Pypath inputs status report

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 2022-04-03 00:13:02 and 2022-04-03 06:38:53; pypath version: 0.14.7 (from git; c907cbb )

Modules collected: 152
Modules failed to import: 0
Functions collected: 479
Functions run without error: 328
Functions returned empty value: 9
Functions skipped due to lack of arguments: 120
Functions run with error: 31

Function Started Finished Elapsed (s) Result type Result repr Result size Error Change since last time Last succeeded
pypath.inputs.abs.abs_interactions 2022-04-03 00:13:08 2022-04-03 00:13:08 0.58 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 {} 2022-04-03 00:13:08
pypath.inputs.acsn.acsn_interactions 2022-04-03 00:13:08 2022-04-03 00:13:10 2.03 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 {} 2022-04-03 00:13:08
pypath.inputs.acsn.acsn_interactions_sif 2022-04-03 00:13:10 2022-04-03 00:13:11 0.47 list [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) 9,570 {} 2022-04-03 00:13:10
pypath.inputs.adhesome.adhesome_annotations 2022-04-03 00:13:11 2022-04-03 00:16:04 173.54 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 {} 2022-04-03 00:13:11
pypath.inputs.adhesome.adhesome_interactions 2022-04-03 00:16:04 2022-04-03 00:18:15 130.18 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) 7,182 {'size': 640} 2022-04-03 00:16:04
pypath.inputs.almen2009.almen2009_annotations 2022-04-03 00:18:15 2022-04-03 00:18:21 6.46 dict {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) 4,826 {} 2022-04-03 00:18:15
pypath.inputs.baccin2019.baccin2019_annotations 2022-04-03 00:18:21 2022-04-03 00:23:04 283.13 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 195, in baccin2019_annotations
    ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 136, in baccin2019_interactions
    ligand_components = raw_to_uniprots(rec[1])
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 83, in raw_to_uniprots
    itertools.product(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 84, in <genexpr>
    *(id_translate(comp) for comp in components)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 65, in id_translate
    itertools.chain(*(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 66, in <genexpr>
    homology_mod.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 1186, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 257, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 171, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 202, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 212, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 484, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 500, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 639, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/homologene.py", line 93, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-04-01 00:17:12
pypath.inputs.baccin2019.baccin2019_interactions 2022-04-03 00:23:04 2022-04-03 00:24:54 109.80 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 136, in baccin2019_interactions
    ligand_components = raw_to_uniprots(rec[1])
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 83, in raw_to_uniprots
    itertools.product(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 84, in <genexpr>
    *(id_translate(comp) for comp in components)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 65, in id_translate
    itertools.chain(*(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/baccin2019.py", line 66, in <genexpr>
    homology_mod.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 1186, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 257, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 171, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 202, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 212, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 484, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 500, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 639, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/homologene.py", line 93, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-04-01 00:28:22
pypath.inputs.biogps.biogps_datasets 2022-04-03 00:24:54 2022-04-03 00:24:54 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 {} 2022-04-03 00:24:54
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
 {} never
pypath.inputs.biogps.biogps_download_all 2022-04-03 00:24:54 2022-04-03 00:30:46 351.63 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 {} 2022-04-03 00:24:54
pypath.inputs.biogrid.biogrid_all_interactions 2022-04-03 00:30:46 2022-04-03 00:37:42 415.63 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/biogrid.py", line 140, in biogrid_all_interactions
    f = next(iter(c.result.values()))
AttributeError: 'NoneType' object has no attribute 'values'
{} 2022-04-01 00:28:58
pypath.inputs.biogrid.biogrid_interactions 2022-04-03 00:37:42 2022-04-03 00:37:43 0.97 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) 6,662 {} 2022-04-03 00:37:42
pypath.inputs.biomart.biomart_homology 2022-04-03 00:37:43 2022-04-03 00:38:17 34.05 list [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) 174,615 {} 2022-04-03 00:37:43
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
 {} never
pypath.inputs.biomart.biomart_microarray_types 2022-04-03 00:38:17 2022-04-03 00:38:18 0.28 list [{'array': 'OneArray', 'vendor': 'PHALANX', 'format': 'EXPRESSION', 'description': None, 'type': 'OLIGO', 'label': 'PHALANX OneArray'}, {'vendor': 'CODELINK', 'array': 'CODELINK', 'format': 'EXPRESSION', 'description': None, 'type': 'OLIGO', 'label': 'CODELINK CODELINK'}, {'vendor': 'ILLUMINA', 'arr...(truncated) 38 {} 2022-04-03 00:38:17
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
 {} never
pypath.inputs.biomodels._get_biomodels 2022-04-03 00:38:18 2022-04-03 00:38:18 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/biomodels.py", line 94, in _get_biomodels
    loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
{} 2022-03-20 00:29:08
pypath.inputs.biomodels.download_single_model 
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments.
 {} never
pypath.inputs.biomodels.get_biomodels 2022-04-03 00:38:18 2022-04-03 00:38:18 0.12 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/biomodels.py", line 159, in get_biomodels
    token = json.loads(fp.read())['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2022-03-20 01:18:55
pypath.inputs.biomodels.get_biomodels_req 2022-04-03 00:38:18 2022-04-03 00:38:19 0.62 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/biomodels.py", line 186, in get_biomodels_req
    token = json.loads(r0.text)['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2022-03-20 01:18:55
pypath.inputs.biomodels.get_single_model 
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments.
 {} never
pypath.inputs.ca1.ca1_interactions 2022-04-03 00:38:19 2022-04-03 00:38:22 3.26 list [Ca1Interaction(source_label='GLYCINE', source_uniprot='NA', source_uniprot_mouse='NA', source_function='Ligand', source_location='Extracellular', target_label='NMDAR', target_uniprot='Q12879', target_uniprot_mouse='P35436', target_function='Receptor', target_location='Membrane', effect='+', interac...(truncated) 1,788 {} 2022-04-03 00:38:19
pypath.inputs.cancercellmap.ccmap_interactions 2022-04-03 00:38:22 2022-04-03 00:38:23 0.94 list [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) 47,644 {} 2022-04-03 00:38:22
pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations 2022-04-03 00:38:23 2022-04-03 00:38:41 18.26 defaultdict defaultdict(<class 'set'>, {'46220502': {CancerDrugsAnnotation(label='Abemaciclib', indications='Advanced Breast Cancer; Metastatic Breast Cancer', last_updated='01/02/2022')}, '132971': {CancerDrugsAnnotation(label='Abiraterone', indications='Metastatic Castration Resistant Prostate Cancer', last_u...(truncated) 199 {} 2022-04-03 00:38:23
pypath.inputs.cancerdrugs_db.cancerdrugs_db_download 2022-04-03 00:38:41 2022-04-03 00:38:41 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) 284 {} 2022-04-03 00:38:41
pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions 2022-04-03 00:38:41 2022-04-03 00:38:42 0.42 list [CancerDrugsInteraction(source={'46220502'}, target={'Q00534'}), CancerDrugsInteraction(source={'46220502'}, target={'P11802'}), CancerDrugsInteraction(source={'46220502'}, target={'P24385'}), CancerDrugsInteraction(source={'46220502'}, target={'P30281'}), CancerDrugsInteraction(source={'46220502'},...(truncated) 2,864 {} 2022-04-03 00:38:41
pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations 2022-04-03 00:38:42 2022-04-03 00:38:42 0.17 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) 188 {} 2022-04-03 00:38:42
pypath.inputs.cancerdrugsdb.cancerdrugsdb_download 2022-04-03 00:38:42 2022-04-03 00:38:42 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) 284 {} 2022-04-03 00:38:42
pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions 2022-04-03 00:38:42 2022-04-03 00:38:42 0.16 list [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P24385', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) 2,378 {} 2022-04-03 00:38:42
pypath.inputs.cancersea.cancersea_annotations 2022-04-03 00:38:42 2022-04-03 00:38:44 1.73 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Metastasis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,247 {} 2022-04-03 00:38:42
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
 {} never
pypath.inputs.cellcall.cellcall_annotations 2022-04-03 00:38:44 2022-04-03 00:38:57 13.13 dict {'Q9H1J7': {CellcallAnnotation(role='ligand')}, 'Q9NPG1': {CellcallAnnotation(role='receptor')}, 'P05014': {CellcallAnnotation(role='ligand')}, 'P17181': {CellcallAnnotation(role='receptor')}, 'P01579': {CellcallAnnotation(role='ligand')}, 'P15260': {CellcallAnnotation(role='receptor')}, 'P05013': {...(truncated) 460 {} 2022-04-03 00:38:44
pypath.inputs.cellcall.cellcall_download 2022-04-03 00:38:57 2022-04-03 00:38:57 0.05 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 {} 2022-04-03 00:38:57
pypath.inputs.cellcall.cellcall_download_all 2022-04-03 00:38:57 2022-04-03 00:38:58 0.99 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 {} 2022-04-03 00:38:57
pypath.inputs.cellcall.cellcall_interactions 2022-04-03 00:38:58 2022-04-03 00:39:00 1.89 list [CellcallInteraction(ligand_uniprot='Q9H1J7', receptor_uniprot='Q9NPG1', core=True), CellcallInteraction(ligand_uniprot='P05014', receptor_uniprot='P17181', core=True), CellcallInteraction(ligand_uniprot='P01579', receptor_uniprot='P15260', core=True), CellcallInteraction(ligand_uniprot='P05013', re...(truncated) 797 {} 2022-04-03 00:38:58
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2022-04-03 00:39:00 2022-04-03 00:39:01 0.86 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinteractions...(truncated) 3,425 {} 2022-04-03 00:39:00
pypath.inputs.cellchatdb._cellchatdb_organism 2022-04-03 00:39:01 2022-04-03 00:39:01 0.00 int 9606 0 {} 2022-04-03 00:39:01
pypath.inputs.cellchatdb._cellchatdb_process_cofactors 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments.
 {} never
pypath.inputs.cellchatdb._cellchatdb_process_complexes 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments.
 {} never
pypath.inputs.cellchatdb.cellchatdb_annotations 2022-04-03 00:39:01 2022-04-03 00:39:09 7.99 dict {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P07996': {CellChatDBAnnotation(role='ligand', pathway='THBS', category='...(truncated) 1,067 {} 2022-04-03 00:39:01
pypath.inputs.cellchatdb.cellchatdb_cofactors 2022-04-03 00:39:09 2022-04-03 00:39:15 5.48 dict {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O60565', 'Q13253', 'O75610', 'O00292', 'P12645', 'Q9H2X0', 'P41271', 'Q9H772'}, 'BMP inhibition receptor': {'Q13145'...(truncated) 31 {} 2022-04-03 00:39:09
pypath.inputs.cellchatdb.cellchatdb_complexes 2022-04-03 00:39:15 2022-04-03 00:39:19 4.90 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) 153 {} 2022-04-03 00:39:15
pypath.inputs.cellchatdb.cellchatdb_download 2022-04-03 00:39:19 2022-04-03 00:39:25 5.44 dict {'interaction': interaction_name ... rownames 0 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 1 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 3 TGFB1_ACVR1B_TGFBR2 ... TGFB1_ACVR1B_TGFBR2 4 TGFB1_ACVR1C_TGFBR...(truncated) 4 {} 2022-04-03 00:39:19
pypath.inputs.cellchatdb.cellchatdb_interactions 2022-04-03 00:39:25 2022-04-03 00:39:30 5.13 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='P07996', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) 11,113 {} 2022-04-03 00:39:25
pypath.inputs.cellinker._cellinker_interactions_raw 2022-04-03 00:39:30 2022-04-03 00:39:31 0.45 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2022-04-03 00:39:30
pypath.inputs.cellinker._cellinker_uniprots 
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments.
 {} never
pypath.inputs.cellinker.cellinker_annotations 2022-04-03 00:39:31 2022-04-03 00:39:31 0.88 dict {'Q9BUR5': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'Q9NZN1': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='...(truncated) 1,921 {} 2022-04-03 00:39:31
pypath.inputs.cellinker.cellinker_complex_annotations 2022-04-03 00:39:31 2022-04-03 00:39:32 0.76 dict {Complex: COMPLEX:P04626_Q15303: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cyto...(truncated) 134 {} 2022-04-03 00:39:31
pypath.inputs.cellinker.cellinker_complexes 2022-04-03 00:39:32 2022-04-03 00:39:32 0.03 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 {} 2022-04-03 00:39:32
pypath.inputs.cellinker.cellinker_complexes_raw 2022-04-03 00:39:32 2022-04-03 00:39:32 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 {} 2022-04-03 00:39:32
pypath.inputs.cellinker.cellinker_lr_interactions 2022-04-03 00:39:32 2022-04-03 00:39:33 0.76 set {CellinkerInteraction(ligand='Q9BUR5', receptor='Q9NZN1', ligand_location='Secreted', receptor_location='Membrane', resources=None, pmids='32589946', type='Secreted protein to receptor interaction'), CellinkerInteraction(ligand='P06858', receptor='P98164', ligand_location='Membrane', receptor_locati...(truncated) 3,812 {} 2022-04-03 00:39:32
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2022-04-03 00:39:33 2022-04-03 00:39:33 0.01 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2022-04-03 00:39:33
pypath.inputs.cellinker.cellinker_protein_annotations 2022-04-03 00:39:33 2022-04-03 00:39:34 0.77 dict {'Q9BUR5': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'Q9NZN1': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='...(truncated) 1,787 {} 2022-04-03 00:39:33
pypath.inputs.cellinker.cellinker_smol_interactions 2022-04-03 00:39:34 2022-04-03 00:39:34 0.23 set {CellinkerInteraction(ligand='681', receptor='P21918', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='1826762', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5497152', receptor='Q99677', ligand_location=None, receptor_location='Membrane', resou...(truncated) 314 {} 2022-04-03 00:39:34
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2022-04-03 00:39:34 2022-04-03 00:39:34 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 {} 2022-04-03 00:39:34
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_annotations 
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_get_entity 
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_hla 
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments.
