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 2021-11-23 00:20:02 and 2021-11-23 03:13:00; pypath version: 0.13.11 (from git; fc45b2b )
| Modules collected: | 146 |
|---|---|
| Modules failed to import: | 0 |
| Functions collected: | 461 |
| Functions run without error: | 319 |
| Functions returned empty value: | 8 |
| Functions skipped due to lack of arguments: | 118 |
| Functions run with error: | 24 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | |
|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2021-11-23 00:20:07 | 2021-11-23 00:20:08 | 0.57 | 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 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2021-11-23 00:20:08 | 2021-11-23 00:20:08 | 0.51 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2021-11-23 00:20:08 | 2021-11-23 00:20:09 | 0.33 | 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 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2021-11-23 00:20:09 | 2021-11-23 00:24:02 | 232.99 | defaultdict | defaultdict(<class 'set'>, {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclas...(truncated) | 239 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2021-11-23 00:24:02 | 2021-11-23 00:24:02 | 0.32 | 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 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2021-11-23 00:24:02 | 2021-11-23 00:24:04 | 2.11 | defaultdict | defaultdict(<class 'set'>, {'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_transme...(truncated) | 4,827 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2021-11-23 00:24:04 | 2021-11-23 00:31:24 | 440.37 | dict | {'P01023': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q07954': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None), Baccin2019Annotation(mainclass='receptor', subclass='growth_factor_receptor', location=None)}, 'P48960': {Baccin2019Annot...(truncated) | 1,055 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2021-11-23 00:31:24 | 2021-11-23 00:31:26 | 1.29 | 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) | 1,708 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2021-11-23 00:31:26 | 2021-11-23 00:31:26 | 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 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
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| ¶ | pypath.inputs.biogps.biogps_download_all | 2021-11-23 00:31:26 | 2021-11-23 00:32:02 | 36.17 | 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 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2021-11-23 00:32:03 | 2021-11-23 00:32:09 | 6.44 | 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) | 6,466 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2021-11-23 00:32:09 | 2021-11-23 00:32:43 | 33.66 | 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) | 168,975 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
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| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2021-11-23 00:32:43 | 2021-11-23 00:32:43 | 0.20 | list | [{'description': None, 'format': 'EXPRESSION', 'array': 'OneArray', 'type': 'OLIGO', 'vendor': 'PHALANX', 'label': 'PHALANX OneArray'}, {'array': 'CODELINK', 'vendor': 'CODELINK', 'type': 'OLIGO', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'array': 'HumanWG_6_V2', '...(truncated) | 37 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
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| ¶ | pypath.inputs.ca1.ca1_interactions | 2021-11-23 00:32:43 | 2021-11-23 00:32:46 | 3.09 | 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 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2021-11-23 00:32:46 | 2021-11-23 00:32:47 | 0.84 | 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 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations | 2021-11-23 00:32:47 | 2021-11-23 00:32:55 | 8.09 | defaultdict | defaultdict(<class 'set'>, {'46220502': {CancerDrugsAnnotation(label='Abemaciclib', indications='Advanced Breast Cancer; Metastatic Breast Cancer', last_updated='17/09/2020')}, '132971': {CancerDrugsAnnotation(label='Abiraterone', indications='Metastatic Castration Resistant Prostate Cancer', last_u...(truncated) | 197 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_download | 2021-11-23 00:32:55 | 2021-11-23 00:32:55 | 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) | 282 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions | 2021-11-23 00:32:55 | 2021-11-23 00:32:56 | 0.25 | 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) | 2,181 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2021-11-23 00:32:56 | 2021-11-23 00:32:57 | 1.73 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,246 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
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| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2021-11-23 00:32:57 | 2021-11-23 00:32:59 | 1.67 | dict | {'P55103': {CellcallAnnotation(role='ligand')}, 'Q13705': {CellcallAnnotation(role='receptor')}, 'O15467': {CellcallAnnotation(role='ligand')}, 'P51681': {CellcallAnnotation(role='receptor')}, 'P52803': {CellcallAnnotation(role='ligand')}, 'P29317': {CellcallAnnotation(role='receptor')}, 'P13501': {...(truncated) | 460 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2021-11-23 00:32:59 | 2021-11-23 00:32:59 | 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 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2021-11-23 00:32:59 | 2021-11-23 00:33:00 | 0.91 | 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 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2021-11-23 00:33:00 | 2021-11-23 00:33:01 | 1.32 | list | [CellcallInteraction(ligand_uniprot='P55103', receptor_uniprot='Q13705', core=True), CellcallInteraction(ligand_uniprot='O15467', receptor_uniprot='P51681', core=True), CellcallInteraction(ligand_uniprot='P52803', receptor_uniprot='P29317', core=True), CellcallInteraction(ligand_uniprot='P13501', re...(truncated) | 797 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2021-11-23 00:33:01 | 2021-11-23 00:33:02 | 0.79 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinterac...(truncated) | 3,427 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2021-11-23 00:33:03 | 2021-11-23 00:33:03 | 0.00 | int | 9606 | None | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
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| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
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| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2021-11-23 00:33:03 | 2021-11-23 00:33:11 | 8.06 | defaultdict | defaultdict(<class 'set'>, {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='agonist'...(truncated) | 1,067 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2021-11-23 00:33:11 | 2021-11-23 00:33:16 | 5.16 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O60565', 'P12645', 'P41271', 'Q9H772', 'O75610', 'Q9H2X0', 'Q13253', 'O00292'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 31 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2021-11-23 00:33:16 | 2021-11-23 00:33:21 | 5.14 | 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 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2021-11-23 00:33:21 | 2021-11-23 00:33:27 | 5.82 | 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 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2021-11-23 00:33:27 | 2021-11-23 00:33:33 | 5.30 | list | [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) | 11,113 | |
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2021-11-23 00:33:33 | 2021-11-23 00:33:33 | 0.34 | 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 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
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| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2021-11-23 00:33:33 | 2021-11-23 00:33:34 | 0.65 | dict | {'P10915': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'Q8TDY8': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type...(truncated) | 1,921 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2021-11-23 00:33:34 | 2021-11-23 00:33:34 | 0.54 | dict | {Complex: COMPLEX:P05107_P11215: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion')}, Complex: COMPLEX:O75581_Q9ULW2: {CellinkerAnnotation(role='receptor', locati...(truncated) | 134 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2021-11-23 00:33:34 | 2021-11-23 00:33:34 | 0.02 | 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 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2021-11-23 00:33:34 | 2021-11-23 00:33:34 | 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 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2021-11-23 00:33:34 | 2021-11-23 00:33:35 | 0.54 | set | {CellinkerInteraction(ligand='P10915', receptor='Q8TDY8', ligand_location='Secreted', receptor_location='Membrane', resources=None, pmids='32822567', type='Secreted protein to receptor interaction'), CellinkerInteraction(ligand='P49765', receptor='P17948', ligand_location='Secreted', receptor_locati...(truncated) | 3,812 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2021-11-23 00:33:35 | 2021-11-23 00:33:35 | 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 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2021-11-23 00:33:35 | 2021-11-23 00:33:35 | 0.55 | dict | {'P10915': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'Q8TDY8': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type...(truncated) | 1,787 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2021-11-23 00:33:35 | 2021-11-23 00:33:36 | 0.21 | set | {CellinkerInteraction(ligand='681', receptor='P21918', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='1826762', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='6262', receptor='Q5T6X5', ligand_location=None, receptor_location='Membrane', resource...(truncated) | 315 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2021-11-23 00:33:36 | 2021-11-23 00:33:36 | 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 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
