From 8188db99452c649e3931ce1ef64e9400866dae99 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 19 Sep 2024 13:28:55 -0700 Subject: [PATCH] Updated serialized Models used in tests --- tests/input/Model-63f809ec00000701.yaml | 81 +++++++++++++++++++++-- tests/input/Model-6606056e00002011.yaml | 86 +++++++++++++++++++++++-- 2 files changed, 156 insertions(+), 11 deletions(-) diff --git a/tests/input/Model-63f809ec00000701.yaml b/tests/input/Model-63f809ec00000701.yaml index 6f50398..eda5ec3 100644 --- a/tests/input/Model-63f809ec00000701.yaml +++ b/tests/input/Model-63f809ec00000701.yaml @@ -7,170 +7,239 @@ status: production activities: - id: gomodel:63f809ec00000701/63f809ec00000742 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:Q96Q11 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0004810 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0001680 + has_input: [] + has_output: [] + causal_associations: [] + provenances: [] - id: gomodel:63f809ec00000701/63f809ec00000726 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:Q9H8Y5 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:31011209 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0004521 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:31011209 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0072344 + has_input: [] has_output: - - evidence: + - type: MoleculeAssociation + evidence: - term: ECO:0000314 reference: PMID:31011209 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: CHEBI:10668 causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000314 reference: PMID:31011209 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] predicate: RO:0002629 downstream_activity: gomodel:63f809ec00000701/63f809ec00000735 + provenances: [] - id: gomodel:63f809ec00000701/63f809ec00000735 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:Q9H777 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0004549 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0042780 has_input: - - evidence: + - type: MoleculeAssociation + evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: CHEBI:10668 + has_output: [] causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000314 reference: PMID:32075755 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] predicate: RO:0002629 downstream_activity: gomodel:63f809ec00000701/63f809ec00000742 + provenances: [] - id: gomodel:63f809ec00000701/63f809ec00000706 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:O60524 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:33909987 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:1904678 occurs_in: + type: CellularAnatomicalEntityAssociation evidence: - term: ECO:0000314 reference: PMID:33909987 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0022626 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:33909987 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: GO:0140708 has_input: - - evidence: + - type: MoleculeAssociation + evidence: - term: ECO:0000314 reference: PMID:33909987 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-01' + provenances: [] term: CHEBI:17732 + has_output: [] causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000314 reference: PMID:33909987 provenances: - contributor: https://orcid.org/0000-0001-7299-6685 date: '2023-03-02' + provenances: [] predicate: RO:0002304 downstream_activity: gomodel:63f809ec00000701/63f809ec00000726 + provenances: [] objects: - id: GO:1904678 label: alpha-aminoacyl-tRNA binding + type: gocam:Object - id: UniProtKB:O60524 label: NEMF Hsap + type: gocam:Object - id: GO:0140708 label: CAT tailing + type: gocam:Object - id: GO:0022626 label: cytosolic ribosome + type: gocam:Object - id: CHEBI:17732 label: Ala-tRNA(Ala) + type: gocam:Object - id: GO:0004521 label: RNA endonuclease activity + type: gocam:Object - id: UniProtKB:Q9H8Y5 label: ANKZF1 Hsap + type: gocam:Object - id: GO:0072344 label: rescue of stalled ribosome + type: gocam:Object - id: ECO:0000314 label: direct assay evidence used in manual assertion + type: gocam:Object - id: CHEBI:10668 label: tRNA precursor + type: gocam:Object - id: GO:0004549 label: tRNA-specific ribonuclease activity + type: gocam:Object - id: UniProtKB:Q9H777 label: ELAC1 Hsap + type: gocam:Object - id: GO:0042780 label: tRNA 3'-end processing + type: gocam:Object - id: GO:0004810 label: CCA tRNA nucleotidyltransferase activity + type: gocam:Object - id: UniProtKB:Q96Q11 label: TRNT1 Hsap + type: gocam:Object - id: GO:0001680 label: tRNA 3'-terminal CCA addition + type: gocam:Object +provenances: [] diff --git a/tests/input/Model-6606056e00002011.yaml b/tests/input/Model-6606056e00002011.yaml index e68cfdd..4b3be1a 100644 --- a/tests/input/Model-6606056e00002011.yaml +++ b/tests/input/Model-6606056e00002011.yaml @@ -6,11 +6,15 @@ status: production activities: - id: gomodel:6606056e00002011/662af8fa00002857 enabled_by: + type: EnabledByProteinComplexAssociation + evidence: [] + provenances: [] term: GO:0019815 members: - UniProtKB:P40259 - UniProtKB:P11912 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000250 