 {} never
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2022-04-03 00:39:34 2022-04-03 00:39:34 0.21 dict {Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('...(truncated) 112 {} 2022-04-03 00:39:34
pypath.inputs.cellphonedb.cellphonedb_complexes 2022-04-03 00:39:34 2022-04-03 00:39:34 0.01 dict {'COMPLEX:P37023_Q13873': Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873, 'COMPLEX:Q04771_Q13873': Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873, 'COMPLEX:P27037_Q04771': Complex ACVR_1A2A receptor: COMPLEX:P27037_Q04771, 'COMPLEX:Q04771_Q13705': Complex ACVR_1A2B receptor: COMPLEX:Q04771_Q13705, 'COMPLEX:...(truncated) 112 {} 2022-04-03 00:39:34
pypath.inputs.cellphonedb.cellphonedb_interactions 2022-04-03 00:39:34 2022-04-03 00:39:35 0.60 list [CellphonedbInteraction(id_a=Complex IL12: COMPLEX:P29459_P29460, id_b=Complex IL12 receptor: COMPLEX:P42701_Q99665, sources='CellPhoneDB', references='', interaction_type='ligand-receptor', type_a='ligand', type_b='receptor'), CellphonedbInteraction(id_a=Complex Activin ligand ab: COMPLEX:P08476_P0...(truncated) 1,396 {} 2022-04-03 00:39:34
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2022-04-03 00:39:35 2022-04-03 00:39:35 0.07 tuple ({'P13236', 'P10451', 'O14944', 'P10747', 'Q96A83', 'P01148', Complex a6b4 complex: COMPLEX:P16144_P23229, 'P06239', 'Q99983', 'P52803', 'P07949', 'P06734', 'Q07092', 'Q9GZV9', Complex IL23: COMPLEX:P29460_Q9NPF7, 'P15248', 'Q9HCQ7', 'Q96S42', 'Q6IA17', 'P12872', 'P05113', 'O75888', 'P13500', 'Q9Y27...(truncated) 2 {} 2022-04-03 00:39:35
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2022-04-03 00:39:35 2022-04-03 00:39:35 0.06 dict {'A4D1S0': CellPhoneDBAnnotation(receptor=True, receptor_class=('klr',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), 'A6NMZ7': CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transme...(truncated) 978 {} 2022-04-03 00:39:35
pypath.inputs.celltalkdb.celltalkdb_annotations 2022-04-03 00:39:35 2022-04-03 00:39:46 11.19 dict {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='15721238'), CellTalkDBAnnotation(role='receptor', pmid='32196115')}, 'Q...(truncated) 1,598 {} 2022-04-03 00:39:35
pypath.inputs.celltalkdb.celltalkdb_download 2022-04-03 00:39:46 2022-04-03 00:39:46 0.00 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 {} 2022-04-03 00:39:46
pypath.inputs.celltalkdb.celltalkdb_interactions 2022-04-03 00:39:46 2022-04-03 00:39:46 0.01 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 {} 2022-04-03 00:39:46
pypath.inputs.celltypist.celltypist_annotations 2022-04-03 00:39:46 2022-04-03 00:39:47 0.31 dict {'P11836': {CelltypistAnnotation(cell_type='B cells', cell_subtype='Transitional B cells', cell_ontology='CL:0000818', marker_type='curated_marker', tissues=('Blood', 'Bone marrow'), datasets=('HCA Immune 2018',)), CelltypistAnnotation(cell_type='B cells', cell_subtype='Memory B cells', cell_ontolog...(truncated) 474 {} 2022-04-03 00:39:46
pypath.inputs.compleat.compleat_complexes 2022-04-03 00:39:47 2022-04-03 00:39:52 5.29 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) 9,693 {'size': -1} 2022-04-03 00:39:47
pypath.inputs.compleat.compleat_raw 2022-04-03 00:39:52 2022-04-03 00:39:52 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 {} 2022-04-03 00:39:52
pypath.inputs.complexportal.complexportal_complexes 2022-04-03 00:39:52 2022-04-03 00:40:49 56.85 dict {'COMPLEX:P84022_Q13485_Q15796': Complex SMAD2-SMAD3-SMAD4 complex: COMPLEX:P84022_Q13485_Q15796, 'COMPLEX:P16220_P18848': Complex bZIP transcription factor complex, ATF4-CREB1: COMPLEX:P16220_P18848, 'COMPLEX:P18846_P18848': Complex bZIP transcription factor complex, ATF1-ATF4: COMPLEX:P18846_P1884...(truncated) 1,261 {} 2022-04-03 00:39:52
pypath.inputs.comppi.comppi_interaction_locations 2022-04-03 00:40:49 2022-04-03 00:42:01 72.64 list [ComppiInteraction(id_a='Q8TES7', id_b='O75478', 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='Q8TES7', id_b='O75478', loc_a=(ComppiLocation(location='cytosol', sc...(truncated) 591,078 {} 2022-04-03 00:40:49
pypath.inputs.comppi.comppi_locations 2022-04-03 00:42:01 2022-04-03 00:43:17 75.15 dict {'Q8TES7': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(location='membrane', score=0.96), ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucl...(truncated) 18,209 {} 2022-04-03 00:42:01
pypath.inputs.connectomedb.connectomedb_annotations 2022-04-03 00:43:17 2022-04-03 00:43:17 0.54 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 {} 2022-04-03 00:43:17
pypath.inputs.connectomedb.connectomedb_interactions 2022-04-03 00:43:17 2022-04-03 00:43:17 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 {} 2022-04-03 00:43:17
pypath.inputs.corum.corum_complexes 2022-04-03 00:43:17 2022-04-03 00:43:18 0.82 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 {} 2022-04-03 00:43:17
pypath.inputs.cosmic.cancer_gene_census_annotations 2022-04-03 00:43:18 2022-04-03 00:43:20 1.86 dict {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',))}, 'Q8IZP0': {CancerGeneCensusAnnotation(tier=1...(truncated) 726 {} 2022-04-03 00:43:18
pypath.inputs.cpad.cpad_annotations 2022-04-03 00:43:20 2022-04-03 00:43:26 5.85 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) 1,038 {} 2022-04-03 00:43:20
pypath.inputs.cpad.cpad_pathway_cancer 2022-04-03 00:43:26 2022-04-03 00:43:26 0.05 tuple ({'Glioma': {CpadPathwayCancer(pathway='PAK5-Egr1-MMP2 signaling pathway', cancer='Glioma', pathway_category='Others', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration and invasion'), CpadPathwayCancer(pathway='Beta-catenin signaling pathway', cancer='Glioma', p...(truncated) 2 {} 2022-04-03 00:43:26
pypath.inputs.cpad.get_cpad 2022-04-03 00:43:26 2022-04-03 00:43:26 0.05 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 {} 2022-04-03 00:43:26
pypath.inputs.cpdb.cpdb_interactions 2022-04-03 00:43:26 2022-04-03 00:43:50 23.72 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 {} 2022-04-03 00:43:26
pypath.inputs.cpdb.cpdb_interactions_ltp 2022-04-03 00:43:50 2022-04-03 00:43:52 2.51 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 {} 2022-04-03 00:43:50
pypath.inputs.cspa.cspa_annotations 2022-04-03 00:43:53 2022-04-03 00:43:55 1.79 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) 1,446 {} 2022-04-03 00:43:53
pypath.inputs.cspa.cspa_cell_type_annotations 2022-04-03 00:43:55 2022-04-03 00:43:58 3.85 dict {'A1A5B4': {CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='NK', value=16.32343)...(truncated) 1,407 {} 2022-04-03 00:43:55
pypath.inputs.cspa.cspa_cell_types 2022-04-03 00:43:58 2022-04-03 00:44:01 2.54 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 {} 2022-04-03 00:43:58
pypath.inputs.cytosig.cytosig_annotations 2022-04-03 00:44:01 2022-04-03 00:44:23 22.42 dict {'Q9NPC4': {CytosigAnnotation(cytokine='O95390', score=0.1075145164614808), CytosigAnnotation(cytokine='P05231', score=0.0084669266516721), CytosigAnnotation(cytokine='P09038', score=-0.0414681704910361), CytosigAnnotation(cytokine='P48061', score=0.0046073476872248), CytosigAnnotation(cytokine='P01...(truncated) 4,889 {} 2022-04-03 00:44:01
pypath.inputs.cytosig.cytosig_df 2022-04-03 00:44:24 2022-04-03 00:44:24 0.04 DataFrame Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) 4,881 {} 2022-04-03 00:44:24
pypath.inputs.dbptm.dbptm_enzyme_substrate 2022-04-03 00:44:24 2022-04-03 00:44:40 16.54 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 {} 2022-04-03 00:44:24
pypath.inputs.dbptm.dbptm_enzyme_substrate_old 2022-04-03 00:44:41 2022-04-03 00:44:44 3.21 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/dbptm.py", line 101, in dbptm_enzyme_substrate_old
    for k, data in iteritems(extra):
  File "/usr/lib/python3/dist-packages/future/utils/__init__.py", line 311, in iteritems
    func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
{} 2022-01-07 23:35:25
pypath.inputs.dbptm.dbptm_interactions 2022-04-03 00:44:44 2022-04-03 00:44:45 1.43 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 {} 2022-04-03 00:44:44
pypath.inputs.deathdomain.deathdomain_interactions 2022-04-03 00:44:45 2022-04-03 00:44:47 1.20 list [] 0 {} 2022-04-03 00:44:45
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2022-04-03 00:44:47 2022-04-03 00:44:47 0.15 list [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) 184 {} 2022-04-03 00:44:47
pypath.inputs.depod.depod_enzyme_substrate 2022-04-03 00:44:47 2022-04-03 00:44:47 0.14 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 {} 2022-04-03 00:44:47
pypath.inputs.depod.depod_interactions 2022-04-03 00:44:47 2022-04-03 00:44:47 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 {} 2022-04-03 00:44:47
pypath.inputs.dgidb.dgidb_annotations 2022-04-03 00:44:47 2022-04-03 00:44:57 9.90 dict {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069': {DgidbAnnotation(category...(truncated) 10,493 {} 2022-04-03 00:44:47
pypath.inputs.dgidb.get_dgidb_old 2022-04-03 00:44:57 2022-04-03 00:46:08 71.73 set {'Q15365', 'Q8N8Q3', 'Q96E52', 'Q9BV47', 'P01148', 'P78368', 'Q14439', 'P08912', 'Q86UK0', 'P0CF51', 'Q8NH00', 'Q13516', 'O00327', 'P61567', 'Q9BRS2', 'O75084', 'P07510', 'P78317', 'Q07011', 'P15248', 'P19793', 'A6NFU8', 'P06753', 'Q14534', 'Q99956', 'P30405', 'P29508', 'Q96D53', 'Q5DID0', 'P08151',...(truncated) 5,900 {} 2022-04-03 00:44:57
pypath.inputs.dip.dip_interactions 2022-04-03 00:46:08 2022-04-03 00:46:09 0.37 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 {} 2022-04-03 00:46:08
pypath.inputs.dip.dip_login 
Not calling `pypath.inputs.dip.dip_login`, not enough arguments.
 {} never
pypath.inputs.disgenet.disgenet_annotations 2022-04-03 00:46:09 2022-04-03 00:46:23 14.11 dict {'P04217': {DisGeNetAnnotation(disease='Schizophrenia', type='disease', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',)), DisGeNetAnnotation(disease='Hepatomegaly', type='phenotype', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',))}, 'P0102...(truncated) 9,203 {} 2022-04-03 00:46:09
pypath.inputs.domino.domino_ddi 2022-04-03 00:46:23 2022-04-03 00:46:41 18.00 list [<pypath.internals.intera.DomainDomain object at 0x7f57928f1a30>, <pypath.internals.intera.DomainDomain object at 0x7f57928f10a0>, <pypath.internals.intera.DomainDomain object at 0x7f57928f1160>, <pypath.internals.intera.DomainDomain object at 0x7f5792376850>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294 {} 2022-04-03 00:46:23
pypath.inputs.domino.domino_enzsub 2022-04-03 00:46:41 2022-04-03 00:46:42 0.97 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f579b44c3a0>, <pypath.internals.intera.DomainDomain object at 0x7f579b44c940>, <pypath.internals.intera.DomainDomain object at 0x7f579b44c970>, <pypath.internals.intera.DomainDomain object at 0x7f5794e54a60>, <pypath.internals.intera.Domain...(truncated) 2 {} 2022-04-03 00:46:41
pypath.inputs.domino.domino_interactions 2022-04-03 00:46:42 2022-04-03 00:46:42 0.38 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 {} 2022-04-03 00:46:42
pypath.inputs.domino.get_domino 2022-04-03 00:46:42 2022-04-03 00:46:43 0.36 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 {} 2022-04-03 00:46:42
pypath.inputs.dorothea._process_resources 
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments.
