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 2025-10-02 02:22:24 and 2025-10-02 09:56:34; pypath version: 0.16.28 (from git, installed by poetry; 1546e5d )
| Modules collected: | 192 |
|---|---|
| Modules failed to import: | 3 |
| Functions collected: | 526 |
| Functions run without error: | 375 |
| Functions returned empty value: | 13 |
| Functions skipped due to lack of arguments: | 111 |
| Functions run with error: | 40 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2025-10-02 02:22:27 | 2025-10-02 02:22:28 | 0.55 | 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 | {} | 2025-10-02 02:22:27 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2025-10-02 02:22:28 | 2025-10-02 02:22:28 | 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 | {} | 2025-10-02 02:22:28 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2025-10-02 02:22:29 | 2025-10-02 02:23:28 | 59.96 | 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 | {} | 2025-10-02 02:22:29 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2025-10-02 02:23:28 | 2025-10-02 02:23:30 | 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 | {} | 2025-10-02 02:23:28 | |
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2025-10-02 02:23:30 | 2025-10-02 02:29:30 | 360.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/common.py", line 123, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Fq4eCasB-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-Fq4eCasB-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-Fq4eCasB-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__20251002-022202/pypath_git/pypath/inputs/adrecs.py", line 113, in adrecs_adr_ontology
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/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
|
{} | 2025-09-28 02:23:31 | |||
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2025-10-02 02:29:30 | 2025-10-02 03:25:03 | 3,333.54 |
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__20251002-022202/pypath_git/pypath/inputs/adrecs.py", line 176, in _adrecs_drug_adr
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{} | 2025-09-28 02:23:47 | |||
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2025-10-02 03:25:03 | 2025-10-02 03:25:06 | 3.23 | list | [AdrecsDrug(badd='BADD_D00001', drug='1,2-hexanediol', synonyms=('1,2-hexanediol',), drugbank='DB14108', pubchem_cid='94335', mesh='C119102', kegg=None, tdd=None), AdrecsDrug(badd='BADD_D00002', drug='2-hydroxy-3-phenylpropanoic acid', synonyms=('3-phenyllactate', '3-phenyllactic acid', '3-phenyllac...(truncated) | 2,526 | {} | 2025-10-02 03:25:03 | |
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2025-10-02 03:25:06 | 2025-10-02 03:31:06 | 360.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/common.py", line 123, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Fq4eCasB-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-Fq4eCasB-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-Fq4eCasB-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__20251002-022202/pypath_git/pypath/inputs/adrecs.py", line 192, in adrecs_hierarchy
adr_ontology = adrecs_adr_ontology()
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/adrecs.py", line 113, in adrecs_adr_ontology
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/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
|
{} | 2025-09-30 03:04:53 | |||
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2025-10-02 03:31:06 | 2025-10-02 03:31:10 | 3.76 | 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 | {} | 2025-10-02 03:31:06 | |
| ¶ | pypath.inputs.alzpathway.alzpathway_interactions | 2025-10-02 03:31:10 | 2025-10-02 03:31:10 | 0.14 | 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 | {} | 2025-10-02 03:31:10 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2025-10-02 03:31:10 | 2025-10-02 03:32:07 | 56.51 |
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__20251002-022202/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__20251002-022202/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__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 78, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 60, in id_translate
itertools.chain(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 61, in <genexpr>
orthology_mod.translate(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Fq4eCasB-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__20251002-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 867, in __init__
Proteomes.__init__(self, only_swissprot = only_swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 760, in __init__
self.load_taxonomy()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 824, in load_taxonomy
self._up_taxonomy = uniprot_input.uniprot_taxonomy(ncbi_tax_ids = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1633, in uniprot_taxonomy
nti = taxonomy.ensure_ncbi_tax_id(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 401, in ensure_ncbi_tax_id
taxid_from_common_name(taxon_id) or
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 310, in taxid_from_common_name
common_to_ncbi = get_db('common')
^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:35:05 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2025-10-02 03:32:07 | 2025-10-02 03:32:38 | 31.34 |
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__20251002-022202/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__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 78, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 60, in id_translate
itertools.chain(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/baccin2019.py", line 61, in <genexpr>
orthology_mod.translate(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 2066, in translate
return manager.translate(**args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Fq4eCasB-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__20251002-022202/pypath_git/pypath/utils/orthology.py", line 329, in translate
table = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 234, in which_table
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/pypath_git/pypath/utils/orthology.py", line 1493, in __init__
ProteinOrthology.__init__(**locals())
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 867, in __init__
Proteomes.__init__(self, only_swissprot = only_swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 760, in __init__
self.load_taxonomy()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/orthology.py", line 824, in load_taxonomy
self._up_taxonomy = uniprot_input.uniprot_taxonomy(ncbi_tax_ids = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1633, in uniprot_taxonomy
nti = taxonomy.ensure_ncbi_tax_id(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 401, in ensure_ncbi_tax_id
taxid_from_common_name(taxon_id) or
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 310, in taxid_from_common_name
common_to_ncbi = get_db('common')
^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:39:06 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2025-10-02 03:32:38 | 2025-10-02 03:32:38 | 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 | {} | 2025-10-02 03:32:38 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2025-10-02 03:32:38 | 2025-10-02 03:33:17 | 38.94 | 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 | {} | 2025-10-02 03:32:38 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2025-10-02 03:33:18 | 2025-10-02 03:33:58 | 40.81 | 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 | {'size': 10} | 2025-10-02 03:33:18 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2025-10-02 03:33:59 | 2025-10-02 03:34:00 | 1.10 | 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 | {'size': 8} | 2025-10-02 03:33:59 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2025-10-02 03:34:00 | 2025-10-02 03:34:30 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/biomart.py", line 194, in biomart_homology
source_organism = ensure_organism(source_organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/biomart.py", line 183, in ensure_organism
organism_ensembl = taxonomy.ensure_ensembl_name(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 253, in ensure_ensembl_name
return _ensure_name(taxon_id, 'ensembl')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:40:28 | |||
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2025-10-02 03:34:30 | 2025-10-02 03:35:00 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/biomart.py", line 237, in biomart_microarray_types
organism = taxonomy.ensure_ensembl_name(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 253, in ensure_ensembl_name
return _ensure_name(taxon_id, 'ensembl')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:40:57 | |||
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2025-10-02 03:35:00 | 2025-10-02 03:35:00 | 0.20 | 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 | {} | 2025-10-02 03:35:00 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2025-10-02 03:35:00 | 2025-10-02 03:35:20 | 19.51 |
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__20251002-022202/pypath_git/pypath/inputs/cancercellmap.py", line 74, in ccmap_interactions
nodes['cell-map-node-attributes.txt'].split('\n')[1:]
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{'broke': True} | 2025-10-01 03:40:57 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2025-10-02 03:35:20 | 2025-10-02 03:35:38 | 18.19 | 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 | {} | 2025-10-02 03:35:20 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2025-10-02 03:35:38 | 2025-10-02 03:35:38 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 330 | {} | 2025-10-02 03:35:38 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2025-10-02 03:35:38 | 2025-10-02 03:35:45 | 7.64 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='Q92731', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 5,157 | {} | 2025-10-02 03:35:38 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2025-10-02 03:35:45 | 2025-10-02 03:35:48 | 2.31 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {} | 2025-10-02 03:35:45 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2025-10-02 03:35:48 | 2025-10-02 03:36:00 | 11.83 | dict | {'P21583': {CellcallAnnotation(role='ligand')}, 'P09619': {CellcallAnnotation(role='receptor')}, 'P32881': {CellcallAnnotation(role='ligand')}, 'P17181': {CellcallAnnotation(role='receptor')}, 'P41221': {CellcallAnnotation(role='ligand')}, 'Q9NPG1': {CellcallAnnotation(role='receptor')}, 'P01566': {...(truncated) | 460 | {} | 2025-10-02 03:35:48 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2025-10-02 03:36:00 | 2025-10-02 03:36:00 | 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 | {} | 2025-10-02 03:36:00 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2025-10-02 03:36:00 | 2025-10-02 03:36:00 | 0.84 | 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 | {} | 2025-10-02 03:36:00 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2025-10-02 03:36:01 | 2025-10-02 03:36:01 | 0.10 | list | [CellcallInteraction(ligand_uniprot='P21583', receptor_uniprot='P09619', core=True), CellcallInteraction(ligand_uniprot='P32881', receptor_uniprot='P17181', core=True), CellcallInteraction(ligand_uniprot='P41221', receptor_uniprot='Q9NPG1', core=True), CellcallInteraction(ligand_uniprot='P01566', re...(truncated) | 797 | {} | 2025-10-02 03:36:01 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2025-10-02 03:36:01 | 2025-10-02 03:36:01 | 0.66 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinterac...(truncated) | 3,425 | {} | 2025-10-02 03:36:01 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2025-10-02 03:36:01 | 2025-10-02 03:36:11 | 9.98 | 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 | {} | 2025-10-02 03:36:01 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2025-10-02 03:36:11 | 2025-10-02 03:36:19 | 7.53 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'P41271', 'Q13253', 'O75610', 'O00292', 'Q9H772', 'Q9H2X0', 'O60565', 'P12645'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 32 | {} | 2025-10-02 03:36:11 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2025-10-02 03:36:19 | 2025-10-02 03:36:26 | 7.05 | 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 | {} | 2025-10-02 03:36:19 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2025-10-02 03:36:26 | 2025-10-02 03:36:33 | 6.94 | 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 | {} | 2025-10-02 03:36:26 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2025-10-02 03:36:33 | 2025-10-02 03:36:40 | 7.24 | list | [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) | 12,424 | {} | 2025-10-02 03:36:33 | |
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2025-10-02 03:36:40 | 2025-10-02 03:37:10 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 311, in cellinker_lr_interactions
raw = cellinker_lr_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 218, in cellinker_lr_interactions_raw
