From 4809e156a08d7bc4e3a1e7c29337bcb772f5398b Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 21 Feb 2022 11:15:15 +0100 Subject: [PATCH 1/6] Create Enzyme quality data.yaml --- STRENDA/Enzyme quality data.yaml | 469 +++++++++++++++++++++++++++++++ 1 file changed, 469 insertions(+) create mode 100644 STRENDA/Enzyme quality data.yaml diff --git a/STRENDA/Enzyme quality data.yaml b/STRENDA/Enzyme quality data.yaml new file mode 100644 index 0000000..fd44c09 --- /dev/null +++ b/STRENDA/Enzyme quality data.yaml @@ -0,0 +1,469 @@ +{ + eln: { + version: '1.0.3', + base_revision: 'c55e64ec712a688f27e80d0be08f8db256da0a08', + current_revision: '1db318d0ab9d2185df284356d43b0af923558fd2\n' + }, + uuid: '2598b5b5-c31f-4ceb-ab0a-c30bea0bc3f6', + klass: 'SegmentKlass', + layers: { + actdet: { + key: 'actdet', + cols: 1, + color: 'none', + label: 'Details on activation data', + style: 'panel_generic_heading', + fields: [ + { + type: 'textarea', + field: 'methods', + label: 'Time-dependence and reversibility methods description', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'types', + label: 'activation types details', + default: '', + position: 2, + required: false, + sub_fields: [], + text_sub_fields: [] + } + ], + position: 8 + }, + details: { + key: 'details', + cols: 1, + label: 'Details on inhibition data', + fields: [ + { + type: 'textarea', + field: 'methods', + label: 'Time-dependence and reversibility methods description', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'types', + label: 'Inhibition types details', + default: '', + position: 2, + required: false, + sub_fields: [], + description: '', + text_sub_fields: [] + } + ], + position: 5 + }, + required: { + key: 'required', + cols: 1, + color: 'none', + label: 'Information required on kinetic parameters', + style: 'panel_generic_heading', + fields: [ + { + type: 'textarea', + field: 'parameter', + label: 'How were the given parameters obtained?', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'e.g., non-linear curve fitting using least squares, non- parametric method such as direct linear plot, linear regression to transformed form of rate equation. Note: if commercial computer programs are used, determine which were used', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Model', + label: 'Model used to determine the parameters', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'With explanation of why is the chosen model considered to be the “right” model. Report any measures of quality of fit, and for any alternative models considered.', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'inhibition', + label: 'high-substrate inhibition', + default: '', + position: 3, + required: false, + sub_fields: [], + description: 'Details on high-substrate inhibition, if observed, with Ki value', + text_sub_fields: [] + } + ], + position: 3 + }, + activation: { + key: 'activation', + cols: 4, + color: 'none', + label: 'Data required for reporting activation data', + style: 'panel_generic_heading', + fields: [ + { + type: 'checkbox', + field: 'Time', + label: 'Time-dependent', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'reversible', + label: 'Reversible', + default: '', + position: 2, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'competitive', + label: 'Competitive', + default: '', + position: 3, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'tight', + label: 'Tight-binding', + default: '', + position: 4, + required: false, + sub_fields: [], + text_sub_fields: [] + } + ], + position: 6 + }, + functional: { + key: 'functional', + cols: 2, + color: 'none', + label: 'Required data for all enzyme functional data', + style: 'panel_generic_heading', + fields: [ + { + type: 'checkbox', + field: 'Specification', + label: 'Relative to subunit', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'relative', + label: 'Relative to oligomeric form', + default: '', + position: 2, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'table', + field: 'table', + label: 'table', + default: '', + position: 3, + required: false, + sub_fields: [ + { + id: '829bdce0-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Experiment no' + }, + { + id: '96bcc180-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Changes' + }, + { + id: 'b6d06d00-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Standard error' + }, + { + id: 'c33fb6e0-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Standard deviation' + }, + { + id: 'e3e1bfb0-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Confidence limits' + }, + { + id: 