Benign Stand Alone

1. Insertar Guia Holística

INSERT INTO "Guideline"(id, title, author, applicability, url, rules, evaluation_type) VALUES

Guía Holística

La guía 8 es la que voy a usar para todos los criterios de mi TFM.

(8, 'Hollistic guideline', 'PROS UPV', NULL, NULL, '{"benign": {"lower": -9999999999, "upper": -6}, "likely benign": {"lower": -6, "upper": -1}, "VUS-ice cold": {"lower": 0, "upper": 0}, "VUS-cold": {"lower": 1, "upper": 1}, "VUS-cool": {"lower": 2, "upper": 2}, "VUS-tepid": {"lower": 3, "upper": 3}, "VUS-warm": {"lower": 4, "upper": 4}, "VUS-hot": {"lower": 5, "upper": 5}, "likely pathogenic": {"lower": 6, "upper": 9}, "pathogenic": {"lower": 10, "upper": 9999999999}}', 'score');

2. Insertar grupo de criterios

INSERT INTO "Criterion"(id, name, dimension, description, pass_rule, strength, direction, suggested_strength, min_accepted_strength, max_accepted_strength) VALUES

Criterio BA1

(INT??, 'BA1', 'Population Frequency', 'used as stand-alone evidence of benign impact. The variant is above the expected carrier frequency for the disorder in a large population/cohort. Implying a ≥5% AF.', 'AND', NULL, NULL, 8, NULL, NULL),;

3. Relacionar Guideline_Criterion

INSERT IGNORE INTO Guideline_Criterion(guideline_id, criterion_id) VALUES

Criterio BA1 con Guía holística

(8, INT??);

4. Insertar Métricas

INSERT INTO Metric(id, name, description, columns_pattern, min_percentage_data_fulfillment, data_evaluation_condition) VALUES

Métrica de BA1

(INT??, 'exon_biologically_relevant', 'The variant is above the expected carrier frequency for the disorder in a large population/cohort. Implying a ≥5% AF.', 'AlleleFrequency.frequency[Population.name={population}]', 1, '{"operation": "MAJOR", "value": "0.05"}');

5. Relacionar Criterion_Metric

INSERT IGNORE INTO Criterion_Metric (criterion_id, metric_id) VALUES

6. Insertar pipeline

el id 3 es el de hereditary cancer-> no es el mío.Tengo que cambiar el ID 3 por el mío. Tengo que averigar cuál fué el ID del pipeline para mi caso.

# Pipeline (id ???) 
INSERT IGNORE INTO Pipeline (id, name, description, filtering_guideline, classification_guideline, report_template_id) VALUES
(3, hereditary_cancer_scores, Pipeline for heriditary cancer with scored based evaluation, 2, 5, 3);

En caso de que ya esté subido tendría que hacer update….(?)

UPDATE nombredelatabla valoraactualizae SET valorquequierocambiar WHERE iddelpipelinequequieroactualizar

7. Relacionar Pipeline_File

De nuevo, cambiar el 3 por el ID que toca. los otros están bien así.


# Pipeline_File
INSERT IGNORE INTO Pipeline_File (Pipeline_id, File_id) VALUES 
(3, 64),
(3, 65),
(3, 66),
(3, 67),
(3, 68),
(3, 69),
(3, 70),
(3, 71),
(3, 72),
(3, 73),
(3, 74),
(3, 75),
(3, 81),
(3, 82),
(3, 83),
(3, 84),
(3, 85),
(3, 88),
(3, 89),
(3, 90),
(3, 99),
(3, 100),
(3, 207),
(3, 208),
(3, 722),
(3, 723),
(3, 727),
(3, 728),
(3, 729),
(3, 733);

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