return _cellinker_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 268, in _cellinker_interactions_raw
_organism = getattr(taxonomy, 'ensure_%s_name' % org_name_type)(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 248, in ensure_latin_name
return _ensure_name(taxon_id, 'latin')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:42:09 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2025-10-02 03:37:10 | 2025-10-02 03:37:40 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 513, in cellinker_complex_annotations
return cellinker_annotations(organism = organism, entity_type = 'complex')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 311, in cellinker_lr_interactions
raw = cellinker_lr_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 218, in cellinker_lr_interactions_raw
return _cellinker_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 268, in _cellinker_interactions_raw
_organism = getattr(taxonomy, 'ensure_%s_name' % org_name_type)(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 248, in ensure_latin_name
return _ensure_name(taxon_id, 'latin')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:42:10 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2025-10-02 03:37:40 | 2025-10-02 03:37:40 | 0.08 | 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 | {} | 2025-10-02 03:37:40 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2025-10-02 03:37:40 | 2025-10-02 03:37:40 | 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 | {} | 2025-10-02 03:37:40 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2025-10-02 03:37:40 | 2025-10-02 03:38:10 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 311, in cellinker_lr_interactions
raw = cellinker_lr_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 218, in cellinker_lr_interactions_raw
return _cellinker_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 268, in _cellinker_interactions_raw
_organism = getattr(taxonomy, 'ensure_%s_name' % org_name_type)(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 248, in ensure_latin_name
return _ensure_name(taxon_id, 'latin')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:42:10 | |||
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2025-10-02 03:38:10 | 2025-10-02 03:38:40 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 218, in cellinker_lr_interactions_raw
return _cellinker_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 268, in _cellinker_interactions_raw
_organism = getattr(taxonomy, 'ensure_%s_name' % org_name_type)(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 248, in ensure_latin_name
return _ensure_name(taxon_id, 'latin')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:42:10 | |||
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2025-10-02 03:38:40 | 2025-10-02 03:39:10 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 495, in cellinker_protein_annotations
return cellinker_annotations(organism = organism, entity_type = 'protein')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 311, in cellinker_lr_interactions
raw = cellinker_lr_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 218, in cellinker_lr_interactions_raw
return _cellinker_interactions_raw(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/cellinker.py", line 268, in _cellinker_interactions_raw
_organism = getattr(taxonomy, 'ensure_%s_name' % org_name_type)(organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 248, in ensure_latin_name
return _ensure_name(taxon_id, 'latin')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 268, in _ensure_name
ncbi_to_name = get_db('ncbi_to_%s' % name_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 470, in get_db
init_db(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/taxonomy.py", line 485, in init_db
ncbi_data = uniprot_input.uniprot_ncbi_taxids_2()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/uniprot.py", line 1707, in uniprot_ncbi_taxids_2
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 03:42:10 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2025-10-02 03:39:10 | 2025-10-02 03:39:10 | 0.14 | set | {CellinkerInteraction(ligand='5280363', receptor='Q9Y5Y4', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='12466225', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='92135', receptor='Q8TDS4', ligand_location=None, receptor_location='Membrane', re...(truncated) | 314 | {} | 2025-10-02 03:39:10 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2025-10-02 03:39:10 | 2025-10-02 03:39:10 | 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 | {} | 2025-10-02 03:39:10 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2025-10-02 03:39:10 | 2025-10-02 03:39:11 | 0.19 | 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 | {} | 2025-10-02 03:39:10 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2025-10-02 03:39:11 | 2025-10-02 03:39:11 | 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 | {} | 2025-10-02 03:39:11 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2025-10-02 03:39:11 | 2025-10-02 03:39:11 | 0.49 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {} | 2025-10-02 03:39:11 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2025-10-02 03:39:11 | 2025-10-02 03:39:11 | 0.02 | tuple | ({Complex Glutamate_byGLS2_and_SLC1A2: COMPLEX:P43004_Q9UI32, 'Q9Y6W8', 'Q14031', 'Q96EP9', 'P19022', 'P21583', 'Q8NFZ3', 'P01275', 'P01178', Complex LeukotrieneB4_byLTA4H: COMPLEX:P09960, Complex Acetylcholine_byCHAT_and_SLC18A3: COMPLEX:P28329_Q16572, 'P56704', 'O95727', 'Q99969', Complex integrin...(truncated) | 2 | {} | 2025-10-02 03:39:11 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2025-10-02 03:39:11 | 2025-10-02 03:39:11 | 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 | {} | 2025-10-02 03:39:11 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2025-10-02 03:39:11 | 2025-10-02 03:39:12 | 0.39 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='26156437')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,598 | {} | 2025-10-02 03:39:11 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2025-10-02 03:39:12 | 2025-10-02 03:39:12 | 0.15 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2025-10-02 03:39:12 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2025-10-02 03:39:12 | 2025-10-02 03:39:12 | 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 | {} | 2025-10-02 03:39:12 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2025-10-02 03:39:12 | 2025-10-02 03:39:12 | 0.29 | dict | {'P11836': {CelltypistAnnotation(cell_type='B cells', cell_subtype='Memory B cells', cell_ontology='CL:0000787', marker_type='celltypist_model', tissues=('Blood', 'Bone marrow', 'Intestine', 'Liver', 'Lung', 'Lung-draining lymph node', 'Mesenteric lymph node', 'Oesophagus', 'Omentum', 'Skeletal musc...(truncated) | 460 | {} | 2025-10-02 03:39:12 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2025-10-02 03:39:12 | 2025-10-02 03:39:52 | 39.78 | list | [Citation(allele='1247404', variation_id='1259194', nsv='', citation_source='PubMed', citation_id='25741868'), Citation(allele='669933', variation_id='669185', nsv='', citation_source='PubMedCentral', citation_id='4544753'), Citation(allele='3019660', variation_id='2864762', nsv='', citation_source=...(truncated) | 4,189,540 | {} | 2025-10-02 03:39:12 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2025-10-02 03:39:57 | 2025-10-02 03:47:24 | 446.59 | list | [Variant(allele='2789394', type='single nucleotide variant', variant='NM_001037329.4(CNGA4):c.152T>A (p.Ile51Asn)', entrez='1262', genesymbol='CNGA4', clinical_significance='Uncertain significance', review_status='criteria provided, single submitter', rs='1248241229', phenotype_ids=('MedGen:CN169374...(truncated) | 7,479,486 | {} | 2025-10-02 03:39:57 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2025-10-02 05:04:28 | 2025-10-02 05:04:40 | 11.46 | 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 | {} | 2025-10-02 05:04:28 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2025-10-02 05:04:40 | 2025-10-02 05:04:40 | 0.08 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2025-10-02 05:04:40 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2025-10-02 05:04:40 | 2025-10-02 05:04:40 | 0.22 | 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 | {} | 2025-10-02 05:04:40 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2025-10-02 05:04:40 | 2025-10-02 05:04:41 | 1.24 | 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 | {} | 2025-10-02 05:04:40 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2025-10-02 05:04:41 | 2025-10-02 05:04:41 | 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 | {} | 2025-10-02 05:04:41 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2025-10-02 05:04:41 | 2025-10-02 05:06:45 | 123.55 | 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 | {} | 2025-10-02 05:04:41 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2025-10-02 05:06:45 | 2025-10-02 05:07:01 | 16.32 | 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 | {} | 2025-10-02 05:06:45 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2025-10-02 05:07:01 | 2025-10-02 05:07:15 | 13.24 | 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='extracellular', score=0.8),...(truncated) | 22,799 | {} | 2025-10-02 05:07:01 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2025-10-02 05:07:15 | 2025-10-02 05:07:15 | 0.33 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {} | 2025-10-02 05:07:15 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2025-10-02 05:07:15 | 2025-10-02 05:07:15 | 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 | {} | 2025-10-02 05:07:15 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2025-10-02 05:07:15 | 2025-10-02 05:07:19 | 3.61 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2025-10-02 05:07:15 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2025-10-02 05:07:19 | 2025-10-02 05:07:19 | 0.16 | 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 | {} | 2025-10-02 05:07:19 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_raw | 2025-10-02 05:07:19 | 2025-10-02 05:07:19 | 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 | {} | 2025-10-02 05:07:19 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2025-10-02 05:07:19 | 2025-10-02 05:08:17 | 58.03 | 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} | 2025-10-02 05:07:19 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2025-10-02 05:08:17 | 2025-10-02 05:08:17 | 0.07 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='ERK signaling pathway', cancer='Glioma', pathway_category='MAPK signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit progression of glioma'), CpadPathwayCancer(pathway='Caspase 3 dependent pathway', cancer='Glioma', pathway_cate...(truncated) | 2 | {} | 2025-10-02 05:08:17 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2025-10-02 05:08:17 | 2025-10-02 05:08:17 | 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 | {} | 2025-10-02 05:08:17 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2025-10-02 05:08:17 | 2025-10-02 05:08:27 | 10.46 | 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 | {} | 2025-10-02 05:08:17 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2025-10-02 05:08:28 | 2025-10-02 05:08:30 | 2.08 | 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 | {} | 2025-10-02 05:08:28 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2025-10-02 05:08:30 | 2025-10-02 05:08:31 | 0.72 | 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 | {} | 2025-10-02 05:08:30 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2025-10-02 05:08:31 | 2025-10-02 05:08:32 | 1.23 | dict | {'A1A5B4': {CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='HDLM2', value...(truncated) | 1,410 | {} | 2025-10-02 05:08:31 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2025-10-02 05:08:32 | 2025-10-02 05:08:32 | 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 | {} | 2025-10-02 05:08:32 | |
| ¶ | 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 | 2025-10-02 05:08:33 | 2025-10-02 05:08:34 | 1.58 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P15692', score=-0.102361116501572, cytokine_genesymbol='VEGFA', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P05231', score=0.0084669266516721, cytokine_genesymbol='IL6', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P12644', score=-0.03...(truncated) | 4,887 | {} | 2025-10-02 05:08:33 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2025-10-02 05:08:34 | 2025-10-02 05:08:34 | 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 | {} | 2025-10-02 05:08:34 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2025-10-02 05:08:34 | 2025-10-02 05:08:37 | 2.91 | 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 | {} | 2025-10-02 05:08:34 | |
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2025-10-02 05:08:38 | 2025-10-02 05:08:39 | 1.22 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2025-10-02 05:08:38 | |