'ec583110-92a3-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Q1' + }, + { + id: '058b4d70-92a4-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Q2' + }, + { + id: '0f68a1d0-92a4-11ec-bdcb-83947351ebe3', + type: 'text', + value: '', + col_name: 'Q3' + } + ], + description: 'Indicate what changed between replicates; just repeat reactions, different enzyme preparations, different ways, alternative staff, different laboratories', + text_sub_fields: [] + } + ], + position: 1 + }, + inhibition: { + key: 'inhibition', + cols: 4, + color: 'none', + label: 'Data required for reporting inhibition data', + style: 'panel_generic_heading', + fields: [ + { + type: 'checkbox', + field: 'Time', + label: 'Time-dependent', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'reversible', + label: 'Reversible', + default: '', + position: 2, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'competitive', + label: 'Competitive', + default: '', + position: 3, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'checkbox', + field: 'tight', + label: 'Tight-binding', + default: '', + position: 4, + required: false, + sub_fields: [], + text_sub_fields: [] + } + ], + position: 4 + }, + parameters: { + key: 'parameters', + cols: 3, + color: 'none', + label: 'Data necessary for reporting kinetic parameters', + style: 'panel_generic_heading', + fields: [ + { + type: 'text', + field: 'equation', + label: 'Kinetic equation', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'text', + field: 'model', + label: 'Model', + default: '', + position: 2, + required: false, + sub_fields: [], + placeholder: 'e.g., Michaelis-Menten', + text_sub_fields: [] + }, + { + type: 'text', + field: 'variable', + label: 'Variables', + default: '', + position: 3, + required: false, + sub_fields: [], + placeholder: 'e.g., varying concentration of ATP, fixed glucose or v = Vmax / (1 + KA/[2-aminopropane] + KB/[2-butanone])', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'kcat', + label: 'Kcat', + default: '', + position: 4, + required: false, + sub_fields: [], + option_layers: 'turnover_number', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Vmax', + label: 'Vmax', + default: '', + position: 5, + required: false, + sub_fields: [], + option_layers: 'reaction_rate', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Km', + label: 'Km', + default: '', + position: 6, + required: false, + sub_fields: [], + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'formula-field', + field: 'kcatKm', + label: 'Kcat/Km', + default: '', + formula: 'kcat/Km', + position: 7, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'S', + label: 'S0.5 ', + default: '', + position: 8, + required: false, + sub_fields: [], + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'text', + field: 'cooperativity', + label: 'cooperativity coefficient', + default: '', + position: 9, + required: false, + sub_fields: [], + description: 'Hill coefficient, saturation ratio (RS) or other coefficients of cooperativity', + placeholder: 'e.g., Hill coefficient', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'value', + label: 'Cooperativity coefficient value', + default: '', + position: 10, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'table', + field: 'KM2', + label: 'KM2', + default: '', + position: 11, + required: false, + sub_fields: [ + { + id: '3c0cb1f0-5847-11ec-ac2d-c11f7a2c60d7', + type: 'text', + value: '', + col_name: 'co-substrates' + }, + { + id: '462adfe0-5847-11ec-ac2d-c11f7a2c60d7', + type: 'text', + value: '', + col_name: 'KM2 constant' + } + ], + text_sub_fields: [] + }, + { + type: 'table', + field: 'KP', + label: 'KP', + default: '', + position: 12, + required: false, + sub_fields: [ + { + id: '907d8430-5847-11ec-ac2d-c11f7a2c60d7', + type: 'text', + value: '', + col_name: 'Product' + }, + { + id: '9386cc90-5847-11ec-ac2d-c11f7a2c60d7', + type: 'text', + value: '', + col_name: 'KP constant' + } + ], + text_sub_fields: [] + } + ], + position: 2 + } + }, + select_options: {} +} From e689aa75252fc6fcf70093b56d7be3e770a743c9 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 21 Feb 2022 11:16:17 +0100 Subject: [PATCH 2/6] Create Enzyme methods data.yaml --- STRENDA/Enzyme methods data.yaml | 1185 ++++++++++++++++++++++++++++++ 1 file changed, 1185 insertions(+) create mode 100644 STRENDA/Enzyme methods data.yaml diff --git a/STRENDA/Enzyme methods data.yaml b/STRENDA/Enzyme methods data.yaml new file mode 100644 index 0000000..064ea06 --- /dev/null +++ b/STRENDA/Enzyme methods data.yaml @@ -0,0 +1,1185 @@ +{ + eln: { + version: '1.0.3', + base_revision: 