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| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
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| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
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| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
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| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2021-11-23 00:33:36 | 2021-11-23 00:33:36 | 0.24 | 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 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2021-11-23 00:33:36 | 2021-11-23 00:33:36 | 0.02 | 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 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2021-11-23 00:33:36 | 2021-11-23 00:33:36 | 0.58 | 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 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2021-11-23 00:33:36 | 2021-11-23 00:33:37 | 0.05 | tuple | ({'P48645', 'P01583', 'Q9ULZ1', 'Q99983', 'P04808', 'Q9NZH7', 'P25063', 'Q16552', 'P20333', 'P23510', 'P15509', 'P14735', 'O43914', Complex IL23: COMPLEX:P29460_Q9NPF7, 'O60462', 'P29320', 'Q969D9', 'Q15109', Complex IL35: COMPLEX:P29459_Q14213, 'P00533', 'P03971', 'P16410', 'P13725', Complex aEb7 c...(truncated) | 2 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2021-11-23 00:33:37 | 2021-11-23 00:33:37 | 0.04 | 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 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2021-11-23 00:33:37 | 2021-11-23 00:33:48 | 11.82 | defaultdict | defaultdict(<class 'set'>, {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='26156437')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='recep...(truncated) | 1,598 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2021-11-23 00:33:48 | 2021-11-23 00:33:48 | 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 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2021-11-23 00:33:48 | 2021-11-23 00:33:48 | 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 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2021-11-23 00:33:48 | 2021-11-23 00:33:52 | 3.73 | 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) | 9,694 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2021-11-23 00:33:52 | 2021-11-23 00:33:52 | 0.06 | 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 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2021-11-23 00:33:52 | 2021-11-23 00:34:39 | 46.67 | 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) | 1,191 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2021-11-23 00:34:39 | 2021-11-23 00:35:33 | 54.24 | 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) | 591,025 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2021-11-23 00:35:33 | 2021-11-23 00:36:29 | 55.82 | dict | {'Q8TES7': {ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='membrane', score=0.96), ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation...(truncated) | 18,233 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2021-11-23 00:36:29 | 2021-11-23 00:36:30 | 0.49 | 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 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2021-11-23 00:36:30 | 2021-11-23 00:36:30 | 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 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2021-11-23 00:36:30 | 2021-11-23 00:36:30 | 0.47 | 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 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2021-11-23 00:36:30 | 2021-11-23 00:36:33 | 2.49 | 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) | 725 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2021-11-23 00:36:33 | 2021-11-23 00:36:39 | 5.99 | defaultdict | defaultdict(<class 'set'>, {'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 cyto...(truncated) | 1,036 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2021-11-23 00:36:39 | 2021-11-23 00:36:39 | 0.06 | tuple | (defaultdict(<class 'set'>, {'Glioma': {CpadPathwayCancer(pathway='5-LO/LTA4 hydrolase pathway', cancer='Glioma', pathway_category='Others', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='partial suppression of tumor growth'), CpadPathwayCancer(pathway='Akt/mTOR signaling pathway', cancer=...(truncated) | 2 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2021-11-23 00:36:39 | 2021-11-23 00:36:39 | 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 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2021-11-23 00:36:39 | 2021-11-23 00:36:41 | 2.08 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2021-11-23 00:36:41 | 2021-11-23 00:36:43 | 2.27 | 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 | |
| ¶ | pypath.inputs.cspa.cspa_annotations | 2021-11-23 00:36:44 | 2021-11-23 00:36:45 | 1.18 | 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 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2021-11-23 00:36:45 | 2021-11-23 00:36:48 | 2.57 | dict | {'A1A5B4': {CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='NK', value=16.32343),...(truncated) | 1,407 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2021-11-23 00:36:48 | 2021-11-23 00:36:51 | 3.02 | dict | {'A431': defaultdict(<class 'dict'>, {'A1A5B4': 16.56885, 'A1A5C7': None, 'P0DN37': None, 'A0A0B4J2A2': 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, 'O0011...(truncated) | 47 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2021-11-23 00:36:51 | 2021-11-23 00:36:52 | 1.36 | 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 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2021-11-23 00:36:52 | 2021-11-23 00:36:56 | 3.51 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/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'
|
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| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2021-11-23 00:36:56 | 2021-11-23 00:36:57 | 1.41 | 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 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2021-11-23 00:36:57 | 2021-11-23 00:36:59 | 1.25 | list | [] | 0 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2021-11-23 00:36:59 | 2021-11-23 00:36:59 | 0.16 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2021-11-23 00:36:59 | 2021-11-23 00:36:59 | 0.13 | 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 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2021-11-23 00:36:59 | 2021-11-23 00:36:59 | 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 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2021-11-23 00:36:59 | 2021-11-23 00:37:01 | 2.55 | defaultdict | defaultdict(<class 'set'>, {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069'...(truncated) | 10,494 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2021-11-23 00:37:01 | 2021-11-23 00:38:06 | 64.26 | set | {'Q8IXE1', 'P48145', 'Q8IYR2', 'O75317', 'Q8TE77', 'Q5TCX8', 'Q96LD4', 'P48595', 'Q16552', 'Q8NEX6', 'P13631', 'P51582', 'Q9UNA1', 'P42262', 'Q8NGR4', 'Q96GM5', 'Q9UIQ6', 'Q7KZI7', 'O00408', 'A0A0C4DH33', 'O95868', 'Q14028', 'P19835', 'Q8TE57', 'Q6PRD1', 'Q6P3R8', 'Q8NH64', 'Q96P09', 'O75908', 'O756...(truncated) | 5,987 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2021-11-23 00:38:06 | 2021-11-23 00:38:06 | 0.29 | 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 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
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| ¶ | pypath.inputs.disgenet.disgenet_annotations | 2021-11-23 00:38:06 | 2021-11-23 00:38:11 | 4.57 | defaultdict | defaultdict(<class 'set'>, {'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, sour...(truncated) | 9,202 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2021-11-23 00:38:11 | 2021-11-23 00:38:16 | 5.37 | list | [<pypath.internals.intera.DomainDomain object at 0x7f4e5b4574c0>, <pypath.internals.intera.DomainDomain object at 0x7f4e5b457460>, <pypath.internals.intera.DomainDomain object at 0x7f4e5b457b20>, <pypath.internals.intera.DomainDomain object at 0x7f4e544e0850>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2021-11-23 00:38:16 | 2021-11-23 00:38:17 | 1.15 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f4e544e7b20>, <pypath.internals.intera.DomainDomain object at 0x7f4e544e7f40>, <pypath.internals.intera.DomainDomain object at 0x7f4e544e78b0>, <pypath.internals.intera.DomainDomain object at 0x7f4e5b2c0b50>, <pypath.internals.intera.Domain...(truncated) | 2 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2021-11-23 00:38:17 | 2021-11-23 00:38:18 | 0.39 | 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 | |
| ¶ | pypath.inputs.domino.get_domino | 2021-11-23 00:38:18 | 2021-11-23 00:38:18 | 0.37 | 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 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
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| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2021-11-23 00:38:18 | 2021-11-23 00:38:26 | 7.94 | 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 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2021-11-23 00:38:26 | 2021-11-23 00:38:34 | 7.65 | list | [DorotheaInteraction(tf='AHR', target='ASAP1', effect=0, level='B', curated=False, chipseq=True, predicted=True, coexp=True, curated_sources='', chipseq_sources='ReMap', predicted_sources='HOCOMOCO', coexp_sources='ARACNe-GTEx', all_sources='ReMap,HOCOMOCO,ARACNe-GTEx', pubmed='', kegg_pathways=''),...(truncated) | 15,252 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2021-11-23 00:38:34 | 2021-11-23 00:38:34 | 0.25 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 619, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
|||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2021-11-23 00:38:34 | 2021-11-23 00:38:34 | 0.10 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 619, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