| ¶ | 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 | 2025-10-02 05:08:39 | 2025-10-02 05:09:22 | 42.67 | list | [DdinterInteraction(drug1_id='DDInter1451', drug1_name='Phenylbutazone', drug2_id='DDInter7', drug2_name='Abemaciclib', level='Moderate'), DdinterInteraction(drug1_id='DDInter1213', drug1_name='Midodrine', drug2_id='DDInter252', drug2_name='Bupropion', level='Moderate'), DdinterInteraction(drug1_id=...(truncated) | 160,235 | {} | 2025-10-02 05:08:39 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2025-10-02 05:09:22 | 2025-10-02 05:56:24 | 2,821.79 | list | [DdinterIdentifiers(ddinter='DDInter364', drugbank='DB00672', chembl='CHEMBL498', pubchem='46506402'), DdinterIdentifiers(ddinter='DDInter1796', drugbank='DB00679', chembl='CHEMBL479', pubchem='46509070'), DdinterIdentifiers(ddinter='DDInter1598', drugbank='DB12457', chembl='CHEMBL2178422', pubchem=...(truncated) | 1,939 | {} | 2025-10-02 05:09:22 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2025-10-02 05:56:24 | 2025-10-02 05:56:24 | 0.43 | int | 1939 | 0 | {} | 2025-10-02 05:56:24 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2025-10-02 05:56:24 | 2025-10-02 05:56:24 | 0.16 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2025-10-02 05:56:24 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2025-10-02 05:56:24 | 2025-10-02 05:56:25 | 0.50 | 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 | {} | 2025-10-02 05:56:24 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2025-10-02 05:56:25 | 2025-10-02 05:56:25 | 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 | {} | 2025-10-02 05:56:25 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2025-10-02 05:56:25 | 2025-10-02 05:56:30 | 5.60 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='dGene'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='BaderLab'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='GO'), DgidbAnnotation(category='DRUGGABLE GENOME', source='HingoraniCasas'), DgidbAn...(truncated) | 9,973 | {} | 2025-10-02 05:56:25 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2025-10-02 05:56:30 | 2025-10-02 05:56:36 | 5.96 | list | [DgidbInteraction(genesymbol='GRIN1', gene_concept_id='hgnc:4584', resource='ChEMBL', type='inhibitor', drug_name='AMANTADINE HYDROCHLORIDE', drug_concept_id='rxcui:282415', score='0.1071585127259071', approved='TRUE', anti_neoplastic='FALSE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='POL...(truncated) | 84,175 | {} | 2025-10-02 05:56:30 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2025-10-02 05:56:37 | 2025-10-02 05:56:37 | 0.23 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2025-10-02 05:56:37 | |
| ¶ | 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 | 2025-10-02 05:56:37 | 2025-10-02 05:56:37 | 0.48 | 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 | {} | 2025-10-02 05:56:37 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2025-10-02 05:56:37 | 2025-10-02 05:56:41 | 3.59 | 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 | {} | 2025-10-02 05:56:37 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2025-10-02 05:56:41 | 2025-10-02 05:56:41 | 0.16 | 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 | {} | 2025-10-02 05:56:41 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2025-10-02 05:56:41 | 2025-10-02 05:56:42 | 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 | {} | 2025-10-02 05:56:41 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2025-10-02 05:56:42 | 2025-10-02 05:56:47 | 5.10 | 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 | {} | 2025-10-02 05:56:42 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2025-10-02 05:56:47 | 2025-10-02 06:02:48 | 360.52 |
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__20251002-022202/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 | 2025-10-02 06:02:48 | 2025-10-02 06:02:54 | 5.85 | list | [<pypath.internals.intera.DomainDomain object at 0x7efd7f3e5190>, <pypath.internals.intera.DomainDomain object at 0x7efdbe8ed7d0>, <pypath.internals.intera.DomainDomain object at 0x7efdd7a22310>, <pypath.internals.intera.DomainDomain object at 0x7efdd7a23ad0>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2025-10-02 06:02:48 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2025-10-02 06:02:54 | 2025-10-02 06:02:55 | 1.16 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7efdfc0625d0>, <pypath.internals.intera.DomainDomain object at 0x7efdfc063350>, <pypath.internals.intera.DomainDomain object at 0x7efdfc062bd0>, <pypath.internals.intera.DomainDomain object at 0x7efdfc061cd0>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2025-10-02 06:02:54 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2025-10-02 06:02:55 | 2025-10-02 06:02:55 | 0.34 | 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 | {} | 2025-10-02 06:02:55 | |
| ¶ | pypath.inputs.domino.get_domino | 2025-10-02 06:02:55 | 2025-10-02 06:02:55 | 0.32 | 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 | {} | 2025-10-02 06:02:55 | |
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2025-10-02 06:02:56 | 2025-10-02 06:03:07 | 11.00 | 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 | {} | 2025-10-02 06:02:56 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-10-02 06:03:07 | 2025-10-02 06:03:22 | 15.37 | 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 | {} | 2025-10-02 06:03:07 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-10-02 06:03:22 | 2025-10-02 06:03:24 | 1.93 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2025-10-02 06:03:22 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-10-02 06:03:24 | 2025-10-02 06:03:25 | 1.35 | 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 | {} | 2025-10-02 06:03:24 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-10-02 06:03:25 | 2025-10-02 06:03:39 | 13.90 | 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 | {} | 2025-10-02 06:03:25 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-10-02 06:03:39 | 2025-10-02 06:03:39 | 0.41 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 06:03:40 | 2025-10-02 06:03:41 | 1.05 | 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 | {} | 2025-10-02 06:03:40 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2025-10-02 06:03:41 | 2025-10-02 06:03:42 | 1.38 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2025-10-02 06:03:41 | |
| ¶ | 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 | 2025-10-02 06:03:42 | 2025-10-02 06:04:04 | 22.26 | 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 | {} | 2025-10-02 06:03:42 | |
| ¶ | pypath.inputs.elm.elm_domains | 2025-10-02 06:04:04 | 2025-10-02 06:04:05 | 0.32 | 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 | {} | 2025-10-02 06:04:04 | |
| ¶ | pypath.inputs.elm.elm_instances | 2025-10-02 06:04:05 | 2025-10-02 06:04:05 | 0.16 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 4,277 | {'size': -1} | 2025-10-02 06:04:05 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2025-10-02 06:04:05 | 2025-10-02 06:04:05 | 0.13 | list | [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) | 2,797 | {} | 2025-10-02 06:04:05 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2025-10-02 06:04:05 | 2025-10-02 06:06:50 | 164.61 | dict | {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=True)}, 'P30411': {EmbraceAnnotation(mainclass='receptor', neu...(truncated) | 844 | {} | 2025-10-02 06:04:05 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2025-10-02 06:06:50 | 2025-10-02 06:06:50 | 0.10 | list | [EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(ligand='O43184', receptor='P05556'), EmbraceInteraction(ligand='O43184', receptor='P31431'), EmbraceInteraction(...(truncated) | 1,273 | {} | 2025-10-02 06:06:50 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2025-10-02 06:06:50 | 2025-10-02 06:06:50 | 0.09 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2025-10-02 06:06:50 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2025-10-02 06:06:50 | 2025-10-02 06:06:50 | 0.10 | list | [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) | 1,832 | {} | 2025-10-02 06:06:50 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2025-10-02 06:06:50 | 2025-10-02 06:06:50 | 0.43 | 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 | {} | 2025-10-02 06:06:50 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2025-10-02 06:06:50 | 2025-10-02 06:06:51 | 0.56 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 348 | {} | 2025-10-02 06:06:50 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.exocarta.get_exocarta | 2025-10-02 06:06:51 | 2025-10-02 06:07:52 | 61.02 | 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 | {} | 2025-10-02 06:06:51 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2025-10-02 06:07:52 | 2025-10-02 06:07:54 | 1.76 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/exocarta.py", line 96, in _get_exocarta_vesiclepedia
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2025-10-01 06:15:09 | |||
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2025-10-02 06:07:54 | 2025-10-02 06:07:55 | 0.93 | 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 | {} | 2025-10-02 06:07:54 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2025-10-02 06:07:55 | 2025-10-02 06:07:56 | 1.79 | 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 | {} | 2025-10-02 06:07:55 | |
| ¶ | 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 | 2025-10-02 06:07:56 | 2025-10-02 06:08:49 | 52.47 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0016020', 'GO:0045275', 'GO:0005743'}, 'A0A023I7H2': {'GO:0005743'}, 'A0A023I7H5': {'GO:0045259', 'GO:0005743'}, 'A0A023I7J4': {'GO:0005743'}, 'A0A023I7L8': {'GO:0045259', 'GO:0005743'}, 'A0A023I7N5': {'GO:0016020', 'GO:0005743'}, 'A0A02...(truncated) | 2 | {} | 2025-10-02 06:07:56 | |
| ¶ | pypath.inputs.go.get_goslim | 2025-10-02 06:08:49 | 2025-10-02 06:08:50 | 1.31 | 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 | {} | 2025-10-02 06:08:49 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-10-02 06:08:50 | 2025-10-02 06:16:24 | 453.99 | dict | {'C': {'GO:0160112': {('GO:0160110', 'part_of'), ('GO:0097649', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0160111': {('GO:0160110', 'part_of'), ('GO:0097649', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:1990657': {('GO:1903958', 'is_a'), ('GO:1990658', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) | 3 | {} | 2025-10-02 06:08:50 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2025-10-02 06:16:24 | 2025-10-02 06:16:24 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 06:16:24 | 2025-10-02 06:16:29 | 4.28 | dict | {'C': {'GO:0160112': {('GO:0160110', 'part_of'), ('GO:0097649', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0160111': {('GO:0160110', 'part_of'), ('GO:0097649', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:1990657': {('GO:1903958', 'is_a'), ('GO:1990658', 'is_a')}, 'GO:0160278': {('GO:0098562', 'is_a'), ('...(truncated) | 3 | {} | 2025-10-02 06:16:24 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-10-02 06:16:29 | 2025-10-02 06:16:31 | 2.58 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005634', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2025-10-02 06:16:29 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2025-10-02 06:16:31 | 2025-10-02 06:16:38 | 6.28 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='involved_in', go_id='GO:1901909', reference='GO_REF:0000033', evidence_code='IBA', with_or_from='PANTHER:PTN000290327|PomBase:SPAC13G6.14|UniProtKB:O95989', aspect='P', db_object_name='Dipho...(truncated) | 19,697 | {} | 2025-10-02 06:16:31 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-10-02 06:16:40 | 2025-10-02 06:16:41 | 1.11 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005634', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005576'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2025-10-02 06:16:40 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2025-10-02 06:16:41 | 2025-10-02 06:16:41 | 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__20251002-022202/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 | 2025-10-02 06:16:41 | 2025-10-02 06:16:53 | 11.92 | 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 | {} | 2025-10-02 06:16:41 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-10-02 06:16:53 | 2025-10-02 06:16:58 | 4.30 | dict | {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160112', 'part_of'), ('GO:0160111', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160280', 'part_of'), ('GO:0160279', 'part_of')}, 'GO:1990676': {(...(truncated) | 3 | {} | 2025-10-02 06:16:53 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2025-10-02 06:16:58 | 2025-10-02 06:16:58 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/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 | 2025-10-02 06:16:58 | 2025-10-02 06:17:02 | 4.34 | dict | {'C': defaultdict(<class 'set'>, {'GO:0160110': {('GO:0160112', 'part_of'), ('GO:0160111', 'part_of')}, 'GO:1990658': {('GO:1990657', 'is_a')}, 'GO:1990674': {('GO:0160278', 'part_of'), ('GO:0160277', 'part_of')}, 'GO:1990675': {('GO:0160280', 'part_of'), ('GO:0160279', 'part_of')}, 'GO:1990676': {(...(truncated) | 3 | {} | 2025-10-02 06:16:58 | |
