Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2025-10-09 02:22:24 and 2025-10-09 09:05:34; pypath version: 0.16.28 (from git, installed by poetry; 32febdc )
| Modules collected: | 193 |
|---|---|
| Modules failed to import: | 3 |
| Functions collected: | 527 |
| Functions run without error: | 383 |
| Functions returned empty value: | 14 |
| Functions skipped due to lack of arguments: | 111 |
| Functions run with error: | 33 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2025-10-09 02:22:28 | 2025-10-09 02:22:28 | 0.46 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2025-10-09 02:22:28 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2025-10-09 02:22:28 | 2025-10-09 02:22:29 | 0.51 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2025-10-09 02:22:28 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2025-10-09 02:22:29 | 2025-10-09 02:23:28 | 59.07 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {} | 2025-10-09 02:22:29 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2025-10-09 02:23:28 | 2025-10-09 02:23:29 | 1.09 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2025-10-09 02:23:28 | |
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2025-10-09 02:23:29 | 2025-10-09 02:23:50 | 21.47 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {} | 2025-10-09 02:23:29 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2025-10-09 02:23:50 | 2025-10-09 02:26:39 | 169.02 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2025-10-09 02:23:50 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2025-10-09 02:26:39 | 2025-10-09 02:29:52 | 192.27 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 123, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-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-Po0PHRhc-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-Po0PHRhc-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__20251009-022202/pypath_git/pypath/inputs/adrecs.py", line 92, in adrecs_drug_identifiers
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/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__20251009-022202/pypath_git/pypath/inputs/common.py", line 133, in read_xls
raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: None
|
{'broke': True} | 2025-10-08 02:26:06 | |||
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2025-10-09 02:29:52 | 2025-10-09 02:29:53 | 0.86 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='17.08.01.028', badd='BADD_A00842'), parent=AdrecsAdr(adr_class='17.08.01', badd='BADD_A00828')), AdrecsChildParent(child=AdrecsAdr(adr_class='11.01.09.016', badd='BADD_A09075'), parent=AdrecsAdr(adr_class='11.01.09', badd='BADD_A02601')), AdrecsChildPare...(truncated) | 13,828 | {} | 2025-10-09 02:29:52 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2025-10-09 02:29:53 | 2025-10-09 02:29:57 | 3.92 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,243 | {} | 2025-10-09 02:29:53 | |
| ¶ | pypath.inputs.alzpathway.alzpathway_interactions | 2025-10-09 02:29:57 | 2025-10-09 02:29:57 | 0.10 | list | [AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='O00213', genesymbol_a='APP', genesymbol_b='APBB1', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05067', uniprot_b='Q8N8S7', genesymbol_a='APP', genesymbol_b='ENAH', pmids='10799711;12927332'), AlzpathwayInteraction(uniprot_a='P05...(truncated) | 119 | {} | 2025-10-09 02:29:57 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2025-10-09 02:29:57 | 2025-10-09 02:34:00 | 243.78 |
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__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 190, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 131, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 78, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 79, in <genexpr>
*(id_translate(comp) for comp in components)
^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 60, in id_translate
itertools.chain(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 61, in <genexpr>
orthology_mod.translate(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 243, in load
self.tables[key] = globals()[f'{key.resource.capitalize()}Orthology'](
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 870, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1507, in load
oma_data = oma_input.oma_orthologs(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/oma.py", line 115, in oma_orthologs
data = inputs_common.json_read(c.result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 362, in json_read
data = json.loads(data)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'broke': True} | 2025-10-08 02:26:11 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2025-10-09 02:34:00 | 2025-10-09 02:34:05 | 4.96 |
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__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 131, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 78, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 79, in <genexpr>
*(id_translate(comp) for comp in components)
^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 60, in id_translate
itertools.chain(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/baccin2019.py", line 61, in <genexpr>
orthology_mod.translate(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 243, in load
self.tables[key] = globals()[f'{key.resource.capitalize()}Orthology'](
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 870, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1507, in load
oma_data = oma_input.oma_orthologs(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/oma.py", line 115, in oma_orthologs
data = inputs_common.json_read(c.result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 362, in json_read
data = json.loads(data)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'broke': True} | 2025-10-08 02:27:30 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2025-10-09 02:34:05 | 2025-10-09 02:34:05 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2025-10-09 02:34:05 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2025-10-09 02:34:05 | 2025-10-09 02:34:44 | 38.68 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2025-10-09 02:34:05 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2025-10-09 02:34:45 | 2025-10-09 02:35:26 | 41.60 | 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) | 8,742 | {} | 2025-10-09 02:34:45 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2025-10-09 02:35:26 | 2025-10-09 02:35:27 | 1.13 | 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) | 7,470 | {} | 2025-10-09 02:35:26 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2025-10-09 02:35:28 | 2025-10-09 02:35:58 | 30.37 | list | [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) | 303,538 | {} | 2025-10-09 02:35:28 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2025-10-09 02:35:58 | 2025-10-09 02:35:59 | 0.08 | list | [{'type': 'OLIGO', 'vendor': 'PHALANX', 'array': 'OneArray', 'description': None, 'format': 'EXPRESSION', 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'array': 'CODELINK', 'vendor': 'CODELINK', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'type': 'OLIGO', 'array': ...(truncated) | 37 | {} | 2025-10-09 02:35:58 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2025-10-09 02:35:59 | 2025-10-09 02:35:59 | 0.18 | list | [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) | 1,788 | {} | 2025-10-09 02:35:59 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2025-10-09 02:35:59 | 2025-10-09 02:36:00 | 1.08 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2025-10-09 02:35:59 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2025-10-09 02:36:00 | 2025-10-09 02:36:07 | 7.59 | dict | {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) | 216 | {} | 2025-10-09 02:36:00 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2025-10-09 02:36:07 | 2025-10-09 02:36:08 | 0.01 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 330 | {} | 2025-10-09 02:36:07 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2025-10-09 02:36:08 | 2025-10-09 02:36:15 | 7.58 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='Q8N726', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 5,157 | {} | 2025-10-09 02:36:08 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2025-10-09 02:36:15 | 2025-10-09 02:36:17 | 2.27 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {} | 2025-10-09 02:36:15 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2025-10-09 02:36:17 | 2025-10-09 02:36:29 | 11.11 | dict | {'P41221': {CellcallAnnotation(role='ligand')}, 'O75084': {CellcallAnnotation(role='receptor')}, 'P22004': {CellcallAnnotation(role='ligand')}, 'P36894': {CellcallAnnotation(role='receptor')}, 'P20827': {CellcallAnnotation(role='ligand')}, 'P54764': {CellcallAnnotation(role='receptor')}, 'Q14393': {...(truncated) | 460 | {} | 2025-10-09 02:36:17 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2025-10-09 02:36:29 | 2025-10-09 02:36:29 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2025-10-09 02:36:29 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2025-10-09 02:36:29 | 2025-10-09 02:36:29 | 0.82 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2025-10-09 02:36:29 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2025-10-09 02:36:30 | 2025-10-09 02:36:30 | 0.11 | list | [CellcallInteraction(ligand_uniprot='P41221', receptor_uniprot='O75084', core=True), CellcallInteraction(ligand_uniprot='P22004', receptor_uniprot='P36894', core=True), CellcallInteraction(ligand_uniprot='P20827', receptor_uniprot='P54764', core=True), CellcallInteraction(ligand_uniprot='Q14393', re...(truncated) | 797 | {} | 2025-10-09 02:36:30 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2025-10-09 02:36:30 | 2025-10-09 02:36:30 | 0.65 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='ECM')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinterac...(truncated) | 3,425 | {} | 2025-10-09 02:36:30 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2025-10-09 02:36:30 | 2025-10-09 02:36:40 | 10.07 | dict | {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='agonist', pathway='NODAL', category...(truncated) | 1,523 | {} | 2025-10-09 02:36:30 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2025-10-09 02:36:40 | 2025-10-09 02:36:47 | 6.86 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'Q9H2X0', 'O00292', 'O75610', 'Q9H772', 'P41271', 'P12645', 'Q13253', 'O60565'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 32 | {} | 2025-10-09 02:36:40 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2025-10-09 02:36:47 | 2025-10-09 02:36:54 | 6.93 | dict | {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) | 330 | {} | 2025-10-09 02:36:47 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2025-10-09 02:36:54 | 2025-10-09 02:37:01 | 6.87 | dict | {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) | 4 | {} | 2025-10-09 02:36:54 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2025-10-09 02:37:01 | 2025-10-09 02:37:09 | 7.75 | list | [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) | 12,424 | {} | 2025-10-09 02:37:01 | |
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.46 | dict | {'Q9HAP6': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'P29972': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, 'Q9NYZ4': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction...(truncated) | 1,919 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.05 | dict | {Complex: COMPLEX:P05106_P06756: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Ce...(truncated) | 134 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.04 | set | {CellinkerInteraction(ligand='Q9HAP6', receptor='P29972', ligand_location='Membrane', receptor_location='Membrane', resources=None, pmids='19584911', type='Cell adhesion'), CellinkerInteraction(ligand='Q9NYZ4', receptor='Q9BY14', ligand_location='Membrane', receptor_location='Membrane', resources=No...(truncated) | 3,810 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2025-10-09 02:37:09 | 2025-10-09 02:37:09 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2025-10-09 02:37:09 | 2025-10-09 02:37:10 | 0.05 | dict | {'Q9HAP6': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion')}, 'P29972': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, 'Q9NYZ4': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction...(truncated) | 1,785 | {} | 2025-10-09 02:37:09 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.11 | set | {CellinkerInteraction(ligand='5280363', receptor='Q9Y5Y4', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='12466225', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='439260', receptor='P25100', ligand_location=None, receptor_location='Membrane', r...(truncated) | 314 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.00 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 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 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.01 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.52 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.02 | tuple | ({'P20809', Complex FZD3_LRP5: COMPLEX:O75197_Q9NPG1, 'Q9BQ51', 'Q86XM0', 'P39905', 'P01833', 'P22455', 'P15692', 'P20382', 'P00734', 'Q02487', 'Q6EMK4', Complex Dopamine_byDDC_and_SLC18A2: COMPLEX:P20711_Q05940, 'P12872', 'Q16787', Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'O00755', 'A6...(truncated) | 2 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2025-10-09 02:37:10 | 2025-10-09 02:37:10 | 0.01 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,359 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2025-10-09 02:37:10 | 2025-10-09 02:37:11 | 0.40 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='15721238'), CellTalkDBAnnotation(role='receptor', pmid='32196115')}, 'Q...