|||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2021-11-23 00:38:34 | 2021-11-23 00:38:36 | 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 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2021-11-23 00:38:36 | 2021-11-23 00:38:36 | 0.33 | 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 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2021-11-23 00:38:36 | 2021-11-23 00:38:38 | 1.24 | 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 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2021-11-23 00:38:38 | 2021-11-23 00:38:45 | 7.59 | list | [DorotheaInteraction(tf='AHR', target='ASAP1', effect=0, level='B', curated=False, chipseq=True, predicted=True, coexp=True, curated_sources='', chipseq_sources='ReMap', predicted_sources='HOCOMOCO', coexp_sources='ARACNe-GTEx', all_sources='ReMap,HOCOMOCO,ARACNe-GTEx', pubmed='', kegg_pathways=''),...(truncated) | 15,252 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2021-11-23 00:38:45 | 2021-11-23 00:38:45 | 0.13 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 619, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/dorothea.py", line 213, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
|||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
||||||
| ¶ | pypath.inputs.elm.elm_classes | 2021-11-23 00:38:45 | 2021-11-23 00:38:58 | 13.04 | 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 | |
| ¶ | pypath.inputs.elm.elm_domains | 2021-11-23 00:38:58 | 2021-11-23 00:38:59 | 0.86 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')]}} | 2 | |
| ¶ | pypath.inputs.elm.elm_instances | 2021-11-23 00:38:59 | 2021-11-23 00:42:11 | 192.16 | list | [ELMInstance(accession='Accession', type='ELMType', identifier='ELMIdentifier', uniprot_id='ProteinName', uniprot='Primary_Acc', synonyms='Accessions', start='Start', end='End', references='References', methods='Methods', logic='InstanceLogic', pdb='PDB', organism='Organism'), ELMInstance(accession=...(truncated) | 3,935 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2021-11-23 00:42:11 | 2021-11-23 00:43:23 | 71.59 | 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 | |
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2021-11-23 00:43:23 | 2021-11-23 00:43:25 | 2.31 | dict | {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'Q07954': {EmbraceAnnotation(mainclass='receptor', neuron=True, mural_cell=False, microglia=True, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neu...(truncated) | 942 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2021-11-23 00:43:25 | 2021-11-23 00:43:26 | 0.26 | 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) | 1,688 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2021-11-23 00:43:26 | 2021-11-23 00:43:26 | 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 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2021-11-23 00:43:26 | 2021-11-23 00:43:26 | 0.26 | 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) | 1,770 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2021-11-23 00:43:26 | 2021-11-23 00:43:27 | 0.72 | 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 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2021-11-23 00:43:27 | 2021-11-23 00:43:27 | 0.61 | 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) | 310 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2021-11-23 00:43:27 | 2021-11-23 00:43:38 | 10.35 | 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 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2021-11-23 00:43:38 | 2021-11-23 00:43:38 | 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 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2021-11-23 00:43:38 | 2021-11-23 00:44:34 | 56.62 | 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 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
||||||
| ¶ | pypath.inputs.go.get_go_quick | 2021-11-23 00:44:34 | 2021-11-23 00:44:35 | 0.43 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 848, in get_go_quick
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
|||
| ¶ | pypath.inputs.go.get_goslim | 2021-11-23 00:44:35 | 2021-11-23 00:44:36 | 0.75 | list | ['GO:0000003', 'GO:0000228', 'GO:0000278', 'GO:0000902', 'GO:0002376', 'GO:0003013', 'GO:0003674', 'GO:0003677', 'GO:0003700', 'GO:0003723', 'GO:0003729', 'GO:0003735', 'GO:0003924', 'GO:0004386', 'GO:0004518', 'GO:0005198', 'GO:0005575', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005622', 'GO:0...(truncated) | 145 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2021-11-23 00:44:36 | 2021-11-23 00:58:50 | 854.59 | dict | {'C': defaultdict(<class 'set'>, {'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0110165', 'is_a'), ('GO:0030694', 'part_of')},...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2021-11-23 00:58:50 | 2021-11-23 00:58:54 | 3.35 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 139, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
|||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2021-11-23 00:58:54 | 2021-11-23 00:58:57 | 3.65 | dict | {'C': defaultdict(<class 'set'>, {'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0110165', 'is_a'), ('GO:0030694', 'part_of')},...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2021-11-23 00:58:57 | 2021-11-23 00:59:00 | 2.80 | dict | {'C': defaultdict(<class 'set'>, {'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'}, 'A0A...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2021-11-23 00:59:00 | 2021-11-23 00:59:01 | 1.09 | dict | {'C': defaultdict(<class 'set'>, {'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'}, 'A0A...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2021-11-23 00:59:01 | 2021-11-23 00:59:04 | 2.76 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 783, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
|||
| ¶ | pypath.inputs.go.go_annotations_solr | 2021-11-23 00:59:04 | 2021-11-23 00:59:05 | 0.97 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 669, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2021-11-23 00:59:05 | 2021-11-23 00:59:12 | 7.32 | dict | {'Entry': ['Gene ontology IDs'], 'Q96NG5': ['GO:0000122', 'GO:0000977', 'GO:0000981', 'GO:0001227', 'GO:0005634', 'GO:0006357', 'GO:0046872'], 'Q6ZN19': ['GO:0000978', 'GO:0001228', 'GO:0005634', 'GO:0006357', 'GO:0046872'], 'Q9UI25': [''], 'Q86XN6': ['GO:0000978', 'GO:0000981', 'GO:0005634', 'GO:00...(truncated) | 20,376 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2021-11-23 00:59:12 | 2021-11-23 00:59:16 | 3.46 | dict | {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0032398', 'is_a'), ('GO:0042612', 'is_a'), ('GO:0042613', '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 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2021-11-23 00:59:16 | 2021-11-23 00:59:19 | 2.68 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 211, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 139, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
|||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2021-11-23 00:59:19 | 2021-11-23 00:59:22 | 3.44 | dict | {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0032398', 'is_a'), ('GO:0042612', 'is_a'), ('GO:0042613', '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 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2021-11-23 00:59:22 | 2021-11-23 00:59:25 | 2.76 | dict | {'C': {'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:0030694': 'bacterial-type flagellum basal body, rod...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2021-11-23 00:59:25 | 2021-11-23 00:59:28 | 2.63 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 507, in go_terms_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
|||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2021-11-23 00:59:28 | 2021-11-23 00:59:30 | 2.78 | dict | {'C': {'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:0030694': 'bacterial-type flagellum basal body, rod...(truncated) | 3 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2021-11-23 00:59:30 | 2021-11-23 00:59:31 | 0.63 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/go.py", line 365, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2021-11-23 00:59:31 | 2021-11-23 00:59:31 | 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 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2021-11-23 00:59:31 | 2021-11-23 00:59:32 | 0.93 | 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 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2021-11-23 00:59:32 | 2021-11-23 00:59:36 | 4.23 | 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 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.havugimana.get_havugimana | 2021-11-23 00:59:36 | 2021-11-23 00:59:38 | 1.63 | 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 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2021-11-23 00:59:38 | 2021-11-23 00:59:38 | 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 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2021-11-23 00:59:38 | 2021-11-23 00:59:48 | 10.27 | defaultdict | defaultdict(<class 'set'>, {'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')}...(truncated) | 14,970 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2021-11-23 00:59:48 | 2021-11-23 01:00:01 | 12.97 | list | [HippieInteraction(id_a='P43686', id_b='P62191', score=0.99, methods=None, references=('17353931', '19490896', '20810900', '21628461', '22275368', '22863883', '22939629', '26344197', '26496610', '28292943', '28514442'), sources=None, organisms=None), HippieInteraction(id_a='P63208', id_b='P38936', s...(truncated) | 39,728 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2021-11-23 01:00:01 | 2021-11-23 01:00:01 | 0.04 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2021-11-23 01:00:01 | 2021-11-23 01:03:11 | 189.52 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2021-11-23 01:03:11 | 2021-11-23 01:03:11 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2021-11-23 01:03:11 | 2021-11-23 01:03:11 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/hpmr.py", line 354, in hpmr_complexes