| ¶ | 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 | 2025-10-02 06:17:02 | 2025-10-02 06:17:06 | 3.63 | 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 | {} | 2025-10-02 06:17:02 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2025-10-02 06:17:06 | 2025-10-02 06:17:06 | 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__20251002-022202/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 | 2025-10-02 06:17:06 | 2025-10-02 06:17:09 | 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 | {} | 2025-10-02 06:17:06 | |
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2025-10-02 06:17:09 | 2025-10-02 06:17:10 | 0.23 | 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 | {} | 2025-10-02 06:17:09 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2025-10-02 06:17:10 | 2025-10-02 06:17:12 | 2.21 | 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 | {} | 2025-10-02 06:17:10 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2025-10-02 06:17:12 | 2025-10-02 06:17:18 | 5.84 | 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 | {} | 2025-10-02 06:17:12 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2025-10-02 06:17:18 | 2025-10-02 06:17:18 | 0.22 | dict | {'P78556': {GutmgeneAnnotation(gut_microbiota='Streptococcus', gut_microbiota_ncbi_id='1301', rank='genus', strain=None, alteration='inhibition', throughput='low-throughput', associative_mode='correlatively', sample='rectum', experimental_method='cell culture', measurement_technique='HPLC analysis,q...(truncated) | 111 | {} | 2025-10-02 06:17:18 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2025-10-02 06:17:18 | 2025-10-02 06:17:18 | 0.01 | list | [GutmgeneRaw(index='1', pmid='31142855', gut_microbiota='Streptococcus', gut_microbiota_ncbi_id='1301', rank='genus', strain=None, gene='CCL20', gene_id='6364', alteration='inhibition', throughput='low-throughput', associative_mode='correlatively', organism='human', sample='rectum', experimental_met...(truncated) | 243 | {} | 2025-10-02 06:17:18 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2025-10-02 06:17:18 | 2025-10-02 06:17:18 | 0.20 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2025-10-02 06:17:18 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2025-10-02 06:17:18 | 2025-10-02 06:17:18 | 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 | {} | 2025-10-02 06:17:18 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2025-10-02 06:17:18 | 2025-10-02 06:17:20 | 2.01 | 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 | {} | 2025-10-02 06:17:18 | |
| ¶ | pypath.inputs.hint.hint_interactions | 2025-10-02 06:17:20 | 2025-10-02 06:17:26 | 5.49 | 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 | {} | 2025-10-02 06:17:20 | |
| ¶ | pypath.inputs.hint.hint_raw | 2025-10-02 06:17:26 | 2025-10-02 06:17:26 | 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 | {} | 2025-10-02 06:17:26 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2025-10-02 06:17:26 | 2025-10-02 06:17:37 | 11.72 | list | [HippieInteraction(id_a='O14498', id_b='Q70JA7', score=0.83, methods=None, references=('26186194', '28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='P40692', id_b='P17661', score=0.78, methods=None, references=('20706999',), sources=None, organisms=None), HippieInteract...(truncated) | 102,409 | {} | 2025-10-02 06:17:26 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2025-10-02 06:17:38 | 2025-10-02 06:18:54 | 76.22 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2025-10-02 06:17:38 | |
| ¶ | 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 | 2025-10-02 06:18:54 | 2025-10-02 06:18:54 | 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 | {} | 2025-10-02 06:18:54 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2025-10-02 06:18:54 | 2025-10-02 06:18:54 | 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 | {} | 2025-10-02 06:18:54 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2025-10-02 06:18:54 | 2025-10-02 06:18:54 | 0.00 | dict | {} | 0 | {} | 2025-10-02 06:18:54 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2025-10-02 06:18:54 | 2025-10-02 06:18:54 | 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 | {} | 2025-10-02 06:18:54 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2025-10-02 06:18:54 | 2025-10-02 06:18:58 | 4.27 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0007034'), HpoAnnotation(entrez_ge...(truncated) | 5,128 | {} | 2025-10-02 06:18:54 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2025-10-02 06:18:58 | 2025-10-02 06:19:03 | 4.26 | 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:613722', name='Developmental and epileptic encephalopat...(truncated) | 11,421 | {} | 2025-10-02 06:18:58 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2025-10-02 06:19:03 | 2025-10-02 06:19:05 | 1.97 | 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 | {} | 2025-10-02 06:19:03 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2025-10-02 06:19:05 | 2025-10-02 06:19:06 | 0.51 | 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 | {} | 2025-10-02 06:19:05 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2025-10-02 06:19:06 | 2025-10-02 06:19:10 | 4.24 | 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 | {} | 2025-10-02 06:19:06 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2025-10-02 06:19:10 | 2025-10-02 06:19:12 | 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 | {} | 2025-10-02 06:19:10 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2025-10-02 06:19:12 | 2025-10-02 06:19:13 | 1.23 | 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 | {} | 2025-10-02 06:19:12 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2025-10-02 06:19:13 | 2025-10-02 06:19:14 | 1.13 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2025-10-02 06:19:13 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2025-10-02 06:19:14 | 2025-10-02 06:19:45 | 30.30 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2025-10-02 06:19:14 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2025-10-02 06:19:45 | 2025-10-02 06:19:55 | 10.38 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 06:19:55 | 2025-10-02 06:19:55 | 0.23 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,545 | {} | 2025-10-02 06:19:55 | |
| ¶ | pypath.inputs.humap.humap2and3_complexes | 2025-10-02 06:19:55 | 2025-10-02 06:19:58 | 2.47 | 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 | {} | 2025-10-02 06:19:55 | |
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2025-10-02 06:19:58 | 2025-10-02 06:20:01 | 2.93 | 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 | {} | 2025-10-02 06:19:58 | |
| ¶ | pypath.inputs.huri.hi_i_interactions | 2025-10-02 06:20:01 | 2025-10-02 06:20:02 | 1.23 |
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__20251002-022202/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 | 2025-10-02 06:20:02 | 2025-10-02 06:20:03 | 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__20251002-022202/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 | 2025-10-02 06:20:03 | 2025-10-02 06:20:04 | 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__20251002-022202/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 | 2025-10-02 06:20:04 | 2025-10-02 06:20:05 | 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__20251002-022202/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 | 2025-10-02 06:20:05 | 2025-10-02 06:20:06 | 1.08 | 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 | {} | 2025-10-02 06:20:05 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2025-10-02 06:20:06 | 2025-10-02 06:20:08 | 1.54 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2025-10-02 06:20:06 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2025-10-02 06:20:08 | 2025-10-02 06:20:10 | 2.28 |
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__20251002-022202/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 | 2025-10-02 06:20:10 | 2025-10-02 06:20:12 | 2.17 | 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 | {} | 2025-10-02 06:20:10 | |
| ¶ | 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 | 2025-10-02 06:20:12 | 2025-10-02 06:20:13 | 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__20251002-022202/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 | 2025-10-02 06:20:13 | 2025-10-02 06:20:15 | 1.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 06:20:15 | 2025-10-02 06:20:26 | 11.88 | 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 | {} | 2025-10-02 06:20:15 | |
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2025-10-02 06:20:27 | 2025-10-02 06:20:27 | 0.27 | dict | {Complex: COMPLEX:P01033_P14780: {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None)}, 'P01033': {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None), IcellnetAnnotation(role='ligand', family='Cell adhesion', subfamily=None, classifica...(truncated) | 1,194 | {'size': 1} | 2025-10-02 06:20:27 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2025-10-02 06:20:27 | 2025-10-02 06:20:27 | 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 | {} | 2025-10-02 06:20:27 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2025-10-02 06:20:27 | 2025-10-02 06:20:27 | 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 | {} | 2025-10-02 06:20:27 | |
| ¶ | 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 | 2025-10-02 06:20:27 | 2025-10-02 06:20:29 | 2.11 | 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 | {} | 2025-10-02 06:20:27 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2025-10-02 06:20:29 | 2025-10-02 06:20:30 | 0.55 | 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 | {} | 2025-10-02 06:20:29 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2025-10-02 06:20:30 | 2025-10-02 06:20:30 | 0.66 | NoneType | None | 0 | {} | 2025-10-02 06:20:30 | |
| ¶ | pypath.inputs.intact.intact_interactions | 2025-10-02 06:20:30 | 2025-10-02 06:23:03 | 152.18 | 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 | {} | 2025-10-02 06:20:30 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2025-10-02 06:23:03 | 2025-10-02 06:23:03 | 0.60 | set | {'Q13797', 'P38570', 'P08648', 'Q13683', 'P23229', 'P08514', 'P53708', 'O75578', 'P20701', 'P05106', 'P26006', 'P56199', 'P26010', 'P18564', 'P06756', 'P18084', 'P16144', 'P26012', 'Q9UKX5', 'P11215', 'P17301', 'P05107', 'P20702', 'P05556', 'Q13349'} | 25 | {} | 2025-10-02 06:23:03 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2025-10-02 06:23:03 | 2025-10-02 06:23:06 | 2.18 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid receptor activity'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOA...(truncated) | 14,743 | {} | 2025-10-02 06:23:03 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2025-10-02 06:23:06 | 2025-10-02 06:23:06 | 0.39 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR000001', organism='9606', start='388', end='471'), InterproAnnotation(interpro_id='IPR000001', organism='9606', start='126', end='208'), InterproAnnotation(interpro_id='IPR018056', organism='9606', start='353', end='365'), Int...(truncated) | 16,611 | {} | 2025-10-02 06:23:06 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2025-10-02 06:23:06 | 2025-10-02 06:23:19 | 12.59 | 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 | {} | 2025-10-02 06:23:06 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2025-10-02 06:23:19 | 2025-10-02 06:23:20 | 0.83 | 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 | {} | 2025-10-02 06:23:19 | |
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2025-10-02 06:23:20 | 2025-10-02 06:23:20 | 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 | {} | 2025-10-02 06:23:20 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2025-10-02 06:23:20 | 2025-10-02 06:23:39 | 19.31 | 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 | {} | 2025-10-02 06:23:20 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2025-10-02 06:23:39 | 2025-10-02 06:23:40 | 0.66 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='growth factor'), ItalkAnnotation(mainclass='receptor', subclass='other')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {} | 2025-10-02 06:23:39 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2025-10-02 06:23:40 | 2025-10-02 06:23:40 | 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 | {} | 2025-10-02 06:23:40 | |
