Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2026-03-22 20:24:25 and 2026-03-23 03:45:55; pypath version: 0.16.31 (from git, installed by poetry; e46d0a7 )
| Modules collected: | 200 |
|---|---|
| Modules failed to import: | 2 |
| Functions collected: | 548 |
| Functions run without error: | 385 |
| Functions returned empty value: | 15 |
| Functions skipped due to lack of arguments: | 128 |
| Functions run with error: | 35 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2026-03-22 20:24:29 | 2026-03-22 20:24:30 | 0.71 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2026-03-22 20:24:29 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2026-03-22 20:24:30 | 2026-03-22 20:24:30 | 0.47 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2026-03-22 20:24:30 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2026-03-22 20:24:30 | 2026-03-22 20:24:31 | 0.44 |
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__20260322-202402/pypath_git/pypath/inputs/adhesome.py", line 71, in adhesome_annotations
data = csv.DictReader(c.result, delimiter = ',')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{} | 2026-03-19 20:24:30 | |||
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2026-03-22 20:24:31 | 2026-03-22 20:24:31 | 0.38 |
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__20260322-202402/pypath_git/pypath/inputs/adhesome.py", line 40, in adhesome_interactions
data = csv.DictReader(c.result, delimiter = ',')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{} | 2026-03-19 20:26:36 | |||
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2026-03-22 20:24:31 | 2026-03-22 20:24:52 | 20.63 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {} | 2026-03-22 20:24:31 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2026-03-22 20:24:52 | 2026-03-22 20:28:14 | 202.36 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2026-03-22 20:24:52 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2026-03-22 20:28:14 | 2026-03-22 20:31:49 | 215.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/common.py", line 123, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-WxRGElZO-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-WxRGElZO-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-WxRGElZO-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__20260322-202402/pypath_git/pypath/inputs/adrecs.py", line 92, in adrecs_drug_identifiers
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/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__20260322-202402/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
|
{} | 2026-03-20 20:28:58 | |||
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2026-03-22 20:31:49 | 2026-03-22 20:31:50 | 0.90 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='13.10.06.013', badd='BADD_A05039'), parent=AdrecsAdr(adr_class='13.10.06', badd='BADD_A04291')), AdrecsChildParent(child=AdrecsAdr(adr_class='10.02.01.010', badd='BADD_A05078'), parent=AdrecsAdr(adr_class='10.02.01', badd='BADD_A02813')), AdrecsChildPare...(truncated) | 13,828 | {} | 2026-03-22 20:31:49 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2026-03-22 20:31:50 | 2026-03-22 20:32:39 | 49.29 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,243 | {} | 2026-03-22 20:31:50 | |
| ¶ | pypath.inputs.alzpathway.alzpathway_interactions | 2026-03-22 20:32:39 | 2026-03-22 20:32:39 | 0.11 | list | [AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='O00213', genesymbol_a='APP', genesymbol_b='APBB1', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='Q8N8S7', genesymbol_a='APP', genesymbol_b='ENAH', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05...(truncated) | 119 | {} | 2026-03-22 20:32:39 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2026-03-22 20:32:39 | 2026-03-22 20:34:58 | 138.94 | 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) | 935 | {} | 2026-03-22 20:32:39 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2026-03-22 20:34:58 | 2026-03-22 20:34:59 | 0.33 | list | [Baccin2019Interaction(ligand='Q15848', receptor='Q96A54', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Baccin2019', 'Ramilowski2015'}, references={'12802337'}), Baccin2019Interaction(ligand='Q15848', receptor='Q86V24', correct='Correct', ligand_location='secre...(truncated) | 1,463 | {} | 2026-03-22 20:34:58 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2026-03-22 20:34:59 | 2026-03-22 20:34:59 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2026-03-22 20:34:59 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2026-03-22 20:34:59 | 2026-03-22 20:35:30 | 31.06 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2026-03-22 20:34:59 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2026-03-22 20:35:30 | 2026-03-22 20:36:15 | 44.28 | 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) | 8,825 | {} | 2026-03-22 20:35:30 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2026-03-22 20:36:15 | 2026-03-22 20:36:16 | 1.16 | list | [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) | 7,605 | {} | 2026-03-22 20:36:15 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2026-03-22 20:36:16 | 2026-03-22 20:36:58 | 42.07 | 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': 303538} | 2026-03-22 20:36:16 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2026-03-22 20:36:58 | 2026-03-22 20:36:59 | 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 | {} | 2026-03-22 20:36:58 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2026-03-22 20:36:59 | 2026-03-22 20:36:59 | 0.14 | list | [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) | 1,788 | {} | 2026-03-22 20:36:59 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2026-03-22 20:36:59 | 2026-03-22 20:37:01 | 1.80 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2026-03-22 20:36:59 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2026-03-22 20:37:01 | 2026-03-22 20:37:10 | 9.68 | 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) | 221 | {} | 2026-03-22 20:37:01 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2026-03-22 20:37:10 | 2026-03-22 20:37:10 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 349 | {} | 2026-03-22 20:37:10 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2026-03-22 20:37:10 | 2026-03-22 20:37:19 | 8.24 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P11802', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 5,075 | {} | 2026-03-22 20:37:10 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2026-03-22 20:37:19 | 2026-03-22 20:37:21 | 2.16 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {} | 2026-03-22 20:37:19 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2026-03-22 20:37:21 | 2026-03-22 20:37:32 | 11.22 | dict | {'Q9Y6Y9': {CellcallAnnotation(role='ligand')}, 'O00206': {CellcallAnnotation(role='receptor')}, 'O43555': {CellcallAnnotation(role='ligand')}, 'P30968': {CellcallAnnotation(role='receptor')}, 'P01303': {CellcallAnnotation(role='ligand')}, 'P25929': {CellcallAnnotation(role='receptor')}, 'P15692': {...(truncated) | 460 | {} | 2026-03-22 20:37:21 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2026-03-22 20:37:32 | 2026-03-22 20:37:32 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2026-03-22 20:37:32 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2026-03-22 20:37:32 | 2026-03-22 20:37:34 | 1.56 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2026-03-22 20:37:32 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2026-03-22 20:37:34 | 2026-03-22 20:37:34 | 0.11 | list | [CellcallInteraction(ligand_uniprot='Q9Y6Y9', receptor_uniprot='O00206', core=True), CellcallInteraction(ligand_uniprot='O43555', receptor_uniprot='P30968', core=True), CellcallInteraction(ligand_uniprot='P01303', receptor_uniprot='P25929', core=True), CellcallInteraction(ligand_uniprot='P15692', re...(truncated) | 797 | {} | 2026-03-22 20:37:34 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2026-03-22 20:37:34 | 2026-03-22 20:37:34 | 0.67 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinteractio...(truncated) | 3,426 | {} | 2026-03-22 20:37:34 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2026-03-22 20:37:34 | 2026-03-22 20:37:44 | 9.68 | 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='antagonist', pathway='ACTIVIN', cat...(truncated) | 1,530 | {} | 2026-03-22 20:37:34 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2026-03-22 20:37:44 | 2026-03-22 20:37:51 | 6.84 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O60565', 'P41271', 'O00292', 'O75610', 'Q9H2X0', 'P12645', 'Q13253', 'Q9H772'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 32 | {} | 2026-03-22 20:37:44 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2026-03-22 20:37:51 | 2026-03-22 20:37:58 | 7.46 | dict | {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) | 330 | {} | 2026-03-22 20:37:51 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2026-03-22 20:37:58 | 2026-03-22 20:38:05 | 6.92 | dict | {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) | 4 | {} | 2026-03-22 20:37:58 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2026-03-22 20:38:05 | 2026-03-22 20:38:13 | 7.24 | list | [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) | 12,436 | {} | 2026-03-22 20:38:05 | |
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.45 | dict | {'Q14031': {CellinkerAnnotation(role='ligand', location='ECM', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='ECM', type='Secreted protein to ECM interaction')}, 'Q16832': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnot...(truncated) | 1,925 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.05 | dict | {Complex: COMPLEX:P78357_Q12860: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, Complex: COMPLEX:O60353_O75581: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:O75581_Q9ULW2: {Cellinker...(truncated) | 134 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.04 | set | {CellinkerInteraction(ligand='Q14031', receptor='Q16832', ligand_location='ECM', receptor_location='Membrane', resources=None, pmids='9659900', type='ECM-receptor interaction'), CellinkerInteraction(ligand='P20827', receptor='P54756', ligand_location='Membrane', receptor_location='Membrane', resourc...(truncated) | 3,816 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.05 | dict | {'Q14031': {CellinkerAnnotation(role='ligand', location='ECM', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='ECM', type='Secreted protein to ECM interaction')}, 'Q16832': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnot...(truncated) | 1,791 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.13 | set | {CellinkerInteraction(ligand='5282411', receptor='P35408', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='10952683', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='6305', receptor='Q6DWJ6', ligand_location=None, receptor_location='Membrane', res...(truncated) | 314 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2026-03-22 20:38:13 | 2026-03-22 20:38:13 | 0.00 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2026-03-22 20:38:13 | 2026-03-22 20:38:14 | 0.18 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 358 | {} | 2026-03-22 20:38:13 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2026-03-22 20:38:14 | 2026-03-22 20:38:14 | 0.02 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {} | 2026-03-22 20:38:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2026-03-22 20:38:14 | 2026-03-22 20:38:14 | 0.87 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {} | 2026-03-22 20:38:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2026-03-22 20:38:15 | 2026-03-22 20:38:15 | 0.03 | tuple | ({Complex Cholesterol_byCEL: COMPLEX:P19835, 'P02751', 'P07949', 'Q8IVG9', 'Q9Y345', Complex fibrinogen: COMPLEX:P02671_P02675_P02679, Complex integrin_aVb8_complex: COMPLEX:P06756_P26012, 'Q96NY8', 'O95399', 'Q29983', 'Q9Y264', Complex ProstaglandinF2a_byPRXL2B: COMPLEX:Q8TBF2, 'P01298', 'O96014', ...(truncated) | 2 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2026-03-22 20:38:15 | 2026-03-22 20:38:15 | 0.01 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,365 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2026-03-22 20:38:15 | 2026-03-22 20:38:15 | 0.61 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,599 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2026-03-22 20:38:15 | 2026-03-22 20:38:15 | 0.15 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2026-03-22 20:38:15 | 2026-03-22 20:38:15 | 0.16 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2026-03-22 20:38:15 | 2026-03-22 20:38:16 | 0.23 | 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='Memory B cells', cell_ontology='CL:00...(truncated) | 466 | {} | 2026-03-22 20:38:15 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2026-03-22 20:38:16 | 2026-03-22 20:38:56 | 40.07 | list | [Citation(allele='250108', variation_id='262591', nsv='', citation_source='PubMed', citation_id='24033266'), Citation(allele='1108035', variation_id='1106239', nsv='', citation_source='PubMed', citation_id='25741868'), Citation(allele='1596538', variation_id='1630016', nsv='', citation_source='PubMe...(truncated) | 4,505,502 | {} | 2026-03-22 20:38:16 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2026-03-22 20:39:02 | 2026-03-22 20:47:42 | 519.64 | list | [Variant(allele='1500889', type='single nucleotide variant', variant='NM_005876.5(SPEG):c.8379G>T (p.Arg2793Ser)', entrez='10290', genesymbol='SPEG', clinical_significance='Uncertain significance', review_status='criteria provided, single submitter', rs='750076433', phenotype_ids=('MedGen:C3661900',...