for cplex in hpmr_data['complexes']
KeyError: 'complexes'
|
|||
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2021-11-23 01:03:11 | 2021-11-23 01:03:11 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2021-11-23 01:03:11 | 2021-11-23 01:03:17 | 6.29 | 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 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2021-11-23 01:03:17 | 2021-11-23 01:03:19 | 1.67 | 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 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2021-11-23 01:03:19 | 2021-11-23 01:03:21 | 1.63 | 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 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2021-11-23 01:03:21 | 2021-11-23 01:03:22 | 1.39 | 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 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2021-11-23 01:03:22 | 2021-11-23 01:03:26 | 3.87 | 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 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2021-11-23 01:03:26 | 2021-11-23 01:03:28 | 1.55 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,371 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2021-11-23 01:03:28 | 2021-11-23 01:03:30 | 2.09 | 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) | 6,943 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2021-11-23 01:03:30 | 2021-11-23 01:03:31 | 1.50 | 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) | 4,495 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2021-11-23 01:03:31 | 2021-11-23 01:03:33 | 2.06 | 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 | |
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2021-11-23 01:03:33 | 2021-11-23 01:03:45 | 11.99 | 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 | |
| ¶ | pypath.inputs.huri.hi_iii_old | 2021-11-23 01:03:45 | 2021-11-23 01:03:45 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 619, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/huri.py", line 94, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
|||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2021-11-23 01:03:45 | 2021-11-23 01:04:20 | 34.76 | list | [HuriInteraction(uniprot_a='P0DP25', uniprot_b='Q9H0B3', isoform_a=1, isoform_b=1, score=0.899116271005), HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0....(truncated) | 231,004 | |
| ¶ | pypath.inputs.huri.huri_interactions | 2021-11-23 01:04:20 | 2021-11-23 01:04:55 | 35.31 | list | [HuriInteraction(uniprot_a='P0DP25', uniprot_b='Q9H0B3', isoform_a=1, isoform_b=1, score=0.899116271005), HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0....(truncated) | 167,638 | |
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2021-11-23 01:04:55 | 2021-11-23 01:04:56 | 0.94 | 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 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2021-11-23 01:04:56 | 2021-11-23 01:04:57 | 0.68 | 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 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2021-11-23 01:04:57 | 2021-11-23 01:06:07 | 70.02 | 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) | 13,675 | |
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2021-11-23 01:06:07 | 2021-11-23 01:06:11 | 4.24 | 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 | |
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2021-11-23 01:06:11 | 2021-11-23 01:06:13 | 1.47 | 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 | |
| ¶ | pypath.inputs.huri.yu2011_interactions | 2021-11-23 01:06:13 | 2021-11-23 01:06:16 | 3.31 | 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 | |
| ¶ | pypath.inputs.i3d.get_i3d | 2021-11-23 01:06:16 | 2021-11-23 01:06:21 | 4.89 | 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 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2021-11-23 01:06:21 | 2021-11-23 01:06:21 | 0.33 | defaultdict | defaultdict(<class 'set'>, {'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': {I...(truncated) | 688 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2021-11-23 01:06:21 | 2021-11-23 01:06:21 | 0.10 | 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 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2021-11-23 01:06:21 | 2021-11-23 01:06:21 | 0.10 | 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 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2021-11-23 01:06:22 | 2021-11-23 01:06:23 | 1.65 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/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
|
|||
| ¶ | pypath.inputs.imweb.get_imweb | 2021-11-23 01:06:23 | 2021-11-23 01:06:23 | 0.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/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)
|
|||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2021-11-23 01:06:23 | 2021-11-23 01:06:24 | 0.61 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/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)
|
|||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2021-11-23 01:06:24 | 2021-11-23 01:06:26 | 1.82 | 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 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2021-11-23 01:06:26 | 2021-11-23 01:06:28 | 2.26 | 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 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2021-11-23 01:06:28 | 2021-11-23 01:06:29 | 0.50 | 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 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2021-11-23 01:06:29 | 2021-11-23 01:07:15 | 45.98 | list | [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, mi_score='0.77', isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}...(truncated) | 70,176 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2021-11-23 01:07:15 | 2021-11-23 01:07:16 | 0.91 | set | {'P56199', 'Q9UKX5', 'Q13349', 'P20702', 'P26010', 'P23229', 'P26006', 'O75578', 'P18564', 'P16144', 'P53708', 'P18084', 'P17301', 'P08648', 'Q13683', 'P08514', 'P11215', 'P06756', 'P38570', 'P05556', 'P20701', 'P05107', 'Q13797', 'P26012', 'P05106'} | 25 | |
| ¶ | pypath.inputs.intogen.intogen_annotations | 2021-11-23 01:07:16 | 2021-11-23 01:07:16 | 0.46 | defaultdict | defaultdict(<class 'set'>, {'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='Activa...(truncated) | 480 | |
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
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| ¶ | pypath.inputs.ipi.ipi_uniprot | 2021-11-23 01:07:16 | 2021-11-23 01:07:16 | 0.31 | 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 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2021-11-23 01:07:17 | 2021-11-23 01:07:28 | 11.59 | 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 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2021-11-23 01:07:28 | 2021-11-23 01:07:29 | 0.78 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2021-11-23 01:07:29 | 2021-11-23 01:07:29 | 0.20 | 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 | |
| ¶ | pypath.inputs.italk.italk_raw | 2021-11-23 01:07:29 | 2021-11-23 01:07:29 | 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 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2021-11-23 01:07:29 | 2021-11-23 01:07:34 | 4.95 | 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 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2021-11-23 01:07:34 | 2021-11-23 01:07:37 | 2.54 | 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 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
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| ¶ | pypath.inputs.kegg.kegg_interactions | 2021-11-23 01:07:37 | 2021-11-23 01:09:39 | 122.66 | 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) | 14,427 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2021-11-23 01:09:39 | 2021-11-23 01:09:56 | 16.13 | set | {KeggMedicusRawInteraction(id_a='1139', id_b='5293', name_a='CHRNA7', name_b='PIK3CD', effect='stimulation', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N01349'), KeggMedicusRawInteraction(id_a=('5836', '178'), id_b='55276', name_a=('PYGL', 'AGL'), name...(truncated) | 12,601 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2021-11-23 01:09:56 | 2021-11-23 01:09:57 | 1.37 | dict | {'COMPLEX:O15488_P13807': Complex: COMPLEX:O15488_P13807, 'COMPLEX:P53992_Q15436': Complex: COMPLEX:P53992_Q15436, 'COMPLEX:P17693_P61769': Complex: COMPLEX:P17693_P61769, 'COMPLEX:A6NGB9_O00401': Complex: COMPLEX:A6NGB9_O00401, 'COMPLEX:P01889_P51572': Complex: COMPLEX:P01889_P51572, 'COMPLEX:P1533...(truncated) | 267 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2021-11-23 01:09:57 | 2021-11-23 01:09:58 | 1.40 | list | [KeggMedicusInteraction(id_a='P36544', id_b='O00329', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a=Complex: COMPLEX:P06737_P35573, id_b='Q96G03', entity_type_a='complex', entity_type_b='protein', interacti...(truncated) | 9,383 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2021-11-23 01:09:58 | 2021-11-23 01:10:05 | 7.07 | defaultdict | defaultdict(<class 'set'>, {'P30305': {KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Cell cycle')}, 'P17535': {KeggPathway(pathway='MAPK signaling pathway')}, 'Q8IVH8': {KeggPathway(pathway='MAPK signaling pathway')}, 'P19419': {KeggPathway(pathway='GnRH signaling pathway'), Ke...(truncated) | 2,569 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2021-11-23 01:10:05 | 2021-11-23 01:10:06 | 0.41 | defaultdict | defaultdict(<class 'set'>, {'A8K7J7': {KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Glycolysis / Gl...(truncated) | 813 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2021-11-23 01:10:06 | 2021-11-23 01:10:13 | 6.86 | tuple | ({'MAPK signaling pathway': {'P30305', 'P17535', 'Q8IVH8', 'P19419', 'Q7RTX0', 'P01583', 'Q96NL6', 'P50897', 'Q13188', 'P11831', 'Q12988', 'Q15750', 'P61244', 'Q7LDG7', 'P52564', 'P07602', 'Q9UPT6', 'O75608', 'O60359', 'Q13233', 'Q9Y2U5', 'P14778', 'P17612', 'Q9HBH9', 'P15336', 'Q12851', 'O95257', '...(truncated) | 2 | |