| ¶ | pypath.inputs.italk.italk_raw | 2025-10-02 06:23:40 | 2025-10-02 06:23:40 | 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 | {} | 2025-10-02 06:23:40 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2025-10-02 06:23:40 | 2025-10-02 06:23:44 | 4.20 | 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 | {} | 2025-10-02 06:23:40 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2025-10-02 06:23:44 | 2025-10-02 06:23:44 | 0.15 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {} | 2025-10-02 06:23:44 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2025-10-02 06:23:44 | 2025-10-02 06:38:35 | 890.62 | 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 | {} | 2025-10-02 06:23:44 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2025-10-02 06:38:35 | 2025-10-02 06:39:13 | 38.41 | set | {KeggMedicusRawInteraction(id_a='35', id_b='3030', name_a='ACADS', name_b='HADHA', effect='enzyme_enzyme', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N00856'), KeggMedicusRawInteraction(id_a='5605', id_b='5595', name_a='MAP2K2', name_b='MAPK3', effect=...(truncated) | 12,946 | {} | 2025-10-02 06:38:35 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2025-10-02 06:39:13 | 2025-10-02 06:39:14 | 0.45 | dict | {'COMPLEX:P36894_Q13705': Complex: COMPLEX:P36894_Q13705, 'COMPLEX:Q8IZP0_Q9Y6W5': Complex: COMPLEX:Q8IZP0_Q9Y6W5, 'COMPLEX:P18206_Q9Y490': Complex: COMPLEX:P18206_Q9Y490, 'COMPLEX:Q2M1P5_Q9UMX1': Complex: COMPLEX:Q2M1P5_Q9UMX1, 'COMPLEX:O43318_Q9NYJ8': Complex: COMPLEX:O43318_Q9NYJ8, 'COMPLEX:P3689...(truncated) | 528 | {} | 2025-10-02 06:39:13 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2025-10-02 06:39:14 | 2025-10-02 06:39:14 | 0.37 | list | [KeggMedicusInteraction(id_a='P16219', id_b='P40939', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='enzyme_enzyme'), KeggMedicusInteraction(id_a='P36507', id_b='P27361', entity_type_a='protein', entity_type_b='protein', interaction_type='post_transl...(truncated) | 9,538 | {} | 2025-10-02 06:39:14 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2025-10-02 06:39:14 | 2025-10-02 06:39:27 | 12.89 | dict | {'Q13233': {KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Tight junction'), KeggPathway(pathway='Growth hormone synthesis, secretion and action'), KeggPathway(pathway='GnRH signaling pathway'), KeggPathway(pathway='Neurotrophin signaling pathway'), KeggPathway(pathway='RIG-I-li...(truncated) | 2,672 | {} | 2025-10-02 06:39:14 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2025-10-02 06:39:27 | 2025-10-02 06:39:28 | 1.14 | dict | {'A8K7J7': {KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Bu...(truncated) | 813 | {} | 2025-10-02 06:39:27 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2025-10-02 06:39:28 | 2025-10-02 06:39:41 | 12.97 | tuple | ({'MAPK signaling pathway': {'Q13233', 'Q9HD43', 'P19419', 'Q9Y6R4', 'Q9Y243', 'P21359', 'P53041', 'Q07889', 'Q03701', 'Q12851', 'P35557', 'P45985', 'O95382', 'Q9UKG9', 'P19838', 'Q99558', 'P62070', 'O95257', 'Q15750', 'Q9BQ95', 'O15111', 'Q99836', 'P16949', 'P51617', 'P49407', 'Q9UK32', 'Q13163', '...(truncated) | 2 | {} | 2025-10-02 06:39:28 | |
| ¶ | 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 | 2025-10-02 06:39:41 | 2025-10-02 06:39:45 | 3.99 |
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__20251002-022202/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__20251002-022202/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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__20251002-022202/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 | 2025-10-02 06:39:45 | 2025-10-02 06:39:46 | 0.56 | 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 | {} | 2025-10-02 06:39:45 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2025-10-02 06:39:46 | 2025-10-02 06:39:46 | 0.20 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2025-10-02 06:39:46 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2025-10-02 06:39:46 | 2025-10-02 06:39:50 | 3.54 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {} | 2025-10-02 06:39:46 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2025-10-02 06:39:50 | 2025-10-02 06:39:52 | 2.08 | 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 | {} | 2025-10-02 06:39:50 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2025-10-02 06:39:52 | 2025-10-02 06:39:52 | 0.41 | 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 | {} | 2025-10-02 06:39:52 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2025-10-02 06:39:52 | 2025-10-02 06:39:53 | 0.92 | 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 | {} | 2025-10-02 06:39:52 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2025-10-02 06:39:53 | 2025-10-02 06:39:54 | 0.85 | 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 | {} | 2025-10-02 06:39:53 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2025-10-02 06:39:54 | 2025-10-02 06:40:06 | 11.65 | 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 | {} | 2025-10-02 06:39:54 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2025-10-02 06:40:06 | 2025-10-02 06:40:06 | 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 | {} | 2025-10-02 06:40:06 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2025-10-02 06:40:06 | 2025-10-02 06:40:06 | 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 | {} | 2025-10-02 06:40:06 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2025-10-02 06:40:06 | 2025-10-02 06:40:07 | 1.30 | 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 | {} | 2025-10-02 06:40:06 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2025-10-02 06:40:07 | 2025-10-02 06:40:08 | 0.69 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2025-10-02 06:40:07 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2025-10-02 06:40:08 | 2025-10-02 06:40:08 | 0.46 | list | [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) | 1,170 | {} | 2025-10-02 06:40:08 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2025-10-02 06:40:08 | 2025-10-02 06:40:09 | 0.47 | 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 | {} | 2025-10-02 06:40:08 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2025-10-02 06:40:09 | 2025-10-02 06:40:10 | 1.16 | 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 | {} | 2025-10-02 06:40:09 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2025-10-02 06:40:10 | 2025-10-02 06:40:10 | 0.36 | 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 | {} | 2025-10-02 06:40:10 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2025-10-02 06:40:10 | 2025-10-02 06:40:45 | 34.93 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI...(truncated) | 9,479 | {} | 2025-10-02 06:40:10 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2025-10-02 06:40:45 | 2025-10-02 06:40:45 | 0.41 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('11560943', '13')), LrdbAnnotation(role='receptor', cell_type=None, s...(truncated) | 1,536 | {} | 2025-10-02 06:40:45 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2025-10-02 06:40:45 | 2025-10-02 06:40:46 | 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 | {} | 2025-10-02 06:40:45 | |
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2025-10-02 06:40:46 | 2025-10-02 06:40:46 | 0.23 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2025-10-02 06:40:46 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2025-10-02 06:40:46 | 2025-10-02 06:40:46 | 0.25 | dict | {'E9PRB5': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YCP4': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'D3YTG3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,501 | {} | 2025-10-02 06:40:46 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2025-10-02 06:40:46 | 2025-10-02 06:40:47 | 0.78 | dict | {} | 0 | {} | 2025-10-02 06:40:46 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2025-10-02 06:40:47 | 2025-10-02 06:40:48 | 1.42 | set | {'P10720', 'P98173', 'Q13162', 'P58062', 'Q14031', 'P21583', 'Q7Z5A8', 'Q9H0B8', 'Q9NQ36', 'Q9NR96', 'P01178', 'P04211', 'Q16842', 'P0DP01', 'P56704', 'Q9BXJ1', 'Q8WWQ2', 'Q17RY6', 'O43927', 'Q5DT21', 'P03950', 'Q12836', 'P04196', 'O60258', 'Q2MV58', 'Q6KF10', 'O60383', 'Q9UBW5', 'Q969D9', 'Q9BZM1',...(truncated) | 2,840 | {} | 2025-10-02 06:40:47 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2025-10-02 06:40:48 | 2025-10-02 06:40:48 | 0.09 | 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 | {} | 2025-10-02 06:40:48 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2025-10-02 06:40:48 | 2025-10-02 06:40:48 | 0.06 | set | set() | 0 | {} | 2025-10-02 06:40:48 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2025-10-02 06:40:48 | 2025-10-02 06:40:48 | 0.06 | set | set() | 0 | {} | 2025-10-02 06:40:48 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2025-10-02 06:40:48 | 2025-10-02 06:40:50 | 1.17 | set | {'Q8TES5', 'Q8WTV0', 'Q68D78', 'O00548', 'P56748', 'Q6UWL6', 'P11215', 'P16671', 'Q9BX67', 'Q6MZM7', 'P35443', 'Q9Y5Y7', 'P13591', 'P56856', 'Q8N726', 'Q6AZ88', 'Q9NY15', 'Q9NZ94', 'Q6ZW63', 'O95500', 'Q92729', 'P02751', 'Q9Y4C0', 'Q9UKX5', 'Q8TAW8', 'P25940', 'Q4G160', 'P18827', 'Q9UQS6', 'Q9BXN2',...(truncated) | 112 | {} | 2025-10-02 06:40:48 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2025-10-02 06:40:50 | 2025-10-02 06:41:20 | 30.10 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {} | 2025-10-02 06:40:50 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2025-10-02 06:41:20 | 2025-10-02 06:41:20 | 0.13 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2025-10-02 06:41:20 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2025-10-02 06:41:20 | 2025-10-02 06:41:23 | 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 | {} | 2025-10-02 06:41:20 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2025-10-02 06:41:23 | 2025-10-02 06:41:24 | 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 | {} | 2025-10-02 06:41:23 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 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 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.17 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0004481', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0010195', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0004481', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0004482', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI...(truncated) | 2,925 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.02 | list | [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0004481', 'hsa-let-7a-3p'), ('MIMAT0004481', 'hsa-let-7a*'), ('MIMAT0010195', 'hsa-let-7a-2-3p'), ('MIMAT0010195', 'hsa-let-7a-2*'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0004482', 'hsa-let...(truncated) | 3,299 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.02 | list | ['MIMAT0000062', 'MIMAT0004481', 'MIMAT0010195', 'MIMAT0000063', 'MIMAT0004482', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0004484', 'MIMAT0000066', 'MIMAT0004485', 'MIMAT0000067', 'MIMAT0004486', 'MIMAT0004487', 'MIMAT0000068', 'MIMAT0004488', 'MIMAT0000069', 'MIMAT0004489', 'MIMAT0000070', 'MIMAT00000...(truncated) | 2,693 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.03 | list | [['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' untr...(truncated) | 39,233 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_mature | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.02 | list | [['75039', 'cel-let-7-5p', 'cel-let-7', 'MIMAT0000001', 'experimental', 'cloned [1-3], Northern [1], PCR [4], 454 [5], Illumina [6], CLIPseq [7]', '', '0'], ['75040', 'cel-let-7-3p', 'cel-let-7*', 'MIMAT0015091', 'experimental', 'CLIPseq [7]', '', '0'], ['75041', 'cel-lin-4-5p', 'cel-lin-4', 'MIMAT0...(truncated) | 49,168 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_mirna_pre_mature | 2025-10-02 06:41:24 | 2025-10-02 06:41:24 | 0.12 | list | [(['64685', 'MI0000001', 'cel-let-7', 'cel-let-7L', 'Caenorhabditis elegans let-7 stem-loop', 'UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA', 'let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' unt...(truncated) | 53,320 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_organisms | 2025-10-02 06:41:24 | 2025-10-02 06:41:26 | 1.79 | 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 | {} | 2025-10-02 06:41:24 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2025-10-02 06:41:26 | 2025-10-02 06:41:26 | 0.03 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,130 | {} | 2025-10-02 06:41:26 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2025-10-02 06:41:26 | 2025-10-02 06:41:26 | 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 | {} | 2025-10-02 06:41:26 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2025-10-02 06:41:26 | 2025-10-02 06:41:26 | 0.08 | list | [('hsa-let-7a-1', 'hsa-let-7a-5p'), ('hsa-let-7a-1', 'hsa-let-7a'), ('hsa-let-7a-1L', 'hsa-let-7a-5p'), ('hsa-let-7a-1L', 'hsa-let-7a'), ('hsa-let-7a-1', 'hsa-let-7a-3p'), ('hsa-let-7a-1', 'hsa-let-7a*'), ('hsa-let-7a-1L', 'hsa-let-7a-3p'), ('hsa-let-7a-1L', 'hsa-let-7a*'), ('hsa-let-7a-2', 'hsa-let...(truncated) | 4,071 | {} | 2025-10-02 06:41:26 | |