'c55e64ec712a688f27e80d0be08f8db256da0a08', + current_revision: '1db318d0ab9d2185df284356d43b0af923558fd2\n' + }, + uuid: 'd956c677-ca99-4642-a4c8-c53a1ed15f51', + klass: 'SegmentKlass', + layers: { + assay: { + key: 'assay', + cols: 4, + label: 'Assay conditions', + fields: [ + { + type: 'table', + field: 'Substrate', + label: 'Identity and purity of all assay components', + default: '', + position: 1, + required: false, + sub_fields: [ + { + id: '9b499cd0-5830-11ec-8e6d-e5da33a42746', + type: 'drag_molecule', + value: 'iupac;', + col_name: 'Component' + }, + { + id: 'b39f5180-5830-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Purity', + value_system: 'p', + option_layers: 'percentage' + }, + { + id: '70fb9360-5831-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Origin' + } + ], + option_layers: 'percentage', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'reaction', + label: 'Measured reaction', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'As a stoichiometrically balanced equation, e.g., 2 mol substrate oxidized per mol O2 consumed', + placeholder: 'e.g., 2 mol substrate oxidized per mol O2 consumed', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Atemperature', + label: 'Assay temperature', + default: '', + position: 3, + required: false, + sub_fields: [], + option_layers: 'temperature', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'pressure', + label: 'Assay pressure', + default: '', + position: 4, + required: false, + sub_fields: [], + option_layers: 'pressure', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Atmosphere', + label: 'Atmosphere', + default: '', + position: 5, + required: false, + sub_fields: [], + description: '', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'ApH', + label: 'Assay pH', + default: '', + position: 6, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'text', + field: 'measure', + label: 'Assay pH measurement', + default: '', + position: 7, + required: false, + sub_fields: [], + description: 'Describe how was the pH measured.', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Buffer', + label: 'Buffer', + default: '', + position: 8, + required: false, + sub_fields: [ + { + id: '54334ce0-5832-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '54d50b20-5832-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'ec48bb50-5deb-11ec-adac-635086d5aeb8', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + description: 'Buffer and concentrations.', + placeholder: 'e.g., 100 mM Tris-HCl, 200 mM potassium phosphate, including counter-ion', + text_sub_fields: [] + }, + { + type: 'table', + field: 'salt', + label: 'Metal salt', + default: '', + position: 9, + required: false, + sub_fields: [ + { + id: '8b087880-5832-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '8b1e9890-5832-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'f115d3c0-5deb-11ec-adac-635086d5aeb8', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + description: 'Metal salt(s) and concentrations.', + placeholder: 'e.g., 10 mM KCl, 1.0 mM MgSO4', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Other', + label: 'Other assay components', + default: '', + position: 10, + required: false, + sub_fields: [ + { + id: 'b0674610-5832-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: 'b0e96e60-5832-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'f5b12dd0-5deb-11ec-adac-635086d5aeb8', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + placeholder: 'e.g., 1.0 mM EDTA, 1.0 mM dithiothreitol', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Coupled', + label: 'Coupled assay components ', + default: '', + position: 11, + required: false, + sub_fields: [], + description: 'if relevant', + text_sub_fields: [] + }, + { + type: 'table', + field: 'ranges', + label: 'Substrate and concentration ranges', + default: '', + position: 12, + required: false, + sub_fields: [ + { + id: '0ba175f0-5833-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '0bb991d0-5833-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Start concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: '36e11b30-5dec-11ec-adac-635086d5aeb8', + type: 'system-defined', + value: '', + col_name: 'End concentration', + value_system: 'mol_l', + option_layers: 'molarity' + } + ], + placeholder: 'e.g., 1 - 100 mM glucose, 5 mM ATP', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'concentration', + label: 'Enzyme molarity', + default: '', + position: 13, + required: false, + sub_fields: [], + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'mconcentration', + label: 