From adc5022d22e68cae6a8cdef0dae37fa00e417fb3 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 14:36:44 -0700 Subject: [PATCH 1/8] Replace minerva JSON data with GO-CAM Model JSON --- src/data/examples/Model-663d668500002178.json | 4876 ++++------------- 1 file changed, 1001 insertions(+), 3875 deletions(-) diff --git a/src/data/examples/Model-663d668500002178.json b/src/data/examples/Model-663d668500002178.json index 377e631..8ce30f8 100644 --- a/src/data/examples/Model-663d668500002178.json +++ b/src/data/examples/Model-663d668500002178.json @@ -1,3964 +1,1090 @@ { "id": "gomodel:663d668500002178", - "individuals": [ - { - "id": "gomodel:663d668500002178/663d668500002179", - "type": [ - { - "type": "class", - "id": "GO:0005366", - "label": "myo-inositol:proton symporter activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002180", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC20G8.03", - "label": "itr2 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002181", - "type": [ - { - "type": "class", - "id": "GO:1904679", - "label": "myo-inositol import across plasma membrane" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002182", - "type": [ - { - "type": "class", - "id": "GO:0005886", - "label": "plasma membrane" - } - ], - "root-type": [ - { - "type": "class", - "id": "UBERON:0001062", - "label": "anatomical entity" - }, - { - "type": "class", - "id": "GO:0110165", - "label": "cellular anatomical entity" - }, - { - "type": "class", - "id": "GO:0005575", - "label": "cellular_component" - }, - { - "type": "class", - "id": "CARO:0000000", - "label": "anatomical entity" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002183", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:9560432" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002184", - "type": [ - { - "type": "class", - "id": "ECO:0000316", - "label": "genetic interaction evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "with", - "value": "PomBase:SPAC4F8.15" - }, - { - "key": "source", - "value": "PMID:9560432" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002185", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "PANTHER:PTN000628316 | PomBase:SPAC20G8.03" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002186", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "PMID:9560432" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002187", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "with", - "value": "PANTHER:PTN000628316 | PomBase:SPAC4F8.15 | PomBase:SPAC20G8.03" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002188", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "with", - "value": "SGD:S000002905" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002205", - "type": [ - { - "type": "class", - "id": "GO:0004430", - "label": "1-phosphatidylinositol 4-kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002206", - "type": [ - { - "type": "class", - "id": "PomBase:SPBC577.06c", - "label": "stt4 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002207", - "type": [ - { - "type": "class", - "id": "GO:0046854", - "label": "phosphatidylinositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002208", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "SGD:S000004296" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002209", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "SGD:S000004296" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002211", - "type": [ - { - "type": "class", - "id": "GO:0052811", - "label": "1-phosphatidylinositol-3-phosphate 4-kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002212", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC19G12.14", - "label": "its3 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002213", - "type": [ - { - "type": "class", - "id": "GO:0046854", - "label": "phosphatidylinositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002214", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "PMID:15249580" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002215", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "PMID:29975157" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002216", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:15249580" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002267", - "type": [ - { - "type": "class", - "id": "GO:0052723", - "label": "inositol hexakisphosphate 1-kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002268", - "type": [ - { - "type": "class", - "id": "PomBase:SPCC1672.06c", - "label": "asp1 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002269", - "type": [ - { - "type": "class", - "id": "GO:0043647", - "label": "inositol phosphate metabolic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002270", - "type": [ - { - "type": "class", - "id": "ECO:0000314", - "label": "direct assay evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "PMID:35536002" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002271", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:25254656" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002281", - "type": [ - { - "type": "class", - "id": "GO:0003881", - "label": "CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002282", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC1D4.08", - "label": "pis1 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002283", - "type": [ - { - "type": "class", - "id": "GO:0006661", - "label": "phosphatidylinositol biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002284", - "type": [ - { - "type": "class", - "id": "ECO:0000269", - "label": "experimental evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "PMID:1324908" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002285", - "type": [ - { - "type": "class", - "id": "ECO:0000269", - "label": "experimental evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "PMID:1324908" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002286", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "PMID:9560432" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002287", - "type": [ - { - "type": "class", - "id": "ECO:0000316", - "label": "genetic interaction evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PomBase:SPAC4F8.15" - }, - { - "key": "source", - "value": "PMID:9560432" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002288", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PANTHER:PTN000628316 | PomBase:SPAC20G8.03" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002289", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "PMID:9560432" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002290", - "type": [ - { - "type": "class", - "id": "ECO:0000316", - "label": "genetic interaction evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PomBase:SPAC4F8.15" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:9560432" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002291", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "with", - "value": "PANTHER:PTN000628316 | PomBase:SPAC20G8.03" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002292", - "type": [ - { - "type": "class", - "id": "ECO:0000269", - "label": "experimental evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "source", - "value": "PMID:1324908" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002293", - "type": [ - { - "type": "class", - "id": "ECO:0000269", - "label": "experimental evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:1324908" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002294", - "type": [ - { - "type": "class", - "id": "GO:0043495", - "label": "protein-membrane adaptor activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002295", - "type": [ - { - "type": "class", - "id": "PomBase:SPCC794.08", - "label": "efr3 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002296", - "type": [ - { - "type": "class", - "id": "GO:0046854", - "label": "phosphatidylinositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002297", - "type": [ - { - "type": "class", - "id": "GO:0005886", - "label": "plasma membrane" - } - ], - "root-type": [ - { - "type": "class", - "id": "UBERON:0001062", - "label": "anatomical entity" - }, - { - "type": "class", - "id": "GO:0110165", - "label": "cellular anatomical entity" - }, - { - "type": "class", - "id": "GO:0005575", - "label": "cellular_component" - }, - { - "type": "class", - "id": "CARO:0000000", - "label": "anatomical entity" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002298", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "SGD:S000004825" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002299", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "with", - "value": "SGD:S000004825" - }, - { - "key": "date", - "value": "2024-05-23" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002300", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "with", - "value": "SGD:S000004825" - }, - { - "key": "source", - "value": "GO_REF:0000024" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002301", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "SGD:S000004825" - }, - { - "key": "source", - "value": "GO_REF:0000024" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002532", - "type": [ - { - "type": "class", - "id": "GO:0004435", - "label": "phosphatidylinositol phospholipase C activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002533", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC22F8.11", - "label": "plc1 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002534", - "type": [ - { - "type": "class", - "id": "GO:0032958", - "label": "inositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002535", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "with", - "value": "PANTHER:PTN007434641 | RGD:61993 | WB:WBGene00004036 | dictyBase:DDB_G0292736 | TAIR:locus:2075696 | RGD:69424 | UniProtKB:Q00722 | MGI:MGI:2150308 | RGD:3347 | UniProtKB:P10894 | UniProtKB:Q9P212 | RGD:3344 | MGI:MGI:97615 | UniProtKB:Q01970 | RGD:3346 | RGD:621004 | MGI:MGI:97613 | UniProtKB:O75038 | UniProtKB:Q86YW0 | UniProtKB:Q9NQ66 | UniProtKB:P19174 | RGD:3348 | UniProtKB:P16885 | UniProtKB:P51178 | RGD:621025 | SGD:S000006189 | MGI:MGI:97616 | FB:FBgn0262738" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002536", - "type": [ - { - "type": "class", - "id": "ECO:0000266", - "label": "sequence orthology evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "SGD:S000006189" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000024" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002537", - "type": [ - { - "type": "class", - "id": "ECO:0000315", - "label": "mutant phenotype evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "PMID:15249580" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002545", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC607.04", - "label": "arg82 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002550", - "type": [ - { - "type": "class", - "id": "GO:0035299", - "label": "inositol pentakisphosphate 2-kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002551", - "type": [ - { - "type": "class", - "id": "PomBase:SPCC4B3.10c", - "label": "ipk1 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002552", - "type": [ - { - "type": "class", - "id": "GO:0032958", - "label": "inositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002553", - "type": [ - { - "type": "class", - "id": "ECO:0000314", - "label": "direct assay evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "PMID:10960485" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002554", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "PANTHER:PTN000374859 | UniProtKB:Q580D3 | UniProtKB:Q9H8X2 | FB:FBgn0050295 | RGD:1311271 | TAIR:locus:2165437 | PomBase:SPCC4B3.10c | SGD:S000002723 | ZFIN:ZDB-GENE-050327-41" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002555", - "type": [ - { - "type": "class", - "id": "ECO:0000314", - "label": "direct assay evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "PMID:10960485" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002556", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "with", - "value": "PANTHER:PTN000374859 | SGD:S000002723 | TAIR:locus:2165437 | PomBase:SPCC4B3.10c | CGD:CAL0000194997 | FB:FBgn0050295" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002565", - "type": [ - { - "type": "class", - "id": "GO:0008440", - "label": "inositol-1,4,5-trisphosphate 3-kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002566", - "type": [ - { - "type": "class", - "id": "PomBase:SPAC607.04", - "label": "arg82 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002567", - "type": [ - { - "type": "class", - "id": "GO:0032958", - "label": "inositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002568", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "with", - "value": "PANTHER:PTN000963723 | SGD:S000002580" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002569", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PANTHER:PTN004357288 | UniProtKB:Q96PC2 | MGI:MGI:1923750 | CGD:CAL0000185409 | TAIR:locus:2159203 | SGD:S000002580 | MGI:MGI:1916968 | FB:FBgn0031267 | SGD:S000002424 | FB:FBgn0283680" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002570", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "with", - "value": "PANTHER:PTN007434641 | RGD:61993 | WB:WBGene00004036 | dictyBase:DDB_G0292736 | TAIR:locus:2075696 | RGD:69424 | UniProtKB:Q00722 | MGI:MGI:2150308 | RGD:3347 | UniProtKB:P10894 | UniProtKB:Q9P212 | RGD:3344 | MGI:MGI:97615 | UniProtKB:Q01970 | RGD:3346 | RGD:621004 | MGI:MGI:97613 | UniProtKB:O75038 | UniProtKB:Q86YW0 | UniProtKB:Q9NQ66 | UniProtKB:P19174 | RGD:3348 | UniProtKB:P16885 | UniProtKB:P51178 | RGD:621025 | SGD:S000006189 | MGI:MGI:97616 | FB:FBgn0262738" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002571", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "with", - "value": "PANTHER:PTN000963723 | SGD:S000002580" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002572", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "PANTHER:PTN000963723 | SGD:S000002580" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002573", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "PANTHER:PTN000963723 | SGD:S000002580" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002574", - "type": [ - { - "type": "class", - "id": "GO:0000828", - "label": "inositol hexakisphosphate kinase activity" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0003674", - "label": "molecular_function" - }, - { - "type": "class", - "id": "obo:go/extensions/reacto.owl#molecular_event", - "label": "Molecular Event" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002575", - "type": [ - { - "type": "class", - "id": "PomBase:SPCC970.08", - "label": "kcs1 Spom" - } - ], - "root-type": [ - { - "type": "class", - "id": "CHEBI:33695", - "label": "information biomacromolecule" - }, - { - "type": "class", - "id": "CHEBI:24431", - "label": "chemical entity" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002576", - "type": [ - { - "type": "class", - "id": "GO:0032958", - "label": "inositol phosphate biosynthetic process" - } - ], - "root-type": [ - { - "type": "class", - "id": "GO:0008150", - "label": "biological_process" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002577", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PANTHER:PTN000274018 | UniProtKB:Q57X56 | MGI:MGI:1923750 | UniProtKB:Q96PC2 | UniProtKB:Q9UHH9 | SGD:S000002424 | dictyBase:DDB_G0278739 | UniProtKB:Q92551" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002578", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "with", - "value": "PANTHER:PTN004357288 | UniProtKB:Q96PC2 | MGI:MGI:1923750 | CGD:CAL0000185409 | TAIR:locus:2159203 | SGD:S000002580 | MGI:MGI:1916968 | FB:FBgn0031267 | SGD:S000002424 | FB:FBgn0283680" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002583", - "type": [ - { - "type": "class", - "id": "ECO:0000314", - "label": "direct assay evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "PMID:10960485" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002584", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PANTHER:PTN000374859 | UniProtKB:Q580D3 | UniProtKB:Q9H8X2 | FB:FBgn0050295 | RGD:1311271 | TAIR:locus:2165437 | PomBase:SPCC4B3.10c | SGD:S000002723 | ZFIN:ZDB-GENE-050327-41" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002585", - "type": [ - { - "type": "class", - "id": "ECO:0000314", - "label": "direct assay evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "source", - "value": "PMID:10960485" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002586", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "with", - "value": "PANTHER:PTN000374859 | UniProtKB:Q580D3 | UniProtKB:Q9H8X2 | FB:FBgn0050295 | RGD:1311271 | TAIR:locus:2165437 | PomBase:SPCC4B3.10c | SGD:S000002723 | ZFIN:ZDB-GENE-050327-41" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "source", - "value": "GO_REF:0000033" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002587", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "with", - "value": "PANTHER:PTN000274018 | UniProtKB:Q57X56 | MGI:MGI:1923750 | UniProtKB:Q96PC2 | UniProtKB:Q9UHH9 | SGD:S000002424 | dictyBase:DDB_G0278739 | UniProtKB:Q92551" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - }, - { - "id": "gomodel:663d668500002178/663d668500002588", - "type": [ - { - "type": "class", - "id": "ECO:0000318", - "label": "biological aspect of ancestor evidence used in manual assertion" - } - ], - "root-type": [ - { - "type": "class", - "id": "ECO:0000000", - "label": "evidence" - } - ], - "annotations": [ - { - "key": "with", - "value": "PANTHER:PTN000274018 | UniProtKB:Q57X56 | MGI:MGI:1923750 | UniProtKB:Q96PC2 | UniProtKB:Q9UHH9 | SGD:S000002424 | dictyBase:DDB_G0278739 | UniProtKB:Q92551" - }, - { - "key": "source", - "value": "GO_REF:0000033" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - } - ] - } + "title": "GO:0046854\tphosphatidylinositol phosphate biosynthetic process and GO:0006661\t\nGO:0006661\tphosphatidylinositol biosynthetic process and GO:0043647 inositol phosphate metabolic process", + "taxon": "NCBITaxon:4896", + "status": "production", + "comments": [ + "Need to add \"inositol phosphate metabolic process\" (GO:0043647) to everything after plc1", + "add major intermediates", + "reference https://www.pombase.org/reference/PMID:38133430" ], - "facts": [ - { - "subject": "gomodel:663d668500002178/663d668500002532", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002533", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002535", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002179", - "property": "BFO:0000066", - "property-label": "BFO:0000066", - "object": "gomodel:663d668500002178/663d668500002182", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002188", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002294", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002295", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002298", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002574", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002576", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002578", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002294", - "property": "RO:0002629", - "property-label": "RO:0002629", - "object": "gomodel:663d668500002178/663d668500002205", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002299", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002300", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002301", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002574", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002267", - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002281", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002211", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002292", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002550", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002574", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002583", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002584", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002267", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002269", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002271", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002179", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002180", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002183", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002184", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002185", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - }, - { - "subject": "gomodel:663d668500002178/663d668500002205", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002207", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002209", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "activities": [ + { + "id": "gomodel:663d668500002178/663d668500002532", + "enabled_by": "PomBase:SPAC22F8.11", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN007434641", + "RGD:61993", + "WB:WBGene00004036", + "dictyBase:DDB_G0292736", + "TAIR:locus:2075696", + "RGD:69424", + "UniProtKB:Q00722", + "MGI:MGI:2150308", + "RGD:3347", + "UniProtKB:P10894", + "UniProtKB:Q9P212", + "RGD:3344", + "MGI:MGI:97615", + "UniProtKB:Q01970", + "RGD:3346", + "RGD:621004", + "MGI:MGI:97613", + "UniProtKB:O75038", + "UniProtKB:Q86YW0", + "UniProtKB:Q9NQ66", + "UniProtKB:P19174", + "RGD:3348", + "UniProtKB:P16885", + "UniProtKB:P51178", + "RGD:621025", + "SGD:S000006189", + "MGI:MGI:97616", + "FB:FBgn0262738" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0004435" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000006189" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0032958" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN007434641", + "RGD:61993", + "WB:WBGene00004036", + "dictyBase:DDB_G0292736", + "TAIR:locus:2075696", + "RGD:69424", + "UniProtKB:Q00722", + "MGI:MGI:2150308", + "RGD:3347", + "UniProtKB:P10894", + "UniProtKB:Q9P212", + "RGD:3344", + "MGI:MGI:97615", + "UniProtKB:Q01970", + "RGD:3346", + "RGD:621004", + "MGI:MGI:97613", + "UniProtKB:O75038", + "UniProtKB:Q86YW0", + "UniProtKB:Q9NQ66", + "UniProtKB:P19174", + "RGD:3348", + "UniProtKB:P16885", + "UniProtKB:P51178", + "RGD:621025", + "SGD:S000006189", + "MGI:MGI:97616", + "FB:FBgn0262738" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002565" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002574", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002267", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002587", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002588", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002294", + "enabled_by": "PomBase:SPCC794.08", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004825" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0043495" + }, + "occurs_in": { + "evidence": [], + "term": "GO:0005886" + }, + "part_of": { + "evidence": [], + "term": "GO:0046854" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004825" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004825" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004825" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "predicate": "RO:0002629", + "downstream_activity": "gomodel:663d668500002178/663d668500002205" + }, + { + "evidence": [], + "predicate": "RO:0002629", + "downstream_activity": "gomodel:663d668500002178/663d668500002205" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002532", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002565", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002570", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002179", + "enabled_by": "PomBase:SPAC20G8.03", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:9560432", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000316", + "reference": "PMID:9560432", + "with_objects": [ + "PomBase:SPAC4F8.15" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000628316", + "PomBase:SPAC20G8.03" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0005366" + }, + "occurs_in": { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000002905" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0005886" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:9560432", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000628316", + "PomBase:SPAC4F8.15", + "PomBase:SPAC20G8.03" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:1904679" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:9560432", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000316", + "reference": "PMID:9560432", + "with_objects": [ + "PomBase:SPAC4F8.15" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000628316", + "PomBase:SPAC20G8.03" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000316", + "reference": "PMID:9560432", + "with_objects": [ + "PomBase:SPAC4F8.15" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002281" + }, + { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:9560432", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000628316", + "PomBase:SPAC20G8.03" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002281" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002550", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002552", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002555", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002556", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002574", + "enabled_by": "PomBase:SPCC970.08", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000274018", + "UniProtKB:Q57X56", + "MGI:MGI:1923750", + "UniProtKB:Q96PC2", + "UniProtKB:Q9UHH9", + "SGD:S000002424", + "dictyBase:DDB_G0278739", + "UniProtKB:Q92551" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0000828" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN004357288", + "UniProtKB:Q96PC2", + "MGI:MGI:1923750", + "CGD:CAL0000185409", + "TAIR:locus:2159203", + "SGD:S000002580", + "MGI:MGI:1916968", + "FB:FBgn0031267", + "SGD:S000002424", + "FB:FBgn0283680" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0032958" + }, + "causal_associations": [ + { + "evidence": [], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002267" + }, + { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000274018", + "UniProtKB:Q57X56", + "MGI:MGI:1923750", + "UniProtKB:Q96PC2", + "UniProtKB:Q9UHH9", + "SGD:S000002424", + "dictyBase:DDB_G0278739", + "UniProtKB:Q92551" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000274018", + "UniProtKB:Q57X56", + "MGI:MGI:1923750", + "UniProtKB:Q96PC2", + "UniProtKB:Q9UHH9", + "SGD:S000002424", + "dictyBase:DDB_G0278739", + "UniProtKB:Q92551" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002267" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002211", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002213", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002215", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002216", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002565", + "enabled_by": "PomBase:SPAC607.04", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000963723", + "SGD:S000002580" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0008440" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN004357288", + "UniProtKB:Q96PC2", + "MGI:MGI:1923750", + "CGD:CAL0000185409", + "TAIR:locus:2159203", + "SGD:S000002580", + "MGI:MGI:1916968", + "FB:FBgn0031267", + "SGD:S000002424", + "FB:FBgn0283680" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0032958" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000963723", + "SGD:S000002580" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002550" + }, + { + "evidence": [ + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000963723", + "SGD:S000002580" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000963723", + "SGD:S000002580" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002550" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002574", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002575", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002577", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002211", + "enabled_by": "PomBase:SPAC19G12.14", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:15249580", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0052811" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:29975157", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + }, + { + "term": "ECO:0000315", + "reference": "PMID:15249580", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0046854" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:15249580", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002532" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002281", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002283", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002285", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002550", + "enabled_by": "PomBase:SPCC4B3.10c", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000314", + "reference": "PMID:10960485", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000374859", + "UniProtKB:Q580D3", + "UniProtKB:Q9H8X2", + "FB:FBgn0050295", + "RGD:1311271", + "TAIR:locus:2165437", + "PomBase:SPCC4B3.10c", + "SGD:S000002723", + "ZFIN:ZDB-GENE-050327-41" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0035299" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000314", + "reference": "PMID:10960485", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000374859", + "SGD:S000002723", + "TAIR:locus:2165437", + "PomBase:SPCC4B3.10c", + "CGD:CAL0000194997", + "FB:FBgn0050295" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "term": "GO:0032958" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000314", + "reference": "PMID:10960485", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000374859", + "UniProtKB:Q580D3", + "UniProtKB:Q9H8X2", + "FB:FBgn0050295", + "RGD:1311271", + "TAIR:locus:2165437", + "PomBase:SPCC4B3.10c", + "SGD:S000002723", + "ZFIN:ZDB-GENE-050327-41" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002574" + }, + { + "evidence": [ + { + "term": "ECO:0000314", + "reference": "PMID:10960485", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + }, + { + "term": "ECO:0000318", + "reference": "GO_REF:0000033", + "with_objects": [ + "PANTHER:PTN000374859", + "UniProtKB:Q580D3", + "UniProtKB:Q9H8X2", + "FB:FBgn0050295", + "RGD:1311271", + "TAIR:locus:2165437", + "PomBase:SPCC4B3.10c", + "SGD:S000002723", + "ZFIN:ZDB-GENE-050327-41" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-24" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002574" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002565", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002566", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002568", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "gomodel:663d668500002178/663d668500002205", + "enabled_by": "PomBase:SPBC577.06c", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004296" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0004430" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000266", + "reference": "GO_REF:0000024", + "with_objects": [ + "SGD:S000004296" + ], + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0046854" + } }, { - "subject": "gomodel:663d668500002178/663d668500002211", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002532", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002537", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "gomodel:663d668500002178/663d668500002281", + "enabled_by": "PomBase:SPAC1D4.08", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000269", + "reference": "PMID:1324908", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0003881" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000269", + "reference": "PMID:1324908", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0006661" + }, + "causal_associations": [ + { + "evidence": [ + { + "term": "ECO:0000269", + "reference": "PMID:1324908", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002211" + }, + { + "evidence": [ + { + "term": "ECO:0000269", + "reference": "PMID:1324908", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "predicate": "RO:0002413", + "downstream_activity": "gomodel:663d668500002178/663d668500002205" } ] }, { - "subject": "gomodel:663d668500002178/663d668500002211", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002212", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002214", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "gomodel:663d668500002178/663d668500002267", + "enabled_by": "PomBase:SPCC1672.06c", + "molecular_function": { + "evidence": [ + { + "term": "ECO:0000314", + "reference": "PMID:35536002", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0052723" + }, + "part_of": { + "evidence": [ + { + "term": "ECO:0000315", + "reference": "PMID:25254656", + "provenances": [ + { + "contributor": "https://orcid.org/0000-0001-6330-7526", + "date": "2024-05-23" + } + ] + } + ], + "term": "GO:0043647" + } + } + ], + "objects": [ + { + "id": "GO:0005366", + "label": "myo-inositol:proton symporter activity" }, { - "subject": "gomodel:663d668500002178/663d668500002565", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002550", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002573", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "PomBase:SPAC20G8.03", + "label": "itr2 Spom" }, { - "subject": "gomodel:663d668500002178/663d668500002550", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002551", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002553", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002554", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:1904679", + "label": "myo-inositol import across plasma membrane" }, { - "subject": "gomodel:663d668500002178/663d668500002532", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002534", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002536", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0005886", + "label": "plasma membrane" }, { - "subject": "gomodel:663d668500002178/663d668500002294", - "property": "BFO:0000066", - "property-label": "BFO:0000066", - "object": "gomodel:663d668500002178/663d668500002297", - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "ECO:0000315", + "label": "mutant phenotype evidence used in manual assertion" }, { - "subject": "gomodel:663d668500002178/663d668500002205", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002206", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002208", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "ECO:0000316", + "label": "genetic interaction evidence used in manual assertion" }, { - "subject": "gomodel:663d668500002178/663d668500002550", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002574", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002585", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002586", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "ECO:0000318", + "label": "biological aspect of ancestor evidence used in manual assertion" }, { - "subject": "gomodel:663d668500002178/663d668500002294", - "property": "RO:0002629", - "property-label": "RO:0002629", - "object": "gomodel:663d668500002178/663d668500002205", - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "ECO:0000266", + "label": "sequence orthology evidence used in manual assertion" }, { - "subject": "gomodel:663d668500002178/663d668500002179", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002281", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002286", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002287", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002288", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002290", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0004430", + "label": "1-phosphatidylinositol 4-kinase activity" }, { - "subject": "gomodel:663d668500002178/663d668500002294", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002296", - "annotations": [ - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "PomBase:SPBC577.06c", + "label": "stt4 Spom" }, { - "subject": "gomodel:663d668500002178/663d668500002281", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002282", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002284", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0046854", + "label": "phosphatidylinositol phosphate biosynthetic process" }, { - "subject": "gomodel:663d668500002178/663d668500002565", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002567", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002569", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0052811", + "label": "1-phosphatidylinositol-3-phosphate 4-kinase activity" }, { - "subject": "gomodel:663d668500002178/663d668500002281", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002205", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002293", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "PomBase:SPAC19G12.14", + "label": "its3 Spom" }, { - "subject": "gomodel:663d668500002178/663d668500002179", - "property": "BFO:0000050", - "property-label": "BFO:0000050", - "object": "gomodel:663d668500002178/663d668500002181", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002186", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002187", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0052723", + "label": "inositol hexakisphosphate 1-kinase activity" }, { - "subject": "gomodel:663d668500002178/663d668500002179", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002281", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002289", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002291", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "PomBase:SPCC1672.06c", + "label": "asp1 Spom" }, { - "subject": "gomodel:663d668500002178/663d668500002267", - "property": "RO:0002333", - "property-label": "RO:0002333", - "object": "gomodel:663d668500002178/663d668500002268", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002270", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-23" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] + "id": "GO:0043647", + "label": "inositol phosphate metabolic process" }, { - "subject": "gomodel:663d668500002178/663d668500002565", - "property": "RO:0002413", - "property-label": "RO:0002413", - "object": "gomodel:663d668500002178/663d668500002550", - "annotations": [ - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002571", - "value-type": "IRI" - }, - { - "key": "evidence", - "value": "gomodel:663d668500002178/663d668500002572", - "value-type": "IRI" - }, - { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" - }, - { - "key": "date", - "value": "2024-05-24" - }, - { - "key": "providedBy", - "value": "http://www.pombase.org" - } - ] - } - ], - "annotations": [ + "id": "ECO:0000314", + "label": "direct assay evidence used in manual assertion" + }, + { + "id": "GO:0003881", + "label": "CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity" + }, + { + "id": "PomBase:SPAC1D4.08", + "label": "pis1 Spom" + }, + { + "id": "GO:0006661", + "label": "phosphatidylinositol biosynthetic process" + }, + { + "id": "ECO:0000269", + "label": "experimental evidence used in manual assertion" + }, + { + "id": "GO:0043495", + "label": "protein-membrane adaptor activity" + }, + { + "id": "PomBase:SPCC794.08", + "label": "efr3 Spom" + }, { - "key": "state", - "value": "production" + "id": "GO:0004435", + "label": "phosphatidylinositol phospholipase C activity" }, { - "key": "contributor", - "value": "https://orcid.org/0000-0001-6330-7526" + "id": "PomBase:SPAC22F8.11", + "label": "plc1 Spom" }, { - "key": "date", - "value": "2024-05-24" + "id": "GO:0032958", + "label": "inositol phosphate biosynthetic process" }, { - "key": "title", - "value": "GO:0046854\tphosphatidylinositol phosphate biosynthetic process and GO:0006661\t\nGO:0006661\tphosphatidylinositol biosynthetic process and GO:0043647 inositol phosphate metabolic process" + "id": "PomBase:SPAC607.04", + "label": "arg82 Spom" }, { - "key": "providedBy", - "value": "http://www.pombase.org" + "id": "GO:0035299", + "label": "inositol pentakisphosphate 2-kinase activity" }, { - "key": "comment", - "value": "Need to add \"inositol phosphate metabolic process\" (GO:0043647) to everything after plc1" + "id": "PomBase:SPCC4B3.10c", + "label": "ipk1 Spom" }, { - "key": "comment", - "value": "add major intermediates" + "id": "GO:0008440", + "label": "inositol-1,4,5-trisphosphate 3-kinase activity" }, { - "key": "comment", - "value": "reference https://www.pombase.org/reference/PMID:38133430" + "id": "GO:0000828", + "label": "inositol hexakisphosphate kinase activity" }, { - "key": "https://w3id.org/biolink/vocab/in_taxon", - "value": "NCBITaxon:4896", - "value-type": "IRI" + "id": "PomBase:SPCC970.08", + "label": "kcs1 Spom" } ] } From 403079ad8a6cd09fd14b42899bafdcef559a2594 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 