| ¶ | pypath.inputs.mirbase.mirbase_taxid | 2025-10-02 06:41:26 | 2025-10-02 06:41:26 | 0.00 | str | 'hsa' | 3 | {} | 2025-10-02 06:41:26 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2025-10-02 06:41:26 | 2025-10-02 06:41:27 | 0.17 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2025-10-02 06:41:26 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2025-10-02 06:41:27 | 2025-10-02 06:41:27 | 0.40 | 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 | {} | 2025-10-02 06:41:27 | |
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2025-10-02 06:41:27 | 2025-10-02 06:47:41 | 373.95 | 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 | {} | 2025-10-02 06:41:27 | |
| ¶ | 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 | 2025-10-02 06:47:41 | 2025-10-02 06:47:41 | 0.27 | 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 | {} | 2025-10-02 06:47:41 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2025-10-02 06:47:41 | 2025-10-02 06:48:16 | 34.59 | dict | {'Q9UBX3': {MsigdbAnnotation(collection='tf_targets_gtrf', geneset='ZNF7_TARGET_GENES'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='MARTINEZ_TP53_TARGETS_UP'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='LASTOWSKA_NEUROBLASTOMA_COPY_NUMB...(truncated) | 20,111 | {} | 2025-10-02 06:47:41 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2025-10-02 06:48:17 | 2025-10-02 06:48:23 | 5.88 | dict | {'MT': {'MT-ND5', 'MT-ND2', 'MT-TR', 'MT-TL1', 'MT-CO3', 'MT-RNR2', 'MT-ND6', 'MT-ND1', 'MT-TS2', 'MT-ND3', 'MT-TM', 'MT-TA', 'MT-RNR1', 'MT-ATP6', 'MT-TS1', 'MT-TW', 'MT-TF', 'MT-TN', 'MT-TK', 'MT-TT', 'MT-ATP8', 'MT-ND4L', 'MT-TG', 'MT-TV', 'MT-TY', 'MT-TD', 'MT-CYB', 'MT-ND4', 'MT-TI', 'MT-CO2', ...(truncated) | 35,134 | {} | 2025-10-02 06:48:17 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2025-10-02 06:48:24 | 2025-10-02 06:48:24 | 0.43 | dict | {('hallmark', 'h.all'): {'HALLMARK_ADIPOGENESIS': {'TANK', 'ATP5PO', 'UBQLN1', 'VEGFB', 'RAB34', 'HSPB8', 'ALDH2', 'CMBL', 'ADIG', 'MGLL', 'ALDOA', 'ME1', 'COQ9', 'ABCA1', 'GBE1', 'ACOX1', 'COX6A1', 'FAH', 'RMDN3', 'DDT', 'SAMM50', 'NMT1', 'ACLY', 'DECR1', 'BAZ2A', 'GADD45A', 'COX8A', 'NDUFAB1', 'PE...(truncated) | 20 | {} | 2025-10-02 06:48:24 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2025-10-02 06:48:24 | 2025-10-02 06:48:25 | 0.38 | 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 | {} | 2025-10-02 06:48:24 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2025-10-02 06:48:25 | 2025-10-02 06:48:25 | 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 | {} | 2025-10-02 06:48:25 | |
| ¶ | pypath.inputs.netbiol.arn_interactions | 2025-10-02 06:48:25 | 2025-10-02 06:48:25 | 0.12 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2025-10-02 06:48:25 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2025-10-02 06:48:25 | 2025-10-02 06:48:25 | 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 | {} | 2025-10-02 06:48:25 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2025-10-02 06:48:25 | 2025-10-02 06:48:27 | 1.98 | 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 | {} | 2025-10-02 06:48:25 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2025-10-02 06:48:27 | 2025-10-02 06:48:27 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2025-10-02 06:48:27 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2025-10-02 06:48:27 | 2025-10-02 06:48:27 | 0.14 | dict | {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Interleukin-3 (IL-...(truncated) | 1,870 | {} | 2025-10-02 06:48:27 | |
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2025-10-02 06:48:27 | 2025-10-02 06:48:52 | 24.12 | 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 | {} | 2025-10-02 06:48:27 | |
| ¶ | pypath.inputs.oma.oma_orthologs | 2025-10-02 06:48:52 | 2025-10-02 06:48:59 | 7.65 | list | [OmaOrthology(a=OmaGene(id='KR105_HUMAN', oma_group=1086880, hog='HOG:E0731798.2d.8c.10d.11c.4f', taxon=9606, chr='21', start=44579763, end=44580578, strand=-1, main_isoform=True), b=OmaGene(id='A0A1W2P709', oma_group=1100759, hog='HOG:E0731798.2d.8c.4b.3b.1b', taxon=10090, chr='10', start=77650516,...(truncated) | 1,000 | {'size': -21374} | 2025-10-02 06:48:52 | |
| ¶ | pypath.inputs.oma.oma_table | 2025-10-02 06:48:59 | 2025-10-02 06:48:59 | 0.14 | defaultdict | defaultdict(<class 'set'>, {'KR105_HUMAN': {'A0A1W2P709', 'E9Q2H5', 'A0A1W2P7N1', 'J3QJV4', 'D3Z5T3', 'J3QMW1', 'A0A1W2P7U0', 'A0A1W2P7W0', 'A0A1W2P7T6', 'A0A1W2P728', 'W4VSP7', 'A0A1W2P739', 'A0A1W2P860', 'J3QMD1', 'E9Q1M3', 'Q08EG8', 'L7N2C3'}, 'SESN1_HUMAN': {'SESN1_MOUSE'}, 'CJ105_HUMAN': {'A0A3...(truncated) | 843 | {'size': -17052} | 2025-10-02 06:48:59 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2025-10-02 06:48:59 | 2025-10-02 06:49:00 | 0.51 | dict | {'ado': "Alzheimer's Disease Ontology (ADO)", 'afpo': 'African Population Ontology', 'agro': 'Agronomy Ontology', 'aism': 'Ontology for the Anatomy of the Insect SkeletoMuscular system', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'apo': 'Ascomycete Phenotype Ontology (APO)', 'apo...(truncated) | 274 | {} | 2025-10-02 06:48:59 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2025-10-02 06:49:00 | 2025-10-02 06:49:58 | 58.40 | 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 | {} | 2025-10-02 06:49:00 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2025-10-02 06:49:58 | 2025-10-02 06:57:30 | 451.49 | 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 | {} | 2025-10-02 06:49:58 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2025-10-02 06:57:30 | 2025-10-02 06:58:07 | 37.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/opentargets.py", line 131, in _opentargets_general
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 07:03:01 | |||
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2025-10-02 06:58:07 | 2025-10-02 06:59:15 | 68.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/inputs/opentargets.py", line 131, in _opentargets_general
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2025-10-01 07:05:52 | |||
| ¶ | pypath.inputs.opm.opm_annotations | 2025-10-02 06:59:16 | 2025-10-02 06:59:32 | 16.86 | 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 | {} | 2025-10-02 06:59:16 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2025-10-02 06:59:32 | 2025-10-02 07:00:04 | 31.72 | 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 | {} | 2025-10-02 06:59:32 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2025-10-02 07:00:04 | 2025-10-02 07:00:08 | 4.05 | 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 | {} | 2025-10-02 07:00:04 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2025-10-02 07:00:08 | 2025-10-02 07:00:13 | 4.67 | 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 | {} | 2025-10-02 07:00:08 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2025-10-02 07:00:13 | 2025-10-02 07:00:13 | 0.03 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2025-10-02 07:00:13 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2025-10-02 07:00:13 | 2025-10-02 07:00:13 | 0.00 | list | [] | 0 | {} | 2025-10-02 07:00:13 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2025-10-02 07:00:13 | 2025-10-02 07:00:46 | 32.85 | 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 | {} | 2025-10-02 07:00:13 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2025-10-02 07:00:47 | 2025-10-02 07:00:48 | 0.27 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2025-10-02 07:00:47 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2025-10-02 07:00:48 | 2025-10-02 07:00:54 | 6.37 | 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 | {} | 2025-10-02 07:00:48 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2025-10-02 07:00:57 | 2025-10-02 07:01:05 | 7.47 | 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) | 49,369 | {} | 2025-10-02 07:00:57 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2025-10-02 07:01:05 | 2025-10-02 07:01:11 | 6.10 | tuple | ({'P02185': {('8ess', 'X-ray', 1.4), ('1mlm', 'X-ray', 1.8), ('4h0b', 'X-ray', 1.26), ('2z6s', 'X-ray', 1.25), ('4mxk', 'X-ray', 1.52), ('5ile', 'X-ray', 1.77), ('3ecx', 'X-ray', 1.21), ('3mn0', 'X-ray', 1.65), ('2blj', 'X-ray', 1.8), ('1mbn', 'X-ray', 2.0), ('4pq6', 'X-ray', 1.45), ('5ojc', 'X-ray'...(truncated) | 2 | {} | 2025-10-02 07:01:05 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2025-10-02 07:01:11 | 2025-10-02 07:01:12 | 1.11 | 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 | {} | 2025-10-02 07:01:11 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2025-10-02 07:01:12 | 2025-10-02 07:12:03 | 651.03 | 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 | {} | 2025-10-02 07:01:12 | |
| ¶ | pypath.inputs.pfam.pfam_names | 2025-10-02 07:12:03 | 2025-10-02 07:12:05 | 1.17 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2025-10-02 07:12:03 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2025-10-02 07:12:05 | 2025-10-02 07:12:09 | 4.44 | 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 | {} | 2025-10-02 07:12:05 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2025-10-02 07:12:10 | 2025-10-02 07:21:05 | 535.26 | tuple | ({}, {}) | 2 | {} | 2025-10-02 07:12:10 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2025-10-02 07:21:05 | 2025-10-02 07:36:31 | 925.95 | tuple | ({}, {}) | 2 | {} | 2025-10-02 07:21:05 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2025-10-02 07:36:31 | 2025-10-02 07:38:58 | 146.75 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {} | 2025-10-02 07:36:31 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2025-10-02 07:38:59 | 2025-10-02 07:39:02 | 3.14 | 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 | {} | 2025-10-02 07:38:59 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2025-10-02 07:39:03 | 2025-10-02 07:39:06 | 3.13 | 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 | {} | 2025-10-02 07:39:03 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2025-10-02 07:39:07 | 2025-10-02 07:39:11 | 3.92 | 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 | {} | 2025-10-02 07:39:07 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2025-10-02 07:39:12 | 2025-10-02 07:39:15 | 3.07 | 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 | {} | 2025-10-02 07:39:12 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2025-10-02 07:39:16 | 2025-10-02 07:40:18 | 62.00 | 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 | {} | 2025-10-02 07:39:16 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2025-10-02 07:40:18 | 2025-10-02 07:40:20 | 2.79 | 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 | {} | 2025-10-02 07:40:18 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2025-10-02 07:40:21 | 2025-10-02 07:40:22 | 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 | {} | 2025-10-02 07:40:21 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2025-10-02 07:40:22 | 2025-10-02 07:40:26 | 4.28 | 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 | {} | 2025-10-02 07:40:22 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2025-10-02 07:40:26 | 2025-10-02 07:40:32 | 6.32 |
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__20251002-022202/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-Fq4eCasB-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 | 2025-10-02 07:40:32 | 2025-10-02 07:40:41 | 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__20251002-022202/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__20251002-022202/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-Fq4eCasB-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 | 2025-10-02 07:40:41 | 2025-10-02 07:40:50 | 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__20251002-022202/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-Fq4eCasB-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 | 2025-10-02 07:40:50 | 2025-10-02 07:40:52 | 1.26 | 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 | {} | 2025-10-02 07:40:50 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 0.02 | list | [['MAPK8', 'SMAD4'], ['MAPK9', 'MAPKAPK5'], ['MAPK1', 'MYC'], ['MAPK8', 'BCL2L1'], ['SCYL2', 'GAPDH'], ['PRKACA', 'CBL'], ['CSNK2A1', 'PKD2'], ['MAPK14', 'SNF1LK'], ['PRKACA', 'CRIP2'], ['SCYL2', 'TMSL3'], ['CDK5', 'ETS1'], ['RPS6KA2', 'CRK'], ['MAPK3', 'ELK1'], ['PRKAA2', 'NFATC4'], ['TNNI3K', 'TRI...(truncated) | 1,821 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 0.32 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 9,164 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2025-10-02 07:40:52 | 2025-10-02 07:40:52 | 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 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2025-10-02 07:40:52 | 2025-10-02 07:40:58 | 5.24 | dict | {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,635 | {} | 2025-10-02 07:40:52 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2025-10-02 07:40:58 | 2025-10-02 07:41:11 | 13.01 | 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 | {} | 2025-10-02 07:40:58 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2025-10-02 07:41:11 | 2025-10-02 07:41:12 | 0.48 | 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 | {} | 2025-10-02 07:41:11 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2025-10-02 07:41:12 | 2025-10-02 07:42:27 | 75.13 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21148409', '24876223', '21209006', '28052875'}, 'isoforms': {1}, 'process': {''}, 'function': {'intracellular localization', 'phosphorylation', 'ubiquitination', 'protein stabilization', 'protein degradation'}...(truncated) | 3,621 | {} | 2025-10-02 07:41:12 | |