(truncated) | 1,598 | {} | 2025-10-09 02:37:10 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2025-10-09 02:37:11 | 2025-10-09 02:37:11 | 0.16 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2025-10-09 02:37:11 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2025-10-09 02:37:11 | 2025-10-09 02:37:11 | 0.16 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2025-10-09 02:37:11 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2025-10-09 02:37:11 | 2025-10-09 02:37:11 | 0.27 | 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) | 460 | {} | 2025-10-09 02:37:11 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2025-10-09 02:37:11 | 2025-10-09 02:37:53 | 41.63 | list | [Citation(allele='17343', variation_id='2304', nsv='', citation_source='PubMed', citation_id='8535454'), Citation(allele='68089', variation_id='53421', nsv='', citation_source='PubMed', citation_id='7691345'), Citation(allele='625899', variation_id='638078', nsv='', citation_source='PubMed', citatio...(truncated) | 4,191,363 | {} | 2025-10-09 02:37:11 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2025-10-09 02:37:59 | 2025-10-09 02:45:12 | 433.78 | list | [Variant(allele='932225', type='single nucleotide variant', variant='NM_001378615.1(CC2D2A):c.2774G>C (p.Arg925Pro)', entrez='57545', genesymbol='CC2D2A', clinical_significance='Pathogenic/Likely pathogenic', review_status='criteria provided, multiple submitters, no conflicts', rs='200707391', pheno...(truncated) | 7,856,076 | {} | 2025-10-09 02:37:59 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2025-10-09 04:10:51 | 2025-10-09 04:11:06 | 15.17 | list | [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) | 64,990 | {} | 2025-10-09 04:10:51 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2025-10-09 04:11:06 | 2025-10-09 04:11:06 | 0.12 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2025-10-09 04:11:06 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2025-10-09 04:11:07 | 2025-10-09 04:11:07 | 0.16 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2025-10-09 04:11:07 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2025-10-09 04:11:07 | 2025-10-09 04:11:08 | 1.08 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,695 | {} | 2025-10-09 04:11:07 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2025-10-09 04:11:08 | 2025-10-09 04:11:08 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2025-10-09 04:11:08 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2025-10-09 04:11:08 | 2025-10-09 04:13:10 | 122.20 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) | 2,275 | {} | 2025-10-09 04:11:08 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2025-10-09 04:13:10 | 2025-10-09 04:13:27 | 16.49 | list | [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) | 587,995 | {} | 2025-10-09 04:13:10 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2025-10-09 04:13:27 | 2025-10-09 04:13:40 | 13.54 | 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='secretory-pathway', score=0...(truncated) | 22,799 | {} | 2025-10-09 04:13:27 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2025-10-09 04:13:40 | 2025-10-09 04:13:40 | 0.31 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {} | 2025-10-09 04:13:40 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2025-10-09 04:13:40 | 2025-10-09 04:13:41 | 0.02 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2025-10-09 04:13:40 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2025-10-09 04:13:41 | 2025-10-09 04:13:41 | 0.57 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2025-10-09 04:13:41 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2025-10-09 04:13:41 | 2025-10-09 04:13:41 | 0.17 | dict | {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, chr_band='10q11.23', tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',), translocation_partner=(()...(truncated) | 762 | {} | 2025-10-09 04:13:41 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_raw | 2025-10-09 04:13:41 | 2025-10-09 04:13:41 | 0.00 | list | [{'Gene Symbol': 'A1CF', 'Name': 'APOBEC1 complementation factor', 'Entrez GeneId': '29974', 'Genome Location': '10:50799421-50885675', 'Tier': '2', 'Hallmark': '', 'Chr Band': '10q11.23', 'Somatic': 'yes', 'Germline': '', 'Tumour Types(Somatic)': 'melanoma', 'Tumour Types(Germline)': '', 'Cancer Sy...(truncated) | 758 | {} | 2025-10-09 04:13:41 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2025-10-09 04:13:41 | 2025-10-09 04:13:51 | 10.10 | dict | {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) | 1,070 | {'size': -1} | 2025-10-09 04:13:41 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2025-10-09 04:13:51 | 2025-10-09 04:13:51 | 0.05 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='miR-107-CDK6 pathway', cancer='Glioma', pathway_category='Others', effect_on_cancer='Activating', effect_on_cancer_outcome='suppress glioma stem-like properties'), CpadPathwayCancer(pathway='Wnt signaling pathway', cancer='Glioma', pathway_category='Wnt signal...(truncated) | 2 | {} | 2025-10-09 04:13:51 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2025-10-09 04:13:51 | 2025-10-09 04:13:52 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2025-10-09 04:13:51 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2025-10-09 04:13:52 | 2025-10-09 04:14:02 | 10.39 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {} | 2025-10-09 04:13:52 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2025-10-09 04:14:02 | 2025-10-09 04:14:05 | 2.70 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2025-10-09 04:14:02 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2025-10-09 04:14:05 | 2025-10-09 04:14:06 | 0.82 | dict | {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) | 1,449 | {} | 2025-10-09 04:14:05 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2025-10-09 04:14:06 | 2025-10-09 04:14:07 | 0.77 | dict | {'A1A5B4': {CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='A431', value=16.5688...(truncated) | 1,410 | {} | 2025-10-09 04:14:06 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2025-10-09 04:14:07 | 2025-10-09 04:14:07 | 0.39 | dict | {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) | 47 | {} | 2025-10-09 04:14:07 | |
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2025-10-09 04:14:07 | 2025-10-09 04:14:09 | 2.12 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P10600', score=0.300776614000001, cytokine_genesymbol='TGFB3', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P56704', score=0.013742799664961, cytokine_genesymbol='WNT3A', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='Q8NEV9', score=-0.04...(truncated) | 4,887 | {} | 2025-10-09 04:14:07 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2025-10-09 04:14:10 | 2025-10-09 04:14:10 | 0.03 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2025-10-09 04:14:10 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2025-10-09 04:14:10 | 2025-10-09 04:14:13 | 3.04 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2025-10-09 04:14:10 | |
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2025-10-09 04:14:13 | 2025-10-09 04:14:15 | 1.32 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2025-10-09 04:14:13 | |
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2025-10-09 04:14:15 | 2025-10-09 04:14:52 | 37.12 | list | [DdinterInteraction(drug1_id='DDInter395', drug1_name='Clemastine', drug2_id='DDInter532', drug2_name='Diamorphine', level='Moderate'), DdinterInteraction(drug1_id='DDInter1309', drug1_name='Nizatidine', drug2_id='DDInter1019', drug2_name='Lamivudine', level='Unknown'), DdinterInteraction(drug1_id='...(truncated) | 160,235 | {} | 2025-10-09 04:14:15 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2025-10-09 04:14:52 | 2025-10-09 05:02:36 | 2,864.52 | list | [DdinterIdentifiers(ddinter='DDInter1365', drugbank='DB01062', chembl='CHEMBL1231', pubchem='46508005'), DdinterIdentifiers(ddinter='DDInter1233', drugbank='DB00648', chembl='CHEMBL1670', pubchem='46508319'), DdinterIdentifiers(ddinter='DDInter171', drugbank='DB15719', chembl=None, pubchem=None), Dd...(truncated) | 1,939 | {} | 2025-10-09 04:14:52 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2025-10-09 05:02:36 | 2025-10-09 05:02:37 | 0.43 | int | 1939 | 0 | {} | 2025-10-09 05:02:36 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2025-10-09 05:02:37 | 2025-10-09 05:02:37 | 0.14 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2025-10-09 05:02:37 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2025-10-09 05:02:37 | 2025-10-09 05:02:38 | 0.64 | list | [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) | 537 | {} | 2025-10-09 05:02:37 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2025-10-09 05:02:38 | 2025-10-09 05:02:38 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2025-10-09 05:02:38 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2025-10-09 05:02:38 | 2025-10-09 05:02:44 | 6.15 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), DgidbAnnotation(category='TRANSCRIPTION FACTOR', source='Pharos'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='GO'), DgidbAnnot...(truncated) | 9,973 | {} | 2025-10-09 05:02:38 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2025-10-09 05:02:44 | 2025-10-09 05:02:50 | 6.36 | list | [DgidbInteraction(genesymbol='NULL', gene_concept_id='NULL', resource='TTD', type='NULL', drug_name='LASOFOXIFENE', drug_concept_id='ncit:C80679', score='NULL', approved='TRUE', anti_neoplastic='FALSE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='KCNH2', gene_concept_id='hgnc:6251', resourc...(truncated) | 84,175 | {} | 2025-10-09 05:02:44 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2025-10-09 05:02:50 | 2025-10-09 05:02:51 | 0.20 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2025-10-09 05:02:50 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2025-10-09 05:02:51 | 2025-10-09 05:02:51 | 0.45 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource='TIGA', source_score=27, confidence=0.865), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:535', disease='Sleep disorder', resource='TIGA'...(truncated) | 30,470 | {} | 2025-10-09 05:02:51 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2025-10-09 05:02:51 | 2025-10-09 05:02:55 | 3.60 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:150', disease='Disease of mental health', resource='TIGA', source_score=18, confidence=0.717), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resou...(truncated) | 345,254 | {} | 2025-10-09 05:02:51 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2025-10-09 05:02:55 | 2025-10-09 05:02:55 | 0.14 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:1928', disease='Williams-Beuren syndrome', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Cranio...(truncated) | 7,775 | {} | 2025-10-09 05:02:55 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2025-10-09 05:02:55 | 2025-10-09 05:02:56 | 0.96 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050177', disease='Monogenic disease', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050736', disease='Autosomal...(truncated) | 98,705 | {} | 2025-10-09 05:02:55 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2025-10-09 05:02:56 | 2025-10-09 05:03:01 | 5.14 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.253, confidence=3.626, 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) | 288,399 | {} | 2025-10-09 05:02:56 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2025-10-09 05:03:01 | 2025-10-09 05:09:01 | 360.53 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/diseases.py", line 132, in _diseases_general
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-13 05:00:57 | |||
| ¶ | pypath.inputs.domino.domino_ddi | 2025-10-09 05:09:02 | 2025-10-09 05:09:08 | 6.85 | list | [<pypath.internals.intera.DomainDomain object at 0x7fbeb4eaa890>, <pypath.internals.intera.DomainDomain object at 0x7fc0149a9d10>, <pypath.internals.intera.DomainDomain object at 0x7fc0149ab590>, <pypath.internals.intera.DomainDomain object at 0x7fc0149ab810>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2025-10-09 05:09:02 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2025-10-09 05:09:08 | 2025-10-09 05:09:10 | 1.18 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7fc188e65f90>, <pypath.internals.intera.DomainDomain object at 0x7fc188e640d0>, <pypath.internals.intera.DomainDomain object at 0x7fc188e67790>, <pypath.internals.intera.DomainDomain object at 0x7fc188e67e50>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2025-10-09 05:09:08 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2025-10-09 05:09:10 | 2025-10-09 05:09:10 | 0.35 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2025-10-09 05:09:10 | |
| ¶ | pypath.inputs.domino.get_domino | 2025-10-09 05:09:10 | 2025-10-09 05:09:10 | 0.33 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2025-10-09 05:09:10 | |
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2025-10-09 05:09:10 | 2025-10-09 05:09:20 | 9.42 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2025-10-09 05:09:10 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-10-09 05:09:20 | 2025-10-09 05:09:34 | 13.97 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-10-09 05:09:20 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-10-09 05:09:34 | 2025-10-09 05:09:36 | 1.89 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-10-09 05:09:34 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-10-09 05:09:36 | 2025-10-09 05:09:37 | 1.37 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-10-09 05:09:36 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-10-09 05:09:37 | 2025-10-09 05:09:51 | 13.86 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2025-10-09 05:09:37 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-10-09 05:09:51 | 2025-10-09 05:09:51 | 0.36 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{} | 2025-08-12 05:02:53 | |||
