delimiter @@

DROP PROCEDURE IF EXISTS Build_Bio_Similarity() @@

CREATE PROCEDURE Build_Bio_Similarity()
BEGIN

-- ----------------------------------------------------------------
-- -- DisGenCoef                                                 --
-- ----------------------------------------------------------------

-- Suma de genes por enfermedad
DROP TABLE IF EXISTS tmp_disgentot;
CREATE TABLE tmp_disgentot AS
SELECT disease_cui, COUNT(*) AS gentot
  FROM disease_gene
 GROUP BY disease_cui;
CREATE INDEX ix_tmp_disgentot ON tmp_disgentot ( disease_cui );

-- Combinaciones de enfermedades con genes coincidentes sin agrupar
DROP TABLE IF EXISTS tmp_disgencomb;
CREATE TABLE tmp_disgencomb AS
SELECT dg1.disease_cui AS id_dis1, dg2.disease_cui AS id_dis2
  FROM disease_gene dg1 INNER JOIN disease_gene dg2
    ON ( dg1.gene_id = dg2.gene_id AND dg2.disease_cui > dg1.disease_cui );
CREATE INDEX ix_tmp_disgencomb ON tmp_disgencomb ( id_dis1, id_dis2 );

-- Coeficientes de los vectores de enfermedades relacionadas por genes
DROP TABLE IF EXISTS tmp_disgencoef;
CREATE TABLE tmp_disgencoef
       ( id_dis1 CHAR(8)
        ,id_dis2 CHAR(8)
        ,gen_cos FLOAT
        ,gen_jac FLOAT
        ,gen_dic FLOAT )
    AS
SELECT dgvc.id_dis1
      ,dgvc.id_dis2
      ,dgvc.gentot / (SQRT(dgv1.gentot) * SQRT(dgv2.gentot)) AS gen_cos
      ,dgvc.gentot / (dgv1.gentot + dgv2.gentot - dgvc.gentot) AS gen_jac
      ,dgvc.gentot * 2 / (dgv1.gentot + dgv2.gentot) AS gen_dic
  FROM (SELECT id_dis1, id_dis2, count(*) AS gentot
          FROM tmp_disgencomb
         GROUP BY id_dis1, id_dis2 ) AS dgvc
       ,tmp_disgentot AS dgv1
       ,tmp_disgentot AS dgv2
 WHERE dgvc.id_dis1 = dgv1.disease_cui
   AND dgvc.id_dis2 = dgv2.disease_cui;
CREATE INDEX ix_tmp_disgencoef ON tmp_disgencoef ( id_dis1, id_dis2 );

-- ----------------------------------------------------------------
-- -- DisProtCoef                                                --
-- ----------------------------------------------------------------

-- Relacion proteinas con enfermedades a traves de genes
DROP TABLE IF EXISTS tmp_disprot;
CREATE TABLE tmp_disprot AS
SELECT DISTINCT disease_cui, prot_id
  FROM disease_gene gd INNER JOIN encodes en
    ON ( gd.gene_id = en.gene_id );
CREATE INDEX ix_tmp_disprot1 ON tmp_disprot ( disease_cui, prot_id );
CREATE INDEX ix_tmp_disprot2 ON tmp_disprot ( prot_id, disease_cui );

-- Suma de proteinas por enfermedad
DROP TABLE IF EXISTS tmp_disprottot;
CREATE TABLE tmp_disprottot AS
SELECT disease_cui, COUNT(*) AS prottot
  FROM tmp_disprot
 GROUP BY disease_cui;
CREATE INDEX ix_tmp_disprottot ON tmp_disprottot ( disease_cui );

-- Combinaciones de enfermedades con proteinas coincidentes sin agrupar
DROP TABLE IF EXISTS tmp_disprotcomb;
CREATE TABLE tmp_disprotcomb AS
SELECT dp1.disease_cui AS id_dis1, dp2.disease_cui AS id_dis2
  FROM tmp_disprot dp1 INNER JOIN tmp_disprot dp2
    ON ( dp1.prot_id = dp2.prot_id AND dp2.disease_cui > dp1.disease_cui );
CREATE INDEX ix_tmp_disprotcomb ON tmp_disprotcomb ( id_dis1, id_dis2 );