| ¶ | 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 | 2025-10-02 07:42:27 | 2025-10-02 07:42:57 | 30.21 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2025-10-02 07:42:27 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2025-10-02 07:42:57 | 2025-10-02 07:42:58 | 0.44 | 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 | {} | 2025-10-02 07:42:57 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2025-10-02 07:42:58 | 2025-10-02 07:44:03 | 65.18 | dict | {'P35250': {ProgenyAnnotation(pathway='p53', weight=-3.3513628049710005, p_value=0.000985568693599589), ProgenyAnnotation(pathway='WNT', weight=0.465622632141, p_value=0.704579815833), ProgenyAnnotation(pathway='Hypoxia', weight=-2.049501418649251, p_value=0.0007040310639538167), ProgenyAnnotation(p...(truncated) | 18,582 | {} | 2025-10-02 07:42:58 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2025-10-02 07:44:04 | 2025-10-02 07:45:09 | 65.56 | 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 | {} | 2025-10-02 07:44:04 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2025-10-02 07:45:09 | 2025-10-02 07:45:14 | 5.17 | 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 | {} | 2025-10-02 07:45:09 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2025-10-02 07:45:16 | 2025-10-02 07:45:25 | 9.65 | dict | {'O43657': {ProtainatlasAnnotation(organ='Lung', tissue='Lung', cell_type='alveolar cells', level='Low', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotation(organ='Skin', tissue='Skin...(truncated) | 15,045 | {} | 2025-10-02 07:45:16 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2025-10-02 07:45:28 | 2025-10-02 07:45:28 | 0.38 | 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 | {} | 2025-10-02 07:45:28 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2025-10-02 07:45:28 | 2025-10-02 07:45:28 | 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 | {} | 2025-10-02 07:45:28 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2025-10-02 07:45:28 | 2025-10-02 07:45:29 | 1.16 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Cytosol', status='main', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', reliability='Approved', m...(truncated) | 13,336 | {} | 2025-10-02 07:45:28 | |
| ¶ | pypath.inputs.proteins.variants | 2025-10-02 07:45:29 | 2025-10-02 07:52:20 | 410.16 | 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 | {} | 2025-10-02 07:45:29 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2025-10-02 07:52:20 | 2025-10-02 07:52:21 | 1.47 | 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 | {} | 2025-10-02 07:52:20 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2025-10-02 07:52:22 | 2025-10-02 07:52:23 | 0.95 | 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 | {} | 2025-10-02 07:52:22 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2025-10-02 07:52:23 | 2025-10-02 07:52:23 | 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 | {} | 2025-10-02 07:52:23 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2025-10-02 07:52:23 | 2025-10-02 07:52:32 | 9.15 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), Ramilo...(truncated) | 18,879 | {} | 2025-10-02 07:52:23 | |
| ¶ | pypath.inputs.reaction.acsn_biopax | 2025-10-02 07:52:33 | 2025-10-02 07:52:33 | 0.41 | NoneType | None | 0 | {} | 2025-10-02 07:52:33 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2025-10-02 07:52:33 | 2025-10-02 07:52:33 | 0.10 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2025-10-02 07:52:33 | |
| ¶ | 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 | 2025-10-02 07:52:33 | 2025-10-02 07:52:33 | 0.37 |
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__20251002-022202/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 07:52:33 | 2025-10-02 07:52:40 | 6.30 | dict | {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) | 178 | {} | 2025-10-02 07:52:33 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2025-10-02 07:52:40 | 2025-10-02 07:52:42 | 2.37 | NoneType | None | 0 | {} | 2025-10-02 07:52:40 | |
| ¶ | 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 | 2025-10-02 07:52:42 | 2025-10-02 07:53:04 | 21.58 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2025-10-02 07:52:42 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2025-10-02 07:53:04 | 2025-10-02 07:59:39 | 394.79 | list | [('R-HSA-1059683', <?xml version="1.0" encoding="utf-8"?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 94 on 9/8/25, 6:26 PM using JSBML version 1.5.</p> </annotati...(truncated) | 2,825 | {} | 2025-10-02 07:53:04 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2025-10-02 08:00:00 | 2025-10-02 08:00:02 | 1.85 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/cache/9c...(truncated) | 2,825 | {} | 2025-10-02 08:00:00 | |
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2025-10-02 08:00:02 | 2025-10-02 08:00:05 | 3.33 | list | [{'parent': 'R-BTA-109581', 'child': 'R-BTA-109606'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-169911'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-5357769'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-75153'}, {'parent': 'R-BTA-109582', 'child': 'R-BTA-140877'}, {'parent': 'R-BTA-109582', 'child'...(truncated) | 23,259 | {'fixed': True} | 2025-10-02 08:00:02 | |
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2025-10-02 08:00:05 | 2025-10-02 08:00:12 | 6.89 |
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__20251002-022202/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 | 2025-10-02 08:00:12 | 2025-10-02 08:00:12 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 922, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 08:00:12 | 2025-10-02 08:00:13 | 1.02 |
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__20251002-022202/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 | 2025-10-02 08:00:13 | 2025-10-02 08:00:28 | 15.06 |
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__20251002-022202/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 | 2025-10-02 08:00:28 | 2025-10-02 08:00:39 | 10.69 | 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 | {} | 2025-10-02 08:00:28 | |
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2025-10-02 08:00:39 | 2025-10-02 08:00:57 | 17.40 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='mouse'), ScconnectAnnota...(truncated) | 3,285 | {} | 2025-10-02 08:00:39 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2025-10-02 08:00:57 | 2025-10-02 08:00:57 | 0.02 | set | {Complex: COMPLEX:P01215_P01222, Complex: COMPLEX:O75462_Q9UBD9, Complex: COMPLEX:O15263, Complex: COMPLEX:Q16552_Q96PD4, Complex: COMPLEX:P01215_P01225, Complex: COMPLEX:P01562, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:P0DML2_P0DML3, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:P08476_P...(truncated) | 17 | {} | 2025-10-02 08:00:57 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2025-10-02 08:00:57 | 2025-10-02 08:04:46 | 229.30 | 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 | {} | 2025-10-02 08:00:57 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2025-10-02 08:04:46 | 2025-10-02 08:04:46 | 0.17 | dict | {'CID111722286': {SiderDrug(name='spinosad', atc=None)}, 'CID100002345': {SiderDrug(name='benzyl', atc='P03AX01')}, 'CID100047319': {SiderDrug(name='atracurium', atc='M03AC04')}, 'CID100002550': {SiderDrug(name='captopril', atc='C09AA01')}, 'CID100003419': {SiderDrug(name='fosinopril', atc='C09AA09'...(truncated) | 1,430 | {} | 2025-10-02 08:04:46 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2025-10-02 08:04:46 | 2025-10-02 08:04:46 | 0.28 | list | [SiderSideeffectMeddra(cid='C0276447', meddra_id='10061494', side_effect_name='Rhinovirus infection'), SiderSideeffectMeddra(cid='C1698397', meddra_id='10065616', side_effect_name='Incision site infection'), SiderSideeffectMeddra(cid='C0863146', meddra_id='10048213', side_effect_name='Xanthochromia'...(truncated) | 20,307 | {} | 2025-10-02 08:04:46 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2025-10-02 08:04:46 | 2025-10-02 08:04:48 | 1.58 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0043094', umls_concept_in_meddra='C0043094', side_effect='Weight increased', frequency='6%'), SiderSideeffetFrequency(umls_concept_on_label='C0020649', umls_concept_in_meddra='C0020649', side_effect='Hypotension', frequency='14%'), Si...(truncated) | 968 | {} | 2025-10-02 08:04:46 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2025-10-02 08:04:48 | 2025-10-02 08:04:49 | 0.89 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0009806', umls_concept_in_meddra='C0009806', side_effect='Constipation'), SiderSideeffect(umls_concept_on_label='C0085595', umls_concept_in_meddra='C0085595', side_effect='Body odor'), SiderSideeffect(umls_concept_on_label='C0003123', umls_co...(truncated) | 1,430 | {} | 2025-10-02 08:04:48 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2025-10-02 08:04:49 | 2025-10-02 08:04:51 | 1.42 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='Toll-like receptor'), Signal...(truncated) | 2 | {} | 2025-10-02 08:04:49 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2025-10-02 08:04:51 | 2025-10-02 08:04:51 | 0.38 | dict | {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 785 | {} | 2025-10-02 08:04:51 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2025-10-02 08:04:51 | 2025-10-02 08:04:51 | 0.37 | 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 | {} | 2025-10-02 08:04:51 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2025-10-02 08:04:51 | 2025-10-02 08:04:52 | 0.98 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(p...(truncated) | 839 | {} | 2025-10-02 08:04:51 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2025-10-02 08:04:52 | 2025-10-02 08:04:53 | 0.77 | 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 | {} | 2025-10-02 08:04:52 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2025-10-02 08:04:53 | 2025-10-02 08:04:57 | 3.97 | list | [{'typ': 'phosphorylation', 'resnum': 324, 'instance': 'RHLSNVSSTGSIDMV', 'substrate': 'P10636', 'start': 317, 'end': 331, 'kinase': 'P17252', 'resaa': 'S', 'motif': 'RHLSNVSSTGSIDMV', 'enzyme_isoform': None, 'substrate_isoform': 2, 'references': {'10090741'}}, {'typ': 'phosphorylation', 'resnum': 3...(truncated) | 13,395 | {} | 2025-10-02 08:04:53 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2025-10-02 08:04:57 | 2025-10-02 08:04:58 | 0.54 | list | [SignorInteraction(source='Q12772', target='P27169', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates quantity by expression', mechanism='transcriptional regulation', ncbi_tax_id='9606', pubmeds='20728021', direct=True, ptm_type='transcript...(truncated) | 95,672 | {'size': 6} | 2025-10-02 08:04:57 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2025-10-02 08:04:58 | 2025-10-02 08:05:20 | 22.21 | dict | {'P05412': {SignorPathway(pathway='Luminal Breast Cancer'), SignorPathway(pathway='GPCR_HCC'), SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='Glucocorticoid receptor Signaling'), SignorPathway(pathway='TNF-alpha Signaling'), SignorPathway(pathway='WNT Signaling'), SignorPath...(truncated) | 782 | {'size': 3} | 2025-10-02 08:04:58 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2025-10-02 08:05:20 | 2025-10-02 08:05:20 | 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 | {} | 2025-10-02 08:05:20 | |
| ¶ | pypath.inputs.slc.slc_annotation | 2025-10-02 08:05:20 | 2025-10-02 08:05:20 | 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 | {} | 2025-10-02 08:05:20 | |
| ¶ | pypath.inputs.slc.slc_chebi_mapping | 2025-10-02 08:05:20 | 2025-10-02 08:05:20 | 0.18 | 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 | {} | 2025-10-02 08:05:20 | |
| ¶ | pypath.inputs.slc.slc_interactions | 2025-10-02 08:05:20 | 2025-10-02 08:05:21 | 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 | {} | 2025-10-02 08:05:20 | |
| ¶ | pypath.inputs.slc.slc_localization_annotations | 2025-10-02 08:05:21 | 2025-10-02 08:05:21 | 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 | {} | 2025-10-02 08:05:21 | |
| ¶ | pypath.inputs.slc.slc_substrate_ontology | 2025-10-02 08:05:21 | 2025-10-02 08:05:21 | 0.63 | 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 | {} | 2025-10-02 08:05:21 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2025-10-02 08:05:21 | 2025-10-02 08:05:32 | 10.70 | 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 | {} | 2025-10-02 08:05:21 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2025-10-02 08:05:32 | 2025-10-02 08:05:35 | 2.57 | 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 | {} | 2025-10-02 08:05:32 | |