14:37:10 -0700 Subject: [PATCH 2/8] Add YAML example data --- src/data/examples/Model-663d668500002178.yaml | 646 ++++++++++++++++++ 1 file changed, 646 insertions(+) create mode 100644 src/data/examples/Model-663d668500002178.yaml diff --git a/src/data/examples/Model-663d668500002178.yaml b/src/data/examples/Model-663d668500002178.yaml new file mode 100644 index 0000000..46fd032 --- /dev/null +++ b/src/data/examples/Model-663d668500002178.yaml @@ -0,0 +1,646 @@ +--- +id: gomodel:663d668500002178 +title: "GO:0046854\tphosphatidylinositol phosphate biosynthetic process and GO:0006661\t\ + \nGO:0006661\tphosphatidylinositol biosynthetic process and GO:0043647 inositol\ + \ phosphate metabolic process" +taxon: NCBITaxon:4896 +status: production +comments: +- Need to add "inositol phosphate metabolic process" (GO:0043647) to everything after + plc1 +- add major intermediates +- reference https://www.pombase.org/reference/PMID:38133430 +activities: +- id: gomodel:663d668500002178/663d668500002532 + enabled_by: PomBase:SPAC22F8.11 + molecular_function: + evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN007434641 + - RGD:61993 + - WB:WBGene00004036 + - dictyBase:DDB_G0292736 + - TAIR:locus:2075696 + - RGD:69424 + - UniProtKB:Q00722 + - MGI:MGI:2150308 + - RGD:3347 + - UniProtKB:P10894 + - UniProtKB:Q9P212 + - RGD:3344 + - MGI:MGI:97615 + - UniProtKB:Q01970 + - RGD:3346 + - RGD:621004 + - MGI:MGI:97613 + - UniProtKB:O75038 + - UniProtKB:Q86YW0 + - UniProtKB:Q9NQ66 + - UniProtKB:P19174 + - RGD:3348 + - UniProtKB:P16885 + - UniProtKB:P51178 + - RGD:621025 + - SGD:S000006189 + - MGI:MGI:97616 + - FB:FBgn0262738 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0004435 + part_of: + evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000006189 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0032958 + causal_associations: + - evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN007434641 + - RGD:61993 + - WB:WBGene00004036 + - dictyBase:DDB_G0292736 + - TAIR:locus:2075696 + - RGD:69424 + - UniProtKB:Q00722 + - MGI:MGI:2150308 + - RGD:3347 + - UniProtKB:P10894 + - UniProtKB:Q9P212 + - RGD:3344 + - MGI:MGI:97615 + - UniProtKB:Q01970 + - RGD:3346 + - RGD:621004 + - MGI:MGI:97613 + - UniProtKB:O75038 + - UniProtKB:Q86YW0 + - UniProtKB:Q9NQ66 + - UniProtKB:P19174 + - RGD:3348 + - UniProtKB:P16885 + - UniProtKB:P51178 + - RGD:621025 + - SGD:S000006189 + - MGI:MGI:97616 + - FB:FBgn0262738 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002565 +- id: gomodel:663d668500002178/663d668500002294 + enabled_by: PomBase:SPCC794.08 + molecular_function: + evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004825 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0043495 + occurs_in: + evidence: [] + term: GO:0005886 + part_of: + evidence: [] + term: GO:0046854 + causal_associations: + - evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004825 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004825 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004825 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + predicate: RO:0002629 + downstream_activity: gomodel:663d668500002178/663d668500002205 + - evidence: [] + predicate: RO:0002629 + downstream_activity: gomodel:663d668500002178/663d668500002205 +- id: gomodel:663d668500002178/663d668500002179 + enabled_by: PomBase:SPAC20G8.03 + molecular_function: + evidence: + - term: ECO:0000315 + reference: PMID:9560432 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000316 + reference: PMID:9560432 + with_objects: + - PomBase:SPAC4F8.15 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000628316 + - PomBase:SPAC20G8.03 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0005366 + occurs_in: + evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000002905 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0005886 + part_of: + evidence: + - term: ECO:0000315 + reference: PMID:9560432 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000628316 + - PomBase:SPAC4F8.15 + - PomBase:SPAC20G8.03 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:1904679 + causal_associations: + - evidence: + - term: ECO:0000315 + reference: PMID:9560432 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000316 + reference: PMID:9560432 + with_objects: + - PomBase:SPAC4F8.15 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000628316 + - PomBase:SPAC20G8.03 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000316 + reference: PMID:9560432 + with_objects: + - PomBase:SPAC4F8.15 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002281 + - evidence: + - term: ECO:0000315 + reference: PMID:9560432 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000628316 + - PomBase:SPAC20G8.03 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002281 +- id: gomodel:663d668500002178/663d668500002574 + enabled_by: PomBase:SPCC970.08 + molecular_function: + evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000274018 + - UniProtKB:Q57X56 + - MGI:MGI:1923750 + - UniProtKB:Q96PC2 + - UniProtKB:Q9UHH9 + - SGD:S000002424 + - dictyBase:DDB_G0278739 + - UniProtKB:Q92551 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0000828 + part_of: + evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN004357288 + - UniProtKB:Q96PC2 + - MGI:MGI:1923750 + - CGD:CAL0000185409 + - TAIR:locus:2159203 + - SGD:S000002580 + - MGI:MGI:1916968 + - FB:FBgn0031267 + - SGD:S000002424 + - FB:FBgn0283680 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0032958 + causal_associations: + - evidence: [] + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002267 + - evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000274018 + - UniProtKB:Q57X56 + - MGI:MGI:1923750 + - UniProtKB:Q96PC2 + - UniProtKB:Q9UHH9 + - SGD:S000002424 + - dictyBase:DDB_G0278739 + - UniProtKB:Q92551 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000274018 + - UniProtKB:Q57X56 + - MGI:MGI:1923750 + - UniProtKB:Q96PC2 + - UniProtKB:Q9UHH9 + - SGD:S000002424 + - dictyBase:DDB_G0278739 + - UniProtKB:Q92551 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002267 +- id: gomodel:663d668500002178/663d668500002565 + enabled_by: PomBase:SPAC607.04 + molecular_function: + evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000963723 + - SGD:S000002580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0008440 + part_of: + evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN004357288 + - UniProtKB:Q96PC2 + - MGI:MGI:1923750 + - CGD:CAL0000185409 + - TAIR:locus:2159203 + - SGD:S000002580 + - MGI:MGI:1916968 + - FB:FBgn0031267 + - SGD:S000002424 + - FB:FBgn0283680 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0032958 + causal_associations: + - evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000963723 + - SGD:S000002580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002550 + - evidence: + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000963723 + - SGD:S000002580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000963723 + - SGD:S000002580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002550 +- id: gomodel:663d668500002178/663d668500002211 + enabled_by: PomBase:SPAC19G12.14 + molecular_function: + evidence: + - term: ECO:0000315 + reference: PMID:15249580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0052811 + part_of: + evidence: + - term: ECO:0000315 + reference: PMID:29975157 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + - term: ECO:0000315 + reference: PMID:15249580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0046854 + causal_associations: + - evidence: + - term: ECO:0000315 + reference: PMID:15249580 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002532 +- id: gomodel:663d668500002178/663d668500002550 + enabled_by: PomBase:SPCC4B3.10c + molecular_function: + evidence: + - term: ECO:0000314 + reference: PMID:10960485 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000374859 + - UniProtKB:Q580D3 + - UniProtKB:Q9H8X2 + - FB:FBgn0050295 + - RGD:1311271 + - TAIR:locus:2165437 + - PomBase:SPCC4B3.10c + - SGD:S000002723 + - ZFIN:ZDB-GENE-050327-41 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0035299 + part_of: + evidence: + - term: ECO:0000314 + reference: PMID:10960485 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000374859 + - SGD:S000002723 + - TAIR:locus:2165437 + - PomBase:SPCC4B3.10c + - CGD:CAL0000194997 + - FB:FBgn0050295 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + term: GO:0032958 + causal_associations: + - evidence: + - term: ECO:0000314 + reference: PMID:10960485 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000374859 + - UniProtKB:Q580D3 + - UniProtKB:Q9H8X2 + - FB:FBgn0050295 + - RGD:1311271 + - TAIR:locus:2165437 + - PomBase:SPCC4B3.10c + - SGD:S000002723 + - ZFIN:ZDB-GENE-050327-41 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002574 + - evidence: + - term: ECO:0000314 + reference: PMID:10960485 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + - term: ECO:0000318 + reference: GO_REF:0000033 + with_objects: + - PANTHER:PTN000374859 + - UniProtKB:Q580D3 + - UniProtKB:Q9H8X2 + - FB:FBgn0050295 + - RGD:1311271 + - TAIR:locus:2165437 + - PomBase:SPCC4B3.10c + - SGD:S000002723 + - ZFIN:ZDB-GENE-050327-41 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-24' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002574 +- id: gomodel:663d668500002178/663d668500002205 + enabled_by: PomBase:SPBC577.06c + molecular_function: + evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004296 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0004430 + part_of: + evidence: + - term: ECO:0000266 + reference: GO_REF:0000024 + with_objects: + - SGD:S000004296 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0046854 +- id: gomodel:663d668500002178/663d668500002281 + enabled_by: PomBase:SPAC1D4.08 + molecular_function: + evidence: + - term: ECO:0000269 + reference: PMID:1324908 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0003881 + part_of: + evidence: + - term: ECO:0000269 + reference: PMID:1324908 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0006661 + causal_associations: + - evidence: + - term: ECO:0000269 + reference: PMID:1324908 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002211 + - evidence: + - term: ECO:0000269 + reference: PMID:1324908 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + predicate: RO:0002413 + downstream_activity: gomodel:663d668500002178/663d668500002205 +- id: gomodel:663d668500002178/663d668500002267 + enabled_by: PomBase:SPCC1672.06c + molecular_function: + evidence: + - term: ECO:0000314 + reference: PMID:35536002 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0052723 + part_of: + evidence: + - term: ECO:0000315 + reference: PMID:25254656 + provenances: + - contributor: https://orcid.org/0000-0001-6330-7526 + date: '2024-05-23' + term: GO:0043647 +objects: +- id: GO:0005366 + label: myo-inositol:proton symporter activity +- id: PomBase:SPAC20G8.03 + label: itr2 Spom +- id: GO:1904679 + label: myo-inositol import across plasma membrane +- id: GO:0005886 + label: plasma membrane +- id: ECO:0000315 + label: mutant phenotype evidence used in manual assertion +- id: ECO:0000316 + label: genetic interaction evidence used in manual assertion +- id: ECO:0000318 + label: biological aspect of ancestor evidence used in manual assertion +- id: ECO:0000266 + label: sequence orthology evidence used in manual assertion +- id: GO:0004430 + label: 1-phosphatidylinositol 4-kinase activity +- id: PomBase:SPBC577.06c + label: stt4 Spom +- id: GO:0046854 + label: phosphatidylinositol phosphate biosynthetic process +- id: GO:0052811 + label: 1-phosphatidylinositol-3-phosphate 4-kinase activity +- id: PomBase:SPAC19G12.14 + label: its3 Spom +- id: GO:0052723 + label: inositol hexakisphosphate 1-kinase activity +- id: PomBase:SPCC1672.06c + label: asp1 Spom +- id: GO:0043647 + label: inositol phosphate metabolic process +- id: ECO:0000314 + label: direct assay evidence used in manual assertion +- id: GO:0003881 + label: CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity +- id: PomBase:SPAC1D4.08 + label: pis1 Spom +- id: GO:0006661 + label: phosphatidylinositol biosynthetic process +- id: ECO:0000269 + label: experimental evidence used in manual assertion +- id: GO:0043495 + label: protein-membrane adaptor activity +- id: PomBase:SPCC794.08 + label: efr3 Spom +- id: GO:0004435 + label: phosphatidylinositol phospholipase C activity +- id: PomBase:SPAC22F8.11 + label: plc1 Spom +- id: GO:0032958 + label: inositol phosphate biosynthetic process +- id: PomBase:SPAC607.04 + label: arg82 Spom +- id: GO:0035299 + label: inositol pentakisphosphate 2-kinase activity +- id: PomBase:SPCC4B3.10c + label: ipk1 Spom +- id: GO:0008440 + label: inositol-1,4,5-trisphosphate 3-kinase activity +- id: GO:0000828 + label: inositol hexakisphosphate kinase activity +- id: PomBase:SPCC970.08 + label: kcs1 Spom + From 3cecd50b156bc2d4ab605c400b55ae86882c82bb Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 14:43:42 -0700 Subject: [PATCH 3/8] Sort imports --- src/gocam/translation/minerva_wrapper.