 {} never
pypath.inputs.dorothea.dorothea_full_raw 2022-04-03 00:46:43 2022-04-03 00:46:51 8.16 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 {} 2022-04-03 00:46:43
pypath.inputs.dorothea.dorothea_interactions 2022-04-03 00:46:51 2022-04-03 00:47:05 13.78 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 {} 2022-04-03 00:46:51
pypath.inputs.dorothea.dorothea_old_csv 2022-04-03 00:47:05 2022-04-03 00:47:05 0.48 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.dorothea.dorothea_old_csv 2022-04-03 00:47:05 2022-04-03 00:47:06 0.28 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.dorothea.dorothea_rda_raw 2022-04-03 00:47:06 2022-04-03 00:47:08 1.85 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 {} 2022-04-03 00:47:06
pypath.inputs.dorothea.get_dorothea_old 2022-04-03 00:47:08 2022-04-03 00:47:09 1.20 list [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) 14,260 {} 2022-04-03 00:47:08
pypath.inputs.dorothea.dorothea_rda_raw 2022-04-03 00:47:09 2022-04-03 00:47:10 1.23 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 {} 2022-04-03 00:47:09
pypath.inputs.dorothea.dorothea_interactions 2022-04-03 00:47:10 2022-04-03 00:47:24 13.87 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2022-04-03 00:47:10
pypath.inputs.dorothea.dorothea_old_csv 2022-04-03 00:47:24 2022-04-03 00:47:24 0.28 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.ebi.ebi_rest 
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments.
 {} never
pypath.inputs.elm.elm_classes 2022-04-03 00:47:24 2022-04-03 00:47:40 15.94 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) 317 {} 2022-04-03 00:47:24
pypath.inputs.elm.elm_domains 2022-04-03 00:47:40 2022-04-03 00:47:41 0.93 dict {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')]}} 2 {} 2022-04-03 00:47:40
pypath.inputs.elm.elm_instances 2022-04-03 00:47:41 2022-04-03 00:49:26 105.19 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) 3,934 {} 2022-04-03 00:47:41
pypath.inputs.elm.elm_interactions 2022-04-03 00:49:26 2022-04-03 00:50:39 72.68 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) 2,394 {} 2022-04-03 00:49:26
pypath.inputs.embrace._embrace_id_translation 
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments.
 {} never
pypath.inputs.embrace.embrace_annotations 2022-04-03 00:50:39 2022-04-03 00:53:44 184.82 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/embrace.py", line 162, in embrace_annotations
    for rec in embrace_translated(organism = organism):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/embrace.py", line 92, in embrace_translated
    ligands = _embrace_id_translation(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/embrace.py", line 71, in _embrace_id_translation
    uniprots = homology.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 1186, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 257, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 171, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 202, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 212, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 484, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 500, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/homology.py", line 639, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/homologene.py", line 93, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-04-01 00:41:13
pypath.inputs.embrace.embrace_interactions 2022-04-03 00:53:44 2022-04-03 01:05:03 679.37 list [EmbraceInteraction(ligand='P01023', receptor='Q07954'), EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O14672', receptor='P29320'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(...(truncated) 1,704 {} 2022-04-03 00:53:44
pypath.inputs.embrace.embrace_raw 2022-04-03 01:05:03 2022-04-03 01:05:03 0.10 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 {} 2022-04-03 01:05:03
pypath.inputs.embrace.embrace_translated 2022-04-03 01:05:03 2022-04-03 01:05:04 0.31 list [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol='Q07954', 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_recepto...(truncated) 1,775 {} 2022-04-03 01:05:03
pypath.inputs.encode.encode_tf_mirna_interactions 2022-04-03 01:05:04 2022-04-03 01:05:04 0.62 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 {} 2022-04-03 01:05:04
pypath.inputs.ensembl.ensembl_organisms 2022-04-03 01:05:04 2022-04-03 01:05:05 0.94 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) 311 {} 2022-04-03 01:05:04
pypath.inputs.exocarta._get_exocarta_vesiclepedia 2022-04-03 01:05:05 2022-04-03 01:05:25 19.71 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2022-04-03 01:05:05
pypath.inputs.exocarta.get_exocarta 2022-04-03 01:05:25 2022-04-03 01:05:25 0.03 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2022-04-03 01:05:25
pypath.inputs.exocarta.get_vesiclepedia 2022-04-03 01:05:25 2022-04-03 01:06:36 71.26 list [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) 290,197 {} 2022-04-03 01:05:25
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 2022-04-03 01:06:36 2022-04-03 01:06:36 0.42 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 860, in get_go_quick
    _ = next(c.result)
TypeError: 'NoneType' object is not an iterator
{} 2022-01-07 23:44:17
pypath.inputs.go.get_goslim 2022-04-03 01:06:36 2022-04-03 01:06:37 0.83 list ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0005635', 'GO:0005654', 'GO:0...(truncated) 141 {} 2022-04-03 01:06:36
pypath.inputs.go.go_ancestors_quickgo 2022-04-03 01:06:37 2022-04-03 01:22:32 954.18 dict {'C': {'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0009426': {('GO:003069...(truncated) 3 {} 2022-04-03 01:06:37
pypath.inputs.go.go_ancestors_goose 2022-04-03 01:22:32 2022-04-03 01:22:36 4.52 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 145, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:57:44
pypath.inputs.go.go_ancestors_quickgo 2022-04-03 01:22:36 2022-04-03 01:22:40 3.56 dict {'C': {'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0009426': {('GO:003069...(truncated) 3 {} 2022-04-03 01:22:36
pypath.inputs.go.go_annotations_goa 2022-04-03 01:22:40 2022-04-03 01:22:50 10.00 dict {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) 3 {} 2022-04-03 01:22:40
pypath.inputs.go.go_annotations_goa 2022-04-03 01:22:50 2022-04-03 01:22:51 1.02 dict {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) 3 {} 2022-04-03 01:22:50
pypath.inputs.go.go_annotations_goose 2022-04-03 01:22:51 2022-04-03 01:22:54 3.22 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 795, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:57:55
pypath.inputs.go.go_annotations_solr 2022-04-03 01:22:54 2022-04-03 01:22:55 1.34 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 681, in go_annotations_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2022-01-07 23:57:58
pypath.inputs.go.go_annotations_uniprot 2022-04-03 01:22:55 2022-04-03 01:23:31 35.66 dict {'Entry': ['Gene ontology IDs'], 'P51451': ['GO:0002431', 'GO:0002513', 'GO:0002576', 'GO:0002902', 'GO:0004712', 'GO:0004713', 'GO:0004715', 'GO:0005102', 'GO:0005524', 'GO:0005829', 'GO:0006974', 'GO:0007169', 'GO:0018108', 'GO:0030154', 'GO:0030889', 'GO:0031175', 'GO:0031234', 'GO:0032024', 'GO:...(truncated) 20,377 {} 2022-04-03 01:22:55
pypath.inputs.go.go_descendants_quickgo 2022-04-03 01:23:31 2022-04-03 01:23:35 3.41 dict {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0032398', 'is_a'), ('GO:0042613', 'is_a'), ('GO:0042612', 'is_a')}, 'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009429', 'part_of'), ('GO:0009426', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:...(truncated) 3 {} 2022-04-03 01:23:31
pypath.inputs.go.go_descendants_goose 2022-04-03 01:23:35 2022-04-03 01:23:38 3.32 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 222, in go_descendants_goose
    anc = go_ancestors_goose(aspects = aspects)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 145, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:58:11
pypath.inputs.go.go_descendants_quickgo 2022-04-03 01:23:38 2022-04-03 01:23:41 3.39 dict {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0032398', 'is_a'), ('GO:0042613', 'is_a'), ('GO:0042612', 'is_a')}, 'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009429', 'part_of'), ('GO:0009426', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:...(truncated) 3 {} 2022-04-03 01:23:38
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 2022-04-03 01:23:41 2022-04-03 01:23:44 2.73 dict {'C': {'GO:0042613': 'MHC class II protein complex', 'GO:0042611': 'MHC protein complex', 'GO:0042612': 'MHC class I protein complex', 'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:00306...(truncated) 3 {} 2022-04-03 01:23:41
pypath.inputs.go.go_terms_goose 2022-04-03 01:23:44 2022-04-03 01:23:48 3.37 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 519, in go_terms_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:58:20
pypath.inputs.go.go_terms_quickgo 2022-04-03 01:23:48 2022-04-03 01:23:50 2.74 dict {'C': {'GO:0042613': 'MHC class II protein complex', 'GO:0042611': 'MHC protein complex', 'GO:0042612': 'MHC class I protein complex', 'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:00306...(truncated) 3 {} 2022-04-03 01:23:48
pypath.inputs.go.go_terms_solr 2022-04-03 01:23:50 2022-04-03 01:23:51 0.61 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/go.py", line 377, in go_terms_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2022-01-07 23:58:26
pypath.inputs.gpcrdb.gpcrdb_annotations 2022-04-03 01:23:51 2022-04-03 01:23:51 0.25 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) 402 {} 2022-04-03 01:23:51
pypath.inputs.graphviz.graphviz_attrs 2022-04-03 01:23:51 2022-04-03 01:23:52 1.04 tuple ({'_background': {'type': 'string', 'default': '<none>', 'min': '', 'notes': ''}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'write only'}, 'bgcolor': {'type': 'colorcolorList', 'default': '<none>', 'min': '', 'notes': ''}, 'center': {'type': 'bool', 'default': 'false', 'min': '', 'no...(truncated) 3 {} 2022-04-03 01:23:51
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
 {} never
pypath.inputs.guide2pharma.guide2pharma_download 2022-04-03 01:23:52 2022-04-03 01:24:01 9.04 tuple ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=9606, target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=True, pubmed_ids=[]), GuideToPharmacologyI...(truncated) 2 {} 2022-04-03 01:23:52
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
 {} never
pypath.inputs.havugimana.get_havugimana 2022-04-03 01:24:01 2022-04-03 01:24:03 2.18 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 {} 2022-04-03 01:24:01
pypath.inputs.havugimana.havugimana_complexes 2022-04-03 01:24:03 2022-04-03 01:24:03 0.04 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 {} 2022-04-03 01:24:03
pypath.inputs.hgnc.hgnc_genegroups 2022-04-03 01:24:03 2022-04-03 01:24:12 8.99 dict {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='C3 and PZP like, alpha-2-macroglobulin domain containing')}, 'A8K2U0': {HGNCGeneGroupA...(truncated) 14,996 {} 2022-04-03 01:24:03
pypath.inputs.hippie.hippie_interactions 2022-04-03 01:24:12 2022-04-03 01:25:03 50.95 list [HippieInteraction(id_a='Q96BK5', id_b='Q9BZE4', score=0.76, methods=None, references=('17353931',), sources=None, organisms=None), HippieInteraction(id_a='Q86U70', id_b='P03372', score=0.75, methods=None, references=('19117995',), sources=None, organisms=None), HippieInteraction(id_a='O15397', id_b...(truncated) 39,727 {} 2022-04-03 01:24:12
pypath.inputs.homologene.get_homologene 2022-04-03 01:25:03 2022-04-03 01:25:04 0.11 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) 851,529 {'size': 576292} 2022-04-03 01:25:03
pypath.inputs.homologene.homologene_dict 
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments.
 {} never
pypath.inputs.homologene.homologene_uniprot_dict 
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments.
 {} never
pypath.inputs.hpmr.get_hpmr 2022-04-03 01:25:04 2022-04-03 01:25:04 0.00 dict {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) 3 {} 2022-04-03 01:25:04
pypath.inputs.hpmr.hpmr_annotations 2022-04-03 01:25:04 2022-04-03 01:25:04 0.00 dict {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) 1,141 {} 2022-04-03 01:25:04
pypath.inputs.hpmr.hpmr_complexes 2022-04-03 01:25:04 2022-04-03 01:25:04 0.00 dict {} 0 {} 2022-04-03 01:25:04
pypath.inputs.hpmr.hpmr_interactions 2022-04-03 01:25:04 2022-04-03 01:25:04 0.00 list [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) 619 {} 2022-04-03 01:25:04
pypath.inputs.hprd.get_hprd 2022-04-03 01:25:04 2022-04-03 01:25:09 5.70 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 {} 2022-04-03 01:25:04
pypath.inputs.hprd.hprd_enzyme_substrate 2022-04-03 01:25:09 2022-04-03 01:25:11 1.59 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 {} 2022-04-03 01:25:09
pypath.inputs.hprd.hprd_interactions 2022-04-03 01:25:11 2022-04-03 01:25:12 1.44 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 {} 2022-04-03 01:25:11
pypath.inputs.hprd.hprd_interactions_htp 2022-04-03 01:25:12 2022-04-03 01:25:14 1.43 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 {} 2022-04-03 01:25:12
pypath.inputs.htri.htri_interactions 2022-04-03 01:25:14 2022-04-03 01:25:17 3.52 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 {} 2022-04-03 01:25:14
pypath.inputs.humancellmap.humancellmap_annotations 2022-04-03 01:25:17 2022-04-03 01:25:20 2.50 dict {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='peroxisome', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) 4,371 {} 2022-04-03 01:25:17
pypath.inputs.humap.humap2_complexes 2022-04-03 01:25:20 2022-04-03 01:25:24 4.31 dict {'COMPLEX:O95900_Q9BQS8': Complex: COMPLEX:O95900_Q9BQS8, 'COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9': Complex: COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9, 'COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6ZRY4_Q93062_Q96S66_Q9NZC3_Q9UF11_Q9Y6M7': Complex: COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6Z...(truncated) 6,942 {} 2022-04-03 01:25:20
pypath.inputs.humap.humap_complexes 2022-04-03 01:25:24 2022-04-03 01:25:26 2.06 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) 4,499 {} 2022-04-03 01:25:24
pypath.inputs.huri._huri_interactions 
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments.