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2025-10-09 05:09:51 | 2025-10-09 05:09:52 | 1.04 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2025-10-09 05:09:51 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2025-10-09 05:09:52 | 2025-10-09 05:09:54 | 1.29 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2025-10-09 05:09:52 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2025-10-09 05:09:54 | 2025-10-09 05:09:54 | 0.22 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 353 | {} | 2025-10-09 05:09:54 | |
| ¶ | pypath.inputs.elm.elm_domains | 2025-10-09 05:09:54 | 2025-10-09 05:09:55 | 0.86 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2025-10-09 05:09:54 | |
| ¶ | pypath.inputs.elm.elm_instances | 2025-10-09 05:09:55 | 2025-10-09 05:13:32 | 217.40 | list | [ELMInstance(accession='Accession', type='ELMType', identifier='ELMIdentifier', uniprot_id='ProteinName', uniprot='Primary_Acc', synonyms='Accessions', start='Start', end='End', references='References', methods='Methods', logic='InstanceLogic', pdb='PDB', organism='Organism'), ELMInstance(accession=...(truncated) | 4,278 | {'size': 1} | 2025-10-09 05:09:55 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2025-10-09 05:13:32 | 2025-10-09 05:16:12 | 160.20 |
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__20251009-022202/pypath_git/pypath/inputs/elm.py", line 177, in elm_interactions
motif_match = reupi.match(l[2])
~^^^
IndexError: tuple index out of range
|
{} | 2025-10-05 04:57:27 | |||
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2025-10-09 05:16:12 | 2025-10-09 05:16:21 | 8.69 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 171, in embrace_annotations
for rec in embrace_translated(organism = organism):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 101, in embrace_translated
ligands = _embrace_id_translation(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 78, in _embrace_id_translation
orthologs = orthology.translate(
^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 243, in load
self.tables[key] = globals()[f'{key.resource.capitalize()}Orthology'](
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 870, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1507, in load
oma_data = oma_input.oma_orthologs(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/oma.py", line 115, in oma_orthologs
data = inputs_common.json_read(c.result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 362, in json_read
data = json.loads(data)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'broke': True} | 2025-10-08 05:07:39 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2025-10-09 05:16:21 | 2025-10-09 05:16:27 | 5.59 |
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__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 137, in embrace_interactions
for rec in embrace_translated(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 101, in embrace_translated
ligands = _embrace_id_translation(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 78, in _embrace_id_translation
orthologs = orthology.translate(
^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 243, in load
self.tables[key] = globals()[f'{key.resource.capitalize()}Orthology'](
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 870, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1507, in load
oma_data = oma_input.oma_orthologs(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/oma.py", line 115, in oma_orthologs
data = inputs_common.json_read(c.result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 362, in json_read
data = json.loads(data)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'broke': True} | 2025-10-08 05:07:46 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2025-10-09 05:16:27 | 2025-10-09 05:16:27 | 0.12 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2025-10-09 05:16:27 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2025-10-09 05:16:27 | 2025-10-09 05:16:32 | 5.45 |
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__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 101, in embrace_translated
ligands = _embrace_id_translation(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/embrace.py", line 78, in _embrace_id_translation
orthologs = orthology.translate(
^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2787, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 243, in load
self.tables[key] = globals()[f'{key.resource.capitalize()}Orthology'](
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 870, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/orthology.py", line 1507, in load
oma_data = oma_input.oma_orthologs(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/oma.py", line 115, in oma_orthologs
data = inputs_common.json_read(c.result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/common.py", line 362, in json_read
data = json.loads(data)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'broke': True} | 2025-10-08 05:07:46 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2025-10-09 05:16:32 | 2025-10-09 05:16:33 | 0.41 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2025-10-09 05:16:32 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2025-10-09 05:16:33 | 2025-10-09 05:16:33 | 0.44 | 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='Y', ensembl_name='cabingdonii'), Ense...(truncated) | 348 | {} | 2025-10-09 05:16:33 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.exocarta.get_exocarta | 2025-10-09 05:16:33 | 2025-10-09 05:17:46 | 73.27 | list | [ExocartaRecord(entrez='967', genesymbol='CD63', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='1803', genesymbol='DPP4', organism=9606, reference=('11487543', (9606,), 'Intestinal epithelial cells')), ExocartaRecord(entrez='79574', genesymbol=...(truncated) | 35,259 | {} | 2025-10-09 05:16:33 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2025-10-09 05:17:46 | 2025-10-09 05:20:56 | 189.40 | list | [VesiclepediaRecord(entrez='31848', genesymbol='His3.3B', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entrez='33736', genesymbol='His3.3A', organism=9606, reference=('16342139', (9606,), 'B cells', ('Microparticles',))), VesiclepediaRecord(entr...(truncated) | 290,197 | {} | 2025-10-09 05:17:46 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2025-10-09 05:20:56 | 2025-10-09 05:20:56 | 0.08 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 354 | {} | 2025-10-09 05:20:56 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2025-10-09 05:20:56 | 2025-10-09 05:20:57 | 1.20 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,405 | {} | 2025-10-09 05:20:56 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2025-10-09 05:20:57 | 2025-10-09 05:21:51 | 54.30 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0005743', 'GO:0016020', 'GO:0045275'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0045259', 'GO:0005743'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0045259', 'GO:0005743'}, 'A0A023I7N5': {'GO:0005743', 'GO:0016020'}, 'A0A02...(truncated) | 2 | {} | 2025-10-09 05:20:57 | |
| ¶ | pypath.inputs.go.get_goslim | 2025-10-09 05:21:51 | 2025-10-09 05:21:53 | 1.25 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 142 | {} | 2025-10-09 05:21:51 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-10-09 05:21:53 | 2025-10-09 05:27:52 | 359.37 | dict | {'C': {'GO:0160111': {('GO:0160110', 'part_of'), ('GO:0110165', 'is_a'), ('GO:0097649', 'part_of')}, 'GO:0160112': {('GO:0160110', 'part_of'), ('GO:0110165', 'is_a'), ('GO:0097649', 'part_of')}, 'GO:1990657': {('GO:1990658', 'is_a'), ('GO:1903958', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) | 3 | {} | 2025-10-09 05:21:53 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2025-10-09 05:27:52 | 2025-10-09 05:27:52 | 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__20251009-022202/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:26 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-10-09 05:27:52 | 2025-10-09 05:27:57 | 4.80 | dict | {'C': {'GO:0160111': {('GO:0160110', 'part_of'), ('GO:0110165', 'is_a'), ('GO:0097649', 'part_of')}, 'GO:0160112': {('GO:0160110', 'part_of'), ('GO:0110165', 'is_a'), ('GO:0097649', 'part_of')}, 'GO:1990657': {('GO:1990658', 'is_a'), ('GO:1903958', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) | 3 | {} | 2025-10-09 05:27:52 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-10-09 05:27:57 | 2025-10-09 05:28:00 | 2.89 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2025-10-09 05:27:57 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2025-10-09 05:28:00 | 2025-10-09 05:28:06 | 6.29 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='located_in', go_id='GO:0005829', reference='GO_REF:0000052', evidence_code='IDA', with_or_from='', aspect='C', db_object_name='Diphosphoinositol polyphosphate phosphohydrolase NUDT4B', db_ob...(truncated) | 19,697 | {} | 2025-10-09 05:28:00 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-10-09 05:28:09 | 2025-10-09 05:28:10 | 1.14 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2025-10-09 05:28:09 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2025-10-09 05:28:10 | 2025-10-09 05:28:10 | 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__20251009-022202/pypath_git/pypath/inputs/go.py", line 860, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:43 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2025-10-09 05:28:10 | 2025-10-09 05:28:21 | 11.04 | dict | {'A0A087X1C5': ['GO:0005506', 'GO:0005737', 'GO:0005739', 'GO:0006805', 'GO:0016020', 'GO:0016712', 'GO:0019369', 'GO:0020037', 'GO:0042178', 'GO:0043231', 'GO:0070330'], 'A0A0B4J2F0': ['GO:0005739', 'GO:0005741', 'GO:0006986', 'GO:1900101'], 'A0A0C5B5G6': ['GO:0001649', 'GO:0003677', 'GO:0005615', ...(truncated) | 19,390 | {} | 2025-10-09 05:28:10 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-10-09 05:28:21 | 2025-10-09 05:28:25 | 4.32 | dict | {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160111', 'part_of'), ('GO:0160112', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160279', 'part_of'), ('GO:0160280', 'part_of')}, 'GO:1990676': {(...(truncated) | 3 | {} | 2025-10-09 05:28:21 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2025-10-09 05:28:25 | 2025-10-09 05:28:26 | 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__20251009-022202/pypath_git/pypath/inputs/go.py", line 291, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/go.py", line 213, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-12 05:19:59 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-10-09 05:28:26 | 2025-10-09 05:28:30 | 4.32 | dict | {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160111', 'part_of'), ('GO:0160112', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160279', 'part_of'), ('GO:0160280', 'part_of')}, 'GO:1990676': {(...(truncated) | 3 | {} | 2025-10-09 05:28:26 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-10-09 05:28:30 | 2025-10-09 05:28:34 | 3.62 | dict | {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) | 3 | {} | 2025-10-09 05:28:30 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2025-10-09 05:28:34 | 2025-10-09 05:28:34 | 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__20251009-022202/pypath_git/pypath/inputs/go.py", line 572, in go_terms_goose
sql_path = os.path.join(common.DATA, 'goose_terms.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{} | 2025-08-12 05:20:07 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-10-09 05:28:34 | 2025-10-09 05:28:37 | 3.64 | dict | {'C': {'GO:0160130': 'mRNA cap methyltransferase RNMT:RAMAC complex', 'GO:0160132': 'meisosome', 'GO:0160115': 'axonemal microtubule doublet ribbon', 'GO:0160110': 'axonemal microtubule doublet inner sheath', 'GO:0160111': 'axonemal A tubule inner sheath', 'GO:0160112': 'axonemal B tubule inner shea...(truncated) | 3 | {} | 2025-10-09 05:28:34 | |
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2025-10-09 05:28:37 | 2025-10-09 05:28:37 | 0.24 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 808 | {} | 2025-10-09 05:28:37 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2025-10-09 05:28:37 | 2025-10-09 05:28:39 | 1.29 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2025-10-09 05:28:37 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2025-10-09 05:28:39 | 2025-10-09 05:28:44 | 5.16 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {} | 2025-10-09 05:28:39 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2025-10-09 05:28:44 | 2025-10-09 05:28:44 | 0.23 | dict | {'Q9P2I0': {GutmgeneAnnotation(gut_microbiota='Lactiplantibacillus plantarum', gut_microbiota_ncbi_id='1590', rank='species', strain='MB452', alteration='inhibition', throughput='high-throughput', associative_mode='causally', sample='Caco-2 cells', experimental_method='cell culture', measurement_tec...(truncated) | 111 | {} | 2025-10-09 05:28:44 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2025-10-09 05:28:44 | 2025-10-09 05:28:44 | 0.01 | list | [GutmgeneRaw(index='48', pmid='21143932', gut_microbiota='Lactiplantibacillus plantarum', gut_microbiota_ncbi_id='1590', rank='species', strain='MB452', gene='CPSF2', gene_id='53981', alteration='inhibition', throughput='high-throughput', associative_mode='causally', organism='human', sample='Caco-2...(truncated) | 243 | {} | 2025-10-09 05:28:44 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2025-10-09 05:28:44 | 2025-10-09 05:28:44 | 0.22 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2025-10-09 05:28:44 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2025-10-09 05:28:44 | 2025-10-09 05:28:44 | 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 | {} | 2025-10-09 05:28:44 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2025-10-09 05:28:44 | 2025-10-09 05:28:46 | 1.75 | dict | {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='Alpha-2-macroglobulin family')}, 'A8K2U0': {HGNCGeneGroupAnnotation(mainclass='Alpha-2...(truncated) | 15,691 | {} | 2025-10-09 05:28:44 | |