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/gocam/translation/minerva_wrapper.py b/src/gocam/translation/minerva_wrapper.py index 4e682a1..6c4bb82 100644 --- a/src/gocam/translation/minerva_wrapper.py +++ b/src/gocam/translation/minerva_wrapper.py @@ -1,20 +1,20 @@ import logging from collections import defaultdict from dataclasses import dataclass, field -from typing import Dict, Iterator, Optional, List, DefaultDict +from typing import DefaultDict, Dict, Iterator, List, Optional import requests import yaml from gocam.datamodel import ( - Model, Activity, - MolecularFunctionAssociation, BiologicalProcessAssociation, - CellularAnatomicalEntityAssociation, CausalAssociation, - Object, + CellularAnatomicalEntityAssociation, EvidenceItem, + Model, + MolecularFunctionAssociation, + Object, ProvenanceInfo, ) From 7eb075d1c226fb50cce0c23a3ffb09aceba95de4 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 14:49:49 -0700 Subject: [PATCH 4/8] Add package for generating CX2 files from Model instances --- poetry.lock | 307 ++++++++++++++++++++- pyproject.toml | 1 + src/gocam/translation/cx2/__init__.py | 1 + src/gocam/translation/cx2/main.py | 89 +++++++ src/gocam/translation/cx2/style.py | 369 ++++++++++++++++++++++++++ tests/__init__.py | 4 +- tests/test_translation/test_cx2.py | 43 +++ 7 files changed, 812 insertions(+), 2 deletions(-) create mode 100644 src/gocam/translation/cx2/__init__.py create mode 100644 src/gocam/translation/cx2/main.py create mode 100644 src/gocam/translation/cx2/style.py create mode 100644 tests/test_translation/test_cx2.py diff --git a/poetry.lock b/poetry.lock index df78108..8effebc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -674,6 +674,109 @@ files = [ {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, ] +[[package]] +name = "ijson" +version = "3.3.0" +description = "Iterative JSON parser with standard Python iterator interfaces" +optional = false +python-versions = "*" +files = [ + {file = "ijson-3.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7f7a5250599c366369fbf3bc4e176f5daa28eb6bc7d6130d02462ed335361675"}, + {file = "ijson-3.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f87a7e52f79059f9c58f6886c262061065eb6f7554a587be7ed3aa63e6b71b34"}, + {file = "ijson-3.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b73b493af9e947caed75d329676b1b801d673b17481962823a3e55fe529c8b8b"}, + {file = "ijson-3.3.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d5576415f3d76290b160aa093ff968f8bf6de7d681e16e463a0134106b506f49"}, + {file = "ijson-3.3.0-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4e9ffe358d5fdd6b878a8a364e96e15ca7ca57b92a48f588378cef315a8b019e"}, + {file = "ijson-3.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8643c255a25824ddd0895c59f2319c019e13e949dc37162f876c41a283361527"}, + {file = "ijson-3.3.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:df3ab5e078cab19f7eaeef1d5f063103e1ebf8c26d059767b26a6a0ad8b250a3"}, + {file = "ijson-3.3.0-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:3dc1fb02c6ed0bae1b4bf96971258bf88aea72051b6e4cebae97cff7090c0607"}, + {file = "ijson-3.3.0-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:e9afd97339fc5a20f0542c971f90f3ca97e73d3050cdc488d540b63fae45329a"}, + {file = "ijson-3.3.0-cp310-cp310-win32.whl", hash = "sha256:844c0d1c04c40fd1b60f148dc829d3f69b2de789d0ba239c35136efe9a386529"}, + {file = "ijson-3.3.0-cp310-cp310-win_amd64.whl", hash = "sha256:d654d045adafdcc6c100e8e911508a2eedbd2a1b5f93f930ba13ea67d7704ee9"}, + {file = "ijson-3.3.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:501dce8eaa537e728aa35810656aa00460a2547dcb60937c8139f36ec344d7fc"}, + {file = "ijson-3.3.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:658ba9cad0374d37b38c9893f4864f284cdcc7d32041f9808fba8c7bcaadf134"}, + {file = "ijson-3.3.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:2636cb8c0f1023ef16173f4b9a233bcdb1df11c400c603d5f299fac143ca8d70"}, + {file = "ijson-3.3.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cd174b90db68c3bcca273e9391934a25d76929d727dc75224bf244446b28b03b"}, + {file = "ijson-3.3.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:97a9aea46e2a8371c4cf5386d881de833ed782901ac9f67ebcb63bb3b7d115af"}, + {file = "ijson-3.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c594c0abe69d9d6099f4ece17763d53072f65ba60b372d8ba6de8695ce6ee39e"}, + {file = "ijson-3.3.0-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8e0ff16c224d9bfe4e9e6bd0395826096cda4a3ef51e6c301e1b61007ee2bd24"}, + {file = "ijson-3.3.0-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:0015354011303175eae7e2ef5136414e91de2298e5a2e9580ed100b728c07e51"}, + {file = "ijson-3.3.0-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:034642558afa57351a0ffe6de89e63907c4cf6849070cc10a3b2542dccda1afe"}, + {file = "ijson-3.3.0-cp311-cp311-win32.whl", hash = "sha256:192e4b65495978b0bce0c78e859d14772e841724d3269fc1667dc6d2f53cc0ea"}, + {file = "ijson-3.3.0-cp311-cp311-win_amd64.whl", hash = "sha256:72e3488453754bdb45c878e31ce557ea87e1eb0f8b4fc610373da35e8074ce42"}, + {file = "ijson-3.3.0-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:988e959f2f3d59ebd9c2962ae71b97c0df58323910d0b368cc190ad07429d1bb"}, + {file = "ijson-3.3.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:b2f73f0d0fce5300f23a1383d19b44d103bb113b57a69c36fd95b7c03099b181"}, + {file = "ijson-3.3.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:0ee57a28c6bf523d7cb0513096e4eb4dac16cd935695049de7608ec110c2b751"}, + {file = "ijson-3.3.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e0155a8f079c688c2ccaea05de1ad69877995c547ba3d3612c1c336edc12a3a5"}, + {file = "ijson-3.3.0-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7ab00721304af1ae1afa4313ecfa1bf16b07f55ef91e4a5b93aeaa3e2bd7917c"}, + {file = "ijson-3.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40ee3821ee90be0f0e95dcf9862d786a7439bd1113e370736bfdf197e9765bfb"}, + {file = "ijson-3.3.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:da3b6987a0bc3e6d0f721b42c7a0198ef897ae50579547b0345f7f02486898f5"}, + {file = "ijson-3.3.0-cp312-cp312-musllinux_1_2_i686.whl", hash = "sha256:63afea5f2d50d931feb20dcc50954e23cef4127606cc0ecf7a27128ed9f9a9e6"}, + {file = "ijson-3.3.0-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:b5c3e285e0735fd8c5a26d177eca8b52512cdd8687ca86ec77a0c66e9c510182"}, + {file = "ijson-3.3.0-cp312-cp312-win32.whl", hash = "sha256:907f3a8674e489abdcb0206723e5560a5cb1fa42470dcc637942d7b10f28b695"}, + {file = "ijson-3.3.0-cp312-cp312-win_amd64.whl", hash = "sha256:8f890d04ad33262d0c77ead53c85f13abfb82f2c8f078dfbf24b78f59534dfdd"}, + {file = "ijson-3.3.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b9d85a02e77ee8ea6d9e3fd5d515bcc3d798d9c1ea54817e5feb97a9bc5d52fe"}, + {file = "ijson-3.3.0-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e6576cdc36d5a09b0c1a3d81e13a45d41a6763188f9eaae2da2839e8a4240bce"}, + {file = "ijson-3.3.0-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e5589225c2da4bb732c9c370c5961c39a6db72cf69fb2a28868a5413ed7f39e6"}, + {file = "ijson-3.3.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ad04cf38164d983e85f9cba2804566c0160b47086dcca4cf059f7e26c5ace8ca"}, + {file = "ijson-3.3.0-cp36-cp36m-musllinux_1_2_aarch64.whl", hash = "sha256:a3b730ef664b2ef0e99dec01b6573b9b085c766400af363833e08ebc1e38eb2f"}, + {file = "ijson-3.3.0-cp36-cp36m-musllinux_1_2_i686.whl", hash = "sha256:4690e3af7b134298055993fcbea161598d23b6d3ede11b12dca6815d82d101d5"}, + {file = "ijson-3.3.0-cp36-cp36m-musllinux_1_2_x86_64.whl", hash = "sha256:aaa6bfc2180c31a45fac35d40e3312a3d09954638ce0b2e9424a88e24d262a13"}, + {file = "ijson-3.3.0-cp36-cp36m-win32.whl", hash = "sha256:44367090a5a876809eb24943f31e470ba372aaa0d7396b92b953dda953a95d14"}, + {file = "ijson-3.3.0-cp36-cp36m-win_amd64.whl", hash = "sha256:7e2b3e9ca957153557d06c50a26abaf0d0d6c0ddf462271854c968277a6b5372"}, + {file = "ijson-3.3.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:47c144117e5c0e2babb559bc8f3f76153863b8dd90b2d550c51dab5f4b84a87f"}, + {file = "ijson-3.3.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:29ce02af5fbf9ba6abb70765e66930aedf73311c7d840478f1ccecac53fefbf3"}, + {file = "ijson-3.3.0-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4ac6c3eeed25e3e2cb9b379b48196413e40ac4e2239d910bb33e4e7f6c137745"}, + {file = "ijson-3.3.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d92e339c69b585e7b1d857308ad3ca1636b899e4557897ccd91bb9e4a56c965b"}, + {file = "ijson-3.3.0-cp37-cp37m-musllinux_1_2_aarch64.whl", hash = "sha256:8c85447569041939111b8c7dbf6f8fa7a0eb5b2c4aebb3c3bec0fb50d7025121"}, + {file = "ijson-3.3.0-cp37-cp37m-musllinux_1_2_i686.whl", hash = "sha256:542c1e8fddf082159a5d759ee1412c73e944a9a2412077ed00b303ff796907dc"}, + {file = "ijson-3.3.0-cp37-cp37m-musllinux_1_2_x86_64.whl", hash = "sha256:30cfea40936afb33b57d24ceaf60d0a2e3d5c1f2335ba2623f21d560737cc730"}, + {file = "ijson-3.3.0-cp37-cp37m-win32.whl", hash = "sha256:6b661a959226ad0d255e49b77dba1d13782f028589a42dc3172398dd3814c797"}, + {file = "ijson-3.3.0-cp37-cp37m-win_amd64.whl", hash = "sha256:0b003501ee0301dbf07d1597482009295e16d647bb177ce52076c2d5e64113e0"}, + {file = "ijson-3.3.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:3e8d8de44effe2dbd0d8f3eb9840344b2d5b4cc284a14eb8678aec31d1b6bea8"}, + {file = "ijson-3.3.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9cd5c03c63ae06d4f876b9844c5898d0044c7940ff7460db9f4cd984ac7862b5"}, + {file = "ijson-3.3.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:04366e7e4a4078d410845e58a2987fd9c45e63df70773d7b6e87ceef771b51ee"}, + {file = "ijson-3.3.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:de7c1ddb80fa7a3ab045266dca169004b93f284756ad198306533b792774f10a"}, + {file = "ijson-3.3.0-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:8851584fb931cffc0caa395f6980525fd5116eab8f73ece9d95e6f9c2c326c4c"}, + {file = "ijson-3.3.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bdcfc88347fd981e53c33d832ce4d3e981a0d696b712fbcb45dcc1a43fe65c65"}, + {file = "ijson-3.3.0-cp38-cp38-musllinux_1_2_aarch64.whl", hash = "sha256:3917b2b3d0dbbe3296505da52b3cb0befbaf76119b2edaff30bd448af20b5400"}, + {file = "ijson-3.3.0-cp38-cp38-musllinux_1_2_i686.whl", hash = "sha256:e10c14535abc7ddf3fd024aa36563cd8ab5d2bb6234a5d22c77c30e30fa4fb2b"}, + {file = "ijson-3.3.0-cp38-cp38-musllinux_1_2_x86_64.whl", hash = "sha256:3aba5c4f97f4e2ce854b5591a8b0711ca3b0c64d1b253b04ea7b004b0a197ef6"}, + {file = "ijson-3.3.0-cp38-cp38-win32.whl", hash = "sha256:b325f42e26659df1a0de66fdb5cde8dd48613da9c99c07d04e9fb9e254b7ee1c"}, + {file = "ijson-3.3.0-cp38-cp38-win_amd64.whl", hash = "sha256:ff835906f84451e143f31c4ce8ad73d83ef4476b944c2a2da91aec8b649570e1"}, + {file = "ijson-3.3.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:3c556f5553368dff690c11d0a1fb435d4ff1f84382d904ccc2dc53beb27ba62e"}, + {file = "ijson-3.3.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:e4396b55a364a03ff7e71a34828c3ed0c506814dd1f50e16ebed3fc447d5188e"}, + {file = "ijson-3.3.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:e6850ae33529d1e43791b30575070670070d5fe007c37f5d06aebc1dd152ab3f"}, + {file = "ijson-3.3.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:36aa56d68ea8def26778eb21576ae13f27b4a47263a7a2581ab2ef58b8de4451"}, + {file = "ijson-3.3.0-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a7ec759c4a0fc820ad5dc6a58e9c391e7b16edcb618056baedbedbb9ea3b1524"}, + {file = "ijson-3.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b51bab2c4e545dde93cb6d6bb34bf63300b7cd06716f195dd92d9255df728331"}, + {file = "ijson-3.3.0-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:92355f95a0e4da96d4c404aa3cff2ff033f9180a9515f813255e1526551298c1"}, + {file = "ijson-3.3.0-cp39-cp39-musllinux_1_2_i686.whl", hash = "sha256:8795e88adff5aa3c248c1edce932db003d37a623b5787669ccf205c422b91e4a"}, + {file = "ijson-3.3.0-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:8f83f553f4cde6d3d4eaf58ec11c939c94a0ec545c5b287461cafb184f4b3a14"}, + {file = "ijson-3.3.0-cp39-cp39-win32.whl", hash = "sha256:ead50635fb56577c07eff3e557dac39533e0fe603000684eea2af3ed1ad8f941"}, + {file = "ijson-3.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:c8a9befb0c0369f0cf5c1b94178d0d78f66d9cebb9265b36be6e4f66236076b8"}, + {file = "ijson-3.3.0-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:2af323a8aec8a50fa9effa6d640691a30a9f8c4925bd5364a1ca97f1ac6b9b5c"}, + {file = "ijson-3.3.0-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f64f01795119880023ba3ce43072283a393f0b90f52b66cc0ea1a89aa64a9ccb"}, + {file = "ijson-3.3.0-pp310-pypy310_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a716e05547a39b788deaf22725490855337fc36613288aa8ae1601dc8c525553"}, + {file = "ijson-3.3.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:473f5d921fadc135d1ad698e2697025045cd8ed7e5e842258295012d8a3bc702"}, + {file = "ijson-3.3.0-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:dd26b396bc3a1e85f4acebeadbf627fa6117b97f4c10b177d5779577c6607744"}, + {file = "ijson-3.3.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:25fd49031cdf5fd5f1fd21cb45259a64dad30b67e64f745cc8926af1c8c243d3"}, + {file = "ijson-3.3.0-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4b72178b1e565d06ab19319965022b36ef41bcea7ea153b32ec31194bec032a2"}, + {file = "ijson-3.3.0-pp37-pypy37_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7d0b6b637d05dbdb29d0bfac2ed8425bb369e7af5271b0cc7cf8b801cb7360c2"}, + {file = "ijson-3.3.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5378d0baa59ae422905c5f182ea0fd74fe7e52a23e3821067a7d58c8306b2191"}, + {file = "ijson-3.3.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:99f5c8ab048ee4233cc4f2b461b205cbe01194f6201018174ac269bf09995749"}, + {file = "ijson-3.3.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:45ff05de889f3dc3d37a59d02096948ce470699f2368b32113954818b21aa74a"}, + {file = "ijson-3.3.0-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1efb521090dd6cefa7aafd120581947b29af1713c902ff54336b7c7130f04c47"}, + {file = "ijson-3.3.0-pp38-pypy38_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:87c727691858fd3a1c085d9980d12395517fcbbf02c69fbb22dede8ee03422da"}, + {file = "ijson-3.3.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0420c24e50389bc251b43c8ed379ab3e3ba065ac8262d98beb6735ab14844460"}, + {file = "ijson-3.3.