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2021-11-23 01:10:13 | 2021-11-23 01:10:18 | 5.70 | defaultdict | defaultdict(<class 'set'>, {'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(g...(truncated) | 503 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2021-11-23 01:10:18 | 2021-11-23 01:10:22 | 3.90 | 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 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2021-11-23 01:10:22 | 2021-11-23 01:10:23 | 0.32 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/laudanna.py", line 56, in laudanna_directions
LaudannaDirection(
TypeError: <lambda>() missing 1 required positional argument: 'target_genesymbol'
|
|||
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2021-11-23 01:10:23 | 2021-11-23 01:10:23 | 0.74 | 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 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2021-11-23 01:10:23 | 2021-11-23 01:10:47 | 23.88 | 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 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2021-11-23 01:10:47 | 2021-11-23 01:11:02 | 14.97 | 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 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2021-11-23 01:11:02 | 2021-11-23 01:11:02 | 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 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2021-11-23 01:11:02 | 2021-11-23 01:11:02 | 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 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2021-11-23 01:11:02 | 2021-11-23 01:11:09 | 6.70 | 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 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2021-11-23 01:11:09 | 2021-11-23 01:11:10 | 1.15 | 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 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2021-11-23 01:11:10 | 2021-11-23 01:11:11 | 0.66 | 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 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2021-11-23 01:11:11 | 2021-11-23 01:11:12 | 0.93 | 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 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2021-11-23 01:11:12 | 2021-11-23 01:11:12 | 0.21 | 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 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2021-11-23 01:11:12 | 2021-11-23 01:11:12 | 0.48 | 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 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2021-11-23 01:11:12 | 2021-11-23 01:11:47 | 34.08 | defaultdict | defaultdict(<class 'set'>, {'P27824': {LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endopl...(truncated) | 9,494 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2021-11-23 01:11:47 | 2021-11-23 01:11:47 | 0.58 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5',), references=('21054788',)), LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', '...(truncated) | 1,536 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2021-11-23 01:11:47 | 2021-11-23 01:11:47 | 0.04 | 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 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
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| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2021-11-23 01:11:47 | 2021-11-23 01:11:47 | 0.21 | 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 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2021-11-23 01:11:47 | 2021-11-23 01:12:03 | 15.63 | set | {'LOX', 'IGFBP4', 'VWA5B1', 'S100a10', 'LOXL1', 'HPX', 'LAMA4', 'ADAMTS5', 'ADAMTS12', 'Sftpd', 'BMP7', 'Lox', 'Try10', 'MEGF6', 'HABP2', 'PODN', 'SEMA6D', 'Srpx2', 'SRPX', 'Col28a1', 'Plxnc1', 'PLOD2', 'Hcfc1', 'PRG3', 'Fbn2', 'Col6a5', 'MFGE8', 'Rptn', 'Mfap2', 'ADAMTSL4', 'SERPINB6', 'Aspn', 'Fra...(truncated) | 744 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2021-11-23 01:12:03 | 2021-11-23 01:12:04 | 0.72 | dict | {'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 1,064 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
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| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2021-11-23 01:12:04 | 2021-11-23 01:12:07 | 2.85 | dict | {'P61158': {MatrixdbAnnotation(mainclass='membrane')}, 'Q96JA3': {MatrixdbAnnotation(mainclass='membrane')}, 'Q9Y5E3': {MatrixdbAnnotation(mainclass='membrane')}, 'Q16563': {MatrixdbAnnotation(mainclass='membrane')}, 'Q5VZ89': {MatrixdbAnnotation(mainclass='membrane')}, 'P51582': {MatrixdbAnnotation...(truncated) | 10,099 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2021-11-23 01:12:07 | 2021-11-23 01:12:07 | 0.06 | set | {'P07355', 'Q99983', 'P10915', 'Q99467', 'Q8IUX8', 'Q9H306', 'Q16270', 'Q8TE57', 'O14936', 'Q14392', 'Q9GZT5', 'Q502W6', 'P21754', 'P23142', 'Q9UMD9', 'Q6PCB0', 'P22105', 'O95460', 'P56703', 'P23352', 'P12107', 'P49747', 'Q8TF66', 'Q14993', 'P53420', 'Q5VXM1', 'O95388', 'Q14393', 'O95428', 'Q99102',...(truncated) | 483 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2021-11-23 01:12:07 | 2021-11-23 01:12:07 | 0.16 | 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 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2021-11-23 01:12:07 | 2021-11-23 01:12:09 | 2.07 | set | {'P61158', 'Q96JA3', 'Q9Y5E3', 'Q16563', 'Q5VZ89', 'P51582', 'Q8NGR4', 'Q9UIQ6', 'Q7KZI7', 'A0A576', 'O00408', 'Q14028', 'Q8TAB3', 'Q8NH64', 'P48165', 'Q86SK9', 'P30518', 'Q6UWH6', 'O75762', 'P43121', 'P47887', 'Q96QT4', 'Q6UXB3', 'P10523', 'O94772', 'Q695T7', 'Q8TF66', 'P29017', 'P05496', 'Q8IY33',...(truncated) | 8,241 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2021-11-23 01:12:09 | 2021-11-23 01:12:09 | 0.31 | set | {'Q9ULZ1', 'P10809', 'Q9ULY5', 'A1L453', 'Q9UF83', 'Q9Y644', 'P48595', 'Q16552', 'Q8NEX6', 'P10915', 'P02810', 'Q6XZB0', 'Q9UIQ6', 'P23510', 'P02812', 'A0A0C4DH33', 'O95868', 'Q8TAV5', 'Q9NS62', 'P19835', 'P01768', 'P29320', 'Q7Z5J1', 'O60462', 'Q8TE57', 'Q16270', 'Q8WWY8', 'P0DOY3', 'P17405', 'P0DP...(truncated) | 2,925 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2021-11-23 01:12:09 | 2021-11-23 01:12:10 | 1.02 | set | {'O14525', 'Q9HDB5', 'O60759', 'P12259', 'Q59H14', 'Q9Y624', 'Q9Y4C0', 'Q9HBB8', 'P28827', 'Q9UQS6', 'Q86WK7', 'Q6ZW63', 'P43121', 'P16144', 'P53708', 'P22105', 'Q49MI3', 'P25942', 'Q92729', 'O95500', 'Q8N6H6', 'Q96KR4', 'O75144', 'Q13895', 'Q05084', 'P18827', 'Q04900', 'P08575', 'P50895', 'Q12816',...(truncated) | 103 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2021-11-23 01:12:10 | 2021-11-23 01:12:35 | 24.77 | 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) | 2,511 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2021-11-23 01:12:35 | 2021-11-23 01:12:36 | 1.28 | 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 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2021-11-23 01:12:36 | 2021-11-23 01:12:41 | 5.04 | 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 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2021-11-23 01:12:41 | 2021-11-23 01:12:42 | 0.37 | 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 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2021-11-23 01:12:42 | 2021-11-23 01:12:42 | 0.21 | 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 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2021-11-23 01:12:42 | 2021-11-23 01:12:42 | 0.09 | tuple | ({'MIMAT0000062': {'hsa-let-7a', 'hsa-let-7a-5p'}, '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 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2021-11-23 01:12:42 | 2021-11-23 01:12:42 | 0.20 | list | [('MIMAT0000062', 'MI0000062'), ('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000068', 'MI...(truncated) | 3,027 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2021-11-23 01:12:42 | 2021-11-23 01:12:42 | 0.06 | list | [('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000062', 'hsa-let-7a-5p'), ('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 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2021-11-23 01:12:42 | 2021-11-23 01:12:43 | 0.09 | list | ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) | 3,027 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2021-11-23 01:12:43 | 2021-11-23 01:12:43 | 0.06 | list | [('MI0000060', 'hsa-let-7a-1L'), ('MI0000060', 'hsa-let-7a-1'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,173 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2021-11-23 01:12:43 | 2021-11-23 01:12:43 | 0.09 | list | ['MI0000062', 'MI0000060', 'MI0000061', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000068', 'MI0000067', 'MI0000069', 'MI0000115', 'MI0000070', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) | 3,027 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2021-11-23 01:12:43 | 2021-11-23 01:12:43 | 0.15 | list | [('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMA...(truncated) | 3,361 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2021-11-23 01:12:43 | 2021-11-23 01:12:43 | 0.20 | 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 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2021-11-23 01:12:43 | 2021-11-23 01:12:46 | 3.41 | 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 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2021-11-23 01:12:46 | 2021-11-23 01:13:05 | 18.19 | 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 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2021-11-23 01:13:05 | 2021-11-23 01:13:05 | 0.38 | 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 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2021-11-23 01:13:05 | 2021-11-23 01:15:02 | 116.84 | dict | {'O60603': {MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='MILI_PSEUDOPODIA_CHEMOTAXIS_DN'), MsigdbAnnotation(collection='reactome_pathways', geneset='REACTOME_MODULATION_BY_MTB_OF_HOST_IMMUNE_SYSTEM'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', gen...(truncated) | 20,047 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2021-11-23 01:15:04 | 2021-11-23 01:15:24 | 20.33 | dict | {'chr1p12': {'AL139420.1', 'GAPDHP33', 'NBPF7', 'LINC01525', 'HSD3BP2', 'PSMC1P12', 'RNU1-75P', 'TBX15', 'WDR3', 'HSD3B2', 'PNRC2P1', 'GAPDHP58', 'RNA5SP56', 'HSD3BP5', 'RPS3AP12', 'PFN1P9', 'HSD3BP4', 'HSD3BP1', 'WARS2-IT1', 'HSD3BP3', 'VPS25P1', 'NOTCH2P1', 'SEC22B', 'GAPDHP23', 'GDAP2', 'VDAC2P3'...(truncated) | 32,284 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2021-11-23 01:15:24 | 2021-11-23 01:15:25 | 0.42 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'FUT4', 'CCND1', 'NR4A3', 'SIK1', 'SPHK1', 'KLF10', 'TRAF1', 'ABCA1', 'B4GALT1', 'IL15RA', 'SAT1', 'PLEK', 'IER3', 'IL7R', 'SNN', 'DUSP5', 'F2RL1', 'SOD2', 'YRDC', 'CXCL11', 'BCL2A1', 'TIPARP', 'SPSB1', 'TNFRSF9', 'CXCL1', 'TRIP10', 'IFIH...(truncated) | 13 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2021-11-23 01:15:25 | 2021-11-23 01:15:26 | 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 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2021-11-23 01:15:26 | 2021-11-23 01:15:26 | 0.08 | 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 | |