| ¶ | pypath.inputs.hint.hint_interactions | 2025-10-09 05:28:46 | 2025-10-09 05:28:52 | 5.68 | list | [HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='LC'), HintInteraction(id_a='A0A024R2I8', id_b='F1D8Q5', pmids=['19211732', '7746322', '9171239', '9368056', '9415406'], quality='HT'), HintInteraction(id_a='A0A024R2I8', id_b='...(truncated) | 88,230 | {} | 2025-10-09 05:28:46 | |
| ¶ | pypath.inputs.hint.hint_raw | 2025-10-09 05:28:52 | 2025-10-09 05:28:52 | 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 | {} | 2025-10-09 05:28:52 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2025-10-09 05:28:52 | 2025-10-09 05:29:03 | 11.09 | list | [HippieInteraction(id_a='P19320', id_b='P42766', score=0.82, methods=None, references=('19738201', '22623428'), sources=None, organisms=None), HippieInteraction(id_a='Q9Y241', id_b='O94829', score=0.82, methods=None, references=('28514442', '33961781'), sources=None, organisms=None), HippieInteracti...(truncated) | 102,409 | {} | 2025-10-09 05:28:52 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2025-10-09 05:29:03 | 2025-10-09 05:30:20 | 76.21 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2025-10-09 05:29:03 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2025-10-09 05:30:20 | 2025-10-09 05:30:20 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {} | 2025-10-09 05:30:20 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2025-10-09 05:30:20 | 2025-10-09 05:30:20 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {} | 2025-10-09 05:30:20 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2025-10-09 05:30:20 | 2025-10-09 05:30:20 | 0.00 | dict | {} | 0 | {} | 2025-10-09 05:30:20 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2025-10-09 05:30:20 | 2025-10-09 05:30:20 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {} | 2025-10-09 05:30:20 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2025-10-09 05:30:20 | 2025-10-09 05:30:24 | 4.27 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0002352'), HpoAnnotation(entrez_ge...(truncated) | 5,128 | {} | 2025-10-09 05:30:20 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2025-10-09 05:30:24 | 2025-10-09 05:30:28 | 4.24 | 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:613254', name='Tuberous sclerosis-2', pmid=None, qualif...(truncated) | 11,421 | {} | 2025-10-09 05:30:24 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2025-10-09 05:30:29 | 2025-10-09 05:30:31 | 2.05 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2025-10-09 05:30:29 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2025-10-09 05:30:31 | 2025-10-09 05:30:31 | 0.52 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 19,232 | {} | 2025-10-09 05:30:31 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2025-10-09 05:30:31 | 2025-10-09 05:30:36 | 4.18 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2025-10-09 05:30:31 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2025-10-09 05:30:36 | 2025-10-09 05:30:38 | 1.81 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2025-10-09 05:30:36 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2025-10-09 05:30:38 | 2025-10-09 05:30:39 | 1.25 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2025-10-09 05:30:38 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2025-10-09 05:30:39 | 2025-10-09 05:30:40 | 1.14 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2025-10-09 05:30:39 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2025-10-09 05:30:40 | 2025-10-09 05:31:10 | 30.29 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2025-10-09 05:30:40 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2025-10-09 05:31:10 | 2025-10-09 05:31:20 | 9.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/humancellmap.py", line 43, in humancellmap_annotations
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{} | 2025-08-31 05:11:31 | |||
| ¶ | pypath.inputs.humap.humap1_complexes | 2025-10-09 05:31:20 | 2025-10-09 05:31:20 | 0.22 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,545 | {} | 2025-10-09 05:31:20 | |
| ¶ | pypath.inputs.humap.humap2and3_complexes | 2025-10-09 05:31:20 | 2025-10-09 05:31:22 | 1.81 | dict | {'COMPLEX:P20963_Q9NWV4_Q9UGQ2': Complex: COMPLEX:P20963_Q9NWV4_Q9UGQ2, 'COMPLEX:O94887_Q9NQ92_Q9NWB1': Complex: COMPLEX:O94887_Q9NQ92_Q9NWB1, 'COMPLEX:Q8N3D4_Q9Y3A4': Complex: COMPLEX:Q8N3D4_Q9Y3A4, 'COMPLEX:O00429_Q5T2D2': Complex: COMPLEX:O00429_Q5T2D2, 'COMPLEX:O95460_P21941_P78540_Q9H267_Q9H9C1...(truncated) | 15,433 | {} | 2025-10-09 05:31:20 | |
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2025-10-09 05:31:22 | 2025-10-09 05:31:25 | 2.81 | dict | {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs893184', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2...(truncated) | 13,122 | {} | 2025-10-09 05:31:22 | |
| ¶ | pypath.inputs.huri.hi_i_interactions | 2025-10-09 05:31:25 | 2025-10-09 05:31:26 | 1.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:38 | |||
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2025-10-09 05:31:26 | 2025-10-09 05:31:27 | 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__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:40 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2025-10-09 05:31:27 | 2025-10-09 05:31:28 | 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__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:11:49 | |||
| ¶ | pypath.inputs.huri.huri_interactions | 2025-10-09 05:31:28 | 2025-10-09 05:31:29 | 1.09 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:20 | |||
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2025-10-09 05:31:29 | 2025-10-09 05:31:31 | 1.16 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2025-10-09 05:31:29 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2025-10-09 05:31:31 | 2025-10-09 05:31:32 | 1.58 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2025-10-09 05:31:31 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2025-10-09 05:31:32 | 2025-10-09 05:31:33 | 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__20251009-022202/pypath_git/pypath/inputs/huri.py", line 279, in lit_bm_interactions
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2025-08-31 05:12:46 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2025-10-09 05:31:33 | 2025-10-09 05:31:35 | 2.15 | list | [Rolland2014Interaction(entrez_a='14', entrez_b='6293', genesymbol_a='AAMP', genesymbol_b='VPS52', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='8553', genesymbol_a='AAMP', genesymbol_b='BHLHE40', numof_screens=1), Rolland2014Interaction(entrez_a='14', entrez_b='64782', genesymbo...(truncated) | 13,944 | {} | 2025-10-09 05:31:33 | |
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2025-10-09 05:31:35 | 2025-10-09 05:31:36 | 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__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:49 | |||
| ¶ | pypath.inputs.huri.yu2011_interactions | 2025-10-09 05:31:36 | 2025-10-09 05:31:38 | 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__20251009-022202/pypath_git/pypath/inputs/huri.py", line 323, in _huri_interactions
c.fileobj.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2025-08-31 05:12:50 | |||
| ¶ | pypath.inputs.i3d.get_i3d | 2025-10-09 05:31:38 | 2025-10-09 05:31:58 | 20.77 | list | [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) | 22,184 | {} | 2025-10-09 05:31:38 | |
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2025-10-09 05:31:58 | 2025-10-09 05:31:59 | 0.26 | 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) | 1,194 | {} | 2025-10-09 05:31:58 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2025-10-09 05:31:59 | 2025-10-09 05:31:59 | 0.04 | dict | {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) | 156 | {} | 2025-10-09 05:31:59 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2025-10-09 05:31:59 | 2025-10-09 05:31:59 | 0.03 | list | [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) | 1,647 | {} | 2025-10-09 05:31:59 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2025-10-09 05:31:59 | 2025-10-09 05:32:01 | 2.16 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2025-10-09 05:31:59 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2025-10-09 05:32:01 | 2025-10-09 05:32:01 | 0.51 | list | [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) | 11,470 | {} | 2025-10-09 05:32:01 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2025-10-09 05:32:02 | 2025-10-09 05:32:02 | 0.62 | NoneType | None | 0 | {} | 2025-10-09 05:32:02 | |
| ¶ | pypath.inputs.intact.intact_interactions | 2025-10-09 05:32:02 | 2025-10-09 05:34:55 | 172.94 | list | [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', i...(truncated) | 78,544 | {} | 2025-10-09 05:32:02 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2025-10-09 05:34:55 | 2025-10-09 05:34:56 | 0.78 | set | {'P18084', 'P20701', 'Q13683', 'P56199', 'O75578', 'P26006', 'P23229', 'P11215', 'Q9UKX5', 'P08648', 'P05556', 'P26012', 'P38570', 'P05107', 'P16144', 'P06756', 'P18564', 'P53708', 'P20702', 'P05106', 'P08514', 'P26010', 'Q13797', 'Q13349', 'P17301'} | 25 | {} | 2025-10-09 05:34:55 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2025-10-09 05:34:56 | 2025-10-09 05:35:01 | 5.28 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0008270', go_term_name='zinc ion binding'), Interpro2GOAnnotation(go_term_id='GO:0006355', go_term_name='regulation of DNA-templated transcription'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA bindin...(truncated) | 14,743 | {} | 2025-10-09 05:34:56 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2025-10-09 05:35:01 | 2025-10-09 05:35:02 | 0.38 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR013806', organism='9606', start='381', end='477'), InterproAnnotation(interpro_id='IPR018056', organism='9606', start='176', end='189'), InterproAnnotation(interpro_id='IPR038178', organism='9606', start='127', end='208'), Int...(truncated) | 16,611 | {} | 2025-10-09 05:35:01 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2025-10-09 05:35:02 | 2025-10-09 05:35:18 | 15.92 | list | [InterproEntry(interpro_id='IPR000001', protein_count='20781', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 48,679 | {} | 2025-10-09 05:35:02 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2025-10-09 05:35:18 | 2025-10-09 05:35:19 | 1.02 | dict | {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) | 483 | {} | 2025-10-09 05:35:18 | |
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2025-10-09 05:35:19 | 2025-10-09 05:35:19 | 0.08 | dict | {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) | 86,754 | {} | 2025-10-09 05:35:19 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2025-10-09 05:35:19 | 2025-10-09 05:35:39 | 19.98 | list | [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', ...(truncated) | 15,834 | {} | 2025-10-09 05:35:19 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2025-10-09 05:35:39 | 2025-10-09 05:35:40 | 0.68 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {} | 2025-10-09 05:35:39 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2025-10-09 05:35:40 | 2025-10-09 05:35:40 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {} | 2025-10-09 05:35:40 | |
| ¶ | pypath.inputs.italk.italk_raw | 2025-10-09 05:35:40 | 2025-10-09 05:35:40 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2025-10-09 05:35:40 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2025-10-09 05:35:40 | 2025-10-09 05:35:42 | 1.96 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,224 | {} | 2025-10-09 05:35:40 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2025-10-09 05:35:42 | 2025-10-09 05:35:42 | 0.14 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {} | 2025-10-09 05:35:42 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2025-10-09 05:35:42 | 2025-10-09 05:51:19 | 937.46 | 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) | 14,739 | {} | 2025-10-09 05:35:42 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2025-10-09 05:51:19 | 2025-10-09 05:51:44 | 24.43 | set | {KeggMedicusRawInteraction(id_a='5155v1', id_b='5159', name_a='(PDGF*) PDGFB overexpression', name_b='PDGFRB', effect='stimulation', itype='post_translational', pw_type='variant', type_a='variant', type_b='gene', network_id='N00016'), KeggMedicusRawInteraction(id_a='4524', id_b='C00440', name_a='MT...(truncated) | 12,946 | {} | 2025-10-09 05:51:19 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2025-10-09 05:51:44 | 2025-10-09 05:51:44 | 0.44 | dict | {'COMPLEX:P28702_P37231': Complex: COMPLEX:P28702_P37231, 'COMPLEX:O00268_Q68CJ9': Complex: COMPLEX:O00268_Q68CJ9, 'COMPLEX:P15336_P18848': Complex: COMPLEX:P15336_P18848, 'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:P18074...(truncated) | 528 | {} | 2025-10-09 05:51:44 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2025-10-09 05:51:44 | 2025-10-09 05:51:45 | 0.37 | list | [KeggMedicusInteraction(id_a='P42345', id_b='Q9UBS0', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P31751', id_b='P42345', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,538 | {} | 2025-10-09 05:51:44 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2025-10-09 05:51:45 | 2025-10-09 05:51:58 | 12.97 | dict | {'P61244': {KeggPathway(pathway='MAPK signaling pathway')}, 'Q9NRY4': {KeggPathway(pathway='Ras signaling pathway'), KeggPathway(pathway='Focal adhesion'), KeggPathway(pathway='Platelet activation'), KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Leukocyte transendothelial migra...(truncated) | 2,672 | {} | 2025-10-09 05:51:45 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2025-10-09 05:51:58 | 2025-10-09 05:51:58 | 0.40 | dict | {'A8K7J7': {KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(...(truncated) | 813 | {} | 2025-10-09 05:51:58 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2025-10-09 05:51:58 | 2025-10-09 05:52:10 | 12.19 | tuple | ({'MAPK signaling pathway': {'P61244', 'Q9NRY4', 'O00622', 'Q9UHA4', 'Q03113', 'Q9Y6R4', 'P35557', 'P46734', 'Q13188', 'P04792', 'Q9Y3M2', 'O43318', 'Q9Y4G8', 'Q15628', 'P17535', 'P49116', 'O95819', 'P01375', 'Q13233', 'Q5STR5', 'P51452', 'Q15283', 'Q9H2K8', 'Q12852', 'Q7LDG7', 'Q13163', 'Q03701', '...(truncated) | 2 | {} | 2025-10-09 05:51:58 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2025-10-09 05:52:10 | 2025-10-09 05:52:14 | 3.98 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
