Pathogenic Supportive

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

Criterios de PP2

(int??, 'PP2', 'Variant Type and Location', 'Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease.', 'AND', NULL, NULL, 1, NULL, NULL),

Criterios de PP3

(INT??, 'PP3', 'Computational and Predictive Information', 'Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) each algorithm should not be counted as an independent criterion.', 'AND', NULL, NULL, 1, NULL, NULL);

3. Relacionar Guideline_Criterion

INSERT IGNORE INTO Guideline_Criterion(guideline_id, criterion_id) VALUES

4. Insertar Métricas

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

Métricas de PP2

(INT??, 'common_mechanism_of_disease', 'Missense variants are a common mechanism of disease of the gene. A gene with a missense z-score > 3.09 is more likely to be intolerant of missense changes.', 'ScorePrediction.score[ScorePrediction.name=Missense_Z-Score]@GnomadConstraints', 1, '{"operation": "MAJOR", "value": "3.09"}'),

#TODO: Se repite missense_variant (quitada)

Métricas de PP3

(INT??, 'bayesdel_d', 'Meta-predictor tool BayesDel as supportive evidence of pathogenicity.', 'ImpactPrediction.impact[ImpactPrediction.name=BayesDel_noAF]@dbNSFP', 1, '{"operation": "EQUALS", "value": "D"}');

#TODO: Se repite deletererious_effect_prediction (quitada)

5. Relacionar Criterion_Metric

INSERT IGNORE INTO Criterion_Metric (criterion_id, metric_id) VALUES

Métricas de PP2 con Criterios de PP2

#TODO: Se repite `missense_variant Recordar incluirla!

(x, x),
(x, x),

Métricas de PP3 con Criterios de PP3

#TODO: Se repite deletererious_effect_prediction Recordar incluirla!

(x, x),
(x, x);

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);

Menú:

  • Pathogenic Strong

  • Pathogenic Moderate

  • Pathogenic Supportive

  • Benign Stand Alone

  • Benign Strong

  • Benign Supportive