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2021-11-23 01:15:26 | 2021-11-23 01:15:26 | 0.13 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2021-11-23 01:15:26 | 2021-11-23 01:15:26 | 0.15 | 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 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2021-11-23 01:15:26 | 2021-11-23 01:15:28 | 2.11 | 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 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2021-11-23 01:15:28 | 2021-11-23 01:15:28 | 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 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2021-11-23 01:15:28 | 2021-11-23 01:15:44 | 15.42 | defaultdict | defaultdict(<class 'set'>, {'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(...(truncated) | 1,868 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2021-11-23 01:15:44 | 2021-11-23 01:15:44 | 0.91 | dict | {'hcao': 'Human Cell Atlas Ontology', 'htn': 'Hypertension Ontology For Clinical Data', 'iceo': 'ICEO: Ontology of Integrative and Conjugative Elements', 'ico': 'Informed Consent Ontology (ICO)', 'ido': 'Infectious Disease Ontology', 'kisao': 'Kinetic Simulation Algorithm Ontology', 'mod': 'Protein ...(truncated) | 268 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
||||||
| ¶ | pypath.inputs.opm.opm_annotations | 2021-11-23 01:15:44 | 2021-11-23 01:15:54 | 9.99 | defaultdict | defaultdict(<class 'set'>, {'O14745': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P59666': {OpmAnnotation(membrane='Secreted', family='Vertebrate defens...(truncated) | 403 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2021-11-23 01:15:54 | 2021-11-23 01:17:52 | 118.00 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2021-11-23 01:17:52 | 2021-11-23 01:18:05 | 12.96 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 5,688,970 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
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| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2021-11-23 01:18:05 | 2021-11-23 01:18:19 | 13.39 | list | [PathwayCommonsInteraction(id_a='A2M', interaction_type='in-complex-with', id_b='ANXA6', resource='CORUM'), PathwayCommonsInteraction(id_a='A2M', interaction_type='in-complex-with', id_b='LRP1', resource='CORUM'), PathwayCommonsInteraction(id_a='AATF', interaction_type='in-complex-with', id_b='NGDN'...(truncated) | 1,261,865 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2021-11-23 01:18:20 | 2021-11-23 01:18:20 | 0.31 | 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 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2021-11-23 01:18:20 | 2021-11-23 01:18:26 | 5.84 | 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 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2021-11-23 01:18:28 | 2021-11-23 01:18:35 | 6.53 | 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) | 38,733 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2021-11-23 01:18:35 | 2021-11-23 01:18:38 | 2.90 | tuple | ({'P02185': {('1bvc', 'X-ray', 1.5), ('5yzf', 'X-ray', 1.77), ('1vxh', 'X-ray', 1.7), ('7a44', 'X-ray', 1.75), ('1mbd', 'X-ray', 1.4), ('1n9h', 'X-ray', 1.8), ('6m8f', 'X-ray', 1.1), ('1bzr', 'X-ray', 1.15), ('3m38', 'X-ray', 1.42), ('2g14', 'X-ray', 1.9), ('2zt0', 'X-ray', 1.21), ('2mye', 'X-ray', ...(truncated) | 2 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2021-11-23 01:18:38 | 2021-11-23 01:18:39 | 0.74 | 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 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2021-11-23 01:18:39 | 2021-11-23 01:31:42 | 783.39 | 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 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2021-11-23 01:31:42 | 2021-11-23 01:31:43 | 0.91 | 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 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2021-11-23 01:31:43 | 2021-11-23 01:31:46 | 2.73 | tuple | (defaultdict(<class 'dict'>, {'101m': {'PF00042': PfamDomain(chain='A', start=7, end=113)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=7, end=113)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': ...(truncated) | 2 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2021-11-23 01:31:46 | 2021-11-23 01:35:44 | 238.13 | tuple | ({}, {}) | 2 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2021-11-23 01:35:44 | 2021-11-23 01:40:40 | 295.46 | tuple | ({'Q92610': {'PF16622', 'PF00096'}, 'Q5SRH9': {'PF10300'}, 'Q6IBS0': {'PF00241'}, 'M5A8F1': set(), 'Q13621': {'PF00324', 'PF03522', 'PF08403'}, 'Q13401': {'PF01352'}, 'A6NEE1': {'PF00169'}, 'Q5VT98': set(), 'Q96DB5': set(), 'Q96FV2': {'PF03577'}, 'Q8WYL5': {'PF00782', 'PF08766'}, 'A0A576': {'PF07686...(truncated) | 2 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2021-11-23 01:40:40 | 2021-11-23 01:40:40 | 0.38 | 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 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2021-11-23 01:40:40 | 2021-11-23 01:40:48 | 7.71 | defaultdict | defaultdict(<class 'set'>, {'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_...(truncated) | 264 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2021-11-23 01:40:48 | 2021-11-23 01:40:50 | 1.50 | 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 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2021-11-23 01:40:50 | 2021-11-23 01:40:50 | 0.63 | 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 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2021-11-23 01:40:50 | 2021-11-23 01:40:50 | 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 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2021-11-23 01:40:50 | 2021-11-23 01:40:51 | 1.18 | 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 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2021-11-23 01:40:51 | 2021-11-23 01:40:51 | 0.02 | list | [['LYN', 'HNRPK'], ['CLK1', 'PTPN1'], ['BMPR1B', 'CTTN'], ['RPS6KA5', 'PRKACA'], ['MAPK9', 'BCL3'], ['NEK4', 'CPSF3'], ['RPS6KA5', 'KLHL25'], ['DYRK1B', 'PRKACB'], ['CLK2', 'SAFB2'], ['CSK', 'SRC'], ['LCK', 'CBL'], ['EIF2AK1', 'EIF2S1'], ['AKT1', 'MEF2C'], ['BMX', 'EIF4B'], ['RPS6KA4', 'MDM2'], ['PR...(truncated) | 1,821 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2021-11-23 01:40:51 | 2021-11-23 01:40:52 | 0.24 | 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 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 0.11 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 0.38 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2021-11-23 01:40:52 | 2021-11-23 01:40:52 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'AB;WB;MA'...(truncated) | 4,732 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2021-11-23 01:40:52 | 2021-11-23 01:40:57 | 4.87 | 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')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) | 198,541 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2021-11-23 01:40:58 | 2021-11-23 01:41:26 | 27.99 | 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 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2021-11-23 01:41:26 | 2021-11-23 01:41:27 | 0.49 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'protein degradation', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,298 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2021-11-23 01:41:27 | 2021-11-23 01:43:12 | 105.48 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'24876223', '28052875', '21148409', '21209006'}, 'isoforms': {1}, 'process': {''}, 'function': {'intracellular localization', 'phosphorylation', 'protein degradation', 'ubiquitination', 'protein stabilization'}...(truncated) | 3,537 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pro.get_pro | 2021-11-23 01:43:12 | 2021-11-23 01:43:34 | 21.67 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | None | |