'Enzyme mass concentration', + default: '', + position: 14, + required: false, + sub_fields: [], + option_layers: 'concentration', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Varied', + label: 'Varied components', + default: '', + position: 15, + required: false, + sub_fields: [ + { + id: '45335090-5833-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '48262ac0-5833-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Start concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: '56ac7310-5dec-11ec-adac-635086d5aeb8', + type: 'system-defined', + value: '', + col_name: 'End concentration', + value_system: 'mol_l', + option_layers: 'molarity' + } + ], + description: 'e.g. inhibitor concentration', + placeholder: '', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'ionic', + label: 'Mixture ionic strength', + default: '', + position: 16, + required: false, + sub_fields: [], + description: 'Total assay mixture ionic strength', + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Comments', + label: 'Comments', + default: '', + position: 17, + required: false, + sub_fields: [], + description: 'Any comment on the above data. e.g., If pH is adjusted by addition of acid or base not shown in buffer name, make this clear – e.g., 50 mM sodium acetate adjusted with HCl.', + text_sub_fields: [] + } + ], + position: 5 + }, + storage: { + key: 'storage', + cols: 4, + label: 'Storage conditions', + fields: [ + { + type: 'checkbox', + field: 'frozen', + label: 'Frozen', + default: '', + position: 1, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'freezingt', + label: 'Freezing temperature', + default: '', + position: 2, + required: false, + sub_fields: [], + option_layers: 'temperature', + text_sub_fields: [] + }, + { + type: 'text', + field: 'freezing', + label: 'Freezing method', + default: '', + position: 3, + required: false, + sub_fields: [], + placeholder: 'e.g., flash', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Stemperature', + label: 'Storage temperature', + default: '', + position: 4, + required: false, + sub_fields: [], + description: 'The temperature at which the enzyme is stored', + option_layers: 'temperature', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Atmosphere', + label: 'Atmosphere', + default: '', + position: 5, + required: false, + sub_fields: [], + placeholder: 'e.g., Air', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'pH', + label: 'pH', + default: '', + position: 6, + required: false, + sub_fields: [], + description: 'The pH of the stored enzyme solution', + placeholder: 'e.g., 7.0', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'pHT', + label: 'pH temperature', + default: '', + position: 7, + required: false, + sub_fields: [], + description: 'At which temperature was the pH measured.', + option_layers: 'temperature', + text_sub_fields: [] + }, + { + type: 'text', + field: 'thawing', + label: 'Thawing procedure', + default: '', + position: 8, + required: false, + sub_fields: [], + description: 'Statement about the thawing procedure.', + placeholder: 'e.g., on ice', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Buffer', + label: 'pH-Buffer', + default: '', + position: 9, + required: false, + sub_fields: [ + { + id: 'd10a8430-582e-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: 'd1a6c430-582e-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'e4a73810-5de9-11ec-b150-952b213f6620', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + description: 'Buffer and concentrations (including counter-ion). ', + placeholder: 'e.g., 200 mM potassium phosphate, 100 mM HEPES- KOH', + text_sub_fields: [] + }, + { + type: 'table', + field: 'salt', + label: 'Metal salt', + default: '', + position: 10, + required: false, + sub_fields: [ + { + id: '34832580-582f-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '34ec6ea0-582f-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'f6322f90-5de9-11ec-b150-952b213f6620', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + description: 'Metal salt(s) and concentrations', + placeholder: 'e.g., 10 mM KCl, 1.0 mM MgSO4', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Other', + label: 'Other components', + default: '', + position: 11, + required: false, + sub_fields: [ + { + id: '5c909850-582f-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '60277ab0-582f-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: '11edf2a0-5dea-11ec-b150-952b213f6620', + type: 'text', + value: '', + col_name: 'Comment' + } + ], + description: 'Other components and concentrations ', + placeholder: 'e.g., 