 {} never
pypath.inputs.huri.hi_i_interactions 2022-04-03 01:25:26 2022-04-03 01:25:40 13.43 list [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 5,676 {} 2022-04-03 01:25:26
pypath.inputs.huri.hi_ii_interactions 2022-04-03 01:25:40 2022-04-03 01:27:05 84.93 list [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P59797', uniprot_b='Q8NF64', isoform_a=1, isoform_b=3, score=None), HuriInteractio...(truncated) 46,898 {} 2022-04-03 01:25:40
pypath.inputs.huri.hi_iii_old 2022-04-03 01:27:05 2022-04-03 01:27:05 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/huri.py", line 94, in hi_iii_old
    url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
{} 2022-01-08 00:02:33
pypath.inputs.huri.hi_union_interactions 2022-04-03 01:27:05 2022-04-03 01:33:05 360.03 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/huri.py", line 302, in _huri_interactions
    c = curl.FileOpener(path)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 592, in __init__
    self.extract()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 622, in extract
    getattr(self, 'open_%s' % self.type)()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 739, in open_plain
    self._log('Opening plain text file `%s`.' % self.fileobj.name)
AttributeError: 'NoneType' object has no attribute 'name'
{} 2022-04-01 01:00:17
pypath.inputs.huri.huri_interactions 2022-04-03 01:33:05 2022-04-03 01:39:05 360.03 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/huri.py", line 302, in _huri_interactions
    c = curl.FileOpener(path)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 592, in __init__
    self.extract()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 622, in extract
    getattr(self, 'open_%s' % self.type)()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/share/curl.py", line 739, in open_plain
    self._log('Opening plain text file `%s`.' % self.fileobj.name)
AttributeError: 'NoneType' object has no attribute 'name'
{} 2022-04-01 01:01:43
pypath.inputs.huri.lit_bm_13_interactions 2022-04-03 01:39:05 2022-04-03 01:39:07 1.88 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 {} 2022-04-03 01:39:05
pypath.inputs.huri.lit_bm_17_interactions 2022-04-03 01:39:07 2022-04-03 01:39:19 12.23 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 {} 2022-04-03 01:39:07
pypath.inputs.huri.lit_bm_interactions 2022-04-03 01:39:19 2022-04-03 01:41:12 113.13 list [LitBmInteraction(uniprot_a='P23511', uniprot_b='Q13952'), LitBmInteraction(uniprot_a='P23511', uniprot_b='P25208'), LitBmInteraction(uniprot_a='P43351', uniprot_b='P43351'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q92843'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q07817'), LitBmInte...(truncated) 13,686 {} 2022-04-03 01:39:19
pypath.inputs.huri.rolland_hi_ii_14 2022-04-03 01:41:12 2022-04-03 01:41:18 5.62 list [['14', '6293', 'AAMP', 'VPS52', '1'], ['14', '8553', 'AAMP', 'BHLHE40', '1'], ['14', '64782', 'AAMP', 'AEN', '2'], ['15', '4188', 'AANAT', 'MDFI', '1'], ['15', '8553', 'AANAT', 'BHLHE40', '1'], ['28', '65983', 'ABO', 'GRAMD3', '2'], ['28', '84283', 'ABO', 'TMEM79', '1'], ['39', '39', 'ACAT2', 'ACAT...(truncated) 13,944 {} 2022-04-03 01:41:12
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 2022-04-03 01:41:18 2022-04-03 01:41:29 11.06 list [HuriInteraction(uniprot_a='P07196', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 2,829 {} 2022-04-03 01:41:18
pypath.inputs.huri.yu2011_interactions 2022-04-03 01:41:29 2022-04-03 01:41:52 23.29 list [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) 7,381 {} 2022-04-03 01:41:29
pypath.inputs.i3d.get_i3d 2022-04-03 01:41:52 2022-04-03 01:42:43 50.96 list [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) 15,984 {} 2022-04-03 01:41:52
pypath.inputs.icellnet._icellnet_get_components 
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_entity 
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_references 
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_resources 
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments.
 {} never
pypath.inputs.icellnet.icellnet_annotations 2022-04-03 01:42:43 2022-04-03 01:42:43 0.39 dict {'P03971': {IcellnetAnnotation(role='ligand', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, Complex: COMPLEX:P36894_Q16671: {IcellnetAnnotation(role='receptor', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, 'P36894': {IcellnetAnnotation(role='rec...(truncated) 688 {} 2022-04-03 01:42:43
pypath.inputs.icellnet.icellnet_complexes 2022-04-03 01:42:43 2022-04-03 01:42:44 0.13 dict {'COMPLEX:P36894_Q16671': Complex: COMPLEX:P36894_Q16671, 'COMPLEX:Q04771_Q16671': Complex: COMPLEX:Q04771_Q16671, 'COMPLEX:P27037_P37023': Complex: COMPLEX:P27037_P37023, 'COMPLEX:P37023_Q13705': Complex: COMPLEX:P37023_Q13705, 'COMPLEX:P37023_Q13873': Complex: COMPLEX:P37023_Q13873, 'COMPLEX:O0023...(truncated) 117 {} 2022-04-03 01:42:43
pypath.inputs.icellnet.icellnet_interactions 2022-04-03 01:42:44 2022-04-03 01:42:44 0.12 list [IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:P36894_Q16671, family='Cytokine', subfamily=None, classification=['Cytokine', 'Tgf'], resources=None, references=['32333774']), IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:Q04771_Q16671, family='Cytokine', subfamily=None, class...(truncated) 743 {} 2022-04-03 01:42:44
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.imweb._get_imweb 2022-04-03 01:42:44 2022-04-03 01:42:55 11.59 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/imweb.py", line 76, in _get_imweb
    hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
  File "/usr/lib/python3.9/json/__init__.py", line 339, in loads
    raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not NoneType
{} 2022-01-08 00:05:26
pypath.inputs.imweb.get_imweb 2022-04-03 01:42:55 2022-04-03 01:42:55 0.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/imweb.py", line 115, in get_imweb
    token = json.loads(fp.read())['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2022-01-08 00:05:27
pypath.inputs.imweb.get_imweb_req 2022-04-03 01:42:55 2022-04-03 01:42:56 0.52 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/imweb.py", line 142, in get_imweb_req
    token = json.loads(r0.text)['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2022-01-08 00:05:27
pypath.inputs.innatedb.innatedb_interactions 2022-04-03 01:42:56 2022-04-03 01:43:00 4.11 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 {} 2022-04-03 01:42:56
pypath.inputs.instruct.get_instruct 2022-04-03 01:43:00 2022-04-03 01:43:14 14.47 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 {} 2022-04-03 01:43:00
pypath.inputs.instruct.get_instruct_offsets 2022-04-03 01:43:15 2022-04-03 01:43:16 1.00 dict {('10gs', 'P09211'): 0, ('11gs', 'P09211'): 0, ('12gs', 'P09211'): 0, ('13gs', 'P09211'): 0, ('14gs', 'P09211'): 0, ('16gs', 'P09211'): 0, ('17gs', 'P09211'): 0, ('18gs', 'P09211'): 0, ('19gs', 'P09211'): 0, ('1a00', 'P68871'): 0, ('1a00', 'P69905'): 0, ('1a01', 'P68871'): 0, ('1a01', 'P69905'): 0, ...(truncated) 11,620 {} 2022-04-03 01:43:15
pypath.inputs.intact._try_isoform 
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments.
 {} never
pypath.inputs.intact.intact_interactions 2022-04-03 01:43:16 2022-04-03 01:51:18 482.00 list [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, interaction_types={'direct interaction'}, mi_score=0.77, isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', i...(truncated) 70,962 {} 2022-04-03 01:43:16
pypath.inputs.integrins.get_integrins 2022-04-03 01:51:18 2022-04-03 01:51:19 1.26 set {'P08514', 'P38570', 'P20702', 'P08648', 'P26010', 'P26006', 'Q13349', 'P56199', 'P16144', 'P05556', 'Q9UKX5', 'P05106', 'P18564', 'P17301', 'P18084', 'P53708', 'P23229', 'Q13797', 'P26012', 'O75578', 'Q13683', 'P20701', 'P05107', 'P11215', 'P06756'} 25 {} 2022-04-03 01:51:18
pypath.inputs.intogen.intogen_annotations 2022-04-03 01:51:19 2022-04-03 01:51:20 0.96 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) 480 {} 2022-04-03 01:51:19
pypath.inputs.ipi._ipi_uniprot_pairs 
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments.
 {} never
pypath.inputs.ipi.ipi_uniprot 2022-04-03 01:51:20 2022-04-03 01:51:20 0.41 dict {'IPI00807623': {'A0A183'}, 'IPI00396341': {'A0AUZ9'}, 'IPI00884975': {'A0AUZ9'}, 'IPI00884987': {'A0AUZ9'}, 'IPI00885003': {'A0AUZ9'}, 'IPI00855723': {'A0AV02'}, 'IPI00867607': {'A0AV02'}, 'IPI00793608': {'A0AV02'}, 'IPI00867726': {'A0AV02'}, 'IPI00867740': {'A0AV02'}, 'IPI00169342': {'A0AV96'}, 'I...(truncated) 51,106 {} 2022-04-03 01:51:20
pypath.inputs.iptmnet.iptmnet_interactions 2022-04-03 01:51:20 2022-04-03 01:55:13 232.13 list [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) 16,686 {} 2022-04-03 01:51:20
pypath.inputs.italk.italk_annotations 2022-04-03 01:55:13 2022-04-03 01:55:13 0.87 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 {} 2022-04-03 01:55:13
pypath.inputs.italk.italk_interactions 2022-04-03 01:55:13 2022-04-03 01:55:14 0.29 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 {} 2022-04-03 01:55:13
pypath.inputs.italk.italk_raw 2022-04-03 01:55:14 2022-04-03 01:55:14 0.01 DataFrame Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) 2,649 {} 2022-04-03 01:55:14
pypath.inputs.kea.kea_enzyme_substrate 2022-04-03 01:55:14 2022-04-03 01:55:26 12.26 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) 35,196 {} 2022-04-03 01:55:14
pypath.inputs.kea.kea_interactions 2022-04-03 01:55:26 2022-04-03 01:55:30 3.66 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) 35,196 {} 2022-04-03 01:55:26
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
 {} never
pypath.inputs.kegg.kegg_interactions 2022-04-03 01:55:30 2022-04-03 01:57:56 146.39 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) 14,431 {} 2022-04-03 01:55:30
pypath.inputs.kegg.kegg_medicus 2022-04-03 01:57:56 2022-04-03 01:58:11 15.25 set {KeggMedicusRawInteraction(id_a='3845', id_b='5894', name_a='KRAS', name_b='RAF1', effect='stimulation', itype='post_translational', pw_type='variant', type_a='gene', type_b='gene', network_id='N00041'), KeggMedicusRawInteraction(id_a='4853', id_b=('11317', '9794'), name_a='NOTCH2', name_b=('RBPJL',...(truncated) 12,601 {} 2022-04-03 01:57:56
pypath.inputs.kegg.kegg_medicus_complexes 2022-04-03 01:58:11 2022-04-03 01:58:13 1.71 dict {'COMPLEX:P15336_Q68CJ9': Complex: COMPLEX:P15336_Q68CJ9, 'COMPLEX:P30279_Q00534': Complex: COMPLEX:P30279_Q00534, 'COMPLEX:P06737_P35573': Complex: COMPLEX:P06737_P35573, 'COMPLEX:Q13547_Q96ST3_Q9UKL0': Complex: COMPLEX:Q13547_Q96ST3_Q9UKL0, 'COMPLEX:P08887_P40189': Complex: COMPLEX:P08887_P40189, ...(truncated) 266 {} 2022-04-03 01:58:11
pypath.inputs.kegg.kegg_medicus_interactions 2022-04-03 01:58:13 2022-04-03 01:58:15 1.74 list [KeggMedicusInteraction(id_a='P01116', id_b='P04049', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='Q04721', id_b=Complex: COMPLEX:Q92585_Q9UBG7, entity_type_a='protein', entity_type_b='complex', interacti...(truncated) 9,383 {} 2022-04-03 01:58:13
pypath.inputs.kegg.kegg_pathway_annotations 2022-04-03 01:58:15 2022-04-03 01:58:22 7.56 dict {'P19419': {KeggPathway(pathway='ErbB signaling pathway'), KeggPathway(pathway='Hepatocellular carcinoma'), KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Focal adhesion'), KeggPathway(pathway='Ras signaling pathway'), KeggPathway(pathway='Oxytocin signaling pathway'), KeggPathw...(truncated) 2,574 {} 2022-04-03 01:58:15
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2022-04-03 01:58:22 2022-04-03 01:58:23 0.46 dict {'A8K7J7': {KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Buti...(truncated) 813 {} 2022-04-03 01:58:22
pypath.inputs.kegg.kegg_pathways 2022-04-03 01:58:23 2022-04-03 01:58:30 7.57 tuple ({'MAPK signaling pathway': {'P19419', 'P28324', 'P21333', 'Q8WTQ7', 'Q99683', 'P49116', 'P15056', 'O95819', 'P01137', 'O75676', 'P25445', 'Q9NRY4', 'O95257', 'P08571', 'P01375', 'Q13233', 'Q96NL6', 'Q03701', 'P10636', 'P28482', 'P17535', 'Q9Y243', 'Q15283', 'Q99836', 'P07333', 'P42574', 'P15976', '...(truncated) 2 {} 2022-04-03 01:58:23
pypath.inputs.kinasedotcom.kinasedotcom_annotations 2022-04-03 01:58:30 2022-04-03 01:58:34 3.31 dict {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) 503 {} 2022-04-03 01:58:30
pypath.inputs.kirouac2010.kirouac2010_interactions 2022-04-03 01:58:34 2022-04-03 01:58:36 2.12 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 {} 2022-04-03 01:58:34
pypath.inputs.laudanna.laudanna_directions 2022-04-03 01:58:36 2022-04-03 01:58:38 1.68 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/laudanna.py", line 56, in laudanna_directions
    LaudannaDirection(
TypeError: <lambda>() missing 1 required positional argument: 'target_genesymbol'
{} 2022-01-08 00:09:37
pypath.inputs.laudanna.laudanna_effects 2022-04-03 01:58:38 2022-04-03 01:58:39 1.52 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 {} 2022-04-03 01:58:38
pypath.inputs.li2012.get_li2012 2022-04-03 01:58:39 2022-04-03 01:59:44 65.25 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 {} 2022-04-03 01:58:39
pypath.inputs.li2012.li2012_dmi 2022-04-03 01:59:44 2022-04-03 02:00:07 22.96 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 {} 2022-04-03 01:59:44
pypath.inputs.li2012.li2012_enzyme_substrate 2022-04-03 02:00:07 2022-04-03 02:00:07 0.03 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 {} 2022-04-03 02:00:07
pypath.inputs.li2012.li2012_interactions 2022-04-03 02:00:07 2022-04-03 02:00:07 0.03 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 {} 2022-04-03 02:00:07
pypath.inputs.lincs.lincs_compounds 2022-04-03 02:00:07 2022-04-03 02:00:34 26.69 dict {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) 1,320 {} 2022-04-03 02:00:07
pypath.inputs.lmpid.lmpid_dmi 2022-04-03 02:00:34 2022-04-03 02:00:35 1.38 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 {} 2022-04-03 02:00:34
pypath.inputs.lmpid.lmpid_interactions 2022-04-03 02:00:35 2022-04-03 02:00:36 0.79 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 {} 2022-04-03 02:00:35
pypath.inputs.lmpid.load_lmpid 2022-04-03 02:00:36 2022-04-03 02:00:37 0.80 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 {} 2022-04-03 02:00:36
pypath.inputs.lncdisease.lncdisease_interactions 2022-04-03 02:00:37 2022-04-03 02:00:37 0.22 list [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) 478 {} 2022-04-03 02:00:37
pypath.inputs.lncrnadb.lncrnadb_interactions 2022-04-03 02:00:37 2022-04-03 02:00:38 0.60 list [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism='Paramecium tetraurelia', pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism='Loris tardigradus', pmid='17175535'), LncrnadbInteraction(lncrna='G22'...(truncated) 773 {} 2022-04-03 02:00:37
pypath.inputs.locate.locate_localizations 2022-04-03 02:00:38 2022-04-03 02:02:53 135.00 dict {'P27824': {LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='type...(truncated) 9,496 {} 2022-04-03 02:00:38
pypath.inputs.lrdb.lrdb_annotations 2022-04-03 02:02:53 2022-04-03 02:02:54 0.71 dict {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD'), references=('14585398',)), LrdbAnnotation(role='receptor', cell_type=None, sources=('Fant...(truncated) 1,536 {} 2022-04-03 02:02:53
pypath.inputs.lrdb.lrdb_interactions 2022-04-03 02:02:54 2022-04-03 02:02:54 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 {} 2022-04-03 02:02:54
pypath.inputs.macrophage._trim_gname 
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments.