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:8fdf3721a2aa7d96577970f5604bd81f426969c1822d467f07b3d844fa2fecc7"}, + {file = "ijson-3.3.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:891f95c036df1bc95309951940f8eea8537f102fa65715cdc5aae20b8523813b"}, + {file = "ijson-3.3.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ed1336a2a6e5c427f419da0154e775834abcbc8ddd703004108121c6dd9eba9d"}, + {file = "ijson-3.3.0-pp39-pypy39_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:f0c819f83e4f7b7f7463b2dc10d626a8be0c85fbc7b3db0edc098c2b16ac968e"}, + {file = "ijson-3.3.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:33afc25057377a6a43c892de34d229a86f89ea6c4ca3dd3db0dcd17becae0dbb"}, + {file = "ijson-3.3.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:7914d0cf083471856e9bc2001102a20f08e82311dfc8cf1a91aa422f9414a0d6"}, + {file = "ijson-3.3.0.tar.gz", hash = "sha256:7f172e6ba1bee0d4c8f8ebd639577bfe429dee0f3f96775a067b8bae4492d8a0"}, +] + [[package]] name = "importlib-metadata" version = "8.0.0" @@ -1186,6 +1289,99 @@ click = "*" [package.extras] tests = ["coverage", "pytest"] +[[package]] +name = "ndex2" +version = "3.9.0" +description = "Nice CX Python includes a client and a data model." +optional = false +python-versions = "*" +files = [ + {file = "ndex2-3.9.0-py2.py3-none-any.whl", hash = "sha256:168a6ed3209f2c9596752897fe535599b11f87305c10d55446bf8ffef4762283"}, + {file = "ndex2-3.9.0.tar.gz", hash = "sha256:388b2f110b2eb1ba787298bc4210ca0cea821c462ec71a4ec4cb6eb0e1b74f70"}, +] + +[package.dependencies] +ijson = "*" +networkx = "*" +numpy = "*" +pandas = "*" +requests = "*" +requests-toolbelt = "*" +six = "*" +urllib3 = ">=1.16" + +[[package]] +name = "networkx" +version = "3.2.1" +description = "Python package for creating and manipulating graphs and networks" +optional = false +python-versions = ">=3.9" +files = [ + {file = "networkx-3.2.1-py3-none-any.whl", hash = "sha256:f18c69adc97877c42332c170849c96cefa91881c99a7cb3e95b7c659ebdc1ec2"}, + {file = "networkx-3.2.1.tar.gz", hash = "sha256:9f1bb5cf3409bf324e0a722c20bdb4c20ee39bf1c30ce8ae499c8502b0b5e0c6"}, +] + +[package.extras] +default = ["matplotlib (>=3.5)", "numpy (>=1.22)", "pandas (>=1.4)", "scipy (>=1.9,!=1.11.0,!=1.11.1)"] +developer = ["changelist (==0.4)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"] +doc = ["nb2plots (>=0.7)", "nbconvert (<7.9)", "numpydoc (>=1.6)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.14)", "sphinx (>=7)", "sphinx-gallery (>=0.14)", "texext (>=0.6.7)"] +extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"] +test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"] + +[[package]] +name = "numpy" +version = "2.0.0" +description = "Fundamental package for array computing in Python" +optional = false +python-versions = ">=3.9" +files = [ + {file = "numpy-2.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:04494f6ec467ccb5369d1808570ae55f6ed9b5809d7f035059000a37b8d7e86f"}, + {file = "numpy-2.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2635dbd200c2d6faf2ef9a0d04f0ecc6b13b3cad54f7c67c61155138835515d2"}, + {file = "numpy-2.0.0-cp310-cp310-macosx_14_0_arm64.whl", hash = "sha256:0a43f0974d501842866cc83471bdb0116ba0dffdbaac33ec05e6afed5b615238"}, + {file = "numpy-2.0.0-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:8d83bb187fb647643bd56e1ae43f273c7f4dbcdf94550d7938cfc32566756514"}, + {file = "numpy-2.0.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:79e843d186c8fb1b102bef3e2bc35ef81160ffef3194646a7fdd6a73c6b97196"}, + {file = "numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6d7696c615765091cc5093f76fd1fa069870304beaccfd58b5dcc69e55ef49c1"}, + {file = "numpy-2.0.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:b4c76e3d4c56f145d41b7b6751255feefae92edbc9a61e1758a98204200f30fc"}, + {file = "numpy-2.0.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:acd3a644e4807e73b4e1867b769fbf1ce8c5d80e7caaef0d90dcdc640dfc9787"}, + {file = "numpy-2.0.0-cp310-cp310-win32.whl", hash = "sha256:cee6cc0584f71adefe2c908856ccc98702baf95ff80092e4ca46061538a2ba98"}, + {file = "numpy-2.0.0-cp310-cp310-win_amd64.whl", hash = "sha256:ed08d2703b5972ec736451b818c2eb9da80d66c3e84aed1deeb0c345fefe461b"}, + {file = "numpy-2.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:ad0c86f3455fbd0de6c31a3056eb822fc939f81b1618f10ff3406971893b62a5"}, + {file = "numpy-2.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:e7f387600d424f91576af20518334df3d97bc76a300a755f9a8d6e4f5cadd289"}, + {file = "numpy-2.0.0-cp311-cp311-macosx_14_0_arm64.whl", hash = "sha256:34f003cb88b1ba38cb9a9a4a3161c1604973d7f9d5552c38bc2f04f829536609"}, + {file = "numpy-2.0.0-cp311-cp311-macosx_14_0_x86_64.whl", hash = "sha256:b6f6a8f45d0313db07d6d1d37bd0b112f887e1369758a5419c0370ba915b3871"}, + {file = "numpy-2.0.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5f64641b42b2429f56ee08b4f427a4d2daf916ec59686061de751a55aafa22e4"}, + {file = "numpy-2.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a7039a136017eaa92c1848152827e1424701532ca8e8967fe480fe1569dae581"}, + {file = "numpy-2.0.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:46e161722e0f619749d1cd892167039015b2c2817296104487cd03ed4a955995"}, + {file = "numpy-2.0.0-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:0e50842b2295ba8414c8c1d9d957083d5dfe9e16828b37de883f51fc53c4016f"}, + {file = "numpy-2.0.0-cp311-cp311-win32.whl", hash = "sha256:2ce46fd0b8a0c947ae047d222f7136fc4d55538741373107574271bc00e20e8f"}, + {file = "numpy-2.0.0-cp311-cp311-win_amd64.whl", hash = "sha256:fbd6acc766814ea6443628f4e6751d0da6593dae29c08c0b2606164db026970c"}, + {file = "numpy-2.0.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:354f373279768fa5a584bac997de6a6c9bc535c482592d7a813bb0c09be6c76f"}, + {file = "numpy-2.0.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:4d2f62e55a4cd9c58c1d9a1c9edaedcd857a73cb6fda875bf79093f9d9086f85"}, + {file = "numpy-2.0.0-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:1e72728e7501a450288fc8e1f9ebc73d90cfd4671ebbd631f3e7857c39bd16f2"}, + {file = "numpy-2.0.0-cp312-cp312-macosx_14_0_x86_64.whl", hash = "sha256:84554fc53daa8f6abf8e8a66e076aff6ece62de68523d9f665f32d2fc50fd66e"}, + {file = "numpy-2.0.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c73aafd1afca80afecb22718f8700b40ac7cab927b8abab3c3e337d70e10e5a2"}, + {file = "numpy-2.0.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:49d9f7d256fbc804391a7f72d4a617302b1afac1112fac19b6c6cec63fe7fe8a"}, + {file = "numpy-2.0.0-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:0ec84b9ba0654f3b962802edc91424331f423dcf5d5f926676e0150789cb3d95"}, + {file = "numpy-2.0.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:feff59f27338135776f6d4e2ec7aeeac5d5f7a08a83e80869121ef8164b74af9"}, + {file = "numpy-2.0.0-cp312-cp312-win32.whl", hash = "sha256:c5a59996dc61835133b56a32ebe4ef3740ea5bc19b3983ac60cc32be5a665d54"}, + {file = "numpy-2.0.0-cp312-cp312-win_amd64.whl", hash = "sha256:a356364941fb0593bb899a1076b92dfa2029f6f5b8ba88a14fd0984aaf76d0df"}, + {file = "numpy-2.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:e61155fae27570692ad1d327e81c6cf27d535a5d7ef97648a17d922224b216de"}, + {file = "numpy-2.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:4554eb96f0fd263041baf16cf0881b3f5dafae7a59b1049acb9540c4d57bc8cb"}, + {file = "numpy-2.0.0-cp39-cp39-macosx_14_0_arm64.whl", hash = "sha256:903703372d46bce88b6920a0cd86c3ad82dae2dbef157b5fc01b70ea1cfc430f"}, + {file = "numpy-2.0.0-cp39-cp39-macosx_14_0_x86_64.whl", hash = "sha256:3e8e01233d57639b2e30966c63d36fcea099d17c53bf424d77f088b0f4babd86"}, + {file = "numpy-2.0.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1cde1753efe513705a0c6d28f5884e22bdc30438bf0085c5c486cdaff40cd67a"}, + {file = "numpy-2.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:821eedb7165ead9eebdb569986968b541f9908979c2da8a4967ecac4439bae3d"}, + {file = "numpy-2.0.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:9a1712c015831da583b21c5bfe15e8684137097969c6d22e8316ba66b5baabe4"}, + {file = "numpy-2.0.0-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:9c27f0946a3536403efb0e1c28def1ae6730a72cd0d5878db38824855e3afc44"}, + {file = "numpy-2.0.0-cp39-cp39-win32.whl", hash = "sha256:63b92c512d9dbcc37f9d81b123dec99fdb318ba38c8059afc78086fe73820275"}, + {file = "numpy-2.0.0-cp39-cp39-win_amd64.whl", hash = "sha256:3f6bed7f840d44c08ebdb73b1825282b801799e325bcbdfa6bc5c370e5aecc65"}, + {file = "numpy-2.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:9416a5c2e92ace094e9f0082c5fd473502c91651fb896bc17690d6fc475128d6"}, + {file = "numpy-2.0.0-pp39-pypy39_pp73-macosx_14_0_x86_64.whl", hash = "sha256:17067d097ed036636fa79f6a869ac26df7db1ba22039d962422506640314933a"}, + {file = "numpy-2.0.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:38ecb5b0582cd125f67a629072fed6f83562d9dd04d7e03256c9829bdec027ad"}, + {file = "numpy-2.0.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:cef04d068f5fb0518a77857953193b6bb94809a806bd0a14983a8f12ada060c9"}, + {file = "numpy-2.0.0.tar.gz", hash = "sha256:cf5d1c9e6837f8af9f92b6bd3e86d513cdc11f60fd62185cc49ec7d1aba34864"}, +] + [[package]] name = "oauthlib" version = "3.2.2" @@ -1248,6 +1444,79 @@ files = [ {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"}, ] +[[package]] +name = "pandas" +version = "2.2.2" +description = "Powerful data structures for data analysis, time series, and statistics" +optional = false +python-versions = ">=3.9" +files = [ + {file = "pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:90c6fca2acf139569e74e8781709dccb6fe25940488755716d1d354d6bc58bce"}, + {file = "pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c7adfc142dac335d8c1e0dcbd37eb8617eac386596eb9e1a1b77791cf2498238"}, + {file = "pandas-2.2.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4abfe0be0d7221be4f12552995e58723c7422c80a659da13ca382697de830c08"}, + {file = "pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8635c16bf3d99040fdf3ca3db669a7250ddf49c55dc4aa8fe0ae0fa8d6dcc1f0"}, + {file = "pandas-2.2.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:40ae1dffb3967a52203105a077415a86044a2bea011b5f321c6aa64b379a3f51"}, + {file = "pandas-2.2.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:8e5a0b00e1e56a842f922e7fae8ae4077aee4af0acb5ae3622bd4b4c30aedf99"}, + {file = "pandas-2.2.2-cp310-cp310-win_amd64.whl", hash = "sha256:ddf818e4e6c7c6f4f7c8a12709696d193976b591cc7dc50588d3d1a6b5dc8772"}, + {file = "pandas-2.2.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:696039430f7a562b74fa45f540aca068ea85fa34c244d0deee539cb6d70aa288"}, + {file = "pandas-2.2.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:8e90497254aacacbc4ea6ae5e7a8cd75629d6ad2b30025a4a8b09aa4faf55151"}, + {file = "pandas-2.2.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:58b84b91b0b9f4bafac2a0ac55002280c094dfc6402402332c0913a59654ab2b"}, + {file = "pandas-2.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6d2123dc9ad6a814bcdea0f099885276b31b24f7edf40f6cdbc0912672e22eee"}, + {file = "pandas-2.2.2-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:2925720037f06e89af896c70bca73459d7e6a4be96f9de79e2d440bd499fe0db"}, + {file = "pandas-2.2.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:0cace394b6ea70c01ca1595f839cf193df35d1575986e484ad35c4aeae7266c1"}, + {file = "pandas-2.2.2-cp311-cp311-win_amd64.whl", hash = "sha256:873d13d177501a28b2756375d59816c365e42ed8417b41665f346289adc68d24"}, + {file = "pandas-2.2.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:9dfde2a0ddef507a631dc9dc4af6a9489d5e2e740e226ad426a05cabfbd7c8ef"}, + {file = "pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:e9b79011ff7a0f4b1d6da6a61aa1aa604fb312d6647de5bad20013682d1429ce"}, + {file = "pandas-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1cb51fe389360f3b5a4d57dbd2848a5f033350336ca3b340d1c53a1fad33bcad"}, + {file = "pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eee3a87076c0756de40b05c5e9a6069c035ba43e8dd71c379e68cab2c20f16ad"}, + {file = "pandas-2.2.2-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:3e374f59e440d4ab45ca2fffde54b81ac3834cf5ae2cdfa69c90bc03bde04d76"}, + {file = "pandas-2.2.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:43498c0bdb43d55cb162cdc8c06fac328ccb5d2eabe3cadeb3529ae6f0517c32"}, + {file = "pandas-2.2.2-cp312-cp312-win_amd64.whl", hash = "sha256:d187d355ecec3629624fccb01d104da7d7f391db0311145817525281e2804d23"}, + {file = "pandas-2.2.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0ca6377b8fca51815f382bd0b697a0814c8bda55115678cbc94c30aacbb6eff2"}, + {file = "pandas-2.2.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9057e6aa78a584bc93a13f0a9bf7e753a5e9770a30b4d758b8d5f2a62a9433cd"}, + {file = "pandas-2.2.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:001910ad31abc7bf06f49dcc903755d2f7f3a9186c0c040b827e522e9cef0863"}, + {file = "pandas-2.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:66b479b0bd07204e37583c191535505410daa8df638fd8e75ae1b383851fe921"}, + {file = "pandas-2.2.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:a77e9d1c386196879aa5eb712e77461aaee433e54c68cf253053a73b7e49c33a"}, + {file = "pandas-2.2.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:92fd6b027924a7e178ac202cfbe25e53368db90d56872d20ffae94b96c7acc57"}, + {file = "pandas-2.2.2-cp39-cp39-win_amd64.whl", hash = "sha256:640cef9aa381b60e296db324337a554aeeb883ead99dc8f6c18e81a93942f5f4"}, + {file = "pandas-2.2.2.tar.gz", hash = "sha256:9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54"}, +] + +[package.dependencies] +numpy = [ + {version = ">=1.26.0", markers = "python_version >= \"3.12\""}, + {version = ">=1.22.4", markers = "python_version < \"3.11\""}, + {version = ">=1.23.2", markers = "python_version == \"3.11\""}, +] +python-dateutil = ">=2.8.2" +pytz = ">=2020.1" +tzdata = ">=2022.7" + +[package.extras] +all = ["PyQt5 (>=5.15.9)", "SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "adbc-driver-sqlite (>=0.8.0)", "beautifulsoup4 (>=4.11.2)", "bottleneck (>=1.3.6)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=2022.12.0)", "fsspec (>=2022.11.0)", "gcsfs (>=2022.11.