(truncated) | 8,907,105 | {} | 2026-03-22 20:39:02 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2026-03-22 23:03:02 | 2026-03-22 23:03:19 | 17.22 | list | [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) | 64,990 | {} | 2026-03-22 23:03:02 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2026-03-22 23:03:19 | 2026-03-22 23:03:19 | 0.08 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2026-03-22 23:03:19 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2026-03-22 23:03:19 | 2026-03-22 23:03:19 | 0.10 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2026-03-22 23:03:19 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2026-03-22 23:03:19 | 2026-03-22 23:03:20 | 0.89 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,695 | {} | 2026-03-22 23:03:19 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2026-03-22 23:03:20 | 2026-03-22 23:03:20 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2026-03-22 23:03:20 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2026-03-22 23:03:20 | 2026-03-22 23:05:23 | 122.43 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) | 2,343 | {} | 2026-03-22 23:03:20 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2026-03-22 23:05:23 | 2026-03-22 23:05:36 | 13.30 | list | [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) | 587,911 | {} | 2026-03-22 23:05:23 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2026-03-22 23:05:36 | 2026-03-22 23:05:49 | 13.55 | dict | {'A0A0R4J2E4': {ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)}, 'A0A024R0Y4': {ComppiLocation(location='nucleus', score=0.8)}, 'A0A087WWR4': {ComppiLocation(location='nucleus', score=0.8)}, 'Q08379': {ComppiLocation(location='cytosol', score=0.958), Com...(truncated) | 22,789 | {} | 2026-03-22 23:05:36 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2026-03-22 23:05:49 | 2026-03-22 23:05:50 | 0.47 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,429 | {} | 2026-03-22 23:05:49 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2026-03-22 23:05:50 | 2026-03-22 23:05:50 | 0.02 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2026-03-22 23:05:50 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2026-03-22 23:05:50 | 2026-03-22 23:05:51 | 0.60 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2026-03-22 23:05:50 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2026-03-22 23:05:51 | 2026-03-22 23:05:51 | 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 | {} | 2026-03-22 23:05:51 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_raw | 2026-03-22 23:05:51 | 2026-03-22 23:05:51 | 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 | {} | 2026-03-22 23:05:51 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2026-03-22 23:05:51 | 2026-03-22 23:06:01 | 10.44 | dict | {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) | 1,071 | {'size': 1} | 2026-03-22 23:05:51 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2026-03-22 23:06:01 | 2026-03-22 23:06:01 | 0.05 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='RAF/MEK/ERK signaling pathway', cancer='Glioma', pathway_category='MAPK signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='enhance sorafenib-induced growth inhibition and apoptosis'), CpadPathwayCancer(pathway='p53/p21 signaling pathw...(truncated) | 2 | {} | 2026-03-22 23:06:01 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2026-03-22 23:06:01 | 2026-03-22 23:06:01 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2026-03-22 23:06:01 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2026-03-22 23:06:01 | 2026-03-22 23:06:01 | 0.08 |
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__20260322-202402/pypath_git/pypath/inputs/cpdb.py", line 40, in cpdb_interactions
for x in data.split('\n')
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2026-03-17 23:12:32 | |||
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2026-03-22 23:06:01 | 2026-03-22 23:06:01 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/cpdb.py", line 75, in cpdb_interactions_ltp
return cpdb_interactions(
^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/cpdb.py", line 40, in cpdb_interactions
for x in data.split('\n')
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2026-03-17 23:12:43 | |||
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2026-03-22 23:06:01 | 2026-03-22 23:06:02 | 0.06 |
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__20260322-202402/pypath_git/pypath/inputs/cspa.py", line 56, in cspa_annotations
xlsname = c.fname
^^^^^^^
AttributeError: 'Curl' object has no attribute 'fname'
|
{} | 2026-03-17 23:12:46 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2026-03-22 23:06:02 | 2026-03-22 23:06:02 | 0.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/cspa.py", line 130, in cspa_cell_type_annotations
cell_type_data = cspa_cell_types(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/cspa.py", line 90, in cspa_cell_types
xlsname = c.fname
^^^^^^^
AttributeError: 'Curl' object has no attribute 'fname'
|
{} | 2026-03-17 23:12:47 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2026-03-22 23:06:02 | 2026-03-22 23:06:02 | 0.04 |
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__20260322-202402/pypath_git/pypath/inputs/cspa.py", line 90, in cspa_cell_types
xlsname = c.fname
^^^^^^^
AttributeError: 'Curl' object has no attribute 'fname'
|
{} | 2026-03-17 23:12:47 | |||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2026-03-22 23:06:02 | 2026-03-22 23:06:03 | 1.37 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P08476', score=-0.1354946121188316, cytokine_genesymbol='Activin A', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P50591', score=-0.0381345829173036, cytokine_genesymbol='TRAIL', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P01133', sco...(truncated) | 4,887 | {} | 2026-03-22 23:06:02 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2026-03-22 23:06:03 | 2026-03-22 23:06:03 | 0.04 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2026-03-22 23:06:03 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2026-03-22 23:06:03 | 2026-03-22 23:06:06 | 2.50 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2026-03-22 23:06:03 | |
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2026-03-22 23:06:06 | 2026-03-22 23:06:08 | 1.28 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2026-03-22 23:06:06 | |
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2026-03-22 23:06:08 | 2026-03-22 23:06:46 | 38.70 | list | [DdinterInteraction(drug1_id='DDInter1533', drug1_name='Promethazine', drug2_id='DDInter954', drug2_name='Iodide I-131', level='Moderate'), DdinterInteraction(drug1_id='DDInter458', drug1_name='Cyclosporine', drug2_id='DDInter1666', drug2_name='Sildenafil', level='Moderate'), DdinterInteraction(drug...(truncated) | 160,235 | {} | 2026-03-22 23:06:08 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2026-03-22 23:06:47 | 2026-03-22 23:49:39 | 2,572.08 | list | [DdinterIdentifiers(ddinter='DDInter1620', drugbank='DB00296', chembl='CHEMBL1077896', pubchem='46504712'), DdinterIdentifiers(ddinter='DDInter1808', drugbank='DB01133', chembl='CHEMBL1350', pubchem='46505302'), DdinterIdentifiers(ddinter='DDInter410', drugbank='DB01242', chembl='CHEMBL415', pubchem...(truncated) | 1,939 | {} | 2026-03-22 23:06:47 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2026-03-22 23:49:39 | 2026-03-22 23:49:39 | 0.44 | int | 1939 | 0 | {} | 2026-03-22 23:49:39 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2026-03-22 23:49:39 | 2026-03-22 23:49:39 | 0.15 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2026-03-22 23:49:39 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2026-03-22 23:49:39 | 2026-03-22 23:49:39 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/depod.py", line 97, in depod_enzyme_substrate
data = [x.split('\t') for x in data.split('\n')]
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2026-03-12 00:00:44 | |||
| ¶ | pypath.inputs.depod.depod_interactions | 2026-03-22 23:49:39 | 2026-03-22 23:49:39 | 0.02 |
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__20260322-202402/pypath_git/pypath/inputs/depod.py", line 39, in depod_interactions
for l in data:
TypeError: 'NoneType' object is not iterable
|
{} | 2026-03-12 00:00:45 | |||
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2026-03-22 23:49:39 | 2026-03-22 23:49:45 | 5.64 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='dGene'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnotation(category='DRUGGABLE GENOME', source='HingoraniCasas'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), Dgi...(truncated) | 9,972 | {} | 2026-03-22 23:49:39 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2026-03-22 23:49:45 | 2026-03-22 23:49:52 | 7.31 | list | [DgidbInteraction(genesymbol='FLT3', gene_concept_id='hgnc:3765', resource='JAX-CKB', type='NULL', drug_name='REBASTINIB', drug_concept_id='ncit:C152162', score='0.108040476', approved='FALSE', anti_neoplastic='TRUE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='PDCD1', gene_concept_id='hgnc...(truncated) | 84,175 | {} | 2026-03-22 23:49:45 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2026-03-22 23:49:52 | 2026-03-22 23:49:53 | 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 | {} | 2026-03-22 23:49:52 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2026-03-22 23:49:53 | 2026-03-22 23:49:53 | 0.36 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:11714', disease='Gestational diabetes', resource='TIGA', source_score=36, confidence=1.004), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resourc...(truncated) | 38,152 | {} | 2026-03-22 23:49:53 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2026-03-22 23:49:53 | 2026-03-22 23:49:55 | 1.93 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:0014667', disease='Disease of metabolism', resource='TIGA', source_score=36, confidence=1.004), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:11714', disease='Gestational diabetes...(truncated) | 413,837 | {} | 2026-03-22 23:49:53 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2026-03-22 23:49:55 | 2026-03-22 23:49:55 | 0.18 | list | [DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Craniosynostosis', resource='UniProtKB-KW', evidence_type='CURATED', confidence=4), DiseasesInteraction(gene_id='ENSP00000003084', genesymbol='CFTR', disease_id='DOID:0111862', disease='Congenital ...(truncated) | 7,806 | {} | 2026-03-22 23:49:55 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2026-03-22 23:49:55 | 2026-03-22 23:49:56 | 0.57 | list | [DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:0080001', disease='Bone disease', resource='UniProtKB-KW', evidence_type='CURATED', confidence=4), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:0080006', disease='Bone deve...(truncated) | 98,568 | {} | 2026-03-22 23:49:55 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2026-03-22 23:49:56 | 2026-03-22 23:49:57 | 1.51 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.244, confidence=3.622, 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) | 288,565 | {} | 2026-03-22 23:49:56 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2026-03-22 23:49:57 | 2026-03-22 23:50:50 | 52.23 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.244, confidence=3.622, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol...(truncated) | 11,424,467 | {} | 2026-03-22 23:49:57 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2026-03-22 23:50:50 | 2026-03-22 23:50:52 | 2.70 | list | [<pypath.internals.intera.DomainDomain object at 0x7f5a454608d0>, <pypath.internals.intera.DomainDomain object at 0x7f5a15c5c0d0>, <pypath.internals.intera.DomainDomain object at 0x7f5a15c5c810>, <pypath.internals.intera.DomainDomain object at 0x7f5a15c5c950>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2026-03-22 23:50:50 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2026-03-22 23:50:52 | 2026-03-22 23:50:53 | 0.63 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f5a15c76fd0>, <pypath.internals.intera.DomainDomain object at 0x7f5a15c77cd0>, <pypath.internals.intera.DomainDomain object at 0x7f5a16a23250>, <pypath.internals.intera.DomainDomain object at 0x7f5a16a22dd0>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2026-03-22 23:50:52 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2026-03-22 23:50:53 | 2026-03-22 23:50:53 | 0.37 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2026-03-22 23:50:53 | |
| ¶ | pypath.inputs.domino.get_domino | 2026-03-22 23:50:53 | 2026-03-22 23:50:54 | 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 | {} | 2026-03-22 23:50:53 | |
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2026-03-22 23:50:54 | 2026-03-22 23:51:04 | 9.90 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2026-03-22 23:50:54 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2026-03-22 23:51:04 | 2026-03-22 23:51:18 | 14.31 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2026-03-22 23:51:04 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2026-03-22 23:51:18 | 2026-03-22 23:51:20 | 1.97 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2026-03-22 23:51:18 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2026-03-22 23:51:20 | 2026-03-22 23:51:21 | 1.36 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2026-03-22 23:51:20 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2026-03-22 23:51:21 | 2026-03-22 23:51:36 | 14.31 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2026-03-22 23:51:21 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2026-03-22 23:51:36 | 2026-03-22 23:51:36 | 0.32 |
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__20260322-202402/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2025-08-12 05:02:53 | |||
