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INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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problems Getting the neighborhood of proteins from the BEL Large Corpus #1019

Closed guerrerosimonl closed 4 years ago

guerrerosimonl commented 4 years ago

Hello,

After trying again the bel.process_pybel_neighborhood command with different protein names, I still get the same error:

INFO: [2019-12-30 10:29:46] indra.sources.bel.api - Loading https://github.com/cthoyt/selventa-knowledge/raw/v1.0.0/selventa_knowledge/large_corpus.bel.nodelink.json.gz INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"1-octadec-9-enoylglycero-3-phosphate") increases tloc(p(HGNC:RHOA), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005856))) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AMP Activated Protein Kinase Complex (complex(SCOMP:"AMP Activated Protein Kinase Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AMP Activated Protein Kinase Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AMP Activated Protein Kinase Complex (complex(SCOMP:"AMP Activated Protein Kinase Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AMP Activated Protein Kinase Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Calcineurin Complex (complex(SCOMP:"Calcineurin Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Calcineurin Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not map EGID56501 to HGNC. INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not map EGID13202 to HGNC. INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Could not map EGID16897 to HGNC. INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex")

INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:06] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"hydrogen peroxide") increases tloc(p(MGI:Aifm1), fromLoc(GOCCID:0005739), toLoc(GOCCID:0005634))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"hydrogen peroxide") increases tloc(p(HGNC:TERT), fromLoc(GOCCID:0005634), toLoc(GOCCID:0005737))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID689226 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID360482 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID54237 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"hydrogen peroxide") increases tloc(p(HGNC:FOXO3), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005634))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"hydrogen peroxide") increases tloc(p(HGNC:BAX), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005739))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"insulin (human)") increases tloc(p(RGD:Akt2), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005886))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID56718 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID56718 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID13177 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID23986 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID56718 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID56718 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"insulin (human)") increases tloc(p(RGD:Prkcz), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005886))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for glucose transport INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"glucose transport") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AMP Activated Protein Kinase Complex (complex(SCOMP:"AMP Activated Protein Kinase Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AMP Activated Protein Kinase Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID54705 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: NADPH Oxidase Complex (complex(SCOMP:"NADPH Oxidase Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"NADPH Oxidase Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID24179 to HGNC. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: GUCY1 Complex (complex(SCOMP:"GUCY1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"GUCY1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Respiratory Chain Complex IV (complex(SCOMP:"Respiratory Chain Complex IV")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Respiratory Chain Complex IV") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Respiratory Chain Complex IV (complex(SCOMP:"Respiratory Chain Complex IV"))

INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Respiratory Chain Complex IV") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Respiratory Chain Complex IV (complex(SCOMP:"Respiratory Chain Complex IV")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Respiratory Chain Complex IV") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for glucose transport INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"glucose transport") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - HGNC entity CKS1BP7 with HGNC ID 1999 has no corresponding Uniprot ID. INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"okadaic acid") decreases tloc(p(MGI:Ptpn14), fromLoc(GOCCID:0005856), toLoc(GOCCID:0005737))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfy Complex (complex(SCOMP:"Nfy Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfy Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfy Complex (complex(SCOMP:"Nfy Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfy Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex")

INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unhandled namespace: SCOMP: Respiratory Chain Complex IV (complex(SCOMP:"Respiratory Chain Complex IV")) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Respiratory Chain Complex IV") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:"reactive oxygen species") increases tloc(p(HGNC:FOXO1), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005634))) INFO: [2019-12-30 10:30:07] indra.sources.bel.processor - Could not map EGID306330 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfy Complex (complex(SCOMP:"Nfy Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfy Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - No Uniprot ID for HGNC ID 9589 INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID27915 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID13851 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Pyruvate Dehydrogenase Complex (complex(SCOMP:"Pyruvate Dehydrogenase Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Pyruvate Dehydrogenase Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID22135 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Calcineurin Complex (complex(SCOMP:"Calcineurin Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Calcineurin Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Calcineurin Complex (complex(SCOMP:"Calcineurin Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Calcineurin Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID24737 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID237877 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID12534 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:androgen) increases tloc(p(HGNC:SREBF1), fromLoc(GOCCID:0005783), toLoc(GOCCID:0005794))) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:androgen) increases tloc(p(HGNC:SREBF2), fromLoc(GOCCID:0005783), toLoc(GOCCID:0005794))) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:androgen) increases tloc(p(RGD:Ezr), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005886))) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID21681 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID22153 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:atorvastatin) increases tloc(p(HGNC:SREBF2), fromLoc(GOCCID:0005783), toLoc(GOCCID:0005634))) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation")

INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID406223 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID12534 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID212377 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: PP2A Complex (complex(SCOMP:"PP2A Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"PP2A Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: PP2A Complex (complex(SCOMP:"PP2A Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"PP2A Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - No Uniprot ID for HGNC ID 4660 INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID21822 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID109543 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:cholesterol) increases tloc(p(MGI:Cycs), fromLoc(GOCCID:0005739), toLoc(GOCCID:0005737))) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID294103 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID305343 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID67836 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID288455 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID22778 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID266806 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID24906 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID299810 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID499422 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID214403 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID290027 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID297961 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID302363 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID71775 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID24157 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID246263 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID298199 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID498940 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID29740 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID24346 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID360504 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID155183 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID287709 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID303689 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID304719 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID361987 to HGNC. INFO: [2019-12-30 10:30:10] indra.sources.bel.processor - Could not map EGID681337 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:corticotropin) increases tloc(p(MGI:Sik1), fromLoc(GOCCID:0005634), toLoc(GOCCID:0005737))) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID59329 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID140910 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID140910 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID29740 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Na/K Exchanging ATPase Complex (complex(SCOMP:"Na/K Exchanging ATPase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Na/K Exchanging ATPase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Respiratory Chain Complex II (complex(SCOMP:"Respiratory Chain Complex II")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Respiratory Chain Complex II")

INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: p85/p110 PI3Kinase Complex (complex(SCOMP:"p85/p110 PI3Kinase Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"p85/p110 PI3Kinase Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID54486 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID29632 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID24737 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID64159 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Controlled translocations are currently not handled: a(CHEBI:estradiol) increases tloc(p(MGI:Ctnnb1), fromLoc(GOCCID:0005737), toLoc(GOCCID:0005634))) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID13909 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Ngf Complex (complex(SCOMP:"Ngf Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Ngf Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID104325 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID13177 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID24157 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID266682 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: AP-1 Complex (complex(SCOMP:"AP-1 Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"AP-1 Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - No Uniprot ID for HGNC ID 11636 INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - No Uniprot ID for HGNC ID 5865

INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unhandled namespace: SCOMP: Nfkb Complex (complex(SCOMP:"Nfkb Complex")) INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: complex(SCOMP:"Nfkb Complex") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID113902 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not find GO ID for cell proliferation INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Unable to get identifier information for node: bp(GOBP:"cell proliferation") INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID52347 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID81879 to HGNC. INFO: [2019-12-30 10:30:11] indra.sources.bel.processor - Could not map EGID18950 to HGNC.

TypeError Traceback (most recent call last)

in 1 from indra.sources import bel ----> 2 bel_processor = bel.process_pybel_neighborhood(['CD80']) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\api.py in process_pybel_neighborhood(entity_names, network_type, network_file, **kwargs) 116 bp.statements. 117 """ --> 118 bp = process_pybel_network(network_type, network_file, **kwargs) 119 filtered_stmts = [] 120 filter_names = set(entity_names) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\api.py in process_pybel_network(network_type, network_file, **kwargs) 79 content = zlib.decompress(res.content, zlib.MAX_WBITS | 32) 80 graph = pybel.from_nodelink_jsons(content) ---> 81 return process_pybel_graph(graph) 82 elif network_type == 'graph_pickle': 83 graph = pybel.from_pickle(network_file) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\api.py in process_pybel_graph(graph) 149 """ 150 bp = PybelProcessor(graph) --> 151 bp.get_statements() 152 if bp.annot_manager.failures: 153 logger.warning('missing %d annotation pairs', ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in get_statements(self) 90 for node_ix, node in enumerate((u_data, v_data)): 91 if isinstance(node, dsl.ComplexAbundance): ---> 92 self._get_enum_complex(u_data, v_data, k, d, node_ix) 93 subj_activity = _get_activity_condition(d.get(pc.SUBJECT)) 94 obj_activity = _get_activity_condition(d.get(pc.OBJECT)) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in _get_enum_complex(self, u_data, v_data, k, edge_data, node_ix) 181 assert node_ix in (0, 1) 182 node = [u_data, v_data][node_ix] --> 183 cplx_agent = get_agent(node, None) 184 if cplx_agent is None: 185 return ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in get_agent(node_data, node_modifier_data) 397 return None 398 bound_conditions = [BoundCondition(get_agent(m), True) --> 399 for m in members[1:]] 400 # Check the bound_conditions for any None agents 401 if any([bc.agent is None for bc in bound_conditions]): ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in (.0) 397 return None 398 bound_conditions = [BoundCondition(get_agent(m), True) --> 399 for m in members[1:]] 400 # Check the bound_conditions for any None agents 401 if any([bc.agent is None for bc in bound_conditions]): ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in get_agent(node_data, node_modifier_data) 414 if not ident: 415 assert name, "Node must have a name if lacking an identifier." --> 416 name, db_refs = get_db_refs_by_name(ns, name, node_data) 417 # We've already got an identifier, look up other identifiers if necessary 418 else: ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\sources\bel\processor.py in get_db_refs_by_name(ns, name, node_data) 466 logger.info("Invalid HGNC name: %s (%s)" % (name, node_data)) 467 return name, None --> 468 name = hgnc_client.get_hgnc_name(hgnc_id) 469 db_refs = {'HGNC': hgnc_id} 470 up_id = _get_up_id(hgnc_id) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\indra\databases\hgnc_client.py in get_hgnc_name(hgnc_id) 120 """ 121 try: --> 122 hgnc_name = hgnc_names[hgnc_id] 123 except KeyError: 124 xml_tree = get_hgnc_entry(hgnc_id) TypeError: unhashable type: 'list' Thank you in advance, Laura
bgyori commented 4 years ago

Have you updated INDRA from Github? The line numbers in your indra\sources\bel\processor.py indicate that you didn't get the latest version which contains the fix in #1018. Please follow the instructions at https://indra.readthedocs.io/en/latest/installation.html#installing-via-github.