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.9.2)", "matplotlib (>=3.6.3)", "numba (>=0.56.4)", "numexpr (>=2.8.4)", "odfpy (>=1.4.1)", "openpyxl (>=3.1.0)", "pandas-gbq (>=0.19.0)", "psycopg2 (>=2.9.6)", "pyarrow (>=10.0.1)", "pymysql (>=1.0.2)", "pyreadstat (>=1.2.0)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "python-calamine (>=0.1.7)", "pyxlsb (>=1.0.10)", "qtpy (>=2.3.0)", "s3fs (>=2022.11.0)", "scipy (>=1.10.0)", "tables (>=3.8.0)", "tabulate (>=0.9.0)", "xarray (>=2022.12.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.5)", "zstandard (>=0.19.0)"] +aws = ["s3fs (>=2022.11.0)"] +clipboard = ["PyQt5 (>=5.15.9)", "qtpy (>=2.3.0)"] +compression = ["zstandard (>=0.19.0)"] +computation = ["scipy (>=1.10.0)", "xarray (>=2022.12.0)"] +consortium-standard = ["dataframe-api-compat (>=0.1.7)"] +excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.1.0)", "python-calamine (>=0.1.7)", "pyxlsb (>=1.0.10)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.5)"] +feather = ["pyarrow (>=10.0.1)"] +fss = ["fsspec (>=2022.11.0)"] +gcp = ["gcsfs (>=2022.11.0)", "pandas-gbq (>=0.19.0)"] +hdf5 = ["tables (>=3.8.0)"] +html = ["beautifulsoup4 (>=4.11.2)", "html5lib (>=1.1)", "lxml (>=4.9.2)"] +mysql = ["SQLAlchemy (>=2.0.0)", "pymysql (>=1.0.2)"] +output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.9.0)"] +parquet = ["pyarrow (>=10.0.1)"] +performance = ["bottleneck (>=1.3.6)", "numba (>=0.56.4)", "numexpr (>=2.8.4)"] +plot = ["matplotlib (>=3.6.3)"] +postgresql = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "psycopg2 (>=2.9.6)"] +pyarrow = ["pyarrow (>=10.0.1)"] +spss = ["pyreadstat (>=1.2.0)"] +sql-other = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "adbc-driver-sqlite (>=0.8.0)"] +test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"] +xml = ["lxml (>=4.9.2)"] + [[package]] name = "parse" version = "1.20.2" @@ -1717,6 +1986,17 @@ files = [ [package.dependencies] sortedcontainers = "*" +[[package]] +name = "pytz" +version = "2024.1" +description = "World timezone definitions, modern and historical" +optional = false +python-versions = "*" +files = [ + {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"}, + {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"}, +] + [[package]] name = "pyyaml" version = "6.0.1" @@ -1901,6 +2181,20 @@ requests = ">=2.0.0" [package.extras] rsa = ["oauthlib[signedtoken] (>=3.0.0)"] +[[package]] +name = "requests-toolbelt" +version = "1.0.0" +description = "A utility belt for advanced users of python-requests" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "requests-toolbelt-1.0.0.tar.gz", hash = "sha256:7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6"}, + {file = "requests_toolbelt-1.0.0-py2.py3-none-any.whl", hash = "sha256:cccfdd665f0a24fcf4726e690f65639d272bb0637b9b92dfd91a5568ccf6bd06"}, +] + +[package.dependencies] +requests = ">=2.0.1,<3.0.0" + [[package]] name = "rfc3339-validator" version = "0.1.4" @@ -2389,6 +2683,17 @@ files = [ {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] +[[package]] +name = "tzdata" +version = "2024.1" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +files = [ + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [[package]] name = "uri-template" version = "1.3.0" @@ -2587,4 +2892,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "3fa1ae4c5d3c4df30a24e9bdbb3f09da3bd1e93ea3a868aaf11cf63e0d4b06c0" +content-hash = "8e13c7f80b53b48f10b7a73b8a696fda2b6b3d8eb86da0b92afc8a984269f3a6" diff --git a/pyproject.toml b/pyproject.toml index b45f2ef..e1558be 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,6 +11,7 @@ include = ["README.md", "src/gocam/schema", "project"] python = "^3.9" click = "^8" linkml-runtime = "^1.1.24" +ndex2 = "^3.9.0" pydantic = "^2" pyyaml = "^6" requests = "^2" diff --git a/src/gocam/translation/cx2/__init__.py b/src/gocam/translation/cx2/__init__.py new file mode 100644 index 0000000..01878d5 --- /dev/null +++ b/src/gocam/translation/cx2/__init__.py @@ -0,0 +1 @@ +from gocam.translation.cx2.main import model_to_cx2 diff --git a/src/gocam/translation/cx2/main.py b/src/gocam/translation/cx2/main.py new file mode 100644 index 0000000..9dccbbc --- /dev/null +++ b/src/gocam/translation/cx2/main.py @@ -0,0 +1,89 @@ +from ndex2.cx2 import CX2Network + +from gocam.datamodel import Model +from gocam.translation.cx2.style import ( + RELATIONS, + VISUAL_EDITOR_PROPERTIES, + VISUAL_PROPERTIES, +) + + +def model_to_cx2(gocam: Model) -> list: + + def _get_object_label(object_id: str) -> str: + object = next((obj for obj in gocam.objects if obj.id == object_id), None) + return object.label if object is not None else "" + + cx2_network = CX2Network() + cx2_network.set_network_attributes( + { + "name": gocam.title if gocam.title is not None else gocam.id, + "represents": gocam.id, + } + ) + + activity_nodes = {} + for activity in gocam.activities: + if activity.enabled_by is None: + continue + + node_attributes = { + "name": _get_object_label(activity.enabled_by), + "represents": activity.enabled_by, + } + + if activity.molecular_function: + node_attributes["molecular_function_id"] = activity.molecular_function.term + node_attributes["molecular_function_label"] = _get_object_label( + activity.molecular_function.term + ) + + if activity.occurs_in: + node_attributes["occurs_in_id"] = activity.occurs_in.term + node_attributes["occurs_in_label"] = _get_object_label( + activity.occurs_in.term + ) + + if activity.part_of: + node_attributes["part_of_id"] = activity.part_of.term + node_attributes["part_of_label"] = _get_object_label(activity.part_of.term) + + if activity.provenances: + node_attributes["provenance"] = [ + p.contributor for p in activity.provenances + ] + + activity_nodes[activity.id] = cx2_network.add_node(attributes=node_attributes) + + for activity in gocam.activities: + for association in activity.causal_associations: + if association.downstream_activity in activity_nodes: + relation_style = RELATIONS.get(association.predicate, None) + name = ( + relation_style.label + if relation_style is not None + else association.predicate + ) + edge_attributes = { + "name": name, + "represents": association.predicate, + } + + if association.evidence: + edge_attributes["evidence"] = [e.term for e in association.evidence] + + if association.provenances: + edge_attributes["provenance"] = [ + p.contributor for p in association.provenances + ] + + cx2_network.add_edge( + source=activity_nodes[activity.id], + target=activity_nodes[association.downstream_activity], + attributes=edge_attributes, + ) + + cx2_network.set_visual_properties(VISUAL_PROPERTIES) + cx2_network.set_opaque_aspect("visualEditorProperties", [VISUAL_EDITOR_PROPERTIES]) + + return cx2_network.to_cx2() diff --git a/src/gocam/translation/cx2/style.py b/src/gocam/translation/cx2/style.py new file mode 100644 index 0000000..7e55a10 --- /dev/null +++ b/src/gocam/translation/cx2/style.py @@ -0,0 +1,369 @@ +from dataclasses import dataclass +from enum import Enum + + +class Color(str, Enum): + LIGHT_BLUE = "#add8e6" + CORNFLOWER_BLUE = "#6495ED" + MEDIUM_AQUAMARINE = "#66CDAA" + DARK_SLATE_GRAY = "#2F4F4F" + RED = "#FF0000" + GREEN = "#008000" + HOT_PINK = "#ED6495" + DARK_SALMON = "#E9967A" + DARK_GOLDENROD = "#B8860B" + DARK_SLATE_BLUE = "#483D8B" + SNOW = "#FFFAFA" + + +class Width(int, Enum): + DEFAULT = 4 + SMALL = 2 + INDIRECT = 3 + DIRECT = 4 + + +class ArrowShape(str, Enum): + CIRCLE = "circle" + DELTA = "delta" + DIAMOND = "diamond" + SQUARE = "square" + + +class LineStyle(str, Enum): + DASHED = "dashed" + SOLID = "solid" + + +@dataclass +class RelationStyle: + line_style: LineStyle + arrow_shape: ArrowShape + label: str + color: Color + width: Width + + +RELATIONS = { + "BFO:0000050": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="part of", + color=Color.LIGHT_BLUE, + width=Width.DEFAULT, + ), + "BFO:0000051": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="has part", + color=Color.CORNFLOWER_BLUE, + width=Width.DEFAULT, + ), + "BFO:0000066": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="occurs in", + color=Color.MEDIUM_AQUAMARINE, + width=Width.DEFAULT, + ), + "RO:0002211": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="regulates", + color=Color.DARK_SLATE_GRAY, + width=Width.INDIRECT, + ), + "RO:0002212": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.SQUARE, + label="negatively regulates", + color=Color.RED, + width=Width.INDIRECT, + ), + "RO:0002630": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.SQUARE, + label="directly negatively regulates", + color=Color.RED, + width=Width.DIRECT, + ), + "RO:0002213": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.DELTA, + label="positively regulates", + color=Color.GREEN, + width=Width.INDIRECT, + ), + "RO:0002629": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.DELTA, + label="directly positively regulates", + color=Color.GREEN, + width=Width.DIRECT, + ), + "RO:0002233": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="has input", + color=Color.CORNFLOWER_BLUE, + width=Width.DEFAULT, + ), + "RO:0002234": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="has output", + color=Color.HOT_PINK, + width=Width.DEFAULT, + ), + "RO:0002331": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="involved in", + color=Color.DARK_SALMON, + width=Width.DEFAULT, + ), + "RO:0002333": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="enabled by", + color=Color.DARK_GOLDENROD, + width=Width.DEFAULT, + ), + "RO:0002411": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of", + color=Color.DARK_SLATE_BLUE, + width=Width.INDIRECT, + ), + "RO:0002418": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of or within", + color=Color.DARK_SLATE_BLUE, + width=Width.INDIRECT, + ), + "RO:0002408": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.SQUARE, + label="directly inhibits", + color=Color.RED, + width=Width.DIRECT, + ), + "RO:0002406": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.DELTA, + label="directly activates", + color=Color.GREEN, + width=Width.DIRECT, + ), + "RO:0002305": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of, negative effect", + color=Color.RED, + width=Width.INDIRECT, + ), + "RO:0004046": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of or within, negative effect", + color=Color.RED, + width=Width.INDIRECT, + ), + "RO:0002304": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of, positive effect", + color=Color.GREEN, + width=Width.INDIRECT, + ), + "RO:0004047": RelationStyle( + line_style=LineStyle.DASHED, + arrow_shape=ArrowShape.CIRCLE, + label="causally upstream of or within, positive effect", + color=Color.GREEN, + width=Width.INDIRECT, + ), + "annotation": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.DIAMOND, + label="annotation", + color=Color.DARK_SLATE_BLUE, + width=Width.DEFAULT, + ), + "instance_of": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="activity", + color=Color.SNOW, + width=Width.DEFAULT, + ), + "RO:0002413": RelationStyle( + line_style=LineStyle.SOLID, + arrow_shape=ArrowShape.CIRCLE, + label="directly provides input for", + color=Color.LIGHT_BLUE, + width=Width.SMALL, + ), +} + +VISUAL_PROPERTIES = { + "default": { + "edge": { + "EDGE_CURVED": True, + "EDGE_LABEL_AUTOROTATE": False, + "EDGE_LABEL_BACKGROUND_COLOR": "#FFFFFF", + "EDGE_LABEL_BACKGROUND_OPACITY": 1, + "EDGE_LABEL_BACKGROUND_SHAPE": "rectangle", + "EDGE_LABEL_COLOR": "#000000", + "EDGE_LABEL_FONT_FACE": { + "FONT_FAMILY": "sans-serif", + "FONT_NAME": "Dialog", + "FONT_STYLE": "normal", + "FONT_WEIGHT": "normal", + }, + "EDGE_LABEL_FONT_SIZE": 10, + "EDGE_LABEL_MAX_WIDTH": 200, + "EDGE_LABEL_OPACITY": 1, + "EDGE_LABEL_POSITION": { + "EDGE_ANCHOR": "C", + "JUSTIFICATION": "center", + "LABEL_ANCHOR": "C", + "MARGIN_X": 0, + "MARGIN_Y": 0, + }, + "EDGE_LABEL_ROTATION": 0, + "EDGE_LINE_COLOR": "#848484", + "EDGE_LINE_STYLE": "solid", + "EDGE_OPACITY": 1, + "EDGE_SELECTED": "false", + "EDGE_SELECTED_PAINT": "#FFFF00", + "EDGE_SOURCE_ARROW_COLOR": "#000000", + "EDGE_SOURCE_ARROW_SELECTED_PAINT": "#FFFF00", + "EDGE_SOURCE_ARROW_SHAPE": "none", + "EDGE_SOURCE_ARROW_SIZE": 6, + "EDGE_STACKING": "AUTO_BEND", + "EDGE_STACKING_DENSITY": 0.5, + "EDGE_STROKE_SELECTED_PAINT": "#FFFF00", + "EDGE_TARGET_ARROW_COLOR": "#000000", + "EDGE_TARGET_ARROW_SELECTED_PAINT": "#FFFF00", + "EDGE_TARGET_ARROW_SHAPE": "none", + "EDGE_TARGET_ARROW_SIZE": 6, + "EDGE_VISIBILITY": "element", + "EDGE_WIDTH": 2, + "EDGE_Z_ORDER": 0, + }, + "network": {"NETWORK_BACKGROUND_COLOR": "#FFFFFF"}, + "node": { + "COMPOUND_NODE_PADDING": "10.0", + "COMPOUND_NODE_SHAPE": "ROUND_RECTANGLE", + "NODE_BACKGROUND_COLOR": "#FFFFFF", + "NODE_BACKGROUND_OPACITY": 1, + "NODE_BORDER_COLOR": "#CCCCCC", + "NODE_BORDER_OPACITY": 1, + "NODE_BORDER_STYLE": "solid", + "NODE_BORDER_WIDTH": 1, + "NODE_HEIGHT": 35, + "NODE_LABEL_BACKGROUND_COLOR": "#B6B6B6", + "NODE_LABEL_BACKGROUND_OPACITY": 1, + "NODE_LABEL_BACKGROUND_SHAPE": "NONE", + "NODE_LABEL_COLOR": "#000000", + "NODE_LABEL_FONT_FACE": { + "FONT_FAMILY": "sans-serif", + "FONT_NAME": "SansSerif", + "FONT_STYLE": "normal", + "FONT_WEIGHT": "normal", + }, + "NODE_LABEL_FONT_SIZE": 12, + "NODE_LABEL_MAX_WIDTH": 200, + "NODE_LABEL_OPACITY": 1, + "NODE_LABEL_POSITION": { + "HORIZONTAL_ALIGN": "center", + "HORIZONTAL_ANCHOR": "center", + "JUSTIFICATION": "center", + "MARGIN_X": 