| ¶ | pypath.inputs.pro.pro_mapping | 2021-11-23 01:43:34 | 2021-11-23 01:43:34 | 0.40 | 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) | 315,413 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2021-11-23 01:43:34 | 2021-11-23 01:44:34 | 59.36 | dict | {'normal': defaultdict(<class 'dict'>, {'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':...(truncated) | 2 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2021-11-23 01:44:35 | 2021-11-23 01:46:28 | 112.44 | defaultdict | defaultdict(<class 'set'>, {'O43657': {ProtainatlasAnnotation(organ='liver cancer', tissue='liver cancer', level='Medium', status=None, n_not_detected=0, n_low=1, n_medium=5, n_high=4, prognostic=False, favourable=True, score=0.104, pathology=True), ProtainatlasAnnotation(organ='smooth muscle', tiss...(truncated) | 19,364 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2021-11-23 01:46:30 | 2021-11-23 01:46:32 | 2.07 | 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) | 2,593 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2021-11-23 01:46:33 | 2021-11-23 01:46:33 | 0.84 | dict | {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) | 6,819 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2021-11-23 01:46:33 | 2021-11-23 01:46:44 | 10.53 | 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 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2021-11-23 01:46:44 | 2021-11-23 01:46:45 | 0.64 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'25728676', '22304920', '25545367', '24357804', '24727247'}, 'substrate': 'P15336', 'databases': {'Sparser', 'SIGNOR', 'REACH', 'PhosphoSite'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) | 22,139 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2021-11-23 01:46:45 | 2021-11-23 01:46:46 | 0.69 | 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 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2021-11-23 01:46:46 | 2021-11-23 01:46:52 | 6.58 | defaultdict | defaultdict(<class 'set'>, {'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=No...(truncated) | 18,868 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2021-11-23 01:46:52 | 2021-11-23 01:46:52 | 0.00 | NoneType | None | None | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2021-11-23 01:46:52 | 2021-11-23 01:46:55 | 2.31 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 957, in _reactome_reactions
soup = reactome_bs()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 135, in reactome_bs
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2021-11-23 01:46:55 | 2021-11-23 01:46:57 | 2.27 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 1014, in _reactome_reactions_et
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2021-11-23 01:46:57 | 2021-11-23 01:46:58 | 0.96 | 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 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2021-11-23 01:46:58 | 2021-11-23 01:46:58 | 0.25 | 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 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2021-11-23 01:46:58 | 2021-11-23 01:49:13 | 134.57 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 619, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 1156, in get_reactions
rea.load_all()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/utils/pyreact.py", line 1303, in load_all
self.load_pid()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/utils/pyreact.py", line 1158, in load_pid
parser.process()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/utils/pyreact.py", line 250, in process
self.open_biopax()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/utils/pyreact.py", line 294, in open_biopax
self.opener = curl.FileOpener(self.biopax, **opener_args)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/share/curl.py", line 583, in __init__
if type(file_param) in common.char_types else file_param.name
AttributeError: 'NoneType' object has no attribute 'name'
|
|||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2021-11-23 01:49:13 | 2021-11-23 01:49:13 | 0.19 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 121, in panther_biopax
c = curl.Curl(url, silent = False, large = True).values()
AttributeError: 'Curl' object has no attribute 'values'
|
|||
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2021-11-23 01:49:13 | 2021-11-23 01:49:15 | 1.66 | NoneType | None | None | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2021-11-23 01:49:15 | 2021-11-23 01:49:27 | 12.47 | TextIOWrapper | <_io.TextIOWrapper name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | None | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2021-11-23 01:49:27 | 2021-11-23 01:49:29 | 2.26 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 135, in reactome_bs
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2021-11-23 01:49:29 | 2021-11-23 01:49:32 | 2.21 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
|||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2021-11-23 01:49:32 | 2021-11-23 01:49:32 | 0.74 | 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 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2021-11-23 01:49:32 | 2021-11-23 01:49:32 | 0.16 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 599, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/scconnect.py", line 152, in scconnect_complexes
return {
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20211123-002002/pypath/inputs/scconnect.py", line 155, in <setcomp>
if entity.Entity._is_complex(cplex)
NameError: name 'entity' is not defined
|
|||
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2021-11-23 01:49:32 | 2021-11-23 02:01:13 | 700.34 | 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 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
||||||
| ¶ | pypath.inputs.signalink.signalink_annotations | 2021-11-23 02:01:13 | 2021-11-23 02:01:14 | 1.28 | dict | {'pathway': defaultdict(<class 'set'>, {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='Rec...(truncated) | 2 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2021-11-23 02:01:14 | 2021-11-23 02:01:15 | 0.56 | defaultdict | defaultdict(<class 'set'>, {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(functi...(truncated) | 784 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2021-11-23 02:01:15 | 2021-11-23 02:01:15 | 0.67 | 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 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2021-11-23 02:01:15 | 2021-11-23 02:01:16 | 0.56 | defaultdict | defaultdict(<class 'set'>, {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='Receptor tyrosi...(truncated) | 836 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2021-11-23 02:01:16 | 2021-11-23 02:01:16 | 0.53 | dict | {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4, 'COMPLEX:P63...(truncated) | 2,986 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2021-11-23 02:01:16 | 2021-11-23 02:01:19 | 2.45 | list | [{'typ': 'dephosphorylation', 'resnum': 661, 'instance': 'QNEFAGFSYTNPEFV', 'substrate': 'P05771', 'start': 654, 'end': 668, 'kinase': 'Q6ZVD8', 'resaa': 'S', 'motif': 'QNEFAGFSYTNPEFV', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'18162466'}}, {'typ': 'dephosphorylation', 'res...(truncated) | 9,902 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2021-11-23 02:01:19 | 2021-11-23 02:01:19 | 0.43 | list | [SignorInteraction(source='Q6T4R5', target='Q9NYB9', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates activity', mechanism='binding', ncbi_tax_id='9606', pubmeds='20332100', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), Si...(truncated) | 31,127 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2021-11-23 02:01:19 | 2021-11-23 02:01:41 | 22.07 | defaultdict | defaultdict(<class 'set'>, {'P23769': {SignorPathway(pathway='Adipogenesis'), SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P31269': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P04637': {SignorPathway(pathway='P38 Signaling'), SignorPathway(pathway='Cell cycle: G2/M phase transition'), ...(truncated) | 555 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2021-11-23 02:01:42 | 2021-11-23 02:01:42 | 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) | 77 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2021-11-23 02:01:42 | 2021-11-23 02:01:52 | 10.75 | 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 | |
| ¶ | pypath.inputs.stitch.stitch_interactions | 2021-11-23 02:01:52 | 2021-11-23 02:03:07 | 75.10 | list | [StitchInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action='', score=150), StitchInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action='', score=150), StitchInteraction(partner_a='23627457', partner_b='ENSP00000353915'...(truncated) | 21,773,491 | |
| ¶ | pypath.inputs.string.string_effects | 2021-11-23 02:03:07 | 2021-11-23 02:03:15 | 8.12 | list | [StringInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target...(truncated) | 2,250,122 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2021-11-23 02:03:17 | 2021-11-23 02:03:20 | 3.59 | dict | {'A0AV02': (0.8363, 'Transporters', {'SLC', 'APC', 'SLC12'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC', 'APC', 'SLC5'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,809 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2021-11-23 02:03:20 | 2021-11-23 02:03:32 | 11.83 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2021-11-23 02:03:32 | 2021-11-23 02:03:33 | 0.75 | defaultdict | defaultdict(<class 'set'>, {'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...(truncated) | 1,346 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2021-11-23 02:03:33 | 2021-11-23 02:03:33 | 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 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2021-11-23 02:03:33 | 2021-11-23 02:03:33 | 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 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2021-11-23 02:03:33 | 2021-11-23 02:03:37 | 3.73 | defaultdict | defaultdict(<class 'set'>, {'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)', t...(truncated) | 2,027 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2021-11-23 02:03:37 | 2021-11-23 02:03:37 | 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) | 21,705 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2021-11-23 02:03:37 | 2021-11-23 02:03:37 | 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) | 1,641 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2021-11-23 02:03:37 | 2021-11-23 02:03:37 | 0.49 | 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) | 1,886 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2021-11-23 02:03:37 | 2021-11-23 02:03:45 | 7.06 | 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 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2021-11-23 02:03:45 | 2021-11-23 02:04:21 | 36.07 | set | {ThreedcomplexContact(pdb='4e7o_1', uniprot_1='Q8DNC2', uniprot_2='Q8DNC2', chain_1='A', chain_2='B', n_residues=7.5, length_1=130, length_2=131, domain_s1=('52172',), domain_p1=('PF00072.19',), domain_s2=('52172',), domain_p2=('PF00072.19',), ident=True, homo=True), ThreedcomplexContact(pdb='1t36_1...(truncated) | 260,282 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2021-11-23 02:04:22 | 2021-11-23 02:07:35 | 192.75 | list | [<pypath.internals.intera.DomainDomain object at 0x7f4e1dcfc7f0>, <pypath.internals.intera.DomainDomain object at 0x7f4e544f05e0>, <pypath.internals.intera.DomainDomain object at 0x7f4e4a77be20>, <pypath.internals.intera.DomainDomain object at 0x7f4e249d6880>, <pypath.internals.intera.DomainDomain o...(truncated) | 525,721 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2021-11-23 02:07:35 | 2021-11-23 02:07:43 | 7.59 | dict | {'4e7o_1': {('Q8DNC2', 'Q8DNC2'): 7.5}, '1t36_1': {('P00968', 'P00968'): 8.5, ('P00968', 'P0A6F1'): 46.0}, '5l5p_1': {('P22141', 'P23638'): 11.5, ('P25043', 'P30657'): 17.5, ('P30656', 'P40303'): 5.0, ('P21243', 'P25043'): 11.5, ('P23638', 'P25043'): 5.5, ('P21242', 'P40302'): 27.5, ('P21243', 'P386...(truncated) | 81,354 | |