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2026-03-22 23:51:36 | 2026-03-22 23:51:37 | 1.00 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2026-03-22 23:51:36 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2026-03-22 23:51:37 | 2026-03-22 23:51:38 | 1.17 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2026-03-22 23:51:37 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2026-03-22 23:51:38 | 2026-03-22 23:51:38 | 0.09 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 353 | {} | 2026-03-22 23:51:38 | |
| ¶ | pypath.inputs.elm.elm_domains | 2026-03-22 23:51:38 | 2026-03-22 23:51:39 | 0.35 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2026-03-22 23:51:38 | |
| ¶ | pypath.inputs.elm.elm_instances | 2026-03-22 23:51:39 | 2026-03-22 23:51:39 | 0.17 | 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} | 2026-03-22 23:51:39 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2026-03-22 23:51:39 | 2026-03-22 23:51:39 | 0.10 | list | [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) | 2,797 | {} | 2026-03-22 23:51:39 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2026-03-22 23:51:39 | 2026-03-22 23:51:43 | 4.15 | 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) | 846 | {} | 2026-03-22 23:51:39 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2026-03-22 23:51:43 | 2026-03-22 23:51:43 | 0.11 | 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) | 1,284 | {} | 2026-03-22 23:51:43 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2026-03-22 23:51:43 | 2026-03-22 23:51:43 | 0.09 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2026-03-22 23:51:43 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2026-03-22 23:51:43 | 2026-03-22 23:51:43 | 0.10 | list | [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) | 1,832 | {} | 2026-03-22 23:51:43 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2026-03-22 23:51:43 | 2026-03-22 23:51:44 | 0.40 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2026-03-22 23:51:43 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2026-03-22 23:51:44 | 2026-03-22 23:51:44 | 0.45 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 348 | {} | 2026-03-22 23:51:44 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.exocarta.get_exocarta | 2026-03-22 23:51:44 | 2026-03-22 23:52:29 | 44.42 | 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 | {} | 2026-03-22 23:51:44 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2026-03-22 23:52:29 | 2026-03-22 23:55:14 | 165.11 | 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 | {} | 2026-03-22 23:52:29 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2026-03-22 23:55:14 | 2026-03-22 23:55:14 | 0.16 | 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) | 410 | {} | 2026-03-22 23:55:14 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2026-03-22 23:55:14 | 2026-03-22 23:55:15 | 0.68 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,441 | {} | 2026-03-22 23:55:14 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2026-03-22 23:55:15 | 2026-03-22 23:56:11 | 55.99 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0016020', 'GO:0005743', 'GO:0045275'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0045259', 'GO:0005743'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0045259', 'GO:0005743'}, 'A0A023I7N5': {'GO:0016020', 'GO:0005743'}, 'A0A02...(truncated) | 2 | {} | 2026-03-22 23:55:15 | |
| ¶ | pypath.inputs.go.get_goslim | 2026-03-22 23:56:11 | 2026-03-22 23:56:12 | 1.01 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {} | 2026-03-22 23:56:11 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2026-03-22 23:56:12 | 2026-03-23 00:01:53 | 340.98 | dict | {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2026-03-22 23:56:12 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2026-03-23 00:01:53 | 2026-03-23 00:01:53 | 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__20260322-202402/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:26 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2026-03-23 00:01:53 | 2026-03-23 00:01:58 | 4.57 | dict | {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2026-03-23 00:01:53 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2026-03-23 00:01:58 | 2026-03-23 00:02:00 | 1.94 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H8': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H9': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6I0': {'GO:0005576', 'GO:0019814', 'G...(truncated) | 3 | {} | 2026-03-23 00:01:58 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2026-03-23 00:02:00 | 2026-03-23 00:02:06 | 6.25 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='involved_in', go_id='GO:1901911', reference='GO_REF:0000033', evidence_code='IBA', with_or_from='PANTHER:PTN000290327|PomBase:SPAC13G6.14', aspect='P', db_object_name='Diphosphoinositol poly...(truncated) | 19,676 | {} | 2026-03-23 00:02:00 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2026-03-23 00:02:08 | 2026-03-23 00:02:09 | 1.07 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H8': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H9': {'GO:0005576', 'GO:0019814', 'GO:0005886'}, 'A0A075B6I0': {'GO:0005576', 'GO:0019814', 'G...(truncated) | 3 | {} | 2026-03-23 00:02:08 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2026-03-23 00:02:09 | 2026-03-23 00:02:09 | 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__20260322-202402/pypath_git/pypath/inputs/go.py", line 860, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:43 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2026-03-23 00:02:09 | 2026-03-23 00:02:19 | 10.20 | dict | {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0070330'], 'A0A096LP01': ['GO:0005739', 'GO:0005741', 'GO:0019901', 'GO:0044325'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'],...(truncated) | 19,406 | {} | 2026-03-23 00:02:09 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2026-03-23 00:02:20 | 2026-03-23 00:02:24 | 4.14 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016014', 'part_of'), ('GO:0016013', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2026-03-23 00:02:20 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2026-03-23 00:02:24 | 2026-03-23 00:02:24 | 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__20260322-202402/pypath_git/pypath/inputs/go.py", line 291, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:59 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2026-03-23 00:02:24 | 2026-03-23 00:02:28 | 4.45 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016014', 'part_of'), ('GO:0016013', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2026-03-23 00:02:24 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2026-03-23 00:02:28 | 2026-03-23 00:02:32 | 3.45 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2026-03-23 00:02:28 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2026-03-23 00:02:32 | 2026-03-23 00:02:32 | 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__20260322-202402/pypath_git/pypath/inputs/go.py", line 572, in go_terms_goose
sql_path = os.path.join(common.DATA, 'goose_terms.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{} | 2025-08-12 05:20:07 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2026-03-23 00:02:32 | 2026-03-23 00:02:35 | 3.62 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2026-03-23 00:02:32 | |
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2026-03-23 00:02:35 | 2026-03-23 00:02:36 | 0.19 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 808 | {} | 2026-03-23 00:02:35 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2026-03-23 00:02:36 | 2026-03-23 00:02:37 | 1.44 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2026-03-23 00:02:36 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2026-03-23 00:02:37 | 2026-03-23 00:02:43 | 6.09 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {} | 2026-03-23 00:02:37 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2026-03-23 00:02:43 | 2026-03-23 00:02:43 | 0.20 | dict | {'Q99541': {GutmgeneAnnotation(gut_microbiota='Segatella copri', gut_microbiota_ncbi_id='165179', rank='species', strain=None, alteration='activation', throughput='low-throughput', associative_mode='causally', sample='intestinal epithelial cells,fecal,HT-29 cells', experimental_method='in vitro bact...(truncated) | 111 | {} | 2026-03-23 00:02:43 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2026-03-23 00:02:43 | 2026-03-23 00:02:43 | 0.01 | list | [GutmgeneRaw(index='119', pmid='30767231', gut_microbiota='Lacticaseibacillus paracasei', gut_microbiota_ncbi_id='1597', rank='species', strain='JS1', gene='IL6', gene_id='3569', alteration='inhibition', throughput='low-throughput', associative_mode='causally', organism='human', sample='NHDF cells',...(truncated) | 243 | {} | 2026-03-23 00:02:43 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2026-03-23 00:02:43 | 2026-03-23 00:02:44 | 0.20 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2026-03-23 00:02:43 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2026-03-23 00:02:44 | 2026-03-23 00:02:44 | 0.03 | dict | {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) | 622 | {} | 2026-03-23 00:02:44 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2026-03-23 00:02:44 | 2026-03-23 00:02:46 | 2.14 | 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) | 15,919 | {} | 2026-03-23 00:02:44 | |
| ¶ | pypath.inputs.hint.hint_interactions | 2026-03-23 00:02:46 | 2026-03-23 00:02:52 | 6.06 | list | [HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='LC'), HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='HT'), HintInteraction(id_a='A0A024R2I8', id_b='...(truncated) | 88,230 | {} | 2026-03-23 00:02:46 | |
| ¶ | pypath.inputs.hint.hint_raw | 2026-03-23 00:02:52 | 2026-03-23 00:02:52 | 0.09 | list | [['A0A024R2I8', 'F1D8Q5', 'NR1A2', 'NR2B1', '15604093:0018:HT:binary|19211732:0018:LC:binary|7746322:0018:LC:binary|9171239:0096:LC:binary|9368056:0096:LC:binary|9415406:0047:LC:binary', '9606', 'True', 'False'], ['A0A024R2I8', 'F1D8Q7', 'NR1A2', 'NR2B3', '15604093:0018:HT:binary', '9606', 'True', '...(truncated) | 163,435 | {} | 2026-03-23 00:02:52 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2026-03-23 00:02:52 | 2026-03-23 00:02:57 | 4.92 | list | [HippieInteraction(id_a='P42566', id_b='Q9Y6I3', score=0.97, methods=None, references=('10791968', '15809337', '16429130', '18200045', '18375383', '21115825', '9723620'), sources=None, organisms=None), HippieInteraction(id_a='O75363', id_b='O75363', score=0.79, methods=None, references=('14567997',)...(truncated) | 102,486 | {} | 2026-03-23 00:02:52 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2026-03-23 00:02:57 | 2026-03-23 00:08:57 | 360.04 | NoneType | None | 0 | {} | 2026-03-23 00:02:57 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2026-03-23 00:08:57 | 2026-03-23 00:08:57 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {} | 2026-03-23 00:08:57 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2026-03-23 00:08:57 | 2026-03-23 00:08:57 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {} | 2026-03-23 00:08:57 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2026-03-23 00:08:57 | 2026-03-23 00:08:57 | 0.00 | dict | {} | 0 | {} | 2026-03-23 00:08:57 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2026-03-23 00:08:57 | 2026-03-23 00:08:57 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {} | 2026-03-23 00:08:57 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2026-03-23 00:08:57 | 2026-03-23 00:09:03 | 5.76 | 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:0001217'), HpoAnnotation(entrez_ge...(truncated) | 5,194 | {} | 2026-03-23 00:08:57 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2026-03-23 00:09:03 | 2026-03-23 00:09:05 | 1.95 | 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:619340', name='Developmental and epileptic encephalopat...(truncated) | 11,614 | {} | 2026-03-23 00:09:03 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2026-03-23 00:09:06 | 2026-03-23 00:09:07 | 1.76 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2026-03-23 00:09:06 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2026-03-23 00:09:07 | 2026-03-23 00:09:08 | 0.53 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 19,389 | {} | 2026-03-23 00:09:07 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2026-03-23 00:09:08 | 2026-03-23 00:09:11 | 2.57 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2026-03-23 00:09:08 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2026-03-23 00:09:11 | 2026-03-23 00:09:12 | 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 | {} | 2026-03-23 00:09:11 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2026-03-23 00:09:12 | 2026-03-23 00:09:14 | 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 | {} | 2026-03-23 00:09:12 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2026-03-23 00:09:14 | 2026-03-23 00:09:15 | 1.16 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2026-03-23 00:09:14 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2026-03-23 00:09:15 | 2026-03-23 00:09:45 | 30.31 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2026-03-23 00:09:15 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2026-03-23 00:09:45 | 2026-03-23 00:09:46 | 1.11 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,384 | {} | 2026-03-23 00:09:45 | |
| ¶ | pypath.inputs.humap.humap1_complexes | 2026-03-23 00:09:46 | 2026-03-23 00:09:47 | 0.22 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,547 | {} | 2026-03-23 00:09:46 | |