0, + "MARGIN_Y": 0, + "VERTICAL_ALIGN": "center", + "VERTICAL_ANCHOR": "center", + }, + "NODE_LABEL_ROTATION": 0, + "NODE_SELECTED": False, + "NODE_SELECTED_PAINT": "#FFFF00", + "NODE_SHAPE": "round-rectangle", + "NODE_VISIBILITY": "element", + "NODE_WIDTH": 75, + "NODE_X_LOCATION": 0, + "NODE_Y_LOCATION": 0, + "NODE_Z_LOCATION": 0, + }, + }, + "edgeMapping": { + "EDGE_LABEL": { + "type": "PASSTHROUGH", + "definition": {"attribute": "name", "type": "string"}, + }, + "EDGE_LINE_COLOR": { + "type": "DISCRETE", + "definition": { + "attribute": "represents", + "map": [ + {"v": key, "vp": value.color} for key, value in RELATIONS.items() + ], + "type": "string", + }, + }, + "EDGE_LINE_STYLE": { + "type": "DISCRETE", + "definition": { + "attribute": "represents", + "map": [ + {"v": key, "vp": value.line_style} + for key, value in RELATIONS.items() + ], + "type": "string", + }, + }, + "EDGE_TARGET_ARROW_COLOR": { + "type": "DISCRETE", + "definition": { + "attribute": "represents", + "map": [ + {"v": key, "vp": value.color} for key, value in RELATIONS.items() + ], + "type": "string", + }, + }, + "EDGE_TARGET_ARROW_SHAPE": { + "type": "DISCRETE", + "definition": { + "attribute": "represents", + "map": [ + {"v": key, "vp": value.arrow_shape} + for key, value in RELATIONS.items() + ], + "type": "string", + }, + }, + "EDGE_WIDTH": { + "type": "DISCRETE", + "definition": { + "attribute": "represents", + "map": [ + {"v": key, "vp": value.width} for key, value in RELATIONS.items() + ], + "type": "integer", + }, + }, + }, + "nodeMapping": { + "NODE_LABEL": { + "type": "PASSTHROUGH", + "definition": {"attribute": "name", "type": "string"}, + } + }, +} + +VISUAL_EDITOR_PROPERTIES = { + "arrowColorMatchesEdge": True, +} diff --git a/tests/__init__.py b/tests/__init__.py index 82cb3fa..d26b6ca 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,5 +1,7 @@ """Tests for gocam.""" + from pathlib import Path +EXAMPLES_DIR = Path(__file__).parent / "../src/data/examples" INPUT_DIR = Path(__file__).parent / "input" -OUTPUT_DIR = Path(__file__).parent / "output" \ No newline at end of file +OUTPUT_DIR = Path(__file__).parent / "output" diff --git a/tests/test_translation/test_cx2.py b/tests/test_translation/test_cx2.py new file mode 100644 index 0000000..82a1b75 --- /dev/null +++ b/tests/test_translation/test_cx2.py @@ -0,0 +1,43 @@ +import pytest +import yaml +from ndex2.cx2 import CX2Network, RawCX2NetworkFactory + +from gocam.datamodel import Model +from gocam.translation.cx2 import model_to_cx2 +from tests import EXAMPLES_DIR + + +@pytest.fixture +def model(): + model_file = EXAMPLES_DIR / "Model-663d668500002178.yaml" + with open(model_file, "r") as f: + deserialized = yaml.safe_load(f) + model = Model.model_validate(deserialized) + return model + + +def test_model_to_cx2(model): + """Test the model_to_cx2 function.""" + cx2 = model_to_cx2(model) + + assert isinstance(cx2, list) + + node_aspect = next((aspect for aspect in cx2 if "nodes" in aspect), None) + assert node_aspect is not None + assert len(node_aspect["nodes"]) == 10, "Incorrect number of nodes in CX2" + + edge_aspect = next((aspect for aspect in cx2 if "edges" in aspect), None) + assert edge_aspect is not None + assert len(edge_aspect["edges"]) == 14, "Incorrect number of edges in CX2" + + +def test_load_cx2_to_ndex(model): + """Test loading generated CX2 file by NDEx library.""" + cx2 = model_to_cx2(model) + + factory = RawCX2NetworkFactory() + cx2_network = factory.get_cx2network(cx2) + + assert isinstance(cx2_network, CX2Network) + assert len(cx2_network.get_nodes()) == 10, "Incorrect number of nodes in CX2" + assert len(cx2_network.get_edges()) == 14, "Incorrect number of edges in CX2" From ad543f4fbe1bb3207a44b81c00de87c0f3864832 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 15:23:04 -0700 Subject: [PATCH 5/8] Add convert subcommand to CLI --- src/gocam/cli.py | 61 +++++++++++++++++++++++++++++++++++++++++++++++ tests/test_cli.py | 56 +++++++++++++++++++++++++++++++++++++++---- 2 files changed, 113 insertions(+), 4 deletions(-) diff --git a/src/gocam/cli.py b/src/gocam/cli.py index a7b7985..475a83f 100644 --- a/src/gocam/cli.py +++ b/src/gocam/cli.py @@ -1,12 +1,16 @@ import json import logging +import os import sys import click +import ndex2 import yaml from gocam import __version__ +from gocam.datamodel import Model from gocam.translation import MinervaWrapper +from gocam.translation.cx2 import model_to_cx2 @click.group() @@ -76,5 +80,62 @@ def fetch(model_ids, format): click.echo(model.model_dump()) +@cli.command() +@click.option( + "--input-format", + "-I", + type=click.Choice(["json", "yaml"]), + help="Input format. Not required unless reading from stdin.", +) +@click.option("--output-format", "-O", type=click.Choice(["cx2"]), required=True) +@click.option("--output", "-o", type=click.File("w"), default="-") +@click.option("--ndex-upload", is_flag=True, help="Upload to NDEx") +@click.argument("model", type=click.File("r"), default="-") +def convert(model, input_format, output_format, output, ndex_upload): + """Convert GO-CAM models.""" + if ndex_upload and output_format != "cx2": + raise click.UsageError("NDEx upload requires output format to be CX2") + + if input_format is None: + if model.name.endswith(".json"): + input_format = "json" + elif model.name.endswith(".yaml"): + input_format = "yaml" + else: + raise click.BadParameter("Could not infer input format") + + if input_format == "json": + deserialized = json.load(model) + elif input_format == "yaml": + deserialized = yaml.safe_load(model) + else: + raise click.UsageError("Invalid input format") + + try: + model = Model.model_validate(deserialized) + except Exception as e: + raise click.UsageError(f"Could not load model: {e}") + + if output_format == "cx2": + cx2 = model_to_cx2(model) + + if ndex_upload: + # This is very basic proof-of-concept usage of the NDEx client. Once we have a better + # idea of how we want to use it, we can refactor this to allow more CLI options for + # connection details, visibility, adding the new network to a group, etc. At that point + # we can also consider moving upload functionality to a separate command. + client = ndex2.client.Ndex2( + host=os.getenv("NDEX_HOST"), + username=os.getenv("NDEX_USERNAME"), + password=os.getenv("NDEX_PASSWORD"), + ) + url = client.save_new_cx2_network(cx2, visibility="PRIVATE") + # This replacement suggested by + # https://ndex2.readthedocs.io/en/latest/quicktutorial.html#upload-new-network-to-ndex + click.echo(f"View network at: {url.replace('v3', 'viewer')}") + else: + click.echo(json.dumps(cx2), file=output) + + if __name__ == "__main__": cli() diff --git a/tests/test_cli.py b/tests/test_cli.py index 09644d0..293e416 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -5,8 +5,8 @@ from click.testing import CliRunner from gocam import __version__ -from gocam.cli import fetch, cli -from tests import INPUT_DIR +from gocam.cli import cli +from tests import EXAMPLES_DIR, INPUT_DIR @pytest.fixture @@ -25,7 +25,7 @@ def api_mock(requests_mock): def test_fetch_yaml(runner, api_mock): - result = runner.invoke(fetch, ["--format", "yaml", "5b91dbd100002057"]) + result = runner.invoke(cli, ["fetch", "--format", "yaml", "5b91dbd100002057"]) assert result.exit_code == 0 parsed_output = yaml.safe_load(result.output) @@ -33,7 +33,7 @@ def test_fetch_yaml(runner, api_mock): def test_fetch_json(runner, api_mock): - result = runner.invoke(fetch, ["--format", "json", "5b91dbd100002057"]) + result = runner.invoke(cli, ["fetch", "--format", "json", "5b91dbd100002057"]) assert result.exit_code == 0 parsed_output = json.loads(result.output) @@ -44,3 +44,51 @@ def test_version(runner): result = runner.invoke(cli, ["--version"]) assert result.exit_code == 0 assert __version__ in result.output + + +@pytest.mark.parametrize("format", ["json", "yaml"]) +def test_convert_to_cx2_from_file(runner, format): + result = runner.invoke( + cli, + [ + "convert", + "-O", + "cx2", + str(EXAMPLES_DIR / f"Model-663d668500002178.{format}"), + ], + ) + assert result.exit_code == 0 + cx2 = json.loads(result.output) + assert isinstance(cx2, list) + + +@pytest.mark.parametrize("format", ["json", "yaml"]) +def test_convert_to_cx2_from_stdin(runner, format): + with open(EXAMPLES_DIR / f"Model-663d668500002178.{format}") as f: + result = runner.invoke( + cli, ["convert", "-O", "cx2", "-I", format], input=f.read() + ) + assert result.exit_code == 0 + cx2 = json.loads(result.output) + assert isinstance(cx2, list) + + +def test_convert_to_cx2_to_file(runner, tmp_path): + output_path = tmp_path / "test.cx2" + result = runner.invoke( + cli, + [ + "convert", + "-O", + "cx2", + "-o", + str(output_path), + str(EXAMPLES_DIR / "Model-663d668500002178.yaml"), + ], + ) + + assert result.exit_code == 0 + assert output_path.exists() + with open(output_path) as f: + cx2 = json.load(f) + assert isinstance(cx2, list) From 23696d954c4144de1c965f505f03da8486ebd0e9 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 1 Aug 2024 15:23:46 -0700 Subject: [PATCH 6/8] Filter uninformative warning from test output --- tests/test_data.py | 13 ++++++++----- tests/test_translation/test_minerva_wrapper.py | 4 +++- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/tests/test_data.py b/tests/test_data.py index f0b8406..a0f01db 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,16 +1,19 @@ """Data test.""" -import os + import glob +import os +import pytest from linkml_runtime.loaders import yaml_loader -from gocam.datamodel import Model -ROOT = os.path.join(os.path.dirname(__file__), '..') -DATA_DIR = os.path.join(ROOT, "src", "data", "examples") +from gocam.datamodel import Model +from tests import EXAMPLES_DIR -EXAMPLE_FILES = glob.glob(os.path.join(DATA_DIR, '*.yaml')) +EXAMPLE_FILES = glob.glob(os.path.join(EXAMPLES_DIR, "*.yaml")) +# linkml-linkml_runtime.loaders.yaml_loader still uses load_obj. Disable capturing this warning. +@pytest.mark.filterwarnings("ignore::pydantic.warnings.PydanticDeprecatedSince20") def test_data(): """Data test.""" for path in EXAMPLE_FILES: diff --git a/tests/test_translation/test_minerva_wrapper.py b/tests/test_translation/test_minerva_wrapper.py index c2374f7..8963fcc 100644 --- a/tests/test_translation/test_minerva_wrapper.py +++ b/tests/test_translation/test_minerva_wrapper.py @@ -17,7 +17,9 @@ def test_api(model_local_id): assert model is not None -@pytest.mark.parametrize("base_name", ["minerva-663d668500002178", "minerva-5b91dbd100002057"]) +@pytest.mark.parametrize( + "base_name", ["minerva-663d668500002178", "minerva-5b91dbd100002057"] +) def test_object(base_name): mw = MinervaWrapper() with open(INPUT_DIR / f"{base_name}.json", "r") as f: From fbd654a88ad6ed54d3f5e751ae76f11f969ddb81 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 7 Aug 2024 10:11:52 -0700 Subject: [PATCH 7/8] Make uploaded networks searchable via NDEx search --- src/gocam/cli.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/gocam/cli.py b/src/gocam/cli.py index 475a83f..9252e96 100644 --- a/src/gocam/cli.py +++ b/src/gocam/cli.py @@ -130,9 +130,12 @@ def convert(model, input_format, output_format, output, ndex_upload): password=os.getenv("NDEX_PASSWORD"), ) url = client.save_new_cx2_network(cx2, visibility="PRIVATE") - # This replacement suggested by - # https://ndex2.readthedocs.io/en/latest/quicktutorial.html#upload-new-network-to-ndex - click.echo(f"View network at: {url.replace('v3', 'viewer')}") + network_id = url.rsplit("/", 1)[-1] + + # Make the network searchable + client.set_network_system_properties(network_id, {"index_level": "META"}) + + click.echo(f"View network at: 'https://www.ndexbio.org/viewer/networks/{network_id}") else: click.echo(json.dumps(cx2), file=output) From 47fd4d41e7b39c315f1ff677f294d63f6d6a031e Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 7 Aug 2024 17:00:04 -0700 Subject: [PATCH 8/8] Use portable style arrow shapes --- src/gocam/translation/cx2/style.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/gocam/translation/cx2/style.py b/src/gocam/translation/cx2/style.py index 7e55a10..f0582f6 100644 --- a/src/gocam/translation/cx2/style.py +++ b/src/gocam/translation/cx2/style.py @@ -25,9 +25,9 @@ class Width(int, Enum): class ArrowShape(str, Enum): CIRCLE = "circle" - DELTA = "delta" DIAMOND = "diamond" - SQUARE = "square" + TEE = "tee" + TRIANGLE = "triangle" class LineStyle(str, Enum): @@ -75,28 +75,28 @@ class RelationStyle: ), "RO:0002212": RelationStyle( line_style=LineStyle.DASHED, - arrow_shape=ArrowShape.SQUARE, + arrow_shape=ArrowShape.TEE, label="negatively regulates", color=Color.RED, width=Width.INDIRECT, ), "RO:0002630": RelationStyle( line_style=LineStyle.SOLID, - arrow_shape=ArrowShape.SQUARE, + arrow_shape=ArrowShape.TEE, label="directly negatively regulates", color=Color.RED, width=Width.DIRECT, ), "RO:0002213": RelationStyle( line_style=LineStyle.DASHED, - arrow_shape=ArrowShape.DELTA, + arrow_shape=ArrowShape.TRIANGLE, label="positively regulates", color=Color.GREEN, width=Width.INDIRECT, ), "RO:0002629": RelationStyle( line_style=LineStyle.SOLID, - arrow_shape=ArrowShape.DELTA, + arrow_shape=ArrowShape.TRIANGLE, label="directly positively regulates", color=Color.GREEN, width=Width.DIRECT, @@ -145,14 +145,14 @@ class RelationStyle: ), "RO:0002408": RelationStyle( line_style=LineStyle.SOLID, - arrow_shape=ArrowShape.SQUARE, + arrow_shape=ArrowShape.TEE, label="directly inhibits", color=Color.RED, width=Width.DIRECT, ), "RO:0002406": RelationStyle( line_style=LineStyle.SOLID, - arrow_shape=ArrowShape.DELTA, + arrow_shape=ArrowShape.TRIANGLE, label="directly activates", color=Color.GREEN, width=Width.DIRECT,