 {} never
pypath.inputs.macrophage.macrophage_interactions 2022-04-03 02:02:54 2022-04-03 02:02:54 0.28 list [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) 4,516 {} 2022-04-03 02:02:54
pypath.inputs.matrisome.__matrisome_annotations_2 2022-04-03 02:02:54 2022-04-03 02:03:10 16.29 set {'Thbs3', 'Fga', 'LAMB4', 'HTRA1', 'COL9A2', 'Emid1', 'Mmp19', 'SEMA3F', 'COLQ', 'COL26A1', 'SERPINB6', 'Sftpc', 'WNT11', 'Pf4', 'MFAP4', 'F13b', 'Pcolce2', 'IL16', 'EMILIN1', 'COL9A1', 'COL22A1', 'ANXA3', 'COL6A5', 'Ntn4', 'LEPREL2', 'Plxnc1', 'FBLN2', 'PODN', 'FGB', 'FN1', 'Efemp1', 'Igfbp6', 'Plo...(truncated) 744 {} 2022-04-03 02:02:54
pypath.inputs.matrisome.matrisome_annotations 2022-04-03 02:03:10 2022-04-03 02:03:13 2.66 dict {'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 1,064 {} 2022-04-03 02:03:10
pypath.inputs.matrixdb._matrixdb_protein_list 
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments.
 {} never
pypath.inputs.matrixdb.matrixdb_annotations 2022-04-03 02:03:13 2022-04-03 02:03:22 8.98 dict {'Q6PL45': {MatrixdbAnnotation(mainclass='secreted'), MatrixdbAnnotation(mainclass='membrane')}, 'Q0VAQ4': {MatrixdbAnnotation(mainclass='membrane')}, 'P0C874': {MatrixdbAnnotation(mainclass='membrane')}, 'Q15365': {MatrixdbAnnotation(mainclass='membrane')}, 'Q9Y5G6': {MatrixdbAnnotation(mainclass='...(truncated) 10,097 {} 2022-04-03 02:03:13
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2022-04-03 02:03:22 2022-04-03 02:03:22 0.09 set {'P10451', 'Q15582', 'Q9UNA0', 'Q96A83', 'Q02509', 'Q6AZY7', 'Q9NT22', 'Q8TER0', 'Q99983', 'Q8TE56', 'Q8WTR8', 'A6NHN0', 'P52803', 'Q9HB63', 'Q9BY76', 'P35625', 'Q07092', 'Q9BXS0', 'Q5KU26', 'Q9UQP3', 'Q8IVL5', 'O43405', 'O00534', 'Q32P28', 'P98066', 'O14594', 'P18065', 'Q9H1J5', 'Q16270', 'Q8WWQ2',...(truncated) 483 {} 2022-04-03 02:03:22
pypath.inputs.matrixdb.matrixdb_interactions 2022-04-03 02:03:22 2022-04-03 02:03:22 0.21 list [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) 425 {} 2022-04-03 02:03:22
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2022-04-03 02:03:22 2022-04-03 02:03:27 4.71 set {'Q6PL45', 'Q0VAQ4', 'P0C874', 'Q15365', 'Q9Y5G6', 'P78368', 'P34810', 'Q86UK0', 'P61567', 'O75084', 'Q86YS6', 'O95178', 'O00161', 'O60292', 'P0C7T8', 'A0A087WSZ9', 'Q96D53', 'Q9UIB8', 'Q6NSJ0', 'Q9Y2P5', 'Q9NPH3', 'P19438', 'Q8NBV8', 'Q8WTT0', 'Q6PCB6', 'Q9HBW1', 'A0A0A0MRZ7', 'Q8NGJ2', 'Q3MJ16', '...(truncated) 8,240 {} 2022-04-03 02:03:22
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2022-04-03 02:03:27 2022-04-03 02:03:27 0.47 set {'Q6PL45', 'P21333', 'Q9HAT1', 'P10451', 'O14944', 'Q6GTS8', 'P30530', 'P60827', 'P01148', 'P08962', 'Q6Q788', 'Q9H6Z9', 'P20851', 'Q9NT22', 'Q03169', 'A6NHN0', 'Q16531', 'Q9H4A4', 'Q96II8', 'Q12884', 'P15248', 'Q9BXS0', 'O60292', 'P29508', 'P00441', 'O43405', 'Q5DID0', 'P01857', 'P01715', 'Q7L592',...(truncated) 2,923 {} 2022-04-03 02:03:27
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2022-04-03 02:03:27 2022-04-03 02:03:28 0.87 set {'Q08174', 'Q9NPY3', 'Q12860', 'P35443', 'O75144', 'Q8TEW0', 'Q12816', 'P56748', 'P18827', 'Q86UP0', 'Q86WK7', 'P28827', 'P25940', 'P42081', 'Q13740', 'Q13477', 'P56746', 'P07359', 'O15394', 'Q13895', 'Q8IUX7', 'Q99418', 'Q59H14', 'Q9Y5Y7', 'Q9BY67', 'Q8WWQ8', 'Q96GP6', 'Q13449', 'P13591', 'Q9UKX5',...(truncated) 103 {} 2022-04-03 02:03:27
pypath.inputs.membranome.membranome_annotations 2022-04-03 02:03:28 2022-04-03 02:05:00 92.12 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) 2,386 {} 2022-04-03 02:03:28
pypath.inputs.mimp.get_kinase_class 2022-04-03 02:05:00 2022-04-03 02:05:01 0.28 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 {} 2022-04-03 02:05:00
pypath.inputs.mimp.mimp_enzyme_substrate 2022-04-03 02:05:01 2022-04-03 02:05:15 14.40 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 {} 2022-04-03 02:05:01
pypath.inputs.mimp.mimp_interactions 2022-04-03 02:05:15 2022-04-03 02:05:16 0.52 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 {} 2022-04-03 02:05:15
pypath.inputs.mir2disease.mir2disease_interactions 2022-04-03 02:05:16 2022-04-03 02:05:16 0.24 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 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.get_mirbase_aliases 2022-04-03 02:05:16 2022-04-03 02:05:16 0.08 tuple ({'MIMAT0000062': {'hsa-let-7a-5p', 'hsa-let-7a'}, 'MIMAT0000063': {'hsa-let-7b-5p', 'hsa-let-7b'}, 'MIMAT0000064': {'hsa-let-7c-5p', 'hsa-let-7c'}, 'MIMAT0000065': {'hsa-let-7d', 'hsa-let-7d-5p'}, 'MIMAT0000066': {'hsa-let-7e-5p', 'hsa-let-7e'}, 'MIMAT0000067': {'hsa-let-7f-5p', 'hsa-let-7f'}, 'MIM...(truncated) 2 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_ids 2022-04-03 02:05:16 2022-04-03 02:05:16 0.08 list [('MIMAT0000062', 'MI0000062'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000062', 'MI0000060'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000068', 'MI...(truncated) 3,027 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_mature 2022-04-03 02:05:16 2022-04-03 02:05:16 0.06 list [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000066', 'hsa-let-7e-5p...(truncated) 3,487 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_mature_all 2022-04-03 02:05:16 2022-04-03 02:05:16 0.08 list ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) 3,027 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_precursor 2022-04-03 02:05:16 2022-04-03 02:05:16 0.06 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-3L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000063', 'hsa-let-7bL'), ('MI0000063', 'hsa-let-7b'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) 2,173 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_precursor_all 2022-04-03 02:05:16 2022-04-03 02:05:16 0.08 list ['MI0000062', 'MI0000061', 'MI0000060', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000115', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) 3,027 {} 2022-04-03 02:05:16
pypath.inputs.mirbase.mirbase_precursor_to_mature 2022-04-03 02:05:16 2022-04-03 02:05:17 0.14 list [('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0000062'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT...(truncated) 3,361 {} 2022-04-03 02:05:16
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2022-04-03 02:05:17 2022-04-03 02:05:17 0.32 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 {} 2022-04-03 02:05:17
pypath.inputs.mirecords.mirecords_interactions 2022-04-03 02:05:17 2022-04-03 02:05:21 4.49 list [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism='Homo sapiens', target_organism='Homo sapiens', pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organ...(truncated) 3,106 {} 2022-04-03 02:05:17
pypath.inputs.mirtarbase._mirtarbase_interactions 
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments.