| ¶ | pypath.inputs.humap.humap2and3_complexes | 2026-03-23 00:09:47 | 2026-03-23 00:09:48 | 1.92 | dict | {'COMPLEX:P20963_Q9NWV4_Q9UGQ2': Complex: COMPLEX:P20963_Q9NWV4_Q9UGQ2, 'COMPLEX:O94887_Q9NQ92_Q9NWB1': Complex: COMPLEX:O94887_Q9NQ92_Q9NWB1, 'COMPLEX:Q8N3D4_Q9Y3A4': Complex: COMPLEX:Q8N3D4_Q9Y3A4, 'COMPLEX:O00429_Q5T2D2': Complex: COMPLEX:O00429_Q5T2D2, 'COMPLEX:O95460_P21941_P78540_Q9H267_Q9H9C1...(truncated) | 15,443 | {} | 2026-03-23 00:09:47 | |
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2026-03-23 00:09:49 | 2026-03-23 00:09:51 | 2.65 | 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) | 13,142 | {} | 2026-03-23 00:09:49 | |
| ¶ | pypath.inputs.huri.hi_i_interactions | 2026-03-23 00:09:51 | 2026-03-23 00:09:53 | 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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:38 | |||
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2026-03-23 00:09:53 | 2026-03-23 00:09:54 | 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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:40 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2026-03-23 00:09:54 | 2026-03-23 00:09:55 | 1.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:49 | |||
| ¶ | pypath.inputs.huri.huri_interactions | 2026-03-23 00:09:55 | 2026-03-23 00:09:56 | 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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:20 | |||
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2026-03-23 00:09:56 | 2026-03-23 00:09:57 | 1.05 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2026-03-23 00:09:56 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2026-03-23 00:09:57 | 2026-03-23 00:09:58 | 0.73 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2026-03-23 00:09:57 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2026-03-23 00:09:58 | 2026-03-23 00:10:00 | 2.19 |
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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 279, in lit_bm_interactions
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-31 05:12:46 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2026-03-23 00:10:00 | 2026-03-23 00:10:01 | 1.19 | list | [Rolland2014Interaction(entrez_a='14', entrez_b='6293', genesymbol_a='AAMP', genesymbol_b='VPS52', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='8553', genesymbol_a='AAMP', genesymbol_b='BHLHE40', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='64782', genesymbo...(truncated) | 13,944 | {} | 2026-03-23 00:10:00 | |
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2026-03-23 00:10:01 | 2026-03-23 00:10:02 | 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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:49 | |||
| ¶ | pypath.inputs.huri.yu2011_interactions | 2026-03-23 00:10:02 | 2026-03-23 00:10:03 | 1.15 |
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__20260322-202402/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:50 | |||
| ¶ | pypath.inputs.i3d.get_i3d | 2026-03-23 00:10:03 | 2026-03-23 00:10:10 | 6.43 | list | [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) | 22,184 | {} | 2026-03-23 00:10:03 | |
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2026-03-23 00:10:10 | 2026-03-23 00:10:10 | 0.51 | dict | {Complex: COMPLEX:P01033_P14780: {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None)}, 'P01033': {IcellnetAnnotation(role='ligand', family='Cell adhesion', subfamily=None, classification=None), IcellnetAnnotation(role='ligand', family=None, subfamily=None, classifica...(truncated) | 1,193 | {'size': -1} | 2026-03-23 00:10:10 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2026-03-23 00:10:10 | 2026-03-23 00:10:10 | 0.04 | dict | {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) | 156 | {} | 2026-03-23 00:10:10 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2026-03-23 00:10:10 | 2026-03-23 00:10:10 | 0.03 | list | [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) | 1,647 | {} | 2026-03-23 00:10:10 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2026-03-23 00:10:10 | 2026-03-23 00:10:13 | 2.76 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2026-03-23 00:10:10 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2026-03-23 00:10:13 | 2026-03-23 00:10:14 | 0.98 | list | [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) | 11,470 | {} | 2026-03-23 00:10:13 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2026-03-23 00:10:14 | 2026-03-23 00:10:15 | 0.57 | NoneType | None | 0 | {} | 2026-03-23 00:10:14 | |
| ¶ | pypath.inputs.intact.intact_interactions | 2026-03-23 00:10:15 | 2026-03-23 00:11:38 | 83.52 | list | [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='O43426', id_type_a='uniprot', i...(truncated) | 79,206 | {} | 2026-03-23 00:10:15 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2026-03-23 00:11:39 | 2026-03-23 00:11:39 | 0.56 | set | {'P56199', 'P17301', 'P38570', 'Q9UKX5', 'P08514', 'P11215', 'P05556', 'P16144', 'P06756', 'P53708', 'P08648', 'P05107', 'P26010', 'Q13683', 'O75578', 'P05106', 'P26012', 'Q13349', 'P20701', 'Q13797', 'P18084', 'P26006', 'P20702', 'P23229', 'P18564'} | 25 | {} | 2026-03-23 00:11:39 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2026-03-23 00:11:39 | 2026-03-23 00:11:40 | 1.14 | 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:0006355', go_term_name='regulation of DNA-templ...(truncated) | 14,808 | {} | 2026-03-23 00:11:39 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2026-03-23 00:11:40 | 2026-03-23 00:11:41 | 0.87 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR018056', organism='9606', start='439', end='452'), InterproAnnotation(interpro_id='IPR000001', organism='9606', start='208', end='290'), InterproAnnotation(interpro_id='IPR024174', organism='9606', start='1', end='723'), Inter...(truncated) | 16,611 | {} | 2026-03-23 00:11:40 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2026-03-23 00:11:41 | 2026-03-23 00:11:52 | 10.60 | list | [InterproEntry(interpro_id='IPR000001', protein_count='21741', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 51,489 | {} | 2026-03-23 00:11:41 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2026-03-23 00:11:52 | 2026-03-23 00:11:53 | 1.05 | dict | {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) | 483 | {} | 2026-03-23 00:11:52 | |
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2026-03-23 00:11:53 | 2026-03-23 00:11:53 | 0.07 | dict | {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) | 86,754 | {} | 2026-03-23 00:11:53 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2026-03-23 00:11:53 | 2026-03-23 00:12:10 | 17.38 | list | [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) | 15,834 | {} | 2026-03-23 00:11:53 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2026-03-23 00:12:10 | 2026-03-23 00:12:11 | 0.70 | 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) | 1,415 | {} | 2026-03-23 00:12:10 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2026-03-23 00:12:11 | 2026-03-23 00:12:11 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {} | 2026-03-23 00:12:11 | |
| ¶ | pypath.inputs.italk.italk_raw | 2026-03-23 00:12:11 | 2026-03-23 00:12:11 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2026-03-23 00:12:11 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2026-03-23 00:12:11 | 2026-03-23 00:12:13 | 1.76 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,224 | {} | 2026-03-23 00:12:11 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2026-03-23 00:12:13 | 2026-03-23 00:12:13 | 0.15 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {} | 2026-03-23 00:12:13 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2026-03-23 00:12:13 | 2026-03-23 00:30:18 | 1,084.46 | list | [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) | 15,357 | {} | 2026-03-23 00:12:13 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2026-03-23 00:30:18 | 2026-03-23 00:30:40 | 22.16 | set | {KeggMedicusRawInteraction(id_a='2534', id_b='5293', name_a='FYN', name_b='PIK3CD', effect='stimulation', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N01204'), KeggMedicusRawInteraction(id_a='C00076', id_b='7419', name_a='Calcium cation', name_b='VDAC3'...(truncated) | 12,946 | {} | 2026-03-23 00:30:18 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2026-03-23 00:30:40 | 2026-03-23 00:30:40 | 0.46 | dict | {'COMPLEX:P46108_P56945': Complex: COMPLEX:P46108_P56945, 'COMPLEX:P15336': Complex: COMPLEX:P15336, 'COMPLEX:O43318_Q8N5C8': Complex: COMPLEX:O43318_Q8N5C8, 'COMPLEX:O14641_Q92837': Complex: COMPLEX:O14641_Q92837, 'COMPLEX:Q6KC79_Q9Y6X3': Complex: COMPLEX:Q6KC79_Q9Y6X3, 'COMPLEX:P02671_P02675_P0267...(truncated) | 530 | {} | 2026-03-23 00:30:40 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2026-03-23 00:30:40 | 2026-03-23 00:30:41 | 0.38 | list | [KeggMedicusInteraction(id_a='P06241', id_b='O00329', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P62993', id_b='Q07889', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,539 | {} | 2026-03-23 00:30:40 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2026-03-23 00:30:41 | 2026-03-23 00:30:54 | 13.64 | dict | {'Q13233': {KeggPathway(pathway='Growth hormone synthesis, secretion and action'), KeggPathway(pathway='RIG-I-like receptor signaling pathway'), KeggPathway(pathway='Neurotrophin signaling pathway'), KeggPathway(pathway='Tight junction'), KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pa...(truncated) | 2,755 | {} | 2026-03-23 00:30:41 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2026-03-23 00:30:54 | 2026-03-23 00:30:55 | 0.35 | dict | {'A8K7J7': {KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Bu...(truncated) | 813 | {} | 2026-03-23 00:30:54 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2026-03-23 00:30:55 | 2026-03-23 00:31:08 | 13.64 | tuple | ({'MAPK signaling pathway': {'Q13233', 'Q15283', 'Q9NYJ8', 'Q9UER7', 'P62070', 'Q12968', 'P19838', 'O95257', 'Q13163', 'P10636', 'P0C869', 'Q07889', 'P17980', 'P17612', 'Q9Y4G8', 'P62993', 'Q9Y6R4', 'Q5STR5', 'P15336', 'P19419', 'Q02750', 'P16949', 'P04792', 'Q03112', 'P18848', 'P04049', 'P36896', '...(truncated) | 2 | {} | 2026-03-23 00:30:55 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2026-03-23 00:31:08 | 2026-03-23 00:31:13 | 4.65 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
self.proc_key(entry[0]): self.proc_value(entry[1])
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
|
{} | 2025-08-12 05:47:03 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2026-03-23 00:31:13 | 2026-03-23 00:31:13 | 0.35 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 503 | {} | 2026-03-23 00:31:13 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2026-03-23 00:31:13 | 2026-03-23 00:31:14 | 0.20 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2026-03-23 00:31:13 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2026-03-23 00:31:14 | 2026-03-23 00:31:16 | 2.80 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {} | 2026-03-23 00:31:14 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2026-03-23 00:31:16 | 2026-03-23 00:31:19 | 2.77 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {} | 2026-03-23 00:31:16 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2026-03-23 00:31:19 | 2026-03-23 00:31:20 | 0.33 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2026-03-23 00:31:19 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2026-03-23 00:31:20 | 2026-03-23 00:31:20 | 0.30 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2026-03-23 00:31:20 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2026-03-23 00:31:20 | 2026-03-23 00:31:20 | 0.46 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2026-03-23 00:31:20 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2026-03-23 00:31:20 | 2026-03-23 00:31:30 | 9.76 | 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 | {} | 2026-03-23 00:31:20 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2026-03-23 00:31:30 | 2026-03-23 00:31:30 | 0.02 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2026-03-23 00:31:30 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2026-03-23 00:31:30 | 2026-03-23 00:31:30 | 0.02 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2026-03-23 00:31:30 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2026-03-23 00:31:30 | 2026-03-23 00:31:31 | 1.07 | dict | {'SciTegic09271913552D': LincsCompound(lincs=None, chembl=None, chebi=None, inchi='InChI=1S/C29H24N4O4S/c1-4-27(34)31-26-16-23(12-5-18(26)2)33-28(35)14-9-21-17-30-25-13-8-20(15-24(25)29(21)33)19-6-10-22(11-7-19)32-38(3,36)37/h4-17,32H,1H2,2-3H3,(H,31,34)', inchi_key='SFMJNHNUOVADRW-UHFFFAOYSA-N', sm...(truncated) | 371 | {} | 2026-03-23 00:31:30 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2026-03-23 00:31:31 | 2026-03-23 00:31:33 | 1.29 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2026-03-23 00:31:31 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2026-03-23 00:31:33 | 2026-03-23 00:31:33 | 0.47 | list | [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) | 1,170 | {} | 2026-03-23 00:31:33 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2026-03-23 00:31:33 | 2026-03-23 00:31:34 | 0.46 | list | [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) | 1,170 | {} | 2026-03-23 00:31:33 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2026-03-23 00:31:34 | 2026-03-23 00:31:34 | 0.44 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {} | 2026-03-23 00:31:34 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2026-03-23 00:31:34 | 2026-03-23 00:31:34 | 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 | {} | 2026-03-23 00:31:34 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2026-03-23 00:31:34 | 2026-03-23 00:32:09 | 34.66 | dict | {'P27824': {LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pm...(truncated) | 9,475 | {} | 2026-03-23 00:31:34 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2026-03-23 00:32:09 | 2026-03-23 00:32:10 | 0.71 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD'), references=('13', '14980518')), LrdbAnnotation(role='receptor', cell_type=None, sources=(...(truncated) | 1,542 | {} | 2026-03-23 00:32:09 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2026-03-23 00:32:10 | 2026-03-23 00:32:10 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2026-03-23 00:32:10 | |
