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 2022-02-25 00:13:02 and 2022-02-25 00:25:16; pypath version: 0.14.2 (from git; d333068 )
| Modules collected: | 16 |
|---|---|
| Modules failed to import: | 0 |
| Functions collected: | 32 |
| Functions run without error: | 28 |
| Functions returned empty value: | 1 |
| Functions skipped due to lack of arguments: | 4 |
| Functions run with error: | 0 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2022-02-25 00:13:08 | 2022-02-25 00:13:09 | 0.56 | 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 | {} | 2022-02-25 00:13:08 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2022-02-25 00:13:09 | 2022-02-25 00:13:09 | 0.62 | 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 | {} | 2022-02-25 00:13:09 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2022-02-25 00:13:09 | 2022-02-25 00:13:10 | 0.51 | 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 | {} | 2022-02-25 00:13:09 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2022-02-25 00:13:10 | 2022-02-25 00:15:10 | 119.60 | 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 | {} | 2022-02-25 00:13:10 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2022-02-25 00:15:10 | 2022-02-25 00:15:10 | 0.23 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2022-02-25 00:15:10 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2022-02-25 00:15:10 | 2022-02-25 00:15:12 | 1.87 | 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) | 4,827 | {} | 2022-02-25 00:15:10 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2022-02-25 00:15:12 | 2022-02-25 00:23:26 | 494.43 | dict | {'P01023': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q07954': {Baccin2019Annotation(mainclass='receptor', subclass='growth_factor_receptor', location=None), Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'P48960': {Baccin2019Annot...(truncated) | 1,063 | {} | 2022-02-25 00:15:12 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2022-02-25 00:23:26 | 2022-02-25 00:23:28 | 1.48 | list | [Baccin2019Interaction(ligand='P01023', receptor='Q07954', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Baccin2019', 'Ramilowski2015'}, references={'10652313', '12194978', '1702392'}), Baccin2019Interaction(ligand='P48960', receptor='P08174', correct='Correct',...(truncated) | 1,739 | {} | 2022-02-25 00:23:26 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2022-02-25 00:23:28 | 2022-02-25 00:23:28 | 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 | {} | 2022-02-25 00:23:28 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2022-02-25 00:23:28 | 2022-02-25 00:24:02 | 34.91 | 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 | {} | 2022-02-25 00:23:28 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2022-02-25 00:24:03 | 2022-02-25 00:24:12 | 8.71 | list | [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridInteraction(partner_a='CDKN3', partner_b='CDK2', pmid='12745075'), BiogridInteraction(partner_a='PPARGC1B', partner_b='ESR1', pmid='11854298'), Biog...(truncated) | 6,582 | {} | 2022-02-25 00:24:03 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2022-02-25 00:24:12 | 2022-02-25 00:24:50 | 38.04 | 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 | {} | 2022-02-25 00:24:12 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2022-02-25 00:24:50 | 2022-02-25 00:24:54 | 3.28 | list | [{'vendor': 'PHALANX', 'type': 'OLIGO', 'description': None, 'format': 'EXPRESSION', 'array': 'OneArray', 'label': 'PHALANX OneArray'}, {'format': 'EXPRESSION', 'array': 'CODELINK', 'vendor': 'CODELINK', 'type': 'OLIGO', 'description': None, 'label': 'CODELINK CODELINK'}, {'description': None, 'type...(truncated) | 38 | {} | 2022-02-25 00:24:50 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2022-02-25 00:24:54 | 2022-02-25 00:24:57 | 3.05 | 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 | {} | 2022-02-25 00:24:54 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2022-02-25 00:24:57 | 2022-02-25 00:24:57 | 0.87 | 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 | {'fixed': True} | 2022-02-25 00:24:57 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations | 2022-02-25 00:24:57 | 2022-02-25 00:25:06 | 8.86 | 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 | {} | 2022-02-25 00:24:57 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_download | 2022-02-25 00:25:06 | 2022-02-25 00:25:06 | 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 | {} | 2022-02-25 00:25:06 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions | 2022-02-25 00:25:06 | 2022-02-25 00:25:07 | 0.31 | 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 | {} | 2022-02-25 00:25:06 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2022-02-25 00:25:07 | 2022-02-25 00:25:07 | 0.13 | 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 | {} | 2022-02-25 00:25:07 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2022-02-25 00:25:07 | 2022-02-25 00:25:07 | 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 | {} | 2022-02-25 00:25:07 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2022-02-25 00:25:07 | 2022-02-25 00:25:07 | 0.12 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P30281', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 2,378 | {} | 2022-02-25 00:25:07 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2022-02-25 00:25:07 | 2022-02-25 00:25:09 | 2.43 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,246 | {} | 2022-02-25 00:25:07 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2022-02-25 00:25:09 | 2022-02-25 00:25:11 | 1.87 | dict | {'P61278': {CellcallAnnotation(role='ligand')}, 'P30872': {CellcallAnnotation(role='receptor')}, 'P01236': {CellcallAnnotation(role='ligand')}, 'P16471': {CellcallAnnotation(role='receptor')}, 'Q9NRA1': {CellcallAnnotation(role='ligand')}, 'P35916': {CellcallAnnotation(role='receptor')}, 'P01583': {...(truncated) | 460 | {} | 2022-02-25 00:25:09 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2022-02-25 00:25:11 | 2022-02-25 00:25:11 | 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 | {} | 2022-02-25 00:25:11 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2022-02-25 00:25:11 | 2022-02-25 00:25:13 | 1.84 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2022-02-25 00:25:11 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2022-02-25 00:25:13 | 2022-02-25 00:25:15 | 1.31 | list | [CellcallInteraction(ligand_uniprot='P61278', receptor_uniprot='P30872', core=True), CellcallInteraction(ligand_uniprot='P01236', receptor_uniprot='P16471', core=True), CellcallInteraction(ligand_uniprot='Q9NRA1', receptor_uniprot='P35916', core=True), CellcallInteraction(ligand_uniprot='P01583', re...(truncated) | 797 | {} | 2022-02-25 00:25:13 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2022-02-25 00:25:15 | 2022-02-25 00:25:15 | 0.79 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), Cellcellinteractions...(truncated) | 3,427 | {} | 2022-02-25 00:25:15 |
The OmniPath Team • Saez Lab • 2022-02-25