 {} never
pypath.inputs.mirtarbase.mirtarbase_interactions 2022-04-03 02:05:21 2022-04-03 02:05:59 37.82 list [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism='Mus musculus', target_genesymbol='Cd320', target_entrez='54219', target_organism='Mus musculus', target_site='AGAGACTGGGGTCCTCAGACACTCCC', method='Luciferase reporter assay//qRT-PCR//Western blot', catego...(truncated) 21,560 {} 2022-04-03 02:05:21
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 2022-04-03 02:05:59 2022-04-03 02:06:00 0.40 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 {} 2022-04-03 02:05:59
pypath.inputs.msigdb.msigdb_annotations 2022-04-03 02:06:00 2022-04-03 02:09:17 197.21 dict {'P38484': {MsigdbAnnotation(collection='immunesigdb', geneset='GSE3982_BCELL_VS_TH2_UP'), MsigdbAnnotation(collection='tf_targets_gtrf', geneset='FOXP2_TARGET_GENES'), MsigdbAnnotation(collection='immunesigdb', geneset='GSE3920_IFNA_VS_IFNB_TREATED_ENDOTHELIAL_CELL_UP'), MsigdbAnnotation(collection...(truncated) 20,065 {} 2022-04-03 02:06:00
pypath.inputs.msigdb.msigdb_download 2022-04-03 02:09:18 2022-04-03 02:09:58 40.05 dict {'chr1p11': {'PDE4DIPP2', 'RNVU1-19', 'EMBP1', 'H3P4', 'PFN1P2', 'NBPF26', 'SRGAP2C', 'RNVU1-4', 'MTIF2P1', 'SRGAP2-AS1', 'NOTCH2NLR', 'RPL22P6', 'LINC02798', 'NBPF8', 'H2BP1', 'LINC00623', 'FCGR1B', 'LINC01691', 'PDE4DIPP4', 'PPIAL4A', 'FAM72B'}, 'chr1p12': {'MAN1A2', 'HSD3BP1', 'ENSG00000236866', ...(truncated) 32,880 {} 2022-04-03 02:09:18
pypath.inputs.msigdb.msigdb_download_collections 2022-04-03 02:09:59 2022-04-03 02:10:00 0.55 dict {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'IFIT2', 'CEBPB', 'NFAT5', 'TNFSF9', 'CCL5', 'CCL2', 'CD83', 'PTGER4', 'B4GALT1', 'IL7R', 'MAP2K3', 'MAP3K8', 'SDC4', 'ICAM1', 'MSC', 'SLC2A6', 'INHBA', 'DENND5A', 'TAP1', 'SMAD3', 'KLF4', 'JUN', 'NINJ1', 'PLPP3', 'ETS2', 'DUSP1', 'PTX3',...(truncated) 18 {} 2022-04-03 02:09:59
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2022-04-03 02:10:00 2022-04-03 02:10:00 0.35 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 {} 2022-04-03 02:10:00
pypath.inputs.negatome.negatome_interactions 2022-04-03 02:10:00 2022-04-03 02:10:00 0.11 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 {} 2022-04-03 02:10:00
pypath.inputs.netbiol._netbiol_interactions 
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments.
 {} never
pypath.inputs.netbiol.arn_interactions 2022-04-03 02:10:00 2022-04-03 02:10:00 0.14 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 {} 2022-04-03 02:10:00
pypath.inputs.netbiol.nrf2ome_interactions 2022-04-03 02:10:00 2022-04-03 02:10:01 0.14 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 {} 2022-04-03 02:10:00
pypath.inputs.netpath.netpath_interactions 2022-04-03 02:10:01 2022-04-03 02:10:03 2.04 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 {} 2022-04-03 02:10:01
pypath.inputs.netpath.netpath_names 2022-04-03 02:10:03 2022-04-03 02:10:03 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 {} 2022-04-03 02:10:03
pypath.inputs.netpath.netpath_pathway_annotations 2022-04-03 02:10:03 2022-04-03 02:10:26 22.92 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-6 (IL-...(truncated) 1,869 {} 2022-04-03 02:10:03
pypath.inputs.ontology.listof_ontologies 2022-04-03 02:10:26 2022-04-03 02:10:27 1.27 dict {'aeo': 'Anatomical Entity Ontology', 'afo': 'Allotrope Merged Ontology Suite', 'agro': 'Agronomy Ontology', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'apo': 'Ascomycete Phenotype Ontology (APO)', 'apollo_sv': 'Apollo Structured Vocabulary (Apollo-SV)', 'aro': 'Antibiotic Resist...(truncated) 273 {} 2022-04-03 02:10:26
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
 {} never
pypath.inputs.opm.opm_annotations 2022-04-03 02:10:27 2022-04-03 02:11:21 53.86 dict {'Q15599': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P59666': {OpmAnnotation(membrane='Secreted', family='Vertebrate defensin', transmembrane=False)},...(truncated) 404 {'size': -1} 2022-04-03 02:10:27
pypath.inputs.oreganno.oreganno_interactions 2022-04-03 02:11:21 2022-04-03 03:11:21 3,600.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/oreganno.py", line 76, in oreganno_interactions
    for l in oreganno_raw():
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/oreganno.py", line 43, in oreganno_raw
    _ = next(data)
TypeError: 'NoneType' object is not an iterator
{} 2022-04-01 01:18:20
pypath.inputs.oreganno.oreganno_raw 2022-04-03 03:11:21 2022-04-03 04:11:21 3,600.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/oreganno.py", line 43, in oreganno_raw
    _ = next(data)
TypeError: 'NoneType' object is not an iterator
{} 2022-04-01 01:20:19
pypath.inputs.panglaodb.panglaodb_annotations 2022-04-03 04:11:21 2022-04-03 04:11:23 2.34 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) 4,807 {} 2022-04-03 04:11:21
pypath.inputs.panglaodb.panglaodb_raw 2022-04-03 04:11:23 2022-04-03 04:11:23 0.04 list [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) 8,286 {} 2022-04-03 04:11:23
pypath.inputs.pathwaycommons._create_single_resource_method 
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, 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._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons.pathwaycommons_interactions 2022-04-03 04:11:23 2022-04-03 04:11:51 27.56 list [PathwayCommonsInteraction(id_a='AAK1', interaction_type='controls-phosphorylation-of', id_b='AP2M1', resource='PhosphoSite'), PathwayCommonsInteraction(id_a='AAK1', interaction_type='controls-state-change-of', id_b='AP2M1', resource='PhosphoSite'), PathwayCommonsInteraction(id_a='AAK1', interaction...(truncated) 1,261,865 {} 2022-04-03 04:11:23
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 2022-04-03 04:11:52 2022-04-03 04:11:52 0.44 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 {} 2022-04-03 04:11:52
pypath.inputs.pdb.pdb_chains 2022-04-03 04:11:52 2022-04-03 04:12:02 9.79 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 {} 2022-04-03 04:11:52
pypath.inputs.pdb.pdb_complexes 2022-04-03 04:12:04 2022-04-03 04:12:11 6.61 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) 39,662 {} 2022-04-03 04:12:04
pypath.inputs.pdb.pdb_uniprot 2022-04-03 04:12:11 2022-04-03 04:12:26 14.77 tuple ({'P02185': {('2mgk', 'X-ray', 2.0), ('1ch7', 'X-ray', 1.9), ('2myb', 'X-ray', 1.9), ('1mgn', 'X-ray', 1.9), ('2zss', 'X-ray', 1.21), ('2zt3', 'X-ray', 1.21), ('5vzo', 'X-ray', 1.78), ('2eb9', 'X-ray', 1.8), ('106m', 'X-ray', 1.99), ('1yoh', 'X-ray', 1.65), ('2g0x', 'X-ray', 1.95), ('4fwy', 'X-ray',...(truncated) 2 {} 2022-04-03 04:12:11
pypath.inputs.pdzbase.pdzbase_interactions 2022-04-03 04:12:26 2022-04-03 04:12:27 1.00 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 {} 2022-04-03 04:12:26
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
 {} never
pypath.inputs.pepcyber.pepcyber_interactions 2022-04-03 04:12:27 2022-04-03 04:25:26 778.85 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 {} 2022-04-03 04:12:27
pypath.inputs.pfam._pfam_uniprot 
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments.
 {} never
pypath.inputs.pfam.pfam_names 2022-04-03 04:25:26 2022-04-03 04:25:27 0.85 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 {} 2022-04-03 04:25:26
pypath.inputs.pfam.pfam_pdb 2022-04-03 04:25:27 2022-04-03 04:25:29 2.67 tuple ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) 2 {} 2022-04-03 04:25:27
pypath.inputs.pfam.pfam_regions 2022-04-03 04:25:30 2022-04-03 05:00:19 2,089.30 tuple ({}, {}) 2 {} 2022-04-03 04:25:30
pypath.inputs.pfam.pfam_uniprot 2022-04-03 05:00:19 2022-04-03 05:05:02 283.15 tuple ({'O95399': {'PF02083'}, 'Q5VT03': {'PF12881'}, 'Q86WH2': {'PF00788', 'PF16517'}, 'Q9P1P5': {'PF00001'}, 'O95178': {'PF14813'}, 'Q5QGS0': {'PF15735'}, 'P18031': {'PF00102'}, 'Q6UVJ0': {'PF18594', 'PF16531'}, 'O00767': set(), 'Q8N614': {'PF15106'}, 'Q6UWJ1': {'PF00999'}, 'Q9BVK6': {'PF01105'}, 'Q9998...(truncated) 2 {} 2022-04-03 05:00:19
pypath.inputs.phobius.phobius_annotations 2022-04-03 05:05:02 2022-04-03 05:05:03 0.35 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 {} 2022-04-03 05:05:02
pypath.inputs.phosphatome.phosphatome_annotations 2022-04-03 05:05:03 2022-04-03 05:05:10 7.61 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 {} 2022-04-03 05:05:03
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2022-04-03 05:05:10 2022-04-03 05:05:13 2.30 list [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) 2,426 {} 2022-04-03 05:05:10
pypath.inputs.phosphoelm.phosphoelm_interactions 2022-04-03 05:05:13 2022-04-03 05:05:13 0.61 list [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) 2,426 {} 2022-04-03 05:05:13
pypath.inputs.phosphoelm.phosphoelm_kinases 2022-04-03 05:05:13 2022-04-03 05:05:13 0.11 dict {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) 247 {} 2022-04-03 05:05:13
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2022-04-03 05:05:13 2022-04-03 05:05:14 1.11 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 {} 2022-04-03 05:05:13
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2022-04-03 05:05:14 2022-04-03 05:05:15 0.02 list [['MAPK1', 'APBB1'], ['CAMK4', 'ATP2A2'], ['CDK4', 'RBL1'], ['MAPK8', 'ZHX1'], ['PDPK1', 'HNRPK'], ['ACVR1', 'RPS6KA2'], ['CSNK2A1', 'NUP62'], ['CDK9', 'NUP133'], ['SCYL1', 'DGCR8'], ['RPS6KB1', 'EEF2K'], ['PAK1', 'LIMK1'], ['PLK1', 'NUDC'], ['NEK2', 'SFRS1'], ['PDK3', 'PDHA1'], ['ILK', 'NOC2L'], ['...(truncated) 1,821 {} 2022-04-03 05:05:14
pypath.inputs.phosphopoint.phosphopoint_directions 2022-04-03 05:05:15 2022-04-03 05:05:15 0.49 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 {} 2022-04-03 05:05:15
pypath.inputs.phosphopoint.phosphopoint_interactions 2022-04-03 05:05:15 2022-04-03 05:05:15 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 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite._phosphosite_filter_organism 
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments.
 {} never
pypath.inputs.phosphosite.phosphosite_directions 2022-04-03 05:05:15 2022-04-03 05:05:15 0.01 list [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) 8,971 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2022-04-03 05:05:15 2022-04-03 05:05:15 0.36 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) 13,127 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_interactions 2022-04-03 05:05:15 2022-04-03 05:05:15 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_interactions_all 2022-04-03 05:05:15 2022-04-03 05:05:15 0.01 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 9,041 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_interactions_curated 2022-04-03 05:05:15 2022-04-03 05:05:15 0.00 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 4,309 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_interactions_new 2022-04-03 05:05:15 2022-04-03 05:05:15 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_interactions_noref 2022-04-03 05:05:15 2022-04-03 05:05:15 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', 'AB;WB;MA'...(truncated) 4,732 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2022-04-03 05:05:15 2022-04-03 05:05:24 8.63 dict {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) 198,541 {} 2022-04-03 05:05:15
pypath.inputs.phosphosite.phosphosite_ptms 2022-04-03 05:05:25 2022-04-03 05:05:54 29.31 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) 239,701 {} 2022-04-03 05:05:25
pypath.inputs.phosphosite.phosphosite_regsites 2022-04-03 05:05:54 2022-04-03 05:05:56 1.98 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) 5,298 {} 2022-04-03 05:05:54
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2022-04-03 05:05:56 2022-04-03 05:07:59 122.47 dict {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'24876223', '21148409', '28052875', '21209006'}, 'isoforms': {1}, 'process': {''}, 'function': {'protein degradation', 'ubiquitination', 'intracellular localization', 'phosphorylation', 'protein stabilization'}...(truncated) 3,538 {} 2022-04-03 05:05:56
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 2022-04-03 05:07:59 2022-04-03 05:13:59 360.02 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> 0 {} 2022-04-03 05:07:59
pypath.inputs.pro.pro_mapping 2022-04-03 05:13:59 2022-04-03 05:13:59 0.37 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) 319,353 {} 2022-04-03 05:13:59
pypath.inputs.progeny.progeny_annotations 2022-04-03 05:13:59 2022-04-03 05:14:18 18.08 dict {'P35250': {ProgenyAnnotation(pathway='EGFR', weight=1.4706466171905381, p_value=0.0016552751715941223), ProgenyAnnotation(pathway='VEGF', weight=-0.15684553639501156, p_value=0.8477560090795286), ProgenyAnnotation(pathway='p53', weight=-3.3513628049710005, p_value=0.000985568693599589), ProgenyAnno...(truncated) 18,598 {} 2022-04-03 05:13:59
pypath.inputs.progeny.progeny_raw 2022-04-03 05:14:18 2022-04-03 05:14:20 2.01 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 {} 2022-04-03 05:14:18
pypath.inputs.proteinatlas.get_proteinatlas 2022-04-03 05:14:20 2022-04-03 05:15:56 96.45 dict {'normal': {'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 detected', 'Approved'...(truncated) 2 {} 2022-04-03 05:14:20
pypath.inputs.proteinatlas.proteinatlas_annotations 2022-04-03 05:15:58 2022-04-03 05:18:39 160.78 dict {'O43657': {ProtainatlasAnnotation(organ='small intestine', tissue='glandular cells', level='Medium', 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='spleen', tissue='cells...(truncated) 19,373 {} 2022-04-03 05:15:58
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2022-04-03 05:18:41 2022-04-03 05:18:43 2.00 dict {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) 2,591 {} 2022-04-03 05:18:41
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2022-04-03 05:18:43 2022-04-03 05:18:44 1.06 dict {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) 6,821 {} 2022-04-03 05:18:43
pypath.inputs.protmapper.get_protmapper 2022-04-03 05:18:44 2022-04-03 05:18:54 10.15 tuple ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) 2 {} 2022-04-03 05:18:44
pypath.inputs.protmapper.protmapper_enzyme_substrate 2022-04-03 05:18:54 2022-04-03 05:18:55 0.72 list [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '25728676', '25545367', '24727247', '24357804'}, 'substrate': 'P15336', 'databases': {'REACH', 'Sparser', 'PhosphoSite', 'SIGNOR'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) 22,139 {} 2022-04-03 05:18:54
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 2022-04-03 05:18:55 2022-04-03 05:18:56 0.60 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 {} 2022-04-03 05:18:55
pypath.inputs.ramilowski2015.ramilowski_locations 2022-04-03 05:18:56 2022-04-03 05:19:32 36.66 dict {'P04217': {RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), Ramilo...(truncated) 18,861 {} 2022-04-03 05:18:56
pypath.inputs.rdata._patch_rdata 2022-04-03 05:19:33 2022-04-03 05:19:33 0.00 NoneType None 0 {} 2022-04-03 05:19:33
pypath.inputs.rdata._rdata_data_frame_get_rownames 
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments.