reference: GO_REF:0000024 @@ -19,16 +23,20 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] term: GO:0004888 occurs_in: + type: CellularAnatomicalEntityAssociation evidence: - term: ECO:0000314 reference: PMID:36426942 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] term: GO:0005886 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000250 reference: GO_REF:0000024 @@ -37,9 +45,11 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] term: GO:0050853 has_input: - - evidence: + - type: MoleculeAssociation + evidence: - term: ECO:0000250 reference: GO_REF:0000024 with_objects: @@ -47,9 +57,12 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] term: UniProtKB:P07948 + has_output: [] causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000250 reference: GO_REF:0000024 with_objects: @@ -57,55 +70,78 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] predicate: RO:0002629 downstream_activity: gomodel:6606056e00002011/6606056e00002040 + provenances: [] - id: gomodel:6606056e00002011/6606056e00002049 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:P29350 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:17562706 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0004725 occurs_in: + type: CellularAnatomicalEntityAssociation evidence: - term: ECO:0000314 reference: PMID:10940933 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0005737 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:35941532 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0050859 + has_input: [] + has_output: [] + causal_associations: [] + provenances: [] - id: gomodel:6606056e00002011/6606056e00002040 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:P07948 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:11823534 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0004713 occurs_in: + type: CellularAnatomicalEntityAssociation evidence: - term: ECO:0000314 reference: PMID:15173188 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0005886 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000250 reference: GO_REF:0000024 @@ -114,9 +150,11 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0001782 has_input: - - evidence: + - type: MoleculeAssociation + evidence: - term: ECO:0000250 reference: GO_REF:0000024 with_objects: @@ -124,87 +162,125 @@ activities: provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-05-07' + provenances: [] term: UniProtKB:P21854 + has_output: [] causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000314 reference: PMID:11823534 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] predicate: RO:0002629 downstream_activity: gomodel:6606056e00002011/6606056e00002014 + provenances: [] - id: gomodel:6606056e00002011/6606056e00002014 enabled_by: + type: EnabledByGeneProductAssociation + evidence: [] + provenances: [] term: UniProtKB:P21854 molecular_function: + type: MolecularFunctionAssociation evidence: - term: ECO:0000314 reference: PMID:27810925 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0004888 occurs_in: + type: CellularAnatomicalEntityAssociation evidence: - term: ECO:0000314 reference: PMID:1711157 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0005886 part_of: + type: BiologicalProcessAssociation evidence: - term: ECO:0000314 reference: PMID:1711157 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] term: GO:0050859 + has_input: [] + has_output: [] causal_associations: - - evidence: + - type: CausalAssociation + evidence: - term: ECO:0000314 reference: PMID:27810925 provenances: - contributor: https://orcid.org/0000-0001-7646-0052 date: '2024-04-09' + provenances: [] predicate: RO:0002629 downstream_activity: gomodel:6606056e00002011/6606056e00002049 + provenances: [] objects: - id: GO:0005615 label: extracellular space + type: gocam:Object - id: GO:0004888 label: transmembrane signaling receptor activity + type: gocam:Object - id: UniProtKB:P21854 label: CD72 Hsap + type: gocam:Object - id: GO:0050859 label: negative regulation of B cell receptor signaling pathway + type: gocam:Object - id: GO:0005886 label: plasma membrane + type: gocam:Object - id: ECO:0000314 label: direct assay evidence used in manual assertion + type: gocam:Object - id: GO:0004713 label: protein tyrosine kinase activity + type: gocam:Object - id: UniProtKB:P07948 label: LYN Hsap + type: gocam:Object - id: GO:0001782 label: B cell homeostasis + type: gocam:Object - id: ECO:0000250 label: sequence similarity evidence used in manual assertion + type: gocam:Object - id: GO:0004725 label: protein tyrosine phosphatase activity + type: gocam:Object - id: UniProtKB:P29350 label: PTPN6 Hsap + type: gocam:Object - id: GO:0005737 label: cytoplasm + type: gocam:Object - id: GO:0019815 label: B cell receptor complex + type: gocam:Object - id: UniProtKB:P11912 label: CD79A Hsap + type: gocam:Object - id: UniProtKB:P40259 label: CD79B Hsap + type: gocam:Object - id: GO:0050853 label: B cell receptor signaling pathway + type: gocam:Object - id: CHEBI:166824 label: peptide antigen + type: gocam:Object +provenances: []