1.0 mM EDTA, 1.0 mM dithiothreitol, 10% glycerol, 20% DMSO, 1 mg/ml PEG2000, 2 mg/ml BSA, peptidase inhibitors', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'concentration', + label: 'Enzyme molarity', + default: '', + position: 12, + required: false, + sub_fields: [], + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Mconcentration', + label: 'Enzyme mass concentration', + default: '', + position: 13, + required: false, + sub_fields: [], + option_layers: 'concentration', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'loss', + label: 'Approximate loss of activity ', + default: '', + position: 14, + required: false, + sub_fields: [], + description: 'Statement about observed loss of activity under the above conditions.', + placeholder: 'e.g., less than 10% loss after 1 month', + option_layers: 'percentage', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'ltime', + label: 'Activity loss time', + default: '', + position: 15, + required: false, + sub_fields: [], + description: 'Time after which activity loss was observed', + option_layers: 'duration', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Comments', + label: 'Comments', + default: '', + position: 16, + required: false, + sub_fields: [], + description: 'Any comment on the above data. ', + text_sub_fields: [] + } + ], + position: 4 + }, + activity: { + key: 'activity', + cols: 4, + label: 'Activity', + fields: [ + { + type: 'system-defined', + field: 'rate', + label: 'Initial rates', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'Initial rate of the reaction measured', + option_layers: 'reaction_rate', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'rateD', + label: 'Initial rate details', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'Determine how initial rate was established. Estimate ranges in substrate/product concentrations at the last data point.', + placeholder: 'e.g., true initial tangent', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Eactivity', + label: 'Enzyme activity', + default: '', + position: 3, + required: false, + sub_fields: [], + option_layers: 'enzyme_activity', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'kcat', + label: 'kcat', + default: '', + position: 4, + required: false, + sub_fields: [], + option_layers: 'turnover_number', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'range', + label: 'Start concentration', + default: '', + position: 5, + required: false, + sub_fields: [], + description: 'Specify at which (range of) enzyme concentration(s) enzyme activity was determined.', + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'system-defined', + field: 'Endconcentration', + label: 'End concentration', + default: '', + position: 6, + required: false, + sub_fields: [], + description: 'Specify at which (range of) enzyme concentration(s) enzyme activity was determined.', + option_layers: 'molarity', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Comments', + label: 'Comments', + default: '', + position: 7, + required: false, + sub_fields: [], + description: 'Any comment on the above data. ', + text_sub_fields: [] + } + ], + position: 6 + }, + identity: { + key: 'identity', + cols: 4, + color: 'none', + label: 'Identity of the enzyme', + style: 'panel_generic_heading', + fields: [ + { + type: 'text', + field: 'Name', + label: 'Name of reaction catalyst', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'Name, preferably the accepted name from the IUBMB Enzyme List', + placeholder: 'e.g., Carboxylic ester hydrolases', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'EC', + label: 'EC number', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'The Enzyme Commission number', + placeholder: 'e.g., 3.4.11.4 ', + text_sub_fields: [] + }, + { + type: 'text', + field: 'accession', + label: 'Uniprot accession number', + default: '', + position: 3, + required: false, + sub_fields: [], + description: '', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'Organism', + label: 'Organism', + default: '', + position: 4, + required: false, + sub_fields: [], + description: 'NCBI Taxonomy ID', + placeholder: 'e.g., 9606', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Oligomeric', + label: 'Oligomeric state', + default: '', + position: 5, + required: false, + sub_fields: [], + description: 'Number of different subunits.', + placeholder: 'e.g., 2a, 2b', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'reaction', + label: 'Reaction equation ', + default: '', + position: 6, + required: false, + sub_fields: [], + description: 'Fully balanced chemical