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2025-10-02 08:05:35 | 2025-10-02 08:06:41 | 66.35 | 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 | {} | 2025-10-02 08:05:35 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2025-10-02 08:06:41 | 2025-10-02 08:08:01 | 79.87 | 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 | {} | 2025-10-02 08:06:41 | |
| ¶ | pypath.inputs.string.string_effects | 2025-10-02 08:08:01 | 2025-10-02 08:08:09 | 7.85 | 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 | {} | 2025-10-02 08:08:01 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2025-10-02 08:08:10 | 2025-10-02 08:08:42 | 32.24 | 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 | {} | 2025-10-02 08:08:10 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2025-10-02 08:08:42 | 2025-10-02 08:08:43 | 1.15 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2025-10-02 08:08:42 | |
| ¶ | pypath.inputs.string.string_species | 2025-10-02 08:08:43 | 2025-10-02 08:08:43 | 0.17 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2025-10-02 08:08:43 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2025-10-02 08:08:44 | 2025-10-02 08:08:46 | 2.43 | dict | {'A0AV02': (0.8363, 'Transporters', {'SLC', 'SLC12', 'APC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC5', 'SLC', 'APC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,844 | {} | 2025-10-02 08:08:44 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2025-10-02 08:08:46 | 2025-10-02 08:08:52 | 6.11 | 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 | {} | 2025-10-02 08:08:46 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2025-10-02 08:08:52 | 2025-10-02 08:08:53 | 0.56 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,344 | {} | 2025-10-02 08:08:52 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2025-10-02 08:08:53 | 2025-10-02 08:08:53 | 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 | {} | 2025-10-02 08:08:53 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2025-10-02 08:08:53 | 2025-10-02 08:08:53 | 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 | {} | 2025-10-02 08:08:53 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2025-10-02 08:08:53 | 2025-10-02 08:08:58 | 5.44 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 902, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20251002-022202/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 | 2025-10-02 08:08:58 | 2025-10-02 08:08:58 | 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 | {} | 2025-10-02 08:08:58 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2025-10-02 08:08:58 | 2025-10-02 08:08:58 | 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 | {'size': 1} | 2025-10-02 08:08:58 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2025-10-02 08:08:58 | 2025-10-02 08:08:58 | 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 | {} | 2025-10-02 08:08:58 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2025-10-02 08:08:58 | 2025-10-02 08:09:03 | 4.09 | 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 | {} | 2025-10-02 08:08:58 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2025-10-02 08:09:03 | 2025-10-02 08:09:25 | 22.38 | set | {ThreedcomplexContact(pdb='2buw_1', uniprot_1='P20372', uniprot_2='P20372', chain_1='B', chain_2='B', n_residues=33.0, length_1=238, length_2=238, domain_s1=('49482',), domain_p1=('PF12391.3', 'PF00775.16'), domain_s2=('49482',), domain_p2=('PF12391.3', 'PF00775.16'), ident=True, homo=True), Threedc...(truncated) | 259,376 | {} | 2025-10-02 08:09:03 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2025-10-02 08:09:26 | 2025-10-02 08:12:33 | 186.82 | list | [<pypath.internals.intera.DomainDomain object at 0x7efd65157b90>, <pypath.internals.intera.DomainDomain object at 0x7efd65157990>, <pypath.internals.intera.DomainDomain object at 0x7efd65157790>, <pypath.internals.intera.DomainDomain object at 0x7efd65157590>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,086 | {} | 2025-10-02 08:09:26 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2025-10-02 08:12:33 | 2025-10-02 08:12:42 | 8.50 | dict | {'2buw_1': {('P20372', 'P20372'): 6.0, ('P20371', 'P20372'): 72.5, ('P20371', 'P20371'): 3.5}, '5cz7_1': {('P25451', 'P30656'): 22.0, ('P21242', 'P23639'): 3.0, ('P21242', 'P23638'): 2.5, ('P23638', 'P25043'): 5.5, ('P23639', 'P25043'): 12.0, ('P23639', 'P25451'): 10.5, ('P23724', 'P25451'): 12.5, (...(truncated) | 80,995 | {} | 2025-10-02 08:12:33 | |
| ¶ | pypath.inputs.threedid.get_3did | 2025-10-02 08:12:42 | 2025-10-02 09:34:14 | 4,891.50 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7efd63ede590>, <pypath.internals.intera.DomainDomain object at 0x7efd120a2d10>, <pypath.internals.intera.DomainDomain object at 0x7efdaf133a90>, <pypath.internals.intera.DomainDomain object at 0x7efd63e67dd0>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2025-10-02 08:12:42 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2025-10-02 09:34:14 | 2025-10-02 09:50:04 | 950.59 | dict | {} | 0 | {} | 2025-10-02 09:34:14 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2025-10-02 09:50:04 | 2025-10-02 09:50:47 | 42.29 | dict | {'P18825': {TopdbAnnotation(membrane='Extracellular', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cytoplasm', topology='Outside', score=70.6, tmregions=6), TopdbAnnotation(membrane='Cell me...(truncated) | 2,027 | {} | 2025-10-02 09:50:04 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2025-10-02 09:50:47 | 2025-10-02 09:50:47 | 0.12 | 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 | {} | 2025-10-02 09:50:47 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2025-10-02 09:50:47 | 2025-10-02 09:50:47 | 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 | {} | 2025-10-02 09:50:47 | |
| ¶ | 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 | 2025-10-02 09:50:47 | 2025-10-02 09:50:47 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;11290752;12601176', 'Patch clamp;Fusion protein-pull down assay;Fluorescence probe lab...(truncated) | 359 | {} | 2025-10-02 09:50:47 | |
| ¶ | pypath.inputs.trip.trip_process | 2025-10-02 09:50:47 | 2025-10-02 09:50:47 | 0.00 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2025-10-02 09:50:47 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2025-10-02 09:50:47 | 2025-10-02 09:50:51 | 3.79 | 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 | {} | 2025-10-02 09:50:47 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2025-10-02 09:50:51 | 2025-10-02 09:50:51 | 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 | {} | 2025-10-02 09:50:51 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2025-10-02 09:50:51 | 2025-10-02 09:50:54 | 2.87 | 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 | {} | 2025-10-02 09:50:51 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2025-10-02 09:50:54 | 2025-10-02 09:54:29 | 215.23 | 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 | {} | 2025-10-02 09:50:54 | |
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2025-10-02 09:54:29 | 2025-10-02 09:54:29 | 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 | {} | 2025-10-02 09:54:29 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2025-10-02 09:54:29 | 2025-10-02 09:54:29 | 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 | {} | 2025-10-02 09:54:29 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2025-10-02 09:54:29 | 2025-10-02 09:54:29 | 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 | {} | 2025-10-02 09:54:29 | |
| ¶ | 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 | 2025-10-02 09:54:29 | 2025-10-02 09:54:40 | 10.81 | 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 | {} | 2025-10-02 09:54:29 | |
| ¶ | 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 | 2025-10-02 09:54:40 | 2025-10-02 09:54:51 | 10.28 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Mitochondrion'), UniprotKeyword(keyword='Transmembrane'), U...(truncated) | 20,420 | {} | 2025-10-02 09:54:40 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2025-10-02 09:54:51 | 2025-10-02 09:54:51 | 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 | {} | 2025-10-02 09:54:51 | |
| ¶ | 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 | 2025-10-02 09:54:51 | 2025-10-02 09:54:52 | 1.26 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'H8ZM71': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies grandis', 'Grand fir', 'Pinu...(truncated) | 558,858 | {} | 2025-10-02 09:54:51 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2025-10-02 09:54:52 | 2025-10-02 09:55:04 | 11.55 | 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 | {} | 2025-10-02 09:54:52 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2025-10-02 09:55:04 | 2025-10-02 09:55:50 | 45.93 | dict | {'A0A087X1C5': {UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', ...(truncated) | 5,244 | {} | 2025-10-02 09:55:04 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2025-10-02 09:55:50 | 2025-10-02 09:55:50 | 0.00 | set | {'P56211', 'Q07687', 'Q9H0E3', 'P27448', 'Q9H2A3', 'Q17RG1', 'P98169', 'Q96K76', 'Q2MJR0', 'P0DOX8', 'Q6ZU45', 'Q562F6', 'O76061', 'Q15800', 'O76039', 'P00395', 'Q8WYK2', 'Q15124', 'P17152', 'Q8N5K1', 'Q8N5H3', 'A0A075B6I9', 'Q6ZVF9', 'P04844', 'P0C5Z0', 'P42694', 'Q86VD9', 'Q9H8X9', 'Q15181', 'Q9Y2...(truncated) | 20,420 | {} | 2025-10-02 09:55:50 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2025-10-02 09:55:50 | 2025-10-02 09:56:27 | 37.52 | set | {'D6RJH7', 'L0BW55', 'A0A343V4Y1', 'A0A7S5EUD4', 'Q8NFC8', 'A0A7S5BZW8', 'A0A7S5EWI0', 'G8HT90', 'A0A5C2GSI3', 'L0R526', 'Q56SI0', 'A0A0U1RRI1', 'A0A678ZFN8', 'A0A7S5C174', 'B3VRI5', 'Q13828', 'Q96JR3', 'C9JAV2', 'G1UD79', 'K7EN35', 'B2CIS9', 'A0A650GAE1', 'D6C521', 'Q5QR36', 'Q38MU6', 'A0A5C2FXZ6',...(truncated) | 184,785 | {} | 2025-10-02 09:55:50 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2025-10-02 09:56:27 | 2025-10-02 09:56:27 | 0.00 | set | {'D6RJH7', 'L0BW55', 'A0A343V4Y1', 'A0A7S5EUD4', 'Q8NFC8', 'A0A7S5BZW8', 'A0A7S5EWI0', 'G8HT90', 'A0A5C2GSI3', 'L0R526', 'Q56SI0', 'A0A0U1RRI1', 'A0A678ZFN8', 'A0A7S5C174', 'B3VRI5', 'Q13828', 'Q96JR3', 'C9JAV2', 'Q07687', 'G1UD79', 'K7EN35', 'B2CIS9', 'A0A650GAE1', 'D6C521', 'Q5QR36', 'Q38MU6', 'A0...(truncated) | 205,205 | {} | 2025-10-02 09:56:27 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2025-10-02 09:56:28 | 2025-10-02 09:56:28 | 0.00 | set | {'D6RJH7', 'L0BW55', 'A0A343V4Y1', 'A0A7S5EUD4', 'Q8NFC8', 'A0A7S5BZW8', 'A0A7S5EWI0', 'G8HT90', 'A0A5C2GSI3', 'L0R526', 'Q56SI0', 'A0A0U1RRI1', 'A0A678ZFN8', 'A0A7S5C174', 'B3VRI5', 'Q13828', 'Q96JR3', 'C9JAV2', 'Q07687', 'G1UD79', 'K7EN35', 'B2CIS9', 'A0A650GAE1', 'D6C521', 'Q5QR36', 'Q38MU6', 'A0...(truncated) | 205,205 | {} | 2025-10-02 09:56:28 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2025-10-02 09:56:28 | 2025-10-02 09:56:28 | 0.05 | NoneType | None | 0 | {} | 2025-10-02 09:56:28 | |
| ¶ | 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 | 2025-10-02 09:56:28 | 2025-10-02 09:56:28 | 0.05 | set | {('UniProtKB-Swiss-Prot', 'Ensembl_Genomes_Protein'), ('UniProtKB_AC-ID', 'GeneTree'), ('Ensembl', 'UniProtKB'), ('UniProtKB', 'PlantReactome'), ('Ensembl', 'UniProtKB-Swiss-Prot'), ('GuidetoPHARMACOLOGY', 'UniProtKB-Swiss-Prot'), ('PHI-base', 'UniProtKB'), ('Allergome', 'UniProtKB'), ('WBParaSite_T...(truncated) | 481 | {} | 2025-10-02 09:56:28 | |
| ¶ | pypath.inputs.wang.cui_interactions | 2025-10-02 09:56:28 | 2025-10-02 09:56:28 | 0.29 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2025-10-02 09:56:28 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2025-10-02 09:56:28 | 2025-10-02 09:56:29 | 0.66 | 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 | {} | 2025-10-02 09:56:28 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2025-10-02 09:56:29 | 2025-10-02 09:56:34 | 4.97 | dict | {'NA': {WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='Adapter', location='Cytosol'), WangAnnotation(function='Ion', location='Cytosol'), WangAnnotation(function='Lipid', location='Cytosol'), WangAnnotation(function='Messenger', location='Cytosol'), WangAnnotation(fu...(truncated) | 1,547 | {} | 2025-10-02 09:56:29 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2025-10-02 09:56:34 | 2025-10-02 09:56:34 | 0.13 | 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 | {} | 2025-10-02 09:56:34 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2025-10-02 09:56:34 | 2025-10-02 09:56:34 | 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 | {} | 2025-10-02 09:56:34 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2025-10-02 09:56:34 | 2025-10-02 09:56:34 | 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 | {} | 2025-10-02 09:56:34 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2025-10-02 09:56:34 | 2025-10-02 09:56:34 | 0.18 | 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 | {} | 2025-10-02 09:56:34 |
The OmniPath Team • Saez Lab • 2025-10-02