligand', location='Extracellular'), Wan...(truncated) | 1,547 | {} | 2025-09-26 08:34:02 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2025-09-26 08:34:06 | 2025-09-26 08:34:06 | 0.14 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2025-09-26 08:34:06 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2025-09-26 08:34:06 | 2025-09-26 08:34:06 | 0.28 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {} | 2025-09-26 08:34:06 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2025-09-26 08:34:06 | 2025-09-26 08:34:07 | 0.10 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {} | 2025-09-26 08:34:06 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2025-09-26 08:34:07 | 2025-09-26 08:34:07 | 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 | {} | 2025-09-26 08:34:07 |
The OmniPath Team • Saez Lab • 2025-09-26