 {} never
pypath.inputs.rdata._rdata_list_get_names 
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments.
 {} never
pypath.inputs.reaction._bp_collect_resources 
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._process_controls 
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_resources 
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_species 
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_compartment 
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_id 
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_res 
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_id 
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reaction 
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reactions 2022-04-03 05:19:33 2022-04-03 05:21:37 124.49 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/reaction.py", line 985, in _reactome_reactions
    for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
AttributeError: 'NoneType' object has no attribute 'find_all'
{} 2022-01-08 00:48:01
pypath.inputs.reaction._reactome_reactions_et 2022-04-03 05:21:37 2022-04-03 05:21:39 2.03 tuple ({}, {}, {}) 3 {} 2022-04-03 05:21:37
pypath.inputs.reaction._reactome_res 
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_species 
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments.
 {} never
pypath.inputs.reaction.acsn_biopax 2022-04-03 05:21:39 2022-04-03 05:21:49 9.55 list ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) 190,854 {} 2022-04-03 05:21:39
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
 {} never
pypath.inputs.reaction.get_acsn_effects 2022-04-03 05:21:49 2022-04-03 05:21:49 0.19 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 {} 2022-04-03 05:21:49
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 2022-04-03 05:21:49 2022-04-03 05:23:37 107.82 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/reaction.py", line 1186, in get_reactions
    rea.load_all()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/pyreact.py", line 1301, in load_all
    self.load_panther()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/utils/pyreact.py", line 1213, in load_panther
    len(biopaxes.files_multipart),
AttributeError: 'Curl' object has no attribute 'files_multipart'
{} 2022-01-08 00:48:07
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
 {} never
pypath.inputs.reaction.panther_biopax 2022-04-03 05:23:37 2022-04-03 05:23:40 3.29 NoneType None 0 {} 2022-04-03 05:23:37
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.pid_biopax 2022-04-03 05:23:40 2022-04-03 05:23:42 2.41 NoneType None 0 {} 2022-04-03 05:23:40
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 2022-04-03 05:23:42 2022-04-03 05:29:42 360.02 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/reaction.py", line 91, in reactome_biopax
    fileobj = c.result[fname]
TypeError: 'NoneType' object is not subscriptable
{} 2022-04-01 01:55:29
pypath.inputs.reaction.reactome_bs 2022-04-03 05:29:42 2022-04-03 05:35:44 361.66 list [('R-HSA-1059683', <?xml version='1.0' encoding='utf-8' standalone='no'?> <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 79 on 1/9/22 9:39 PM using JSBML version 1.5....(truncated) 2,553 {} 2022-04-03 05:29:42
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_sbml 2022-04-03 05:36:01 2022-04-03 05:36:03 2.03 dict {'R-HSA-1059683.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-00130...(truncated) 2,553 {} 2022-04-03 05:36:01
pypath.inputs.scconnect.scconnect_annotations 2022-04-03 05:36:03 2022-04-03 05:36:04 0.98 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 {} 2022-04-03 05:36:03
pypath.inputs.scconnect.scconnect_complexes 2022-04-03 05:36:04 2022-04-03 05:36:05 0.21 set {Complex: COMPLEX:P01215_P01222, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:P01562, Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:P29459_P29460, Complex: COMPLEX:P01215_P01229, Complex: CO...(truncated) 17 {} 2022-04-03 05:36:04
pypath.inputs.scconnect.scconnect_interactions 2022-04-03 05:36:05 2022-04-03 05:50:55 890.76 list [ScconnectInteraction(ligand_id='ML355', target_id='P18054', ligand_organism=None, target_organism=9606, ligand_type='small_molecule', target_type='protein', effect='Inhibition', references='24393039'), ScconnectInteraction(ligand_id='PKUMDL_MH_1001', target_id='P16050', ligand_organism=None, target...(truncated) 20,434 {} 2022-04-03 05:36:05
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
 {} never
pypath.inputs.signalink.signalink_annotations 2022-04-03 05:50:55 2022-04-03 05:50:57 2.01 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 {} 2022-04-03 05:50:55
pypath.inputs.signalink.signalink_function_annotations 2022-04-03 05:50:57 2022-04-03 05:50:58 0.61 dict {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) 784 {} 2022-04-03 05:50:57
pypath.inputs.signalink.signalink_interactions 2022-04-03 05:50:58 2022-04-03 05:50:59 0.70 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 {} 2022-04-03 05:50:58
pypath.inputs.signalink.signalink_pathway_annotations 2022-04-03 05:50:59 2022-04-03 05:50:59 0.61 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) 836 {} 2022-04-03 05:50:59
pypath.inputs.signor.signor_complexes 2022-04-03 05:50:59 2022-04-03 05:51:01 1.77 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) 3,211 {} 2022-04-03 05:50:59
pypath.inputs.signor.signor_enzyme_substrate 2022-04-03 05:51:01 2022-04-03 05:51:22 20.95 list [{'typ': 'phosphorylation', 'resnum': 11, 'instance': 'TKQTARKSTGGKAPR', 'substrate': 'P68431', 'start': 4, 'end': 18, 'kinase': 'P21980', 'resaa': 'S', 'motif': 'TKQTARKSTGGKAPR', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'16407273'}}, {'typ': 'phosphorylation', 'resnum': 35...(truncated) 9,985 {'size': 2} 2022-04-03 05:51:01
pypath.inputs.signor.signor_interactions 2022-04-03 05:51:22 2022-04-03 05:51:23 0.43 list [SignorInteraction(source='P21860', target='P62993', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates', mechanism='binding', ncbi_tax_id='9606', pubmeds='14967450', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), SignorInter...(truncated) 36,564 {'size': 36} 2022-04-03 05:51:22
pypath.inputs.signor.signor_pathway_annotations 2022-04-03 05:51:23 2022-04-03 05:51:52 29.16 dict {'Q8IXJ9': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q8TEK3': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P31269': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P42229': {SignorPathway(pathway='Leptin Signaling'), SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway...(truncated) 645 {} 2022-04-03 05:51:23
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
 {} never
pypath.inputs.signor.signor_protein_families 2022-04-03 05:51:52 2022-04-03 05:51:52 0.00 dict {'SIGNOR-PF1': ['P28482', 'P27361'], 'SIGNOR-PF2': ['Q9HBW0', 'Q9UBY5', 'Q92633'], 'SIGNOR-PF3': ['O14610', 'O60262', 'Q9P2W3', 'P63215', 'P63211', 'P50150', 'P59768', 'P63218', 'P61952', 'Q9UK08', 'Q9UBI6', 'P50151'], 'SIGNOR-PF4': ['P28482', 'P27361'], 'SIGNOR-PF5': ['P01137', 'P10600', 'P61812'],...(truncated) 93 {} 2022-04-03 05:51:52
pypath.inputs.spike.spike_interactions 2022-04-03 05:51:52 2022-04-03 05:52:08 16.38 list [['836', 'CASP3', '8669', 'EIF3J', '1', '10672017', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['836', 'CASP3', '3691', 'ITGB4', '1', '17178732', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['407042', 'MIR34C', '4609', 'MYC', '1', '20212154', '1', '2', ...(truncated) 3,842 {} 2022-04-03 05:51:52
pypath.inputs.stitch.stitch_actions_interactions 2022-04-03 05:52:08 2022-04-03 05:54:17 128.33 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 {} 2022-04-03 05:52:08
pypath.inputs.stitch.stitch_links_interactions 2022-04-03 05:54:17 2022-04-03 05:56:07 110.85 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 {} 2022-04-03 05:54:17
pypath.inputs.string.string_effects 2022-04-03 05:56:07 2022-04-03 05:56:18 11.01 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 {} 2022-04-03 05:56:07
pypath.inputs.string.string_links_interactions 2022-04-03 05:56:20 2022-04-03 05:57:16 56.05 list [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000440005', neighborhood_score=0, fusion=0, cooccurence=50, coexpression=99, experimental=679, database=900, textmining=59, combined_score=969, physical_combined_score=740), StringLinksInteraction(protein_a='ENSP00000000233', prot...(truncated) 247,200 {} 2022-04-03 05:56:20
pypath.inputs.string.string_physical_interactions 2022-04-03 05:57:16 2022-04-03 05:57:17 1.68 list [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000221957', experimental=483, database=600, textmining=821, combined_score=959), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=932, database=0, textmining=0, combined_score=932...(truncated) 83,896 {} 2022-04-03 05:57:16
pypath.inputs.surfaceome.surfaceome_annotations 2022-04-03 05:57:18 2022-04-03 05:57:23 5.94 dict {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC12', 'SLC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC5', 'SLC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'TMEM30', 'Unknown_function'}), '...(truncated) 2,808 {} 2022-04-03 05:57:18
pypath.inputs.switches_elm.get_switches_elm 2022-04-03 05:57:23 2022-04-03 05:58:45 81.94 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/switches_elm.py", line 95, in get_switches_elm
    mod_ont = ontology.ontology('MOD')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/ontology.py", line 46, in ontology
    result = ebi.ebi_rest(url = url, fields = _fields)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220403-001302/pypath/inputs/ebi.py", line 73, in ebi_rest
    this_result = json.loads(c.result)
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{'broke': True} 2022-04-02 05:49:39
pypath.inputs.talklr.talklr_annotations 2022-04-03 05:58:45 2022-04-03 05:58:46 0.71 dict {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) 1,345 {} 2022-04-03 05:58:45
pypath.inputs.talklr.talklr_interactions 2022-04-03 05:58:46 2022-04-03 05:58:46 0.05 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 {} 2022-04-03 05:58:46
pypath.inputs.talklr.talklr_raw 2022-04-03 05:58:46 2022-04-03 05:58:46 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 {} 2022-04-03 05:58:46
pypath.inputs.tcdb.tcdb_annotations 2022-04-03 05:58:46 2022-04-03 05:58:52 5.85 dict {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', tcid='1.F.1.1.1')}, 'O00299'...(truncated) 2,047 {'size': 1} 2022-04-03 05:58:46
pypath.inputs.tcdb.tcdb_classes 2022-04-03 05:58:52 2022-04-03 05:58:52 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) 21,882 {'size': 1} 2022-04-03 05:58:52
pypath.inputs.tcdb.tcdb_families 2022-04-03 05:58:52 2022-04-03 05:58:52 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) 1,666 {} 2022-04-03 05:58:52
pypath.inputs.tfcensus.tfcensus_annotations 2022-04-03 05:58:52 2022-04-03 05:58:53 0.42 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) 1,885 {} 2022-04-03 05:58:52
pypath.inputs.threedcomplex.threedcomplex_chains 2022-04-03 05:58:53 2022-04-03 05:59:00 7.28 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 {} 2022-04-03 05:58:53