self.proc_key(entry[0]): self.proc_value(entry[1])
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
|
{} | 2025-08-12 05:47:03 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2025-10-09 05:52:14 | 2025-10-09 05:52:15 | 0.47 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 503 | {} | 2025-10-09 05:52:14 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2025-10-09 05:52:15 | 2025-10-09 05:52:15 | 0.16 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2025-10-09 05:52:15 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2025-10-09 05:52:15 | 2025-10-09 05:52:19 | 3.63 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {} | 2025-10-09 05:52:15 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2025-10-09 05:52:19 | 2025-10-09 05:52:21 | 2.63 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {} | 2025-10-09 05:52:19 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2025-10-09 05:52:21 | 2025-10-09 05:52:22 | 0.48 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2025-10-09 05:52:21 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2025-10-09 05:52:22 | 2025-10-09 05:52:22 | 0.31 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2025-10-09 05:52:22 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2025-10-09 05:52:22 | 2025-10-09 05:52:23 | 0.83 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2025-10-09 05:52:22 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2025-10-09 05:52:23 | 2025-10-09 05:52:34 | 10.86 | list | [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) | 593 | {} | 2025-10-09 05:52:23 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2025-10-09 05:52:34 | 2025-10-09 05:52:34 | 0.02 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2025-10-09 05:52:34 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2025-10-09 05:52:34 | 2025-10-09 05:52:34 | 0.02 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2025-10-09 05:52:34 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2025-10-09 05:52:34 | 2025-10-09 05:52:35 | 1.21 | dict | {'SciTegic09271913552D': LincsCompound(lincs=None, chembl=None, chebi=None, inchi='InChI=1S/C29H24N4O4S/c1-4-27(34)31-26-16-23(12-5-18(26)2)33-28(35)14-9-21-17-30-25-13-8-20(15-24(25)29(21)33)19-6-10-22(11-7-19)32-38(3,36)37/h4-17,32H,1H2,2-3H3,(H,31,34)', inchi_key='SFMJNHNUOVADRW-UHFFFAOYSA-N', sm...(truncated) | 371 | {} | 2025-10-09 05:52:34 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2025-10-09 05:52:35 | 2025-10-09 05:52:36 | 0.66 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2025-10-09 05:52:35 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2025-10-09 05:52:36 | 2025-10-09 05:52:36 | 0.44 | list | [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) | 1,170 | {} | 2025-10-09 05:52:36 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2025-10-09 05:52:36 | 2025-10-09 05:52:37 | 1.11 | list | [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) | 1,170 | {} | 2025-10-09 05:52:36 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2025-10-09 05:52:37 | 2025-10-09 05:52:38 | 0.39 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {} | 2025-10-09 05:52:37 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2025-10-09 05:52:38 | 2025-10-09 05:52:38 | 0.37 | list | [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism=5888, pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism=9468, pmid='17175535'), LncrnadbInteraction(lncrna='G22', partner='SRP9', type='protein', o...(truncated) | 773 | {} | 2025-10-09 05:52:38 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2025-10-09 05:52:38 | 2025-10-09 05:53:14 | 35.90 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='lysosomes', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None...(truncated) | 9,479 | {} | 2025-10-09 05:52:38 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2025-10-09 05:53:14 | 2025-10-09 05:53:15 | 0.49 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPMR'), references=('146', '8626456')), LrdbAnnotation(role='receptor', cell_type=None, sources=(...(truncated) | 1,536 | {} | 2025-10-09 05:53:14 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2025-10-09 05:53:15 | 2025-10-09 05:53:15 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2025-10-09 05:53:15 | |
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2025-10-09 05:53:15 | 2025-10-09 05:53:15 | 0.28 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2025-10-09 05:53:15 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2025-10-09 05:53:15 | 2025-10-09 05:53:15 | 0.25 | dict | {'H0YF18': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YEL2': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C4X4': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,501 | {} | 2025-10-09 05:53:15 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2025-10-09 05:53:15 | 2025-10-09 05:53:17 | 1.62 | dict | {} | 0 | {} | 2025-10-09 05:53:15 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2025-10-09 05:53:17 | 2025-10-09 05:53:19 | 1.99 | set | {'P35237', 'Q9UBQ6', 'A0A0B4J264', 'Q9H400', 'Q9BQ51', 'P29017', 'O95197', 'Q8WTQ1', 'Q8NBX0', 'P60153', 'O95025', 'O00264', 'P00734', 'O75200', 'Q8TF66', 'Q9BWP8', 'Q8TCZ2', 'Q6WRI0', 'Q8IWU5', 'Q00LT1', 'P17066', 'Q8N136', 'Q96QU1', 'P10147', 'O75493', 'Q9BVM2', 'P37802', 'Q9NQR4', 'P14923', 'Q8N2...(truncated) | 2,840 | {} | 2025-10-09 05:53:17 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2025-10-09 05:53:19 | 2025-10-09 05:53:19 | 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 | {} | 2025-10-09 05:53:19 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2025-10-09 05:53:19 | 2025-10-09 05:53:19 | 0.07 | set | set() | 0 | {} | 2025-10-09 05:53:19 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2025-10-09 05:53:19 | 2025-10-09 05:53:19 | 0.07 | set | set() | 0 | {} | 2025-10-09 05:53:19 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2025-10-09 05:53:19 | 2025-10-09 05:53:20 | 1.09 | set | {'Q92729', 'Q14956', 'Q8TD84', 'P42771', 'Q6FIB4', 'Q49MI3', 'Q13797', 'Q8N726', 'Q15223', 'Q13449', 'Q7Z3B1', 'Q6AZ88', 'Q05084', 'P16144', 'P16671', 'Q9BX67', 'P08F94', 'P25940', 'Q9BRX2', 'Q13835', 'Q9Y4C0', 'P16284', 'Q6MZF4', 'Q9BXN2', 'O95297', 'Q4G160', 'Q6MZK0', 'Q86SJ6', 'P56748', 'O43854',...(truncated) | 112 | {} | 2025-10-09 05:53:19 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2025-10-09 05:53:20 | 2025-10-09 05:53:45 | 24.58 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {} | 2025-10-09 05:53:20 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2025-10-09 05:53:45 | 2025-10-09 05:53:45 | 0.11 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2025-10-09 05:53:45 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2025-10-09 05:53:45 | 2025-10-09 05:53:48 | 3.17 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2025-10-09 05:53:45 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2025-10-09 05:53:48 | 2025-10-09 05:53:49 | 0.79 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2025-10-09 05:53:48 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.16 | list | [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) | 805 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.18 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) | 2,925 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.02 | list | [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0004481', 'hsa-let-7a-3p'), ('MIMAT0004481', 'hsa-let-7a*'), ('MIMAT0010195', 'hsa-let-7a-2-3p'), ('MIMAT0010195', 'hsa-let-7a-2*'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0004482', 'hsa-let...(truncated) | 3,299 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.02 | list | ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) | 2,693 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.03 | list | [['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' untr...(truncated) | 39,233 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_mature | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.02 | list | [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) | 49,168 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_pre_mature | 2025-10-09 05:53:49 | 2025-10-09 05:53:49 | 0.12 | list | [(['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' unt...(truncated) | 53,320 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_organisms | 2025-10-09 05:53:49 | 2025-10-09 05:53:51 | 1.74 | dict | {400682: 'aqu', 45351: 'nve', 6085: 'hma', 10224: 'sko', 7668: 'spu', 7719: 'cin', 51511: 'csa', 34765: 'odi', 7739: 'bfl', 8355: 'xla', 8364: 'xtr', 9031: 'gga', 9615: 'cfa', 13616: 'mdo', 9509: 'age', 9519: 'lla', 78454: 'sla', 9544: 'mml', 9545: 'mne', 61621: 'pbi', 9593: 'ggo', 9606: 'hsa', 9597...(truncated) | 285 | {} | 2025-10-09 05:53:49 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2025-10-09 05:53:51 | 2025-10-09 05:53:51 | 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 | {} | 2025-10-09 05:53:51 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2025-10-09 05:53:51 | 2025-10-09 05:53:51 | 0.03 | list | ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', 'MI0000081', 'MI0000082', ...(truncated) | 1,984 | {} | 2025-10-09 05:53:51 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2025-10-09 05:53:51 | 2025-10-09 05:53:51 | 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 | {} | 2025-10-09 05:53:51 | |
| ¶ | pypath.inputs.mirbase.mirbase_taxid | 2025-10-09 05:53:51 | 2025-10-09 05:53:51 | 0.00 | str | 'hsa' | 3 | {} | 2025-10-09 05:53:51 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2025-10-09 05:53:51 | 2025-10-09 05:53:52 | 0.16 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2025-10-09 05:53:51 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2025-10-09 05:53:52 | 2025-10-09 05:53:52 | 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 | {} | 2025-10-09 05:53:52 | |
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2025-10-09 05:53:52 | 2025-10-09 06:00:04 | 371.55 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=10090, target_genesymbol='Cd320', target_entrez='54219', target_organism=10090, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', data...(truncated) | 27,595 | {} | 2025-10-09 05:53:52 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2025-10-09 06:00:04 | 2025-10-09 06:00:04 | 0.29 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2025-10-09 06:00:04 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2025-10-09 06:00:04 | 2025-10-09 06:00:38 | 34.30 | dict | {'Q92766': {MsigdbAnnotation(collection='mirna_targets_legacy', geneset='CACCAGC_MIR138'), MsigdbAnnotation(collection='mirna_targets_mirdb', geneset='MIR4755_5P'), MsigdbAnnotation(collection='cancer_gene_neighborhoods', geneset='MORF_PPP2R5B'), MsigdbAnnotation(collection='immunesigdb', geneset='G...(truncated) | 20,111 | {} | 2025-10-09 06:00:04 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2025-10-09 06:00:40 | 2025-10-09 06:00:46 | 5.88 | dict | {'MT': {'MT-ND2', 'MT-TH', 'MT-TT', 'MT-ND5', 'MT-ATP6', 'MT-TV', 'MT-TK', 'MT-TR', 'MT-CO2', 'MT-TS2', 'MT-CO3', 'MT-TF', 'MT-TD', 'MT-TA', 'MT-TW', 'MT-TQ', 'MT-ND4', 'MT-ND3', 'MT-TE', 'MT-TC', 'MT-TS1', 'MT-TG', 'MT-TN', 'MT-TP', 'MT-ND4L', 'MT-TL2', 'MT-CYB', 'MT-TI', 'MT-TY', 'MT-RNR1', 'MT-TM...(truncated) | 35,134 | {} | 2025-10-09 06:00:40 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2025-10-09 06:00:46 | 2025-10-09 06:00:46 | 0.42 | dict | {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'COL15A1', 'ECH1', 'PGM1', 'ADIPOR2', 'QDPR', 'IMMT', 'PPARG', 'CCNG2', 'ACOX1', 'CHUK', 'DHCR7', 'PFKL', 'ALDH2', 'ACADS', 'COQ3', 'DNAJC15', 'TALDO1', 'ACAA2', 'GADD45A', 'CAVIN2', 'DHRS7B', 'PHLDB1', 'MRAP', 'SCARB1', 'SSPN', 'BAZ2A', 'MCCC1', 'N...(truncated) | 20 | {} | 2025-10-09 06:00:46 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2025-10-09 06:00:47 | 2025-10-09 06:00:47 | 0.50 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2025-10-09 06:00:47 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2025-10-09 06:00:47 | 2025-10-09 06:00:47 | 0.16 | list | [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) | 2,171 | {} | 2025-10-09 06:00:47 | |
| ¶ | pypath.inputs.netbiol.arn_interactions | 2025-10-09 06:00:47 | 2025-10-09 06:00:48 | 0.13 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2025-10-09 06:00:47 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2025-10-09 06:00:48 | 2025-10-09 06:00:48 | 0.12 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2025-10-09 06:00:48 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2025-10-09 06:00:48 | 2025-10-09 06:00:49 | 1.48 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2025-10-09 06:00:48 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2025-10-09 06:00:49 | 2025-10-09 06:00:49 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2025-10-09 06:00:49 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2025-10-09 06:00:49 | 2025-10-09 06:00:49 | 0.12 | 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='Brain-derived neur...(truncated) | 1,870 | {} | 2025-10-09 06:00:49 | |