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2026-03-23 00:32:10 | 2026-03-23 00:32:10 | 0.14 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2026-03-23 00:32:10 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2026-03-23 00:32:10 | 2026-03-23 00:32:10 | 0.28 | dict | {'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YEA0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C524': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,500 | {} | 2026-03-23 00:32:10 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2026-03-23 00:32:10 | 2026-03-23 00:32:11 | 0.48 | dict | {} | 0 | {} | 2026-03-23 00:32:10 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2026-03-23 00:32:11 | 2026-03-23 00:32:13 | 2.06 | set | {'Q16206', 'Q96RT1', 'P12821', 'P53634', 'Q6UXV3', 'P55290', 'Q9Y6N6', 'Q96KX0', 'P16671', 'P16035', 'Q6ZWH5', 'A0A0J9YXX1', 'Q8NCC3', 'P15291', 'Q9UBU3', 'Q9UI46', 'Q7Z5A8', 'Q5TF21', 'P0CJ72', 'Q9Y240', 'Q14766', 'P0C862', 'Q9H324', 'O15229', 'P42025', 'P16278', 'O43827', 'P01148', 'P04792', 'Q8N2...(truncated) | 2,847 | {} | 2026-03-23 00:32:11 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2026-03-23 00:32:13 | 2026-03-23 00:32:13 | 0.08 | list | [MatrixdbInteraction(id_a='"chebi:""CHEBI:29105"""', id_b='uniprotkb:P05067', alt_ids_a='matrixdb:CAT_1', alt_ids_b='-', aliases_a='matrixdb:Zinc(short label)', aliases_b='"uniprotkb:""APP""(gene name)"', detection_method='"psi-mi:""MI:0004""(""affinity chromatography technology"")"', author='Bush A...(truncated) | 1,264 | {} | 2026-03-23 00:32:13 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2026-03-23 00:32:13 | 2026-03-23 00:32:13 | 0.06 | set | set() | 0 | {} | 2026-03-23 00:32:13 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2026-03-23 00:32:13 | 2026-03-23 00:32:13 | 0.06 | set | set() | 0 | {} | 2026-03-23 00:32:13 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2026-03-23 00:32:13 | 2026-03-23 00:32:14 | 1.07 | set | {'Q13835', 'Q9BX67', 'Q9HBB8', 'P02751', 'Q9UKX5', 'P56856', 'Q9UQS6', 'P16671', 'Q02763', 'Q9Y4C0', 'P16284', 'Q49MI3', 'Q86SJ6', 'O95500', 'Q6MZF4', 'O15394', 'O00548', 'O14525', 'Q6UWL6', 'P12259', 'Q8N6H6', 'Q6ZW63', 'Q6NW40', 'Q8TD84', 'Q7Z3B1', 'Q05084', 'Q6MZM7', 'Q96QR6', 'Q96GP6', 'O75144',...(truncated) | 112 | {} | 2026-03-23 00:32:13 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2026-03-23 00:32:14 | 2026-03-23 00:32:49 | 34.53 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {} | 2026-03-23 00:32:14 | |
| ¶ | pypath.inputs.metanetx.metanetx_metabolite_chebi | 2026-03-23 00:32:49 | 2026-03-23 00:33:18 | 29.07 | dict | {'MNXM02': 'CHEBI:13365', 'MNXM03': 'CHEBI:29412', 'MNXM1': 'CHEBI:10744', 'MNXM10': 'CHEBI:13395', 'MNXM100': 'CHEBI:14299', 'MNXM100000': 'CHEBI:165749', 'MNXM100003': 'CHEBI:179593', 'MNXM100004': 'CHEBI:196064', 'MNXM100005': 'CHEBI:196177', 'MNXM100006': 'CHEBI:179952', 'MNXM100007': 'CHEBI:169...(truncated) | 188,747 | {} | 2026-03-23 00:32:49 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2026-03-23 00:33:18 | 2026-03-23 00:33:18 | 0.13 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2026-03-23 00:33:18 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2026-03-23 00:33:18 | 2026-03-23 00:33:21 | 2.65 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2026-03-23 00:33:18 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 0.19 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 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 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 0.19 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) | 2,925 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 0.02 | list | [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0004481', 'hsa-let-7a-3p'), ('MIMAT0004481', 'hsa-let-7a*'), ('MIMAT0010195', 'hsa-let-7a-2-3p'), ('MIMAT0010195', 'hsa-let-7a-2*'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0004482', 'hsa-let...(truncated) | 3,299 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 0.02 | list | ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) | 2,693 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 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 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_mature | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 0.02 | list | [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) | 49,168 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_pre_mature | 2026-03-23 00:33:21 | 2026-03-23 00:33:21 | 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 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_organisms | 2026-03-23 00:33:21 | 2026-03-23 00:33:22 | 0.14 | dict | {400682: 'aqu', 45351: 'nve', 6085: 'hma', 10224: 'sko', 7668: 'spu', 7719: 'cin', 51511: 'csa', 34765: 'odi', 7739: 'bfl', 8355: 'xla', 8364: 'xtr', 9031: 'gga', 9615: 'cfa', 13616: 'mdo', 9509: 'age', 9519: 'lla', 78454: 'sla', 9544: 'mml', 9545: 'mne', 61621: 'pbi', 9593: 'ggo', 9606: 'hsa', 9597...(truncated) | 285 | {} | 2026-03-23 00:33:21 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.05 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,130 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.03 | list | ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', 'MI0000081', 'MI0000082', ...(truncated) | 1,984 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.09 | list | [('hsa-let-7a-1', 'hsa-let-7a-5p'), ('hsa-let-7a-1', 'hsa-let-7a'), ('hsa-let-7a-1L', 'hsa-let-7a-5p'), ('hsa-let-7a-1L', 'hsa-let-7a'), ('hsa-let-7a-1', 'hsa-let-7a-3p'), ('hsa-let-7a-1', 'hsa-let-7a*'), ('hsa-let-7a-1L', 'hsa-let-7a-3p'), ('hsa-let-7a-1L', 'hsa-let-7a*'), ('hsa-let-7a-2', 'hsa-let...(truncated) | 4,071 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirbase.mirbase_taxid | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.00 | str | 'hsa' | 3 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.16 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2026-03-23 00:33:22 | 2026-03-23 00:33:22 | 0.42 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism=9606, target_organism=9606, pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organism=10090, target_or...(truncated) | 3,106 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2026-03-23 00:33:22 | 2026-03-23 00:35:35 | 132.73 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=10090, target_genesymbol='Cd320', target_entrez='54219', target_organism=10090, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', data...(truncated) | 27,595 | {} | 2026-03-23 00:33:22 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_interactions |
Not calling `pypath.inputs.mitab.mitab_interactions`, not enough arguments. |
{} | 2025-11-18 23:16:47 | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_aliases |
Not calling `pypath.inputs.mitab.mitab_parse_aliases`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_confidence |
Not calling `pypath.inputs.mitab.mitab_parse_confidence`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_features |
Not calling `pypath.inputs.mitab.mitab_parse_features`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_identifier |
Not calling `pypath.inputs.mitab.mitab_parse_identifier`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_identifiers |
Not calling `pypath.inputs.mitab.mitab_parse_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_mi_term |
Not calling `pypath.inputs.mitab.mitab_parse_mi_term`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_mi_terms |
Not calling `pypath.inputs.mitab.mitab_parse_mi_terms`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_parameters |
Not calling `pypath.inputs.mitab.mitab_parse_parameters`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_pubmeds |
Not calling `pypath.inputs.mitab.mitab_parse_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_parse_taxid |
Not calling `pypath.inputs.mitab.mitab_parse_taxid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2026-03-23 00:35:35 | 2026-03-23 00:35:36 | 0.86 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2026-03-23 00:35:35 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2026-03-23 00:35:36 | 2026-03-23 00:36:10 | 34.44 | dict | {'Q16698': {MsigdbAnnotation(collection='immunesigdb', geneset='GSE18281_SUBCAPSULAR_CORTICAL_REGION_VS_WHOLE_CORTEX_THYMUS_UP'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE13493_DP_VS_CD4INTCD8POS_THYMOCYTE_DN'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE29617_CTRL_VS_TIV_F...(truncated) | 20,120 | {} | 2026-03-23 00:35:36 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2026-03-23 00:36:12 | 2026-03-23 00:36:19 | 7.50 | dict | {'MT': {'MT-CO3', 'MT-TI', 'MT-TM', 'MT-RNR2', 'MT-TV', 'MT-CYB', 'MT-ATP8', 'MT-TS1', 'MT-ND5', 'MT-ND1', 'MT-TE', 'MT-TF', 'MT-TH', 'MT-TN', 'MT-TS2', 'MT-TW', 'MT-ND4L', 'MT-TY', 'MT-ND3', 'MT-TQ', 'MT-ATP6', 'MT-TC', 'MT-TT', 'MT-RNR1', 'MT-TK', 'MT-TP', 'MT-ND2', 'MT-CO2', 'MT-TD', 'MT-CO1', 'M...(truncated) | 35,134 | {} | 2026-03-23 00:36:12 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2026-03-23 00:36:20 | 2026-03-23 00:36:20 | 0.48 | dict | {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'MTCH2', 'NMT1', 'HSPB8', 'SNCG', 'SOD1', 'VEGFB', 'ATP5PO', 'ITGA7', 'CDKN2C', 'PFKL', 'ADIPOQ', 'UQCR11', 'ABCB8', 'ACAA2', 'RMDN3', 'IDH3A', 'CD302', 'JAGN1', 'CCNG2', 'PTGER3', 'GADD45A', 'CD151', 'YWHAG', 'ACADL', 'MGST3', 'CYP4B1', 'DBT', 'GPX...(truncated) | 20 | {} | 2026-03-23 00:36:20 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2026-03-23 00:36:21 | 2026-03-23 00:36:21 | 0.31 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2026-03-23 00:36:21 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2026-03-23 00:36:21 | 2026-03-23 00:36:21 | 0.14 | list | [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) | 2,171 | {} | 2026-03-23 00:36:21 | |
| ¶ | pypath.inputs.netbiol.arn_interactions | 2026-03-23 00:36:21 | 2026-03-23 00:36:21 | 0.11 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2026-03-23 00:36:21 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2026-03-23 00:36:21 | 2026-03-23 00:36:21 | 0.12 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2026-03-23 00:36:21 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2026-03-23 00:36:21 | 2026-03-23 00:36:24 | 2.10 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2026-03-23 00:36:21 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2026-03-23 00:36:24 | 2026-03-23 00:36:24 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2026-03-23 00:36:24 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2026-03-23 00:36:24 | 2026-03-23 00:36:24 | 0.13 | dict | {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Notch'), NetpathPa...(truncated) | 1,870 | {} | 2026-03-23 00:36:24 | |
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2026-03-23 00:36:24 | 2026-03-23 00:36:51 | 27.48 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2026-03-23 00:36:24 | |
| ¶ | pypath.inputs.oma.oma_orthologs | 2026-03-23 00:36:51 | 2026-03-23 00:37:50 | 58.43 | list | [OmaOrthology(a=OmaGene(id='KLK1_HUMAN', oma_group=1228743, hog='HOG:E0794303.3kh.151b', taxon=9606, chr='19', start=50819194, end=50823748, strand=-1, main_isoform=True), b=OmaGene(id='KLK1_MOUSE', oma_group=1228743, hog='HOG:E0794303.3kh.151b.113b.68b.37k', taxon=10090, chr='7', start=43874903, en...(truncated) | 22,374 | {} | 2026-03-23 00:36:51 | |