reaction equation, elements and charges balanced. ', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'sequence', + label: 'sequence', + default: '', + position: 7, + required: false, + sub_fields: [], + description: 'If the sequence doesn\'t have an accession number, please provide the full sequence', + text_sub_fields: [] + } + ], + position: 1 + }, + material: { + key: 'material', + cols: 2, + color: 'none', + label: 'Additional material desirable', + style: 'panel_generic_heading', + fields: [ + { + type: 'table', + field: 'constant', + label: 'Free metal cation concentrations', + default: '', + position: 1, + required: false, + sub_fields: [ + { + id: 'a9071e50-5840-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: 'a93bc2e0-5840-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: 'a9b55fb0-5840-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'How concentration calculated' + } + ], + placeholder: 'e.g., 2', + text_sub_fields: [] + } + ], + position: 9 + }, + additional: { + key: 'additional', + cols: 3, + label: 'Additional information on the enzyme', + fields: [ + { + type: 'text', + field: 'Isoenzyme', + label: 'Isoenzyme', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'Naturally occurring variant or indication of selection of alternative', + placeholder: 'e.g., Hexokinase-1', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Tissue', + label: 'Tissue', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'The source of an enzyme comprising tissue, preferably from BRENDA Tissue Ontology (BTO)', + placeholder: 'e.g., epineurium', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Organelle', + label: 'Organelle', + default: '', + position: 3, + required: false, + sub_fields: [], + description: 'The source of an enzyme comprising organelle, preferably from Gene Ontology (GO)', + placeholder: 'e.g., lysosome', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Localization', + label: 'Localization', + default: '', + position: 4, + required: false, + sub_fields: [], + description: 'Within cell. Specify what localization is based on. preferably from NCI Thesaurus', + placeholder: 'e.g., Cellular Membrane', + text_sub_fields: [] + }, + { + type: 'text', + field: 'modification', + label: 'Post-translational modification', + default: '', + position: 5, + required: false, + sub_fields: [], + description: 'Add only when determined, preferably from PSI-MOD', + placeholder: '', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Sequencemodifications', + label: 'Sequence modifications', + default: '', + position: 6, + required: false, + sub_fields: [], + text_sub_fields: [] + } + ], + position: 2 + }, + equilibrium: { + key: 'equilibrium', + cols: 2, + label: 'Equilibrium measurements', + fields: [ + { + type: 'textarea', + field: 'Evidence', + label: 'Evidence that reaction reached equilibrium', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'e.g., approached from both (or all if multiple substrates/products) directions', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Complexing', + label: 'Complexing metal ions', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'if the reaction involved species that might bind these (e.g., phosphate esters), essential to report estimated pMg and/or pCa', + text_sub_fields: [] + }, + { + type: 'integer', + field: 'pMg', + label: 'pMg', + default: '', + position: 3, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'integer', + field: 'pCa', + label: 'pCa', + default: '', + position: 4, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'table', + field: 'directly', + label: 'State which of all reactants were measured directly', + default: '', + position: 5, + required: false, + sub_fields: [ + { + id: 'cde631c0-7ab4-11ec-b768-23aca4358195', + type: 'text', + value: '', + col_name: 'Reactant' + }, + { + id: 'd824b8f0-7ab4-11ec-b768-23aca4358195', + type: 'text', + value: '', + col_name: 'Was it measured directly?' + } + ], + description: 'e.g., glucose phosphate and glucose measured directly, excess phosphate estimated by mass balance', + text_sub_fields: [] + }, + { + type: 'table', + field: 'Range', + label: 'Concentrations ranges', + default: '', + position: 6, + required: false, + sub_fields: [ + { + id: '95811b20-5835-11ec-8e6d-e5da33a42746', + type: 'text', + value: '', + col_name: 'Name' + }, + { + id: '9a9bb750-5835-11ec-8e6d-e5da33a42746', + type: 'system-defined', + value: '', + col_name: 'Start concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: '29b21670-5e7e-11ec-adac-635086d5aeb8', + type: 'system-defined', + value: '', + col_name: 'End concentration', + value_system: 'mol_l', + option_layers: 'molarity' + }, + { + id: '2a5de6d0-5e7e-11ec-adac-635086d5aeb8', + type: 'text', + value: 'initial vs equilibrium', + col_name: 'Time point' + } + ], + description: 'Range of all initial and measured equilibrium concentrations of the starting material and products in the experiment ', + text_sub_fields: [] + } + ], + position: 7 + }, + methodology: { + key: 'methodology', + cols: 1, + color: 'none', + label: 'Methodology', + style: 'panel_generic_heading', + fields: [ + { + type: 'text', + field: 'method', + label: 'Assay method name', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'a literature reference may suffice for an established procedure but any modification should be detailed', + text_sub_fields: [] + }, + { + type: 'text', + field: 'link', + label: 'Method reference', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'a literature reference may suffice for an established procedure but any modification should be detailed', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'mod', + label: 'Description', + default: '', + position: 3, + required: false, + sub_fields: [], + description: 'any modification on the method, or full description if not an established procedure', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'assay', + label: 'Type of assay', + default: '', + position: 4, + required: false, + sub_fields: [], + description: 'e.g., continuous or discontinuous, direct or coupled', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Reaction', + label: 'Reaction stopping procedure', + default: '', + position: 5, + required: false, + sub_fields: [], + description: 'In the case of discontinuous assays', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Direction', + label: 'Direction of the assay ', + default: '', + position: 6, + required: false, + sub_fields: [], + description: 'With respect to the reaction equation provided e.g., NAD reduction by alcohol dehydrogenase; alcohol + NAD+ -> aldehyde or ketone + NADH + H+', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Reactant', + label: 'Reactant determined', + default: '', + position: 7, + required: false, + sub_fields: [], + placeholder: 'e.g., NADH formation, O2 utilization', + text_sub_fields: [] + } + ], + position: 8 + }, + preparation: { + key: 'preparation', + cols: 2, + color: 'none', + label: 'Preparation', + style: 'panel_generic_heading', + fields: [ + { + type: 'checkbox', + field: 'Purified', + label: 'Purified', + default: '', + position: 1, + required: false, + sub_fields: [], + description: 'Specify whether protein or enzyme was purified.', + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'purity', + label: 'Purity criteria', + default: '', + position: 2, + required: false, + sub_fields: [], + description: 'Methodology for purification', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Artificial', + label: 'Artificial modification', + default: '', + position: 3, + required: false, + sub_fields: [], + description: '', + placeholder: 'e.g., truncated, His-tagged, fusion protein, lacking native glycosylation...', + text_sub_fields: [] + }, + { + type: 'text', + field: 'Metalloenzyme', + label: 'Metalloenzyme mutation', + default: '', + position: 4, + required: false, + sub_fields: [], + description: '', + text_sub_fields: [] + }, + { + type: 'text', + field: 'content', + label: 'Metalloenzyme content', + default: '', + position: 5, + required: false, + sub_fields: [], + placeholder: '', + text_sub_fields: [] + }, + { + type: 'text', + field: 'cofactors', + label: 'Metalloenzyme cofactors', + default: '', + position: 6, + required: false, + sub_fields: [], + text_sub_fields: [] + }, + { + type: 'textarea', + field: 'Description', + label: 'Description', + default: '', + position: 7, + required: false, + sub_fields: [], + description: 'Commercial source, procedure used or reference along with modifications...', + text_sub_fields: [] + } + ], + position: 3 + } + }, + select_options: {} + } From 93cdc0743eb47d604f64a26444e9aba68ced3bc0 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Wed, 9 Nov 2022 11:34:18 +0100 Subject: [PATCH 3/6] Create README.md --- NMR/README.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 NMR/README.md diff --git a/NMR/README.md b/NMR/README.md new file mode 100644 index 0000000..3d7488a --- /dev/null +++ b/NMR/README.md @@ -0,0 +1 @@ +This folder contains NMR templates for 1H and 13C. We aim at one NMR template in the future. 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