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2025-10-09 06:00:49 | 2025-10-09 06:01:15 | 25.30 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2025-10-09 06:00:49 | |
| ¶ | pypath.inputs.oma.oma_orthologs | 2025-10-09 06:01:15 | 2025-10-09 06:01:23 | 8.78 | list | [OmaOrthology(a=OmaGene(id='TBC30_HUMAN', oma_group=1078191, hog='HOG:E0746702.2a.3a.3b', taxon=9606, chr='12', start=64830437, end=64875788, strand=1, main_isoform=True), b=OmaGene(id='TBC30_MOUSE', oma_group=1077973, hog='HOG:E0746702.2a', taxon=10090, chr='10', start=121102730, end=121146705, str...(truncated) | 1,000 | {'size': 1000} | 2025-10-09 06:01:15 | |
| ¶ | pypath.inputs.oma.oma_table | 2025-10-09 06:01:23 | 2025-10-09 06:01:23 | 0.09 | defaultdict | defaultdict(<class 'set'>, {'TBC30_HUMAN': {'TBC30_MOUSE'}, 'P36268': {'GGT1_MOUSE'}, 'KR105_HUMAN': {'A0A1W2P7T6', 'A0A1W2P728', 'Q08EG8', 'A0A1W2P7U0', 'E9Q1M3', 'A0A1W2P860', 'A0A1W2P739', 'A0A1W2P7N1', 'W4VSP7', 'D3Z5T3', 'L7N2C3', 'J3QMD1', 'J3QMW1', 'J3QJV4', 'A0A1W2P709', 'A0A1W2P7W0', 'E9Q2H...(truncated) | 843 | {'size': 843} | 2025-10-09 06:01:23 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2025-10-09 06:01:23 | 2025-10-09 06:01:24 | 0.40 | dict | {'ado': "Alzheimer's Disease Ontology (ADO)", 'afpo': 'African Population Ontology', 'agro': 'Agronomy Ontology', 'aism': 'Ontology for the Anatomy of the Insect SkeletoMuscular system', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'apo': 'Ascomycete Phenotype Ontology (APO)', 'apo...(truncated) | 275 | {} | 2025-10-09 06:01:23 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2025-10-09 06:01:24 | 2025-10-09 06:02:04 | 39.94 | list | [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) | 112,928 | {'fixed': True} | 2025-10-09 06:01:24 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2025-10-09 06:02:04 | 2025-10-09 06:07:33 | 329.52 | list | [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) | 43,791 | {} | 2025-10-09 06:02:04 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2025-10-09 06:07:33 | 2025-10-09 06:09:01 | 87.27 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {} | 2025-10-09 06:07:33 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2025-10-09 06:09:01 | 2025-10-09 06:12:14 | 193.02 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) | 6,960,486 | {'fixed': True} | 2025-10-09 06:09:01 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2025-10-09 06:12:14 | 2025-10-09 06:12:31 | 17.63 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 88 | {} | 2025-10-09 06:12:14 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2025-10-09 06:12:31 | 2025-10-09 06:13:03 | 31.65 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {} | 2025-10-09 06:12:31 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2025-10-09 06:13:03 | 2025-10-09 06:13:07 | 3.96 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 2,219,572 | {} | 2025-10-09 06:13:03 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2025-10-09 06:13:07 | 2025-10-09 06:13:11 | 3.98 | defaultdict | defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=False, cell_type='Enterocytes', organ='GI tract', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=0.0, mouse_sensitivity=0.00331126, human_specificity=0.00439422, mouse_specifici...(truncated) | 4,492 | {} | 2025-10-09 06:13:07 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2025-10-09 06:13:11 | 2025-10-09 06:13:11 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2025-10-09 06:13:11 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2025-10-09 06:13:11 | 2025-10-09 06:13:11 | 0.00 | list | [] | 0 | {} | 2025-10-09 06:13:11 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2025-10-09 06:13:11 | 2025-10-09 06:13:36 | 25.06 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='controls-expression-of', id_b='A2M', resource='pid'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b=...(truncated) | 2,524,906 | {} | 2025-10-09 06:13:11 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2025-10-09 06:13:38 | 2025-10-09 06:13:38 | 0.22 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2025-10-09 06:13:38 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2025-10-09 06:13:38 | 2025-10-09 06:13:47 | 8.39 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2025-10-09 06:13:38 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2025-10-09 06:13:49 | 2025-10-09 06:13:58 | 8.56 | dict | {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) | 49,431 | {} | 2025-10-09 06:13:49 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2025-10-09 06:13:58 | 2025-10-09 06:14:04 | 5.98 | tuple | ({'P02185': {('8j4l', 'X-ray', 1.45), ('6f17', 'X-ray', 1.45), ('1ufp', 'X-ray', 2.1), ('1ajh', 'X-ray', 1.69), ('8fdj', 'X-ray', 1.75), ('1mlh', 'X-ray', 2.0), ('2g0r', 'X-ray', 1.95), ('5ojc', 'X-ray', 1.25), ('6e03', 'X-ray', 1.76), ('1f65', 'X-ray', 1.7), ('5vnu', 'X-ray', 1.58), ('1mbn', 'X-ray...(truncated) | 2 | {} | 2025-10-09 06:13:58 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2025-10-09 06:14:05 | 2025-10-09 06:14:05 | 0.53 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2025-10-09 06:14:05 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2025-10-09 06:14:05 | 2025-10-09 06:25:39 | 693.68 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2025-10-09 06:14:05 | |
| ¶ | pypath.inputs.pfam.pfam_names | 2025-10-09 06:25:39 | 2025-10-09 06:25:40 | 1.18 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2025-10-09 06:25:39 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2025-10-09 06:25:40 | 2025-10-09 06:25:43 | 3.53 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) | 2 | {} | 2025-10-09 06:25:40 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2025-10-09 06:25:44 | 2025-10-09 06:34:38 | 534.02 | tuple | ({}, {}) | 2 | {} | 2025-10-09 06:25:44 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2025-10-09 06:34:38 | 2025-10-09 06:50:04 | 926.15 | tuple | ({}, {}) | 2 | {} | 2025-10-09 06:34:38 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2025-10-09 06:50:04 | 2025-10-09 06:58:28 | 503.29 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 06:50:04 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2025-10-09 06:58:29 | 2025-10-09 06:58:32 | 3.29 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 06:58:29 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2025-10-09 06:58:33 | 2025-10-09 06:58:36 | 2.92 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 06:58:33 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2025-10-09 06:58:37 | 2025-10-09 06:58:40 | 3.32 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 06:58:37 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2025-10-09 06:58:41 | 2025-10-09 06:58:45 | 4.11 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 06:58:41 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2025-10-09 06:58:46 | 2025-10-09 07:04:54 | 368.22 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2025-10-09 06:58:46 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2025-10-09 07:04:54 | 2025-10-09 07:04:58 | 3.46 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-09 07:04:54 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2025-10-09 07:04:59 | 2025-10-09 07:04:59 | 0.43 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2025-10-09 07:04:59 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2025-10-09 07:04:59 | 2025-10-09 07:05:04 | 4.34 | dict | {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) | 264 | {} | 2025-10-09 07:04:59 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2025-10-09 07:05:04 | 2025-10-09 07:05:13 | 9.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
n for d, n in iteritems(data)
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2025-08-31 06:30:34 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2025-10-09 07:05:13 | 2025-10-09 07:05:22 | 9.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/phosphoelm.py", line 101, in phosphoelm_interactions
data = phosphoelm_enzyme_substrate(ltp_only = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/phosphoelm.py", line 54, in phosphoelm_enzyme_substrate
n for d, n in iteritems(data)
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2025-08-31 06:30:36 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2025-10-09 07:05:22 | 2025-10-09 07:05:31 | 9.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/phosphoelm.py", line 121, in phosphoelm_kinases
soup = bs4.BeautifulSoup(data, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Po0PHRhc-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{} | 2025-08-31 06:30:37 | |||
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2025-10-09 07:05:31 | 2025-10-09 07:05:32 | 1.27 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2025-10-09 07:05:31 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2025-10-09 07:05:32 | 2025-10-09 07:05:32 | 0.02 | list | [['FYN', 'MAP2'], ['TNNI3K', 'PPP1R8'], ['MAPK8', 'IRS1'], ['PLK1', 'CDC27'], ['MAP2K1', 'MAPK3'], ['TBK1', 'PPP1R13L'], ['MAPK3', 'ELK1'], ['WEE1', 'SNRP70'], ['STK24', 'HLCS'], ['CDK5', 'APBB1'], ['CDK5', 'SOX10'], ['TTK', 'EIF2S1'], ['BMPR1B', 'CSNK1G2'], ['LYN', 'FCGR2A'], ['IKBKB', 'FOXO3'], ['...(truncated) | 1,821 | {} | 2025-10-09 07:05:32 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2025-10-09 07:05:32 | 2025-10-09 07:05:32 | 0.22 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2025-10-09 07:05:32 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2025-10-09 07:05:32 | 2025-10-09 07:05:32 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2025-10-09 07:05:32 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2025-10-09 07:05:32 | 2025-10-09 07:05:32 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {} | 2025-10-09 07:05:32 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2025-10-09 07:05:32 | 2025-10-09 07:05:33 | 0.33 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2025-10-09 07:05:32 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2025-10-09 07:05:33 | 2025-10-09 07:05:33 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2025-10-09 07:05:33 | 2025-10-09 07:05:33 | 0.01 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 9,164 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2025-10-09 07:05:33 | 2025-10-09 07:05:33 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2025-10-09 07:05:33 | 2025-10-09 07:05:33 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2025-10-09 07:05:33 | 2025-10-09 07:05:33 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) | 4,790 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2025-10-09 07:05:33 | 2025-10-09 07:05:37 | 4.60 | dict | {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,635 | {} | 2025-10-09 07:05:33 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2025-10-09 07:05:38 | 2025-10-09 07:05:52 | 14.15 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {} | 2025-10-09 07:05:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2025-10-09 07:05:52 | 2025-10-09 07:05:53 | 0.49 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'phosphorylation', 'intracellular localization', 'protein degradation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2025-10-09 07:05:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2025-10-09 07:05:53 | 2025-10-09 07:07:22 | 88.83 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21209006', '28052875', '21148409', '24876223'}, 'isoforms': {1}, 'process': {''}, 'function': {'intracellular localization', 'phosphorylation', 'ubiquitination', 'protein degradation', 'protein stabilization'}...(truncated) | 3,621 | {} | 2025-10-09 07:05:53 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2025-10-09 07:07:22 | 2025-10-09 07:07:53 | 30.95 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2025-10-09 07:07:22 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2025-10-09 07:07:53 | 2025-10-09 07:07:53 | 0.47 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 394,059 | {} | 2025-10-09 07:07:53 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2025-10-09 07:07:53 | 2025-10-09 07:09:00 | 66.15 | dict | {'P35250': {ProgenyAnnotation(pathway='Androgen', weight=-1.28437624907, p_value=0.121273439673), ProgenyAnnotation(pathway='PI3K', weight=-0.23892575535137267, p_value=0.8037183514291981), ProgenyAnnotation(pathway='p53', weight=-3.3513628049710005, p_value=0.000985568693599589), ProgenyAnnotation(...(truncated) | 18,582 | {} | 2025-10-09 07:07:53 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2025-10-09 07:09:00 | 2025-10-09 07:10:07 | 67.16 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2025-10-09 07:09:00 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2025-10-09 07:10:07 | 2025-10-09 07:10:12 | 5.08 | dict | {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) | 2 | {} | 2025-10-09 07:10:07 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2025-10-09 07:10:13 | 2025-10-09 07:10:24 | 10.85 | dict | {'O43657': {ProtainatlasAnnotation(organ='Bone marrow', tissue='Bone marrow', cell_type='hematopoietic cells', level='Not detected', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotatio...(truncated) | 15,045 | {} | 2025-10-09 07:10:13 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2025-10-09 07:10:27 | 2025-10-09 07:10:27 | 0.35 | list | [ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interac...(truncated) | 46,472 | {} | 2025-10-09 07:10:27 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2025-10-09 07:10:27 | 2025-10-09 07:10:27 | 0.28 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,590 | {} | 2025-10-09 07:10:27 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2025-10-09 07:10:27 | 2025-10-09 07:10:28 | 0.51 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Cytosol', status='approved', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', reliability='Approved...(truncated) | 13,336 | {} | 2025-10-09 07:10:27 | |