| ¶ | pypath.inputs.oma.oma_table | 2026-03-23 00:37:50 | 2026-03-23 00:37:55 | 4.81 | defaultdict | defaultdict(<class 'set'>, {'KLK1_HUMAN': {'K1B27_MOUSE', 'K1KB1_MOUSE', 'KLK1_MOUSE', 'K1B22_MOUSE', 'K1KB3_MOUSE', 'K1B21_MOUSE', 'K1KB9_MOUSE', 'K1KB5_MOUSE', 'K1B16_MOUSE', 'K1KB8_MOUSE', 'K1B11_MOUSE', 'K1B26_MOUSE', 'K1KB4_MOUSE', 'K1B24_MOUSE'}, 'H2A1_HUMAN': {'H2A2C_MOUSE', 'H2A2B_MOUSE', 'H...(truncated) | 17,895 | {} | 2026-03-23 00:37:50 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2026-03-23 00:37:55 | 2026-03-23 00:37:55 | 0.48 | dict | {'addicto': 'Addiction Ontology', 'ado': "Alzheimer's Disease Ontology (ADO)", 'aeo': 'Anatomical Entity Ontology', 'afo': 'Allotrope Merged Ontology Suite', 'afpo': 'African Population Ontology', 'agro': 'Agronomy Ontology', 'aism': 'Ontology for the Anatomy of the Insect SkeletoMuscular system', '...(truncated) | 270 | {} | 2026-03-23 00:37:55 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2026-03-23 00:37:55 | 2026-03-23 00:38:14 | 18.84 | list | [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) | 112,928 | {} | 2026-03-23 00:37:55 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2026-03-23 00:38:14 | 2026-03-23 00:39:43 | 89.17 | list | [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) | 43,791 | {} | 2026-03-23 00:38:14 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2026-03-23 00:39:43 | 2026-03-23 00:40:25 | 42.01 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {} | 2026-03-23 00:39:43 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2026-03-23 00:40:25 | 2026-03-23 00:41:34 | 69.19 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) | 6,960,486 | {} | 2026-03-23 00:40:25 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2026-03-23 00:41:34 | 2026-03-23 00:41:51 | 16.98 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 88 | {} | 2026-03-23 00:41:34 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2026-03-23 00:41:51 | 2026-03-23 00:42:08 | 16.68 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {} | 2026-03-23 00:41:51 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2026-03-23 00:42:08 | 2026-03-23 00:42:12 | 3.90 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 2,219,572 | {} | 2026-03-23 00:42:08 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2026-03-23 00:42:12 | 2026-03-23 00:42:15 | 3.16 | 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) | 4,491 | {} | 2026-03-23 00:42:12 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2026-03-23 00:42:15 | 2026-03-23 00:42:15 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2026-03-23 00:42:15 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2026-03-23 00:42:15 | 2026-03-23 00:42:37 | 21.87 | list | [DiseasePathogen(disease_id='DOID:4166', disease='syphilitic chancre', pathogen_taxid='168', pathogen='Treponema pallidum\xa0subspecies\xa0pertenue', evidence='automatic assertion'), DiseasePathogen(disease_id='DOID:1564', disease='fungal infectious disease', pathogen_taxid='46472', pathogen='Asperg...(truncated) | 4,111 | {} | 2026-03-23 00:42:15 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2026-03-23 00:42:37 | 2026-03-23 00:42:51 | 14.22 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='controls-expression-of', id_b='A2M', resource='pid'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b=...(truncated) | 2,524,906 | {} | 2026-03-23 00:42:37 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2026-03-23 00:42:53 | 2026-03-23 00:42:53 | 0.19 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2026-03-23 00:42:53 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2026-03-23 00:42:53 | 2026-03-23 00:43:00 | 6.81 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2026-03-23 00:42:53 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2026-03-23 00:43:03 | 2026-03-23 00:43:12 | 8.84 | dict | {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:Q12791': Complex: COMPLEX:Q12791, 'COMPLEX:Q4E2L0': Complex: COMPLEX:Q4E2L0, 'COMPLEX:Q13UJ9': Complex: COMPLEX:Q13UJ9, 'COMPLEX:P06241': Complex: COMPLEX:P06241, 'COMPLEX:Q5NHB4': Complex: COMPLEX:Q5NHB4, 'COMPLEX:C3SSQ8_P02358_P02359_P0A7R5_P0A7...(truncated) | 50,550 | {} | 2026-03-23 00:43:03 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2026-03-23 00:43:12 | 2026-03-23 00:43:17 | 5.03 | tuple | ({'P02185': {('6m8f', 'X-ray', 1.1), ('5vzo', 'X-ray', 1.78), ('5utd', 'X-ray', 1.78), ('1mlf', 'X-ray', 2.0), ('1l2k', 'Neutron', 1.5), ('4mxl', 'X-ray', 1.5), ('3h58', 'X-ray', 1.8), ('3e4n', 'X-ray', 1.21), ('7l3u', 'X-ray', 1.47), ('2mgc', 'X-ray', 1.9), ('6n02', 'X-ray', 2.0), ('1duo', 'X-ray',...(truncated) | 2 | {} | 2026-03-23 00:43:12 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2026-03-23 00:43:18 | 2026-03-23 00:43:18 | 0.58 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2026-03-23 00:43:18 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2026-03-23 00:43:18 | 2026-03-23 00:55:09 | 711.20 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2026-03-23 00:43:18 | |
| ¶ | pypath.inputs.pfam.pfam_names | 2026-03-23 00:55:09 | 2026-03-23 00:55:10 | 1.06 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'Ion_trans': {'PF00520'}, 'Slo-like_RCK': {'PF22614'}, 'BK_channel_a': {'PF03493'}, 'Slowpoke_C': {'PF21014'}, 'Pro_isomerase': {'PF00160'}, 'Pkinase': {'PF00069'}, 'RS_preATP-grasp-like': {'PF22660'}, 'ATP-gras...(truncated) | 2 | {} | 2026-03-23 00:55:09 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2026-03-23 00:55:11 | 2026-03-23 00:55:15 | 4.01 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) | 2 | {} | 2026-03-23 00:55:11 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2026-03-23 00:55:15 | 2026-03-23 01:01:18 | 363.08 | tuple | ({}, {}) | 2 | {} | 2026-03-23 00:55:15 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2026-03-23 01:01:18 | 2026-03-23 01:16:44 | 925.43 | tuple | ({}, {}) | 2 | {} | 2026-03-23 01:01:18 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2026-03-23 01:16:44 | 2026-03-23 01:28:56 | 731.84 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:16:44 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2026-03-23 01:28:56 | 2026-03-23 01:29:00 | 3.31 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:28:56 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2026-03-23 01:29:01 | 2026-03-23 01:29:05 | 4.10 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:29:01 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2026-03-23 01:29:06 | 2026-03-23 01:29:09 | 3.49 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:29:06 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2026-03-23 01:29:10 | 2026-03-23 01:29:14 | 3.34 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:29:10 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2026-03-23 01:29:15 | 2026-03-23 01:37:44 | 509.37 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2026-03-23 01:29:15 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2026-03-23 01:37:44 | 2026-03-23 01:37:47 | 2.83 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2026-03-23 01:37:44 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2026-03-23 01:37:48 | 2026-03-23 01:37:48 | 0.51 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2026-03-23 01:37:48 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2026-03-23 01:37:48 | 2026-03-23 01:37:52 | 4.30 | dict | {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) | 264 | {} | 2026-03-23 01:37:48 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2026-03-23 01:37:52 | 2026-03-23 01:37:54 | 1.38 | list | [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) | 2,426 | {} | 2026-03-23 01:37:52 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2026-03-23 01:37:54 | 2026-03-23 01:37:54 | 0.40 | list | [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) | 2,426 | {} | 2026-03-23 01:37:54 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2026-03-23 01:37:54 | 2026-03-23 01:37:54 | 0.10 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {} | 2026-03-23 01:37:54 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2026-03-23 01:37:54 | 2026-03-23 01:37:56 | 1.25 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2026-03-23 01:37:54 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.02 | list | [['RAF1', 'RNUXA'], ['PAK4', 'BAD'], ['CSNK1G1', 'C21orf66'], ['STK38L', 'PRKCD'], ['RPS6KA4', 'NFATC4'], ['RIOK1', 'YWHAH'], ['MAPK1', 'PITPNM1'], ['CDK7', 'ZYX'], ['MAPK3', 'CEBPA'], ['CSNK2A1', 'PKD2'], ['MAPKAPK5', 'NEUROD1'], ['ILK', 'PPP1R14B'], ['MAPK3', 'MAPK8'], ['PRKACA', 'CAMKK1'], ['FYN'...(truncated) | 1,821 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.23 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 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 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2026-03-23 01:37:56 | 2026-03-23 01:37:56 | 0.01 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 9,164 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2026-03-23 01:37:56 | 2026-03-23 01:37:57 | 0.61 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {} | 2026-03-23 01:37:56 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2026-03-23 01:37:57 | 2026-03-23 01:37:57 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2026-03-23 01:37:57 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2026-03-23 01:37:57 | 2026-03-23 01:37:57 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) | 4,790 | {} | 2026-03-23 01:37:57 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2026-03-23 01:37:57 | 2026-03-23 01:38:01 | 4.20 | 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 | {} | 2026-03-23 01:37:57 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2026-03-23 01:38:02 | 2026-03-23 01:38:15 | 13.17 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {} | 2026-03-23 01:38:02 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2026-03-23 01:38:15 | 2026-03-23 01:38:16 | 1.01 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'protein degradation', 'intracellular localization', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2026-03-23 01:38:15 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2026-03-23 01:38:16 | 2026-03-23 01:44:16 | 360.25 |
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__20260322-202402/pypath_git/pypath/inputs/phosphosite.py", line 512, in phosphosite_regsites_one_organism
dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/phosphosite.py", line 517, in <lambda>
homologene.homologene_uniprot_dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/homologene.py", line 137, in homologene_uniprot_dict
hge = homologene_dict(source, target, 'entrez')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/homologene.py", line 88, in homologene_dict
for l in hg:
TypeError: 'NoneType' object is not iterable
|
{} | 2026-02-16 01:54:08 | |||
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2026-03-23 01:44:17 | 2026-03-23 01:44:39 | 22.36 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2026-03-23 01:44:17 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2026-03-23 01:44:39 | 2026-03-23 01:44:39 | 0.47 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 395,915 | {} | 2026-03-23 01:44:39 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2026-03-23 01:44:40 | 2026-03-23 01:45:52 | 72.40 | dict | {'P35250': {ProgenyAnnotation(pathway='JAK-STAT', weight=0.0012188579040493524, p_value=0.998388257483376), ProgenyAnnotation(pathway='p53', weight=-3.3513628049710005, p_value=0.000985568693599589), ProgenyAnnotation(pathway='MAPK', weight=2.277341180050157, p_value=3.324844332731664e-11), ProgenyA...(truncated) | 18,581 | {} | 2026-03-23 01:44:40 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2026-03-23 01:45:52 | 2026-03-23 01:47:04 | 71.40 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2026-03-23 01:45:52 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2026-03-23 01:47:04 | 2026-03-23 01:47:08 | 4.47 | dict | {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) | 2 | {} | 2026-03-23 01:47:04 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2026-03-23 01:47:09 | 2026-03-23 01:47:19 | 9.74 | dict | {'O43657': {ProtainatlasAnnotation(organ='Testis', tissue='Testis', cell_type='Leydig cells', level='Low', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotation(organ='Skeletal muscle',...(truncated) | 15,058 | {} | 2026-03-23 01:47:09 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2026-03-23 01:47:21 | 2026-03-23 01:47:22 | 0.37 | list | [ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interac...(truncated) | 47,188 | {} | 2026-03-23 01:47:21 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2026-03-23 01:47:22 | 2026-03-23 01:47:22 | 0.31 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,591 | {} | 2026-03-23 01:47:22 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2026-03-23 01:47:22 | 2026-03-23 01:47:23 | 1.05 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Nucleoli fibrillar center', status='additional', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', r...(truncated) | 13,407 | {} | 2026-03-23 01:47:22 | |
| ¶ | pypath.inputs.proteins.variants | 2026-03-23 01:47:23 | 2026-03-23 01:53:29 | 366.26 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 29,523 | {} | 2026-03-23 01:47:23 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2026-03-23 01:53:30 | 2026-03-23 01:53:31 | 1.21 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q05513', 'CTRL_GENE_NAME': 'PRKCZ', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P27448', 'TARGET_GENE_NAME': 'MARK3', 'TARGET_RES': 'T', 'TARGET_POS': '564', 'SOURCES': 'psp,signor', 'BELIEF': '1'}, {'ID': '1', 'CTRL_NS': 'UP', 'CTRL_ID': 'P41743', 'CTRL_GEN...(truncated) | 2 | {} | 2026-03-23 01:53:30 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2026-03-23 01:53:31 | 2026-03-23 01:53:32 | 0.96 | list | [{'kinase': 'Q05513', 'resaa': 'T', 'resnum': 564, 'references': {'15084291'}, 'substrate': 'P27448', 'databases': {'SIGNOR', 'PhosphoSite'}}, {'kinase': 'P41743', 'resaa': 'T', 'resnum': 564, 'references': set(), 'substrate': 'P27448', 'databases': {'PhosphoSite'}}, {'kinase': 'Q9NRM7', 'resaa': 'S...(truncated) | 31,263 | {} | 2026-03-23 01:53:31 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.psimi.psimi_ontology | 2026-03-23 01:53:32 | 2026-03-23 01:53:33 | 0.45 | list | [PsimiRecord(id='MI:0000', name='molecular interaction', definition='Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.', definition_refs='[PMID:14755292]', parent_ids=None, parent_names=None, synonyms=['mi'], alt_ids=None), PsimiRe...(truncated) | 1,653 | {} | 2026-03-23 01:53:32 | |
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_name_cids |
Not calling `pypath.inputs.pubchem.pubchem_name_cids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_names_cids |
Not calling `pypath.inputs.pubchem.pubchem_names_cids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2026-03-23 01:53:33 | 2026-03-23 01:53:33 | 0.38 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2026-03-23 01:53:33 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2026-03-23 01:53:33 | 2026-03-23 01:53:42 | 9.00 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), Rami...(truncated) | 18,879 | {} | 2026-03-23 01:53:33 | |
| ¶ | pypath.inputs.ramp.ramp_id_types | 2026-03-23 01:53:42 | 2026-03-23 01:53:43 | 0.99 | set | {'pubchem', 'CAS', 'ncbiprotein', 'kegg', 'plantfa', 'entrez', 'chebi', 'LIPIDMAPS', 'swisslipids', 'EN', 'refmet', 'lipidbank', 'kegg_glycan', 'polymer', 'gene_symbol', 'uniprot', 'brenda', 'hmdb', 'ensembl', 'rhea-comp', 'chemspider', 'wikidata'} | 22 | {} | 2026-03-23 01:53:42 | |