pypath.inputs.threedcomplex.threedcomplex_contacts 2022-04-03 05:59:00 2022-04-03 05:59:53 53.53 set {ThreedcomplexContact(pdb='3sqg_1', uniprot_1='D1JBK3', uniprot_2='D1JBK4', chain_1='F', chain_2='D', n_residues=63.0, length_1=278, length_2=574, domain_s1=('55088',), domain_p1=('PF02240.11',), domain_s2=('55088', '48081'), domain_p2=('PF02745.10', 'PF02249.12'), ident=False, homo=False), Threedco...(truncated) 260,239 {} 2022-04-03 05:59:00
pypath.inputs.threedcomplex.threedcomplex_ddi 2022-04-03 05:59:54 2022-04-03 06:03:12 197.82 list [<pypath.internals.intera.DomainDomain object at 0x7f579051f5e0>, <pypath.internals.intera.DomainDomain object at 0x7f579051f400>, <pypath.internals.intera.DomainDomain object at 0x7f579051f5b0>, <pypath.internals.intera.DomainDomain object at 0x7f579051f6d0>, <pypath.internals.intera.DomainDomain o...(truncated) 525,428 {} 2022-04-03 05:59:54
pypath.inputs.threedcomplex.threedcomplex_nresidues 2022-04-03 06:03:13 2022-04-03 06:03:21 7.88 dict {'3sqg_1': {('D1JBK3', 'D1JBK4'): 64.0, ('D1JBK2', 'D1JBK4'): 22.0, ('D1JBK4', 'D1JBK4'): 115.0, ('D1JBK2', 'D1JBK3'): 55.5, ('D1JBK2', 'D1JBK2'): 33.0}, '2x86_4': {('P67911', 'P67911'): 16.0}, '3he3_6': {('Q9RYF1', 'Q9RYF1'): 21.0}, '5l6a_1': {('P25043', 'P30656'): 2.0, ('P23724', 'P30657'): 19.0, ...(truncated) 81,381 {} 2022-04-03 06:03:13
pypath.inputs.threedid.get_3did 2022-04-03 06:03:21 2022-04-03 06:34:39 1,877.82 tuple ([<pypath.internals.intera.DomainDomain object at 0x7f57a95d6220>, <pypath.internals.intera.DomainDomain object at 0x7f57a95d6f70>, <pypath.internals.intera.DomainDomain object at 0x7f57a95d6fd0>, <pypath.internals.intera.DomainDomain object at 0x7f57a95d6670>, <pypath.internals.intera.DomainDomain ...(truncated) 2 {} 2022-04-03 06:03:21
pypath.inputs.threedid.get_3did_ddi 2022-04-03 06:34:39 2022-04-03 06:35:10 30.93 dict {('Q13162', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}, ('PF00578', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}}, ('Q06830', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0...(truncated) 3,274,970 {} 2022-04-03 06:34:39
pypath.inputs.topdb.topdb_annotations 2022-04-03 06:36:18 2022-04-03 06:36:22 3.45 dict {'P05067': {TopdbAnnotation(membrane='Cytoplasm', topology='Outside', score=89, tmregions=1), TopdbAnnotation(membrane='Extracellular', topology='Signal', score=89, tmregions=1), TopdbAnnotation(membrane='Extracellular', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplas...(truncated) 1,245 {'size': 2} 2022-04-03 06:36:18
pypath.inputs.transmir.transmir_interactions 2022-04-03 06:36:22 2022-04-03 06:36:23 1.10 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 {} 2022-04-03 06:36:22
pypath.inputs.trip.take_a_trip 2022-04-03 06:36:23 2022-04-03 06:36:23 0.01 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 {} 2022-04-03 06:36:23
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 2022-04-03 06:36:23 2022-04-03 06:36:23 0.01 list [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;12601176;11290752', 'Calcium measurement;Fluorescence probe labeling;Fusion protein-pu...(truncated) 359 {} 2022-04-03 06:36:23
pypath.inputs.trip.trip_process 2022-04-03 06:36:23 2022-04-03 06:36:23 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 {} 2022-04-03 06:36:23
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
 {} never
pypath.inputs.unichem._unichem_mapping 
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_info 2022-04-03 06:36:23 2022-04-03 06:36:23 0.02 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='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) 41 {} 2022-04-03 06:36:23
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_sources 2022-04-03 06:36:23 2022-04-03 06:36:23 0.02 dict {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '11': 'ibm', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma'...(truncated) 41 {} 2022-04-03 06:36:23
pypath.inputs.uniprot._all_uniprots 2022-04-03 06:36:23 2022-04-03 06:36:23 0.05 set {'H0YD55', 'G3V4N8', 'H3BN68', 'Q6IBP4', 'L0EP99', 'A0A5C2G2P8', 'A4ZL80', 'Q549K4', 'K7ERC8', 'A0A678ZG40', 'A0A0C4DGK5', 'B3KVU0', 'A0A6H0MV12', 'A0A5H2UYU9', 'D3U3Y5', 'M0QXS6', 'A0A0G2JJL1', 'F8WCN2', 'W0GBI5', 'A0A7I2V498', 'C9JU26', 'F8VQX3', 'A0A5C2GBG5', 'H3BQM9', 'A0A0S2Z4T5', 'O95178', 'A0...(truncated) 204,185 {} 2022-04-03 06:36:23
pypath.inputs.uniprot._cleanup 2022-04-03 06:36:23 2022-04-03 06:36:23 0.00 NoneType None 0 {} 2022-04-03 06:36:23
pypath.inputs.uniprot._protein_datasheet 
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot._remove 
Not calling `pypath.inputs.uniprot._remove`, not enough arguments.
 {} never
pypath.inputs.uniprot._swissprot_param 
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments.
 {} never
pypath.inputs.uniprot.all_swissprots 2022-04-03 06:36:23 2022-04-03 06:36:23 0.00 set {'P0DI81', 'P61567', 'O95178', 'Q9Y2P5', 'Q6NSJ0', 'Q14582', 'Q7Z5L3', 'A6NJG6', 'A0A0A0MRZ7', 'Q86XD5', 'Q3MJ16', 'A1X283', 'Q5JNZ3', 'Q9BVK6', 'P31994', 'P0DN77', 'Q96IR3', 'Q8N5C1', 'Q15170', 'Q6ZRR7', 'A2VDJ0', 'Q86WH2', 'Q15291', 'P31949', 'O15287', 'O95399', 'Q9UIM3', 'P08185', 'P40425', 'Q8N6...(truncated) 20,376 {} 2022-04-03 06:36:23
pypath.inputs.uniprot.all_trembls 2022-04-03 06:36:23 2022-04-03 06:37:36 73.14 set {'H0YD55', 'G3V4N8', 'H3BN68', 'Q6IBP4', 'L0EP99', 'A0A5C2G2P8', 'A4ZL80', 'Q549K4', 'K7ERC8', 'A0A678ZG40', 'A0A0C4DGK5', 'B3KVU0', 'A0A6H0MV12', 'A0A5H2UYU9', 'D3U3Y5', 'M0QXS6', 'A0A0G2JJL1', 'F8WCN2', 'W0GBI5', 'A0A7I2V498', 'C9JU26', 'F8VQX3', 'A0A5C2GBG5', 'H3BQM9', 'A0A0S2Z4T5', 'A0A7L4X6Y0',...(truncated) 183,809 {} 2022-04-03 06:36:23
pypath.inputs.uniprot.all_uniprots 2022-04-03 06:37:36 2022-04-03 06:37:36 0.00 set {'H0YD55', 'G3V4N8', 'H3BN68', 'Q6IBP4', 'L0EP99', 'A0A5C2G2P8', 'A4ZL80', 'Q549K4', 'K7ERC8', 'A0A678ZG40', 'A0A0C4DGK5', 'B3KVU0', 'A0A6H0MV12', 'A0A5H2UYU9', 'D3U3Y5', 'M0QXS6', 'A0A0G2JJL1', 'F8WCN2', 'W0GBI5', 'A0A7I2V498', 'C9JU26', 'F8VQX3', 'A0A5C2GBG5', 'H3BQM9', 'A0A0S2Z4T5', 'O95178', 'A0...(truncated) 204,185 {} 2022-04-03 06:37:36
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
 {} never
pypath.inputs.uniprot.get_db 2022-04-03 06:37:36 2022-04-03 06:37:36 0.00 set {'H0YD55', 'G3V4N8', 'H3BN68', 'Q6IBP4', 'L0EP99', 'A0A5C2G2P8', 'A4ZL80', 'Q549K4', 'K7ERC8', 'A0A678ZG40', 'A0A0C4DGK5', 'B3KVU0', 'A0A6H0MV12', 'A0A5H2UYU9', 'D3U3Y5', 'M0QXS6', 'A0A0G2JJL1', 'F8WCN2', 'W0GBI5', 'A0A7I2V498', 'C9JU26', 'F8VQX3', 'A0A5C2GBG5', 'H3BQM9', 'A0A0S2Z4T5', 'O95178', 'A0...(truncated) 204,185 {} 2022-04-03 06:37:36
pypath.inputs.uniprot.get_uniprot_sec 2022-04-03 06:37:36 2022-04-03 06:37:37 0.72 list [['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R077', 'Q96S94'], ['A0A024R079', 'G3V1E2'], ['A0A024R081', 'J3QRY6'], ['A0A024R...(truncated) 71,902 {} 2022-04-03 06:37:36
pypath.inputs.uniprot.init_db 2022-04-03 06:37:37 2022-04-03 06:37:37 0.06 NoneType None 0 {} 2022-04-03 06:37:37
pypath.inputs.uniprot.is_swissprot 
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_trembl 
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_uniprot 
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.protein_datasheet 
Not calling `pypath.inputs.uniprot.protein_datasheet`, 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 2022-04-03 06:37:37 2022-04-03 06:37:49 12.39 dict {'P51451': {UniprotFamily(family='Protein kinase superfamily, Tyr protein kinase', subfamily='SRC')}, 'P09871': {UniprotFamily(family='Peptidase S1', subfamily=None)}, 'Q9ULX7': {UniprotFamily(family='Alpha-carbonic anhydrase', subfamily=None)}, 'Q01518': {UniprotFamily(family='CAP', subfamily=None)...(truncated) 14,355 {} 2022-04-03 06:37:37
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 2022-04-03 06:37:49 2022-04-03 06:37:57 7.08 dict {'P51451': {UniprotKeyword(keyword='Kinase'), UniprotKeyword(keyword='SH3 domain'), UniprotKeyword(keyword='ATP-binding'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Nucleotide-binding'), UniprotKeyword(keyword='Tyrosine-protein kinase'), UniprotKeyword(keyword='Reference proteome')...(truncated) 20,376 {} 2022-04-03 06:37:49
pypath.inputs.uniprot.uniprot_locations 2022-04-03 06:37:57 2022-04-03 06:38:05 8.17 dict {'P51451': {UniprotLocation(location='Cell membrane', features=('Lipid-anchor',))}, 'A6H8Y1': {UniprotLocation(location='Nucleus', features=None)}, 'O60885': {UniprotLocation(location='Nucleus', features=None), UniprotLocation(location='Chromosome', features=None)}, 'P22223': {UniprotLocation(locati...(truncated) 16,856 {} 2022-04-03 06:37:57
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2022-04-03 06:38:05 2022-04-03 06:38:05 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) 26,873 {} 2022-04-03 06:38:05
pypath.inputs.uniprot.uniprot_preprocess 
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, 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 2022-04-03 06:38:05 2022-04-03 06:38:13 8.46 dict {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'H8ZM71': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'Q9MV51': {'Momi fir', 'Abies firma'}, 'O81086': {'Grand fir', 'Pinus grandis', 'Abie...(truncated) 552,780 {} 2022-04-03 06:38:05
pypath.inputs.uniprot.uniprot_tissues 2022-04-03 06:38:14 2022-04-03 06:38:22 8.00 dict {'P51451': {UniprotTissue(tissue='Leydig cells', level='undefined'), UniprotTissue(tissue='Hair follicles', level='undefined'), UniprotTissue(tissue='Striate ducts of salivary glands', level='undefined'), UniprotTissue(tissue='Lymphatic organs', level='undefined'), UniprotTissue(tissue='Pancreatic i...(truncated) 9,938 {} 2022-04-03 06:38:14
pypath.inputs.uniprot.uniprot_topology 2022-04-03 06:38:22 2022-04-03 06:38:49 26.71 dict {'P22223': {UniprotTopology(topology='Transmembrane', start=655, end=677), UniprotTopology(topology='Cytoplasmic', start=678, end=829), UniprotTopology(topology='Extracellular', start=108, end=654)}, 'Q9ULX7': {UniprotTopology(topology='Transmembrane', start=291, end=311), UniprotTopology(topology='...(truncated) 5,217 {} 2022-04-03 06:38:22
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
 {} never
pypath.inputs.wang.get_hsn 2022-04-03 06:38:49 2022-04-03 06:38:51 1.99 list [['1909', 'EDNRA', '4683', 'NBN', 'Pos'], ['7040', 'TGFB1', '7040', 'TGFB1', 'Neg'], ['9669', 'EIF5B', '6135', 'RPL11', 'Pos'], ['367', 'AR', '7337', 'UBE3A', 'Phy'], ['5291', 'PIK3CB', '57580', 'PREX1', 'Pos'], ['5568', 'PRKACG', '1499', 'CTNNB1', 'Pos'], ['156', 'ADRBK1', '155', 'ADRB3', 'Pos'], [...(truncated) 62,937 {} 2022-04-03 06:38:49
pypath.inputs.wang.wang_interactions 2022-04-03 06:38:51 2022-04-03 06:38:51 0.78 list [['EDNRA', 'NBN', '+'], ['TGFB1', 'TGFB1', '-'], ['EIF5B', 'RPL11', '+'], ['AR', 'UBE3A', '0'], ['PIK3CB', 'PREX1', '+'], ['PRKACG', 'CTNNB1', '+'], ['ADRBK1', 'ADRB3', '+'], ['ITGA2B', 'ACTN4', '0'], ['MCM7', 'UBE3A', '-'], ['CD4', 'ITK', '+'], ['STAT3', 'MYC', '+'], ['ZBTB17', 'NDRG2', '-'], ['CSN...(truncated) 62,937 {} 2022-04-03 06:38:51
pypath.inputs.wojtowicz2020._id_translate 
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments.
 {} never
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2022-04-03 06:38:52 2022-04-03 06:38:53 1.56 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 {} 2022-04-03 06:38:52
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2022-04-03 06:38:53 2022-04-03 06:38:53 0.06 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 {} 2022-04-03 06:38:53
pypath.inputs.zhong2015.zhong2015_annotations 2022-04-03 06:38:53 2022-04-03 06:38:53 0.22 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 {} 2022-04-03 06:38:53

The OmniPath Team • Saez Lab • 2022-04-03