| ¶ | pypath.inputs.proteins.variants | 2025-10-09 07:10:28 | 2025-10-09 07:17:32 | 424.40 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 30,452 | {} | 2025-10-09 07:10:28 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2025-10-09 07:17:33 | 2025-10-09 07:17:34 | 1.28 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q05513', 'CTRL_GENE_NAME': 'PRKCZ', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P27448', 'TARGET_GENE_NAME': 'MARK3', 'TARGET_RES': 'T', 'TARGET_POS': '564', 'SOURCES': 'psp,signor', 'BELIEF': '1'}, {'ID': '1', 'CTRL_NS': 'UP', 'CTRL_ID': 'P41743', 'CTRL_GEN...(truncated) | 2 | {} | 2025-10-09 07:17:33 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2025-10-09 07:17:35 | 2025-10-09 07:17:36 | 1.12 | list | [{'kinase': 'Q05513', 'resaa': 'T', 'resnum': 564, 'references': {'15084291'}, 'substrate': 'P27448', 'databases': {'SIGNOR', 'PhosphoSite'}}, {'kinase': 'P41743', 'resaa': 'T', 'resnum': 564, 'references': set(), 'substrate': 'P27448', 'databases': {'PhosphoSite'}}, {'kinase': 'Q9NRM7', 'resaa': 'S...(truncated) | 31,263 | {} | 2025-10-09 07:17:35 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.psimi.psimi_ontology | 2025-10-09 07:17:36 | 2025-10-09 07:17:36 | 0.33 | list | [PsimiRecord(id='MI:0000', name='molecular interaction', definition='Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.', definition_refs='[PMID:14755292]', parent_ids=None, parent_names=None, synonyms='mi', alt_ids=None), PsimiReco...(truncated) | 1,647 | {} | 2025-10-09 07:17:36 | |
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2025-10-09 07:17:36 | 2025-10-09 07:17:36 | 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 | {} | 2025-10-09 07:17:36 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2025-10-09 07:17:36 | 2025-10-09 07:17:45 | 8.99 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), Ram...(truncated) | 18,879 | {} | 2025-10-09 07:17:36 | |
| ¶ | pypath.inputs.reaction.acsn_biopax | 2025-10-09 07:17:46 | 2025-10-09 07:17:46 | 0.33 | NoneType | None | 0 | {} | 2025-10-09 07:17:46 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2025-10-09 07:17:46 | 2025-10-09 07:17:47 | 0.70 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2025-10-09 07:17:46 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2025-10-09 07:17:47 | 2025-10-09 07:17:47 | 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__20251009-022202/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
len(biopaxes.result),
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
|
{} | 2025-08-12 06:52:15 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2025-10-09 07:17:47 | 2025-10-09 07:17:53 | 6.34 | dict | {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) | 178 | {} | 2025-10-09 07:17:47 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2025-10-09 07:17:53 | 2025-10-09 07:17:55 | 2.05 | NoneType | None | 0 | {} | 2025-10-09 07:17:53 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2025-10-09 07:17:55 | 2025-10-09 07:18:26 | 30.55 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2025-10-09 07:17:55 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2025-10-09 07:18:26 | 2025-10-09 07:18:56 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reaction.py", line 136, in reactome_bs
for k, v in sbml.items():
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{'broke': True} | 2025-10-08 06:55:52 | |||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2025-10-09 07:18:56 | 2025-10-09 07:19:26 | 30.01 | NoneType | None | 0 | {'size': -2825, 'type': {'previous': 'dict', 'current': 'NoneType'}} | 2025-10-09 07:18:56 | |
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2025-10-09 07:19:26 | 2025-10-09 07:19:56 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reactome/__init__.py", line 17, in pathway_hierarchy
yield from _reactome_txt(url = url, colnames = ['parent', 'child'])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reactome/__init__.py", line 10, in _reactome_txt
yield from csv.DictReader(c.fileobj, delimiter='\t', fieldnames=colnames)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-08 07:02:52 | |||
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2025-10-09 07:19:56 | 2025-10-09 07:20:26 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:10 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathway_relations | 2025-10-09 07:20:26 | 2025-10-09 07:20:56 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:23 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathways | 2025-10-09 07:20:56 | 2025-10-09 07:21:04 | 7.90 |
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__20251009-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:23 | |||
| ¶ | pypath.inputs.reactome_old.reactome_uniprots | 2025-10-09 07:21:04 | 2025-10-09 07:21:34 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251009-022202/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{} | 2025-08-12 07:00:24 | |||
| ¶ | pypath.inputs.rhea.rhea_gui | 2025-10-09 07:21:34 | 2025-10-09 07:21:51 | 16.97 | list | [{'Reaction identifier': 'RHEA:21252', 'Equation': '(S)-2-hydroxyglutarate + A = 2-oxoglutarate + AH2', 'ChEBI name': '(S)-2-hydroxyglutarate;A;2-oxoglutarate;AH2', 'ChEBI identifier': 'CHEBI:16782;CHEBI:13193;CHEBI:16810;CHEBI:17499', 'EC number': 'EC:1.1.99.2', 'Enzymes': '4258', 'Gene Ontology': ...(truncated) | 17,783 | {} | 2025-10-09 07:21:34 | |
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2025-10-09 07:21:51 | 2025-10-09 07:21:52 | 0.66 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human'), ScconnectAnnota...(truncated) | 3,285 | {} | 2025-10-09 07:21:51 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2025-10-09 07:21:52 | 2025-10-09 07:21:52 | 0.02 | set | {Complex: COMPLEX:O15263, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:P01562, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P01215_P01222, Complex: CO...(truncated) | 17 | {} | 2025-10-09 07:21:52 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2025-10-09 07:21:52 | 2025-10-09 07:26:57 | 304.99 | list | [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) | 1,766 | {} | 2025-10-09 07:21:52 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2025-10-09 07:26:57 | 2025-10-09 07:26:57 | 0.12 | dict | {'CID100002366': {SiderDrug(name='betahistine', atc='N07CA01')}, 'CID100110635': {SiderDrug(name='tadalafil', atc='G04BE08')}, 'CID100160352': {SiderDrug(name='zidovudine/lamivudine', atc=None)}, 'CID100003143': {SiderDrug(name='docetaxel', atc='L01CD02')}, 'CID100004868': {SiderDrug(name='polymyxin...(truncated) | 1,430 | {} | 2025-10-09 07:26:57 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2025-10-09 07:26:57 | 2025-10-09 07:26:57 | 0.24 | list | [SiderSideeffectMeddra(cid='C1141978', meddra_id='10058385', side_effect_name='Urogenital fistula repair'), SiderSideeffectMeddra(cid='C0192720', meddra_id='10052991', side_effect_name='Intestinal fistula repair'), SiderSideeffectMeddra(cid='C0948525', meddra_id='10052904', side_effect_name='Musculo...(truncated) | 20,307 | {} | 2025-10-09 07:26:57 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2025-10-09 07:26:57 | 2025-10-09 07:26:58 | 0.88 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0042373', umls_concept_in_meddra='C0042373', side_effect='Angiopathy', frequency='2%'), SiderSideeffetFrequency(umls_concept_on_label='C0019080', umls_concept_in_meddra='C0019080', side_effect='Haemorrhage', frequency='9%'), SiderSide...(truncated) | 968 | {} | 2025-10-09 07:26:57 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2025-10-09 07:26:58 | 2025-10-09 07:26:59 | 0.85 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0003123', umls_concept_in_meddra='C0003123', side_effect='Anorexia'), SiderSideeffect(umls_concept_on_label='C0231528', umls_concept_in_meddra='C0948594', side_effect='Musculoskeletal discomfort'), SiderSideeffect(umls_concept_on_label='C0003...(truncated) | 1,430 | {} | 2025-10-09 07:26:58 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2025-10-09 07:26:59 | 2025-10-09 07:27:00 | 1.37 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate immune pathways'), Signalin...(truncated) | 2 | {} | 2025-10-09 07:26:59 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2025-10-09 07:27:00 | 2025-10-09 07:27:01 | 1.01 | 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) | 785 | {} | 2025-10-09 07:27:00 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2025-10-09 07:27:01 | 2025-10-09 07:27:02 | 0.39 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2025-10-09 07:27:01 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2025-10-09 07:27:02 | 2025-10-09 07:27:02 | 0.40 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pat...(truncated) | 839 | {} | 2025-10-09 07:27:02 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2025-10-09 07:27:02 | 2025-10-09 07:27:03 | 0.65 | 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) | 4,892 | {} | 2025-10-09 07:27:02 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2025-10-09 07:27:03 | 2025-10-09 07:27:07 | 4.10 | list | [{'typ': 'phosphorylation', 'resnum': 1203, 'instance': 'LHSVSSKSFRDFLLE', 'substrate': 'Q9P2D0', 'start': 1196, 'end': 1210, 'kinase': 'P05771', 'resaa': 'S', 'motif': 'LHSVSSKSFRDFLLE', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'21482705'}}, {'typ': 'phosphorylation', 'resn...(truncated) | 13,396 | {} | 2025-10-09 07:27:03 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2025-10-09 07:27:07 | 2025-10-09 07:27:08 | 1.18 | list | [SignorInteraction(source='P05771', target='Q9P2D0', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates', mechanism='phosphorylation', ncbi_tax_id='9606', pubmeds='21482705', direct=True, ptm_type='phosphorylation', ptm_residue='Ser1203', p...(truncated) | 95,675 | {} | 2025-10-09 07:27:07 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2025-10-09 07:27:08 | 2025-10-09 07:27:28 | 19.54 | dict | {'P49715': {SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='Adipogenesis')}, 'Q5H9F3': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q12913': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P05412': {SignorPathway(pathway='GPCR_HCC'), SignorPathway(pathway='EGFR Sig...(truncated) | 782 | {} | 2025-10-09 07:27:08 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2025-10-09 07:27:28 | 2025-10-09 07:27:28 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 91 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.slc.slc_annotation | 2025-10-09 07:27:28 | 2025-10-09 07:27:28 | 0.27 | list | [SlcAnnotation(Entrez_ID=56172, Ensembl_ID='ENSG00000154122', HGNC_symbol='ANKH', Substrate_class='Orphan', Substrates='', Substrates_PMID='', Coupled_ions='Unknown', Coupled_ions_PMID='', Transport_mechanism='Unknown', Transport_system_PMID='', Subcellular_localization='Unknown', Subcellular_locali...(truncated) | 446 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.slc.slc_chebi_mapping | 2025-10-09 07:27:28 | 2025-10-09 07:27:28 | 0.16 | list | [SlcChebiMapping(Substrate_name_annotation='17-beta-glucuronosyl estradiol', chebi_id='CHEBI:791', chebi_term='17beta-estradiol 17-glucosiduronic acid', synonym='3-hydroxyestra-1,3,5(10)-trien-17beta-yl beta-D-glucopyranosiduronic acid', description='A steroid glucosiduronic acid that consists of 17...(truncated) | 382 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.slc.slc_interactions | 2025-10-09 07:27:28 | 2025-10-09 07:27:28 | 0.10 | list | [SlcInteraction(transporter=SlcTransporter(uniprot='Q9Y5Y0', genesymbol='FLVCR1', entrez=28982, ensg='ENSG00000162769'), substrate=SlcSubstrate(slc_name='Heme', chebi='CHEBI:30413', label='heme', synonyms=['heme', 'hemes']), role='substrate', pmids='15369674', localization='Plasma membrane', transpo...(truncated) | 1,288 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.slc.slc_localization_annotations | 2025-10-09 07:27:28 | 2025-10-09 07:27:28 | 0.06 | dict | {'Q9HCJ1': {SlcLocalization(localization='Unknown', pmids=None)}, 'Q13286': {SlcLocalization(localization='Endosome; Lysosome', pmids='15471887;22261744')}, 'Q96SL1': {SlcLocalization(localization='Lysosome', pmids='21692750')}, 'Q9Y5Y0': {SlcLocalization(localization='Plasma membrane', pmids='18815...(truncated) | 447 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.slc.slc_substrate_ontology | 2025-10-09 07:27:28 | 2025-10-09 07:27:29 | 0.64 | list | [SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='heme', ChEBI_ID='CHEBI:30413', ChEBI_subontology='chemical entity'), SlcSubstrateOntology(Entrez_ID=28982, Ensembl_ID='ENSG00000162769', HGNC_symbol='FLVCR1', ChEBI_term='cyclic tetrapyrrole', ChEB...(truncated) | 24,810 | {} | 2025-10-09 07:27:28 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2025-10-09 07:27:29 | 2025-10-09 07:27:38 | 9.13 | dict | {'COMPLEX:P67775_Q15172_Q15257': Complex PP2A: COMPLEX:P67775_Q15172_Q15257, 'COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478': Complex AMPK: COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478, 'COMPLEX:P67870_P68400': Complex CK2: COMPLEX:P67870_P68400, 'COMPLEX:P05412_P15336': Compl...(truncated) | 154 | {} | 2025-10-09 07:27:29 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2025-10-09 07:27:38 | 2025-10-09 07:27:40 | 1.92 | list | [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) | 8,903 | {} | 2025-10-09 07:27:38 | |
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2025-10-09 07:27:40 | 2025-10-09 07:28:47 | 66.38 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2025-10-09 07:27:40 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2025-10-09 07:28:47 | 2025-10-09 07:30:08 | 81.53 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2025-10-09 07:28:47 | |