| ¶ | pypath.inputs.ramp.ramp_list_tables | 2026-03-23 01:53:43 | 2026-03-23 01:53:51 | 7.77 | dict | {'analyte': ['rampId', 'type'], 'analytehasontology': ['rampCompoundId', 'rampOntologyId'], 'analytehaspathway': ['rampId', 'pathwayRampId', 'pathwaySource'], 'catalyzed': ['rampCompoundId', 'rampGeneId', 'proteinType'], 'chem_props': ['ramp_id', 'chem_data_source', 'chem_source_id', 'iso_smiles', '...(truncated) | 19 | {'fixed': True} | 2026-03-23 01:53:43 | |
| ¶ | pypath.inputs.ramp.ramp_raw |
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_show_tables | 2026-03-23 01:53:51 | 2026-03-23 01:53:51 | 0.00 | NoneType | None | 0 | {'fixed': True} | 2026-03-23 01:53:51 | |
| ¶ | pypath.inputs.ramp.ramp_table |
Not calling `pypath.inputs.ramp.ramp_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_table_df |
Not calling `pypath.inputs.ramp.ramp_table_df`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_table_fields |
Not calling `pypath.inputs.ramp.ramp_table_fields`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2026-03-23 01:53:51 | 2026-03-23 01:53:51 | 0.33 | NoneType | None | 0 | {} | 2026-03-23 01:53:51 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2026-03-23 01:53:51 | 2026-03-23 01:53:52 | 0.10 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2026-03-23 01:53:51 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2026-03-23 01:53:52 | 2026-03-23 01:53:52 | 0.33 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
len(biopaxes.result),
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
|
{} | 2025-08-12 06:52:15 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2026-03-23 01:53:52 | 2026-03-23 01:54:22 | 30.01 | NoneType | None | 0 | {} | 2026-03-23 01:53:52 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2026-03-23 01:54:22 | 2026-03-23 01:54:24 | 1.73 | NoneType | None | 0 | {} | 2026-03-23 01:54:22 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2026-03-23 01:54:24 | 2026-03-23 01:54:49 | 25.07 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2026-03-23 01:54:24 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2026-03-23 01:54:49 | 2026-03-23 02:01:37 | 408.30 | list | [('R-HSA-1059683', <?xml version="1.0" encoding="utf-8"?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 95 on 11/25/25, 4:17 AM using JSBML version 1.5.</p> </annota...(truncated) | 2,848 | {} | 2026-03-23 01:54:49 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2026-03-23 02:02:01 | 2026-03-23 02:02:02 | 1.88 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/cache/9c...(truncated) | 2,848 | {} | 2026-03-23 02:02:01 | |
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2026-03-23 02:02:02 | 2026-03-23 02:02:03 | 0.79 | list | [{'parent': 'R-BTA-109581', 'child': 'R-BTA-109606'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-169911'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-5357769'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-75153'}, {'parent': 'R-BTA-109582', 'child': 'R-BTA-140877'}, {'parent': 'R-BTA-109582', 'child'...(truncated) | 23,403 | {} | 2026-03-23 02:02:02 | |
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2026-03-23 02:02:03 | 2026-03-23 02:02:15 | 11.26 |
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__20260322-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:10 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathway_relations | 2026-03-23 02:02:15 | 2026-03-23 02:02:15 | 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__20260322-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:23 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathways | 2026-03-23 02:02:15 | 2026-03-23 02:02:16 | 1.05 |
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__20260322-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:23 | |||
| ¶ | pypath.inputs.reactome_old.reactome_uniprots | 2026-03-23 02:02:16 | 2026-03-23 02:02:33 | 17.88 |
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__20260322-202402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:24 | |||
| ¶ | pypath.inputs.rhea.rhea_gui | 2026-03-23 02:02:34 | 2026-03-23 02:02:38 | 4.75 | list | [{'Reaction identifier': 'RHEA:10000', 'Equation': 'pentanamide + H2O = pentanoate + NH4(+)', 'ChEBI name': 'pentanamide;water;valerate;ammonium', 'ChEBI identifier': 'CHEBI:16459;CHEBI:15377;CHEBI:31011;CHEBI:28938', 'EC number': 'EC:3.5.1.50', 'Enzymes': '0', 'Gene Ontology': 'GO:0050168 pentanami...(truncated) | 18,343 | {} | 2026-03-23 02:02:34 | |
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2026-03-23 02:02:38 | 2026-03-23 02:02:55 | 16.62 | 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='mouse'), ScconnectAnnota...(truncated) | 3,290 | {} | 2026-03-23 02:02:38 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2026-03-23 02:02:55 | 2026-03-23 02:02:55 | 0.02 | set | {Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:A0A087WWS6_P0DY56, Complex: COMPLEX:Q16552_Q96PD4, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:O15263, Complex: COMPLEX:P0DML2_P0DML3, ...(truncated) | 17 | {} | 2026-03-23 02:02:55 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2026-03-23 02:02:55 | 2026-03-23 02:07:58 | 302.94 | list | [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) | 1,784 | {} | 2026-03-23 02:02:55 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2026-03-23 02:07:58 | 2026-03-23 02:07:58 | 0.09 | dict | {'CID100003310': {SiderDrug(name='etoposide', atc='L01CB01')}, 'CID100001546': {SiderDrug(name='cladribine', atc='L01BB04')}, 'CID100477468': {SiderDrug(name='FK463', atc='J02AX05')}, 'CID100002082': {SiderDrug(name='albendazole', atc='P02CA03')}, 'CID100000813': {SiderDrug(name='potassium', atc=Non...(truncated) | 1,430 | {} | 2026-03-23 02:07:58 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2026-03-23 02:07:58 | 2026-03-23 02:07:58 | 0.29 | list | [SiderSideeffectMeddra(cid='C0850638', meddra_id='10021769', side_effect_name='Infected bites'), SiderSideeffectMeddra(cid='C2609205', meddra_id='10069249', side_effect_name='Product size issue'), SiderSideeffectMeddra(cid='C0198187', meddra_id='10053296', side_effect_name='Middle ear prosthesis rem...(truncated) | 20,307 | {} | 2026-03-23 02:07:58 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2026-03-23 02:07:58 | 2026-03-23 02:07:59 | 0.86 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0020649', umls_concept_in_meddra='C0020649', side_effect='Hypotension', frequency='19%'), SiderSideeffetFrequency(umls_concept_on_label='C0037199', umls_concept_in_meddra='C0037199', side_effect='Sinusitis', frequency='5%'), SiderSide...(truncated) | 968 | {} | 2026-03-23 02:07:58 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2026-03-23 02:07:59 | 2026-03-23 02:08:01 | 1.43 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0007222', umls_concept_in_meddra='C0007222', side_effect='Cardiovascular disorder'), SiderSideeffect(umls_concept_on_label='C0231528', umls_concept_in_meddra='C0231528', side_effect='Myalgia'), SiderSideeffect(umls_concept_on_label='C0020538'...(truncated) | 1,430 | {} | 2026-03-23 02:07:59 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2026-03-23 02:08:01 | 2026-03-23 02:08:02 | 1.21 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(p...(truncated) | 2 | {} | 2026-03-23 02:08:01 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2026-03-23 02:08:02 | 2026-03-23 02:08:02 | 0.40 | dict | {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 786 | {} | 2026-03-23 02:08:02 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2026-03-23 02:08:02 | 2026-03-23 02:08:03 | 0.39 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2026-03-23 02:08:02 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2026-03-23 02:08:03 | 2026-03-23 02:08:03 | 0.41 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='Rece...(truncated) | 840 | {} | 2026-03-23 02:08:03 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2026-03-23 02:08:03 | 2026-03-23 02:08:04 | 0.75 | 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) | 4,992 | {} | 2026-03-23 02:08:03 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2026-03-23 02:08:04 | 2026-03-23 02:08:07 | 3.03 | list | [{'typ': 'dephosphorylation', 'resnum': 896, 'instance': 'EPKSPGEYVNIEFGS', 'substrate': 'P35568', 'start': 889, 'end': 903, 'kinase': 'Q06124', 'resaa': 'Y', 'motif': 'EPKSPGEYVNIEFGS', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'7515062'}}, {'typ': 'phosphorylation', 'resnum...(truncated) | 13,473 | {} | 2026-03-23 02:08:04 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2026-03-23 02:08:07 | 2026-03-23 02:08:08 | 0.56 | list | [SignorInteraction(source='Q06124', target='P35568', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates', mechanism='dephosphorylation', ncbi_tax_id='9606', pubmeds='7515062', direct=True, ptm_type='dephosphorylation', ptm_residue='Tyr896',...(truncated) | 96,940 | {} | 2026-03-23 02:08:07 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2026-03-23 02:08:08 | 2026-03-23 02:08:33 | 24.89 | dict | {'Q06124': {SignorPathway(pathway='LIF in PDAC'), SignorPathway(pathway='EGFR Signaling'), SignorPathway(pathway='Leptin Signaling'), SignorPathway(pathway='Noonan syndrome'), SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q13363': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'O60216': {Si...(truncated) | 811 | {} | 2026-03-23 02:08:08 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2026-03-23 02:08:33 | 2026-03-23 02:08:33 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 91 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.slc.slc_annotation | 2026-03-23 02:08:33 | 2026-03-23 02:08:33 | 0.37 | list | [SlcAnnotation(Entrez_ID=56172, Ensembl_ID='ENSG00000154122', HGNC_symbol='ANKH', Substrate_class='Orphan', Substrates='', Substrates_PMID='', Coupled_ions='Unknown', Coupled_ions_PMID='', Transport_mechanism='Unknown', Transport_system_PMID='', Subcellular_localization='Unknown', Subcellular_locali...(truncated) | 446 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.slc.slc_chebi_mapping | 2026-03-23 02:08:33 | 2026-03-23 02:08:33 | 0.17 | list | [SlcChebiMapping(Substrate_name_annotation='17-beta-glucuronosyl estradiol', chebi_id='CHEBI:791', chebi_term='17beta-estradiol 17-glucosiduronic acid', synonym='3-hydroxyestra-1,3,5(10)-trien-17beta-yl beta-D-glucopyranosiduronic acid', description='A steroid glucosiduronic acid that consists of 17...(truncated) | 382 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.slc.slc_interactions | 2026-03-23 02:08:33 | 2026-03-23 02:08:33 | 0.10 | list | [SlcInteraction(transporter=SlcTransporter(uniprot='Q9Y5Y0', genesymbol='FLVCR1', entrez=28982, ensg='ENSG00000162769'), substrate=SlcSubstrate(slc_name='Heme', chebi='CHEBI:30413', label='heme', synonyms=['heme', 'hemes']), role='substrate', pmids='15369674', localization='Plasma membrane', transpo...(truncated) | 1,288 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.slc.slc_localization_annotations | 2026-03-23 02:08:33 | 2026-03-23 02:08:33 | 0.06 | dict | {'Q9HCJ1': {SlcLocalization(localization='Unknown', pmids=None)}, 'Q13286': {SlcLocalization(localization='Endosome; Lysosome', pmids='15471887;22261744')}, 'Q96SL1': {SlcLocalization(localization='Lysosome', pmids='21692750')}, 'Q9Y5Y0': {SlcLocalization(localization='Plasma membrane', pmids='18815...(truncated) | 446 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.slc.slc_substrate_ontology | 2026-03-23 02:08:33 | 2026-03-23 02:08:34 | 0.66 | list | [SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='heme', ChEBI_ID='CHEBI:30413', ChEBI_subontology='chemical entity'), SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='cyclic tetrapyrrole', ChEB...(truncated) | 24,810 | {} | 2026-03-23 02:08:33 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2026-03-23 02:08:34 | 2026-03-23 02:09:04 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/spike.py", line 197, in spike_complexes
interactions = spike_interactions(min_confidence = min_confidence)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/spike.py", line 50, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2026-02-16 02:18:22 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2026-03-23 02:09:04 | 2026-03-23 02:09:34 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/spike.py", line 50, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2026-02-16 02:18:26 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2026-03-23 02:09:34 | 2026-03-23 02:10:27 | 53.28 | 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 | {} | 2026-03-23 02:09:34 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2026-03-23 02:10:27 | 2026-03-23 02:11:46 | 78.31 | 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 | {} | 2026-03-23 02:10:27 | |
| ¶ | pypath.inputs.string.string_effects | 2026-03-23 02:11:46 | 2026-03-23 02:11:55 | 8.71 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2026-03-23 02:11:46 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2026-03-23 02:11:56 | 2026-03-23 02:12:20 | 23.93 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {} | 2026-03-23 02:11:56 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2026-03-23 02:12:20 | 2026-03-23 02:12:21 | 1.15 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2026-03-23 02:12:20 | |