| ¶ | pypath.inputs.threedid.get_3did | 2021-11-23 02:07:43 | 2021-11-23 02:40:26 | 1,963.14 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7f4e8961a370>, <pypath.internals.intera.DomainDomain object at 0x7f4e2b82a790>, <pypath.internals.intera.DomainDomain object at 0x7f4e2b82a280>, <pypath.internals.intera.DomainDomain object at 0x7f4e2b82af70>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2021-11-23 02:40:26 | 2021-11-23 02:40:57 | 31.10 | dict | {('P30048', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}, ('PF00578', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}}, ('Q13162', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0...(truncated) | 3,079,747 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2021-11-23 02:41:45 | 2021-11-23 02:41:49 | 4.44 | defaultdict | defaultdict(<class 'set'>, {'P05067': {TopdbAnnotation(membrane='Plasma membrane', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Plasma membrane', topology='Signal', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Signal', score=89, tmregions=1), Topd...(truncated) | 1,243 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2021-11-23 02:41:49 | 2021-11-23 02:41:51 | 1.74 | 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 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2021-11-23 02:41:51 | 2021-11-23 02:43:30 | 98.81 | 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 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 0.01 | list | [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;11983166;12601176', 'Calcium measurement;Fluorescence probe labeling;Fusion protein-pu...(truncated) | 359 | |
| ¶ | pypath.inputs.trip.trip_process | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'Rat aortic vascular smooth muscle cell', 'HEK293', 'Porcine coronary artery', 'Rat vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
||||||
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 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 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 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 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 0.05 | set | {'A0A804HLH2', 'A0A1S7SKF3', 'A0A7S5C2Q7', 'Q8IUC1', 'C9J368', 'A8KAH6', 'A0A0A7C6K9', 'G0ZDX3', 'H0YDH9', 'Q9GZZ0', 'Q16563', 'A0A6B7HHK1', 'C0KLR6', 'A0A3Q5AD24', 'Q9UIQ6', 'Q9UNG0', 'A0A494BZW8', 'G9I2M2', 'A0A5C2GNQ4', 'A0A5C2FWI7', 'H3BQ38', 'D2DKN8', 'A0A1J0Q2N5', 'A8K5W5', 'A0A7D5BS20', 'K7EQ...(truncated) | 203,711 | |
| ¶ | pypath.inputs.uniprot._cleanup | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 0.00 | NoneType | None | None | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot._remove |
Not calling `pypath.inputs.uniprot._remove`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.all_swissprots | 2021-11-23 02:43:30 | 2021-11-23 02:43:30 | 0.00 | set | {'O75317', 'D6RBM5', 'Q8IUC1', 'Q9GZZ0', 'Q16563', 'Q8TE77', 'P51582', 'Q8NGR4', 'Q9UIQ6', 'A0A576', 'Q9H0I3', 'B1AJZ9', 'Q2M5E4', 'O75762', 'P55103', 'P43121', 'Q8WYH8', 'Q86W56', 'Q8NEG2', 'Q96QT4', 'P10523', 'O94772', 'Q2M329', 'Q9BXI9', 'Q9P265', 'Q5T6R2', 'P30990', 'P0C874', 'Q8NHM5', 'Q9UPS8',...(truncated) | 20,375 | |
| ¶ | pypath.inputs.uniprot.all_trembls | 2021-11-23 02:43:30 | 2021-11-23 02:43:57 | 27.03 | set | {'A0A804HLH2', 'A0A1S7SKF3', 'A0A7S5C2Q7', 'C9J368', 'A8KAH6', 'A0A0A7C6K9', 'G0ZDX3', 'H0YDH9', 'C0KLR6', 'A0A6B7HHK1', 'A0A3Q5AD24', 'Q9UNG0', 'A0A494BZW8', 'G9I2M2', 'A0A5C2GNQ4', 'A0A5C2FWI7', 'H3BQ38', 'D2DKN8', 'A0A1J0Q2N5', 'A8K5W5', 'A0A7D5BS20', 'K7EQR9', 'A0A0A0MRK9', 'A0A1C3PI48', 'A0A059...(truncated) | 183,336 | |
| ¶ | pypath.inputs.uniprot.all_uniprots | 2021-11-23 02:43:57 | 2021-11-23 02:43:57 | 0.00 | set | {'A0A804HLH2', 'A0A1S7SKF3', 'A0A7S5C2Q7', 'Q8IUC1', 'C9J368', 'A8KAH6', 'A0A0A7C6K9', 'G0ZDX3', 'H0YDH9', 'Q9GZZ0', 'Q16563', 'A0A6B7HHK1', 'C0KLR6', 'A0A3Q5AD24', 'Q9UIQ6', 'Q9UNG0', 'A0A494BZW8', 'G9I2M2', 'A0A5C2GNQ4', 'A0A5C2FWI7', 'H3BQ38', 'D2DKN8', 'A0A1J0Q2N5', 'A8K5W5', 'A0A7D5BS20', 'K7EQ...(truncated) | 203,711 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.get_db | 2021-11-23 02:43:57 | 2021-11-23 02:43:57 | 0.00 | set | {'A0A804HLH2', 'A0A1S7SKF3', 'A0A7S5C2Q7', 'Q8IUC1', 'C9J368', 'A8KAH6', 'A0A0A7C6K9', 'G0ZDX3', 'H0YDH9', 'Q9GZZ0', 'Q16563', 'A0A6B7HHK1', 'C0KLR6', 'A0A3Q5AD24', 'Q9UIQ6', 'Q9UNG0', 'A0A494BZW8', 'G9I2M2', 'A0A5C2GNQ4', 'A0A5C2FWI7', 'H3BQ38', 'D2DKN8', 'A0A1J0Q2N5', 'A8K5W5', 'A0A7D5BS20', 'K7EQ...(truncated) | 203,711 | |
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2021-11-23 02:43:57 | 2021-11-23 02:43:58 | 0.74 | 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) | 71,862 | |
| ¶ | pypath.inputs.uniprot.init_db | 2021-11-23 02:43:58 | 2021-11-23 02:43:58 | 0.06 | NoneType | None | None | |
| ¶ | pypath.inputs.uniprot.is_swissprot |
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.is_trembl |
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.is_uniprot |
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2021-11-23 02:43:58 | 2021-11-23 02:44:03 | 5.59 | defaultdict | defaultdict(<class 'set'>, {'Q96NG5': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None)}, 'Q6ZN19': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None)}, 'Q86XN6': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None...(truncated) | 14,348 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2021-11-23 02:44:03 | 2021-11-23 02:44:10 | 6.80 | defaultdict | defaultdict(<class 'set'>, {'Q96NG5': {UniprotKeyword(keyword='Zinc-finger'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Zinc'), UniprotKeyword(keyword='DNA-binding'), UniprotKeyword(keyword='Repeat'), UniprotKeyword(keyword='Transc...(truncated) | 20,375 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2021-11-23 02:44:10 | 2021-11-23 02:44:18 | 7.76 | defaultdict | defaultdict(<class 'set'>, {'Q96NG5': {UniprotLocation(location='Nucleus', features=None)}, 'Q6ZN19': {UniprotLocation(location='Nucleus', features=None)}, 'Q86XN6': {UniprotLocation(location='Nucleus', features=None)}, 'A8MUZ8': {UniprotLocation(location='Nucleus', features=None)}, 'Q08ER8': {Unipr...(truncated) | 16,812 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids | 2021-11-23 02:44:18 | 2021-11-23 03:11:36 | 1,637.94 | dict | {1980042: Taxon(ncbi_id=1980042, latin='1,4-dioxane-degrading enrichment culture', english='', latin_synonym=None), 85621: Taxon(ncbi_id=85621, latin='16SrII (Peanut WB group)', english='', latin_synonym=None), 85623: Taxon(ncbi_id=85623, latin='16SrIII (X-disease group)', english='', latin_synonym=...(truncated) | 2,686,944 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2021-11-23 03:11:38 | 2021-11-23 03:11:38 | 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) | 26,745 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2021-11-23 03:11:38 | 2021-11-23 03:11:40 | 1.81 | defaultdict | defaultdict(<class 'set'>, {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'H8ZM71': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies g...(truncated) | 551,796 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2021-11-23 03:11:41 | 2021-11-23 03:11:53 | 12.37 | defaultdict | defaultdict(<class 'set'>, {'Q9GZX5': {UniprotTissue(tissue='Wide', level='undefined')}, 'Q9GZP7': {UniprotTissue(tissue='Lung', level='low'), UniprotTissue(tissue='Brain', level='low'), UniprotTissue(tissue='Olfactory mucosa', level='undefined'), UniprotTissue(tissue='Kidney', level='low')}, 'Q9NY8...(truncated) | 9,904 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2021-11-23 03:11:53 | 2021-11-23 03:12:56 | 63.17 | defaultdict | defaultdict(<class 'set'>, {'Q9GZP7': {UniprotTopology(topology='Transmembrane', start=170, end=190), UniprotTopology(topology='Cytoplasmic', start=154, end=169), UniprotTopology(topology='Cytoplasmic', start=78, end=84), UniprotTopology(topology='Extracellular', start=296, end=303), UniprotTopology...(truncated) | 5,210 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
||||||
| ¶ | pypath.inputs.wang.get_hsn | 2021-11-23 03:12:56 | 2021-11-23 03:12:57 | 0.39 | 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 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2021-11-23 03:12:57 | 2021-11-23 03:12:57 | 0.31 | 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 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2021-11-23 03:12:57 | 2021-11-23 03:12:59 | 2.27 | 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 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2021-11-23 03:12:59 | 2021-11-23 03:12:59 | 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 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2021-11-23 03:12:59 | 2021-11-23 03:13:00 | 0.21 | defaultdict | defaultdict(<class 'set'>, {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM'...(truncated) | 466 |
The OmniPath Team • Saez Lab • 2021-11-23