| ¶ | pypath.inputs.string.string_effects | 2025-10-09 07:30:08 | 2025-10-09 07:30:16 | 8.16 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2025-10-09 07:30:08 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2025-10-09 07:30:17 | 2025-10-09 07:30:50 | 32.88 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {} | 2025-10-09 07:30:17 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2025-10-09 07:30:50 | 2025-10-09 07:30:51 | 1.18 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2025-10-09 07:30:50 | |
| ¶ | pypath.inputs.string.string_species | 2025-10-09 07:30:52 | 2025-10-09 07:30:52 | 0.16 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2025-10-09 07:30:52 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2025-10-09 07:30:52 | 2025-10-09 07:30:54 | 2.41 | dict | {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC', 'SLC12'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC', 'SLC5'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,844 | {} | 2025-10-09 07:30:52 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2025-10-09 07:30:54 | 2025-10-09 07:31:13 | 18.78 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2025-10-09 07:30:54 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2025-10-09 07:31:13 | 2025-10-09 07:31:14 | 0.58 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,344 | {} | 2025-10-09 07:31:13 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2025-10-09 07:31:14 | 2025-10-09 07:31:14 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2025-10-09 07:31:14 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2025-10-09 07:31:14 | 2025-10-09 07:31:14 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2025-10-09 07:31:14 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2025-10-09 07:31:14 | 2025-10-09 07:31:20 | 5.97 |
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__20251009-022202/pypath_git/pypath/inputs/tcdb/__init__.py", line 95, in tcdb_annotations
for ac, (tc, family) in iteritems(classes):
^^^^^^^^^
NameError: name 'iteritems' is not defined
|
{} | 2025-08-13 07:12:59 | |||
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2025-10-09 07:31:20 | 2025-10-09 07:31:20 | 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) | 24,302 | {} | 2025-10-09 07:31:20 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2025-10-09 07:31:20 | 2025-10-09 07:31:20 | 0.01 | dict | {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) | 2,122 | {} | 2025-10-09 07:31:20 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2025-10-09 07:31:20 | 2025-10-09 07:31:20 | 0.23 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,871 | {} | 2025-10-09 07:31:20 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2025-10-09 07:31:20 | 2025-10-09 07:31:23 | 3.25 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2025-10-09 07:31:20 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2025-10-09 07:31:23 | 2025-10-09 07:31:45 | 22.00 | set | {ThreedcomplexContact(pdb='4ywl_1', uniprot_1='Q8U3I4', uniprot_2='Q8U3I4', chain_1='G', chain_2='B', n_residues=7.0, length_1=254, length_2=254, domain_s1=('50249',), domain_p1=('PF14551.1',), domain_s2=('50249',), domain_p2=('PF14551.1',), ident=True, homo=True), ThreedcomplexContact(pdb='1kca_1',...(truncated) | 259,376 | {} | 2025-10-09 07:31:23 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2025-10-09 07:31:46 | 2025-10-09 07:34:56 | 190.12 | list | [<pypath.internals.intera.DomainDomain object at 0x7fc15b0dcc10>, <pypath.internals.intera.DomainDomain object at 0x7fc15b0dc9d0>, <pypath.internals.intera.DomainDomain object at 0x7fc15b0de210>, <pypath.internals.intera.DomainDomain object at 0x7fc15b0dcbd0>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,086 | {} | 2025-10-09 07:31:46 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2025-10-09 07:34:57 | 2025-10-09 07:35:06 | 8.68 | dict | {'4ywl_1': {('Q8U3I4', 'Q8U3I4'): 15.5}, '1kca_1': {('P03034', 'P03034'): 7.5}, '1kiu_11': {('P08191', 'P31697'): 33.5, ('P08191', 'P08191'): 15.0, ('P31697', 'P31697'): 11.0}, '3q5v_1': {('H2L2L6', 'H2L2L6'): 16.5}, '2yad_2': {('P11686', 'P11686'): 10.5}, '1ict_1': {('P02766', 'P02766'): 9.0}, '1vp...(truncated) | 80,995 | {} | 2025-10-09 07:34:57 | |
| ¶ | pypath.inputs.threedid.get_3did | 2025-10-09 07:35:06 | 2025-10-09 08:43:14 | 4,087.90 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7fc159fc8f90>, <pypath.internals.intera.DomainDomain object at 0x7fc17a1f3c50>, <pypath.internals.intera.DomainDomain object at 0x7fc1438b0a10>, <pypath.internals.intera.DomainDomain object at 0x7fbfc6e5ff10>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2025-10-09 07:35:06 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2025-10-09 08:43:14 | 2025-10-09 08:59:04 | 949.67 | dict | {} | 0 | {} | 2025-10-09 08:43:14 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2025-10-09 08:59:04 | 2025-10-09 08:59:43 | 38.91 | dict | {'P18825': {TopdbAnnotation(membrane='Extracellular', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell membrane', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cyt...(truncated) | 2,027 | {} | 2025-10-09 08:59:04 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2025-10-09 08:59:43 | 2025-10-09 08:59:43 | 0.07 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2025-10-09 08:59:43 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2025-10-09 08:59:43 | 2025-10-09 08:59:43 | 0.00 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2025-10-09 08:59:43 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2025-10-09 08:59:43 | 2025-10-09 08:59:43 | 0.01 | list | [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;12601176;11983166', 'Calcium measurement;Patch clamp;Fusion protein-pull down assay;Fl...(truncated) | 359 | {} | 2025-10-09 08:59:43 | |
| ¶ | pypath.inputs.trip.trip_process | 2025-10-09 08:59:43 | 2025-10-09 08:59:43 | 0.00 | dict | {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'Rat vascular smooth muscle cell', 'Rat aortic vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2025-10-09 08:59:43 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2025-10-09 08:59:43 | 2025-10-09 08:59:48 | 4.93 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-10-09 08:59:43 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2025-10-09 08:59:48 | 2025-10-09 08:59:48 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2025-10-09 08:59:48 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2025-10-09 08:59:48 | 2025-10-09 08:59:50 | 2.86 | list | [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) | 7,057 | {} | 2025-10-09 08:59:48 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2025-10-09 08:59:50 | 2025-10-09 09:03:18 | 207.37 | list | [TwosidesInteraction(drug1_rxnorm='10355', drug1='Temazepam', drug2_rxnorm='136411', drug2='sildenafil', condition_meddra='10003239', condition='Arthralgia', prr='2.91667', pee_error='0.421275', mean_reporting_frequency='0.0448718'), TwosidesInteraction(drug1_rxnorm='1808', drug1='Bumetanide', drug2...(truncated) | 42,920,391 | {} | 2025-10-09 08:59:50 | |
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2025-10-09 09:03:18 | 2025-10-09 09:03:18 | 0.01 | list | [UnichemSource(number=1, label='ChEMBL', name='chembl', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='2024-12-11'), UnichemSource(number=2, label='DrugBank', name='drugbank', description='A database that com...(truncated) | 41 | {} | 2025-10-09 09:03:18 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2025-10-09 09:03:18 | 2025-10-09 09:03:18 | 0.00 | dict | {1: 'ChEMBL', 2: 'DrugBank', 3: 'PDBe', 4: 'Guide to Pharmacology', 5: 'PubChem: Drugs of the Future ', 6: 'KEGG Ligand', 7: 'ChEBI', 8: 'NIH Clinical Collection', 9: 'ZINC', 10: 'eMolecules', 12: 'Atlas', 14: 'FDA SRS', 15: 'SureChEMBL', 17: 'PharmGKB', 18: 'Human Metabolome Database', 20: 'Selleck...(truncated) | 41 | {} | 2025-10-09 09:03:18 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2025-10-09 09:03:18 | 2025-10-09 09:03:18 | 0.51 | list | [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ13', 'K7EN86'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZ66', 'K7EQ86'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZK0', 'A0A024QZP7'], ['A0A024Q...(truncated) | 72,358 | {} | 2025-10-09 09:03:18 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2025-10-09 09:03:18 | 2025-10-09 09:03:30 | 11.71 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0AV02': {UniprotFamily(family='SLC12A transporter', subfamily=None)}, 'A0AV96': {UniprotFam...(truncated) | 14,485 | {} | 2025-10-09 09:03:18 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2025-10-09 09:03:30 | 2025-10-09 09:03:42 | 11.56 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Heme'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Glycoprotein'), ...(truncated) | 20,420 | {} | 2025-10-09 09:03:30 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2025-10-09 09:03:42 | 2025-10-09 09:03:42 | 0.08 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,837 | {} | 2025-10-09 09:03:42 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2025-10-09 09:03:42 | 2025-10-09 09:03:44 | 1.84 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'H8ZM71': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies grandis', 'Grand fir', 'Pinu...(truncated) | 558,858 | {} | 2025-10-09 09:03:42 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2025-10-09 09:03:44 | 2025-10-09 09:03:58 | 14.17 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Lymphocytes nor granulocytes', level='none'), UniprotTissue(ti...(truncated) | 10,169 | {} | 2025-10-09 09:03:44 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2025-10-09 09:03:58 | 2025-10-09 09:04:51 | 52.60 | dict | {'A0A087X1C5': {UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Transmembrane', ...(truncated) | 5,244 | {} | 2025-10-09 09:03:58 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2025-10-09 09:04:51 | 2025-10-09 09:04:51 | 0.00 | set | {'P51788', 'Q8N9W7', 'O95278', 'P41181', 'Q902F9', 'Q9Y294', 'Q8NB91', 'Q9NQG1', 'Q7Z6M2', 'Q96AE7', 'Q2KHM9', 'Q7Z403', 'P32321', 'P61925', 'Q6PIV2', 'Q9Y6E2', 'P07360', 'Q14008', 'Q8N743', 'Q9NVF9', 'Q6ZV77', 'Q9UJU3', 'P08134', 'P61604', 'Q9Y5H3', 'Q86YI8', 'Q6UXA7', 'P82912', 'O15049', 'Q6N069',...(truncated) | 20,420 | {} | 2025-10-09 09:04:51 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2025-10-09 09:04:51 | 2025-10-09 09:05:28 | 36.87 | set | {'A0A5H2UZZ8', 'D6ML77', 'A0A7S5ETV0', 'S4T722', 'Q06HC1', 'T1R3B0', 'E7ER95', 'B7ZLW8', 'A2MZT1', 'A0A0D6K9K5', 'Q59FX4', 'Q5SAW0', 'U3KPX1', 'C9JP48', 'A0A345W497', 'F5H598', 'H9XFB9', 'Q59F91', 'A0A059RXD3', 'A0A096LPK8', 'A0A2S0RAQ9', 'A0A5C2G2R6', 'Q13514', 'Q6ZT55', 'F8W0U9', 'B4E3C4', 'G5D831...(truncated) | 184,785 | {} | 2025-10-09 09:04:51 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2025-10-09 09:05:28 | 2025-10-09 09:05:28 | 0.00 | set | {'A0A5H2UZZ8', 'D6ML77', 'A0A7S5ETV0', 'S4T722', 'Q06HC1', 'O95278', 'T1R3B0', 'E7ER95', 'Q8NB91', 'B7ZLW8', 'A2MZT1', 'A0A0D6K9K5', 'Q9NQG1', 'Q59FX4', 'Q5SAW0', 'U3KPX1', 'C9JP48', 'A0A345W497', 'F5H598', 'H9XFB9', 'Q59F91', 'A0A059RXD3', 'A0A096LPK8', 'A0A2S0RAQ9', 'A0A5C2G2R6', 'Q13514', 'Q6ZT55...(truncated) | 205,205 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2025-10-09 09:05:28 | 2025-10-09 09:05:28 | 0.00 | set | {'A0A5H2UZZ8', 'D6ML77', 'A0A7S5ETV0', 'S4T722', 'Q06HC1', 'O95278', 'T1R3B0', 'E7ER95', 'Q8NB91', 'B7ZLW8', 'A2MZT1', 'A0A0D6K9K5', 'Q9NQG1', 'Q59FX4', 'Q5SAW0', 'U3KPX1', 'C9JP48', 'A0A345W497', 'F5H598', 'H9XFB9', 'Q59F91', 'A0A059RXD3', 'A0A096LPK8', 'A0A2S0RAQ9', 'A0A5C2G2R6', 'Q13514', 'Q6ZT55...(truncated) | 205,205 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2025-10-09 09:05:28 | 2025-10-09 09:05:28 | 0.05 | NoneType | None | 0 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2025-10-09 09:05:28 | 2025-10-09 09:05:28 | 0.05 | set | {('SGD', 'UniProtKB-Swiss-Prot'), ('UniProtKB', 'DisProt'), ('UniProtKB', 'IDEAL'), ('UniProtKB', 'GeneTree'), ('UniProtKB', 'DNASU'), ('UniProtKB_AC-ID', 'PDB'), ('UniProtKB', 'CCDS'), ('UniProtKB_AC-ID', 'FlyBase'), ('UniProtKB', 'Ensembl_Protein'), ('GI_number', 'UniProtKB'), ('UniProtKB-Swiss-Pr...(truncated) | 481 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.wang.cui_interactions | 2025-10-09 09:05:28 | 2025-10-09 09:05:28 | 0.33 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2025-10-09 09:05:28 | 2025-10-09 09:05:29 | 0.44 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2025-10-09 09:05:28 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2025-10-09 09:05:29 | 2025-10-09 09:05:34 | 4.76 | dict | {'NA': {WangAnnotation(function='RNA', location='Ribosomes'), WangAnnotation(function='Messenger', location='Cytosol'), WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='Adapter', location='Ribosomes'), WangAnnotation(function='Adapter', location='Cytosol'), WangAnnotat...(truncated) | 1,547 | {} | 2025-10-09 09:05:29 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2025-10-09 09:05:34 | 2025-10-09 09:05:34 | 0.14 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2025-10-09 09:05:34 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2025-10-09 09:05:34 | 2025-10-09 09:05:34 | 0.29 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {} | 2025-10-09 09:05:34 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2025-10-09 09:05:34 | 2025-10-09 09:05:34 | 0.10 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {} | 2025-10-09 09:05:34 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2025-10-09 09:05:34 | 2025-10-09 09:05:34 | 0.14 | dict | {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) | 466 | {} | 2025-10-09 09:05:34 |
The OmniPath Team • Saez Lab • 2025-10-09