| ¶ | pypath.inputs.string.string_species | 2026-03-23 02:12:21 | 2026-03-23 02:12:21 | 0.11 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2026-03-23 02:12:21 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2026-03-23 02:12:21 | 2026-03-23 02:12:24 | 2.63 | dict | {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC12', 'SLC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC5', 'SLC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,844 | {} | 2026-03-23 02:12:21 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2026-03-23 02:12:24 | 2026-03-23 02:12:27 | 3.76 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2026-03-23 02:12:24 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2026-03-23 02:12:27 | 2026-03-23 02:12:29 | 1.10 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,345 | {} | 2026-03-23 02:12:27 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2026-03-23 02:12:29 | 2026-03-23 02:12:29 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2026-03-23 02:12:29 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2026-03-23 02:12:29 | 2026-03-23 02:12:29 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2026-03-23 02:12:29 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2026-03-23 02:12:29 | 2026-03-23 02:12:34 | 5.79 |
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__20260322-202402/pypath_git/pypath/inputs/tcdb/__init__.py", line 95, in tcdb_annotations
for ac, (tc, family) in iteritems(classes):
^^^^^^^^^
NameError: name 'iteritems' is not defined
|
{} | 2025-08-13 07:12:59 | |||
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2026-03-23 02:12:34 | 2026-03-23 02:12:34 | 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) | 24,437 | {} | 2026-03-23 02:12:34 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2026-03-23 02:12:34 | 2026-03-23 02:12:34 | 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) | 2,155 | {} | 2026-03-23 02:12:34 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2026-03-23 02:12:35 | 2026-03-23 02:12:35 | 0.31 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,873 | {} | 2026-03-23 02:12:35 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2026-03-23 02:12:35 | 2026-03-23 02:12:39 | 4.51 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2026-03-23 02:12:35 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2026-03-23 02:12:39 | 2026-03-23 02:13:01 | 21.75 | set | {ThreedcomplexContact(pdb='1q6r_2', uniprot_1='P39304', uniprot_2='P39304', chain_1='A', chain_2='B', n_residues=26.5, length_1=214, length_2=215, domain_s1=('51366',), domain_p1=('PF00215.19',), domain_s2=('51366',), domain_p2=('PF00215.19',), ident=True, homo=True), ThreedcomplexContact(pdb='2g2q_...(truncated) | 259,347 | {} | 2026-03-23 02:12:39 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2026-03-23 02:13:02 | 2026-03-23 02:16:31 | 209.13 | list | [<pypath.internals.intera.DomainDomain object at 0x7f5a43c59850>, <pypath.internals.intera.DomainDomain object at 0x7f5a306e6c50>, <pypath.internals.intera.DomainDomain object at 0x7f5a35e79c10>, <pypath.internals.intera.DomainDomain object at 0x7f5a521caed0>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,076 | {} | 2026-03-23 02:13:02 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2026-03-23 02:16:32 | 2026-03-23 02:16:41 | 9.15 | dict | {'1q6r_2': {('P39304', 'P39304'): 26.5}, '2g2q_4': {('P68460', 'P68460'): 1.0}, '3e3g_2': {('P45148', 'P45148'): 13.5}, '1zp3_3': {('P0AEZ1', 'P0AEZ1'): 41.0}, '1vk8_1': {('Q9WYV6', 'Q9WYV6'): 10.0}, '2xwn_1': {('P9WKG9', 'P9WKG9'): 36.0}, '4by7_1': {('P16370', 'P40422'): 12.5, ('P16370', 'P22139'):...(truncated) | 80,976 | {} | 2026-03-23 02:16:32 | |
| ¶ | pypath.inputs.threedid.get_3did | 2026-03-23 02:16:41 | 2026-03-23 03:21:58 | 3,917.00 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7f5974f74710>, <pypath.internals.intera.DomainDomain object at 0x7f5a3fe01c50>, <pypath.internals.intera.DomainDomain object at 0x7f5a4aaf2290>, <pypath.internals.intera.DomainDomain object at 0x7f59fa537590>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2026-03-23 02:16:41 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2026-03-23 03:21:58 | 2026-03-23 03:37:55 | 956.10 | dict | {} | 0 | {} | 2026-03-23 03:21:58 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2026-03-23 03:37:55 | 2026-03-23 03:38:14 | 19.55 | dict | {'P18825': {TopdbAnnotation(membrane='Cytoplasm', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='Extracellular', topology='Membrane', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell membrane', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='...(truncated) | 2,025 | {} | 2026-03-23 03:37:55 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2026-03-23 03:38:14 | 2026-03-23 03:38:14 | 0.08 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2026-03-23 03:38:14 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2026-03-23 03:38:14 | 2026-03-23 03:38:14 | 0.00 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2026-03-23 03:38:14 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2026-03-23 03:38:14 | 2026-03-23 03:38:14 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;11290752;12601176', 'Fusion protein-pull down assay;Patch clamp;Calcium measurement;Fl...(truncated) | 359 | {} | 2026-03-23 03:38:14 | |
| ¶ | pypath.inputs.trip.trip_process | 2026-03-23 03:38:14 | 2026-03-23 03:38:14 | 0.00 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2026-03-23 03:38:14 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2026-03-23 03:38:14 | 2026-03-23 03:38:45 | 30.73 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/trrust.py", line 87, in trrust_human
return trrust_interactions('human')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
interactions = [TrrustInteraction(line) for line in c.result]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{} | 2026-02-15 02:04:18 | |||
| ¶ | pypath.inputs.trrust.trrust_interactions | 2026-03-23 03:38:45 | 2026-03-23 03:39:15 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
interactions = [TrrustInteraction(line) for line in c.result]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{} | 2026-02-15 02:04:22 | |||
| ¶ | pypath.inputs.trrust.trrust_mouse | 2026-03-23 03:39:15 | 2026-03-23 03:39:45 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/trrust.py", line 92, in trrust_mouse
return trrust_interactions('mouse')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20260322-202402/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
interactions = [TrrustInteraction(line) for line in c.result]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{} | 2026-02-15 02:04:22 | |||
| ¶ | pypath.inputs.twosides.twosides_interactions | 2026-03-23 03:39:45 | 2026-03-23 03:43:35 | 230.13 | 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 | {} | 2026-03-23 03:39:45 | |
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2026-03-23 03:43:35 | 2026-03-23 03:43:35 | 0.01 | list | [UnichemSource(number=49, label='Probes&Drugs', name='probes_and_drugs', description='Source of chemical probes and drugs', acquisition='2026-03-22'), UnichemSource(number=22, label='PubChem', name='pubchem', description='A database of normalized PubChem compounds (CIDs) from the PubChem Database.',...(truncated) | 19 | {} | 2026-03-23 03:43:35 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2026-03-23 03:43:35 | 2026-03-23 03:43:35 | 0.00 | dict | {49: 'Probes&Drugs', 22: 'PubChem', 31: 'BindingDB', 33: 'LIPID MAPS®', 14: 'FDA SRS', 24: 'NMRShiftDB', 34: 'DrugCentral', 1: 'ChEMBL', 3: 'RSCB PDB', 38: 'Rhea', 15: 'SureChEMBL', 37: 'Brenda', 41: 'SwissLipids', 50: 'CSD', 28: 'MolPort', 4: 'Guide to Pharmacology', 7: 'ChEBI', 2: 'DrugBank', 18: 'HMDB'} | 19 | {} | 2026-03-23 03:43:35 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2026-03-23 03:43:35 | 2026-03-23 03:43:36 | 0.54 | list | [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ13', 'K7EN86'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZ66', 'K7EQ86'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZK0', 'A0A024QZP7'], ['A0A024Q...(truncated) | 72,409 | {} | 2026-03-23 03:43:35 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2026-03-23 03:43:36 | 2026-03-23 03:43:52 | 16.15 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A096LP01': {UniprotFamily(family='SMIM26', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0A8I5KQE6': {UniprotFamily(...(truncated) | 14,503 | {} | 2026-03-23 03:43:36 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2026-03-23 03:43:52 | 2026-03-23 03:44:02 | 10.10 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Reference proteome'),...(truncated) | 20,431 | {} | 2026-03-23 03:43:52 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2026-03-23 03:44:02 | 2026-03-23 03:44:02 | 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) | 27,908 | {} | 2026-03-23 03:44:02 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2026-03-23 03:44:02 | 2026-03-23 03:44:04 | 1.72 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Pinus balsamea', 'Abies balsamea'}, 'H8ZM71': {'Balsam fir', 'Pinus balsamea', 'Abies balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Grand fir', 'Abies grandis', 'Pinu...(truncated) | 559,781 | {} | 2026-03-23 03:44:02 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2026-03-23 03:44:04 | 2026-03-23 03:44:20 | 15.64 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A096LP01': {UniprotTissue(tissue='Kidney', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Plasma', level='undefined'), UniprotTissue(tissue='Skeletal muscle', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tis...(truncated) | 10,185 | {} | 2026-03-23 03:44:04 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2026-03-23 03:44:20 | 2026-03-23 03:45:08 | 48.17 | dict | {'A0A087X1C5': {UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', ...(truncated) | 5,253 | {} | 2026-03-23 03:44:20 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2026-03-23 03:45:08 | 2026-03-23 03:45:08 | 0.01 | set | {'P07949', 'Q96T52', 'O95429', 'Q86XK7', 'Q6UXN8', 'P27694', 'P04424', 'Q08477', 'P17482', 'Q6ZMD2', 'Q9Y3D9', 'P56199', 'Q712K3', 'Q8NB50', 'P22681', 'A6NGZ8', 'P55735', 'Q8TF74', 'O14519', 'Q8TCJ0', 'Q92540', 'Q16134', 'Q6UW60', 'Q9Y5G8', 'Q8IUR7', 'Q9UH17', 'P30041', 'Q9BXA5', 'Q8N8V2', 'Q495M9',...(truncated) | 20,431 | {} | 2026-03-23 03:45:08 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2026-03-23 03:45:08 | 2026-03-23 03:45:48 | 39.69 | set | {'A0A6H0MU04', 'A0A0A7C9W8', 'A6NAF0', 'E7EQE8', 'A0A1C8DSJ8', 'Q4LEK1', 'Q9GIL1', 'Q5SBK2', 'A0A343H8T4', 'A0A343SUV0', 'R4KW00', 'E0WBY1', 'H9NRP1', 'Q9H657', 'A0A804HIG1', 'A0A494C023', 'H9T0Z6', 'A0A0A7C5M3', 'A0A0E3DC51', 'Q6UXV5', 'A0A5C2GQQ6', 'A0A059RG71', 'A0A141PNN4', 'A0A7P0T9L0', 'A0A5C2...(truncated) | 184,724 | {} | 2026-03-23 03:45:08 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2026-03-23 03:45:48 | 2026-03-23 03:45:48 | 0.00 | set | {'A0A6H0MU04', 'P07949', 'A0A0A7C9W8', 'E7EQE8', 'A0A1C8DSJ8', 'A6NAF0', 'Q4LEK1', 'Q9GIL1', 'Q5SBK2', 'A0A343H8T4', 'O95429', 'Q86XK7', 'A0A343SUV0', 'R4KW00', 'E0WBY1', 'H9NRP1', 'Q9H657', 'A0A804HIG1', 'A0A494C023', 'H9T0Z6', 'A0A0A7C5M3', 'A0A0E3DC51', 'Q6UXV5', 'P17482', 'A0A5C2GQQ6', 'A0A059RG...(truncated) | 205,155 | {} | 2026-03-23 03:45:48 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2026-03-23 03:45:48 | 2026-03-23 03:45:48 | 0.00 | set | {'A0A6H0MU04', 'P07949', 'A0A0A7C9W8', 'E7EQE8', 'A0A1C8DSJ8', 'A6NAF0', 'Q4LEK1', 'Q9GIL1', 'Q5SBK2', 'A0A343H8T4', 'O95429', 'Q86XK7', 'A0A343SUV0', 'R4KW00', 'E0WBY1', 'H9NRP1', 'Q9H657', 'A0A804HIG1', 'A0A494C023', 'H9T0Z6', 'A0A0A7C5M3', 'A0A0E3DC51', 'Q6UXV5', 'P17482', 'A0A5C2GQQ6', 'A0A059RG...(truncated) | 205,155 | {} | 2026-03-23 03:45:48 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2026-03-23 03:45:48 | 2026-03-23 03:45:48 | 0.06 | NoneType | None | 0 | {} | 2026-03-23 03:45:48 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2026-03-23 03:45:48 | 2026-03-23 03:45:48 | 0.04 | set | {('UCSC', 'UniProtKB'), ('UniProtKB', 'SGD'), ('UniProtKB-Swiss-Prot', 'ComplexPortal'), ('UniProtKB', 'GeneID'), ('eggNOG', 'UniProtKB-Swiss-Prot'), ('SGD', 'UniProtKB'), ('UniProtKB', 'CollecTF'), ('REBASE', 'UniProtKB'), ('UniProtKB_AC-ID', 'TCDB'), ('MIM', 'UniProtKB-Swiss-Prot'), ('UniProtKB', ...(truncated) | 475 | {} | 2026-03-23 03:45:48 | |
| ¶ | pypath.inputs.wang.cui_interactions | 2026-03-23 03:45:48 | 2026-03-23 03:45:49 | 0.47 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2026-03-23 03:45:48 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2026-03-23 03:45:49 | 2026-03-23 03:45:49 | 0.41 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2026-03-23 03:45:49 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2026-03-23 03:45:49 | 2026-03-23 03:45:54 | 4.90 | dict | {'NA': {WangAnnotation(function='Ligand', location='Extracellular'), WangAnnotation(function='Adapter', location='Cytosol'), WangAnnotation(function='DNA', location='Nucleus'), WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='Peptide', location='Ribosomes'), WangAnnota...(truncated) | 1,547 | {} | 2026-03-23 03:45:49 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2026-03-23 03:45:54 | 2026-03-23 03:45:54 | 0.14 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2026-03-23 03:45:54 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2026-03-23 03:45:54 | 2026-03-23 03:45:55 | 0.33 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {} | 2026-03-23 03:45:54 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2026-03-23 03:45:55 | 2026-03-23 03:45:55 | 0.10 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {} | 2026-03-23 03:45:55 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2026-03-23 03:45:55 | 2026-03-23 03:45:55 | 0.16 | dict | {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) | 466 | {} | 2026-03-23 03:45:55 |
The OmniPath Team • Saez Lab • 2026-03-23