-- Coeficientes de los vectores de enfermedades relacionadas por proteinas
DROP TABLE IF EXISTS tmp_disprotcoef;
CREATE TABLE tmp_disprotcoef
       ( id_dis1 CHAR(8)
        ,id_dis2 CHAR(8)
        ,prot_cos FLOAT
        ,prot_jac FLOAT
        ,prot_dic FLOAT )
    AS
SELECT dpvc.id_dis1
      ,dpvc.id_dis2
      ,dpvc.prottot / (SQRT(dpv1.prottot) * SQRT(dpv2.prottot)) AS prot_cos
      ,dpvc.prottot / (dpv1.prottot + dpv2.prottot - dpvc.prottot) AS prot_jac
      ,dpvc.prottot * 2 / (dpv1.prottot + dpv2.prottot) AS prot_dic
  FROM (SELECT id_dis1, id_dis2, count(*) AS prottot
          FROM tmp_disprotcomb
         GROUP BY id_dis1, id_dis2 ) AS dpvc
       ,tmp_disprottot AS dpv1
       ,tmp_disprottot AS dpv2
 WHERE dpvc.id_dis1 = dpv1.disease_cui
   AND dpvc.id_dis2 = dpv2.disease_cui;
CREATE INDEX ix_tmp_disprotcoef ON tmp_disprotcoef ( id_dis1, id_dis2 );

-- ----------------------------------------------------------------
-- -- DisPathCoef                                                --
-- ----------------------------------------------------------------

-- Relacion rutas con enfermedades a traves de genes
DROP TABLE IF EXISTS tmp_dispath;
CREATE TABLE tmp_dispath AS
SELECT DISTINCT disease_cui, path_id
  FROM disease_gene gd INNER JOIN gene_pathway gp
    ON ( gd.gene_id = gp.gen_id );
CREATE INDEX ix_tmp_dispath1 ON tmp_dispath ( disease_cui, path_id );
CREATE INDEX ix_tmp_dispath2 ON tmp_dispath ( path_id, disease_cui );

-- Suma de rutas por enfermedad
DROP TABLE IF EXISTS tmp_dispathtot;
CREATE TABLE tmp_dispathtot AS
SELECT disease_cui, COUNT(*) AS pathtot
  FROM tmp_dispath
 GROUP BY disease_cui;
CREATE INDEX ix_tmp_dispathtot ON tmp_dispathtot ( disease_cui );

-- Combinaciones de enfermedades con rutas coincidentes sin agrupar
DROP TABLE IF EXISTS tmp_dispathcomb;
CREATE TABLE tmp_dispathcomb AS
SELECT dp1.disease_cui AS id_dis1, dp2.disease_cui AS id_dis2
  FROM tmp_dispath dp1 INNER JOIN tmp_dispath dp2
    ON ( dp1.path_id = dp2.path_id AND dp2.disease_cui > dp1.disease_cui );
CREATE INDEX ix_tmp_dispathcomb ON tmp_dispathcomb ( id_dis1, id_dis2 );

-- Coeficientes de los vectores de enfermedades relacionadas por rutas
DROP TABLE IF EXISTS tmp_dispathcoef;
CREATE TABLE tmp_dispathcoef
       ( id_dis1 CHAR(8)
        ,id_dis2 CHAR(8)
        ,path_cos FLOAT
        ,path_jac FLOAT
        ,path_dic FLOAT )
    AS
SELECT dpvc.id_dis1
      ,dpvc.id_dis2
      ,dpvc.pathtot / (SQRT(dpv1.pathtot) * SQRT(dpv2.pathtot)) AS path_cos
      ,dpvc.pathtot / (dpv1.pathtot + dpv2.pathtot - dpvc.pathtot) AS path_jac
      ,dpvc.pathtot * 2 / (dpv1.pathtot + dpv2.pathtot) AS path_dic
  FROM (SELECT id_dis1, id_dis2, count(*) AS pathtot
          FROM tmp_dispathcomb
         GROUP BY id_dis1, id_dis2 ) AS dpvc
       ,tmp_dispathtot AS dpv1
       ,tmp_dispathtot AS dpv2
 WHERE dpvc.id_dis1 = dpv1.disease_cui
   AND dpvc.id_dis2 = dpv2.disease_cui;
CREATE INDEX ix_tmp_dispathcoef ON tmp_dispathcoef ( id_dis1, id_dis2 );

-- ----------------------------------------------------------------
-- -- DisPPiCoef                                                 --
-- ----------------------------------------------------------------

-- Relacion interaccion proteinas con enfermedades a traves de genes
DROP TABLE IF EXISTS tmp_disppi;
CREATE TABLE tmp_disppi AS
SELECT DISTINCT dp1.disease_cui, ppi.id_p1, ppi.id_p2
  FROM p_interacts_with_p ppi
       INNER JOIN edsssdb.tmp_disprot dp1
         ON ( dp1.prot_id = ppi.id_p1 )
       INNER JOIN edsssdb.tmp_disprot dp2
         ON ( dp2.prot_id = ppi.id_p2 AND dp1.disease_cui = dp2.disease_cui);
CREATE INDEX ix_tmp_disppi1 ON tmp_disppi ( id_p1, id_p2, disease_cui );
CREATE INDEX ix_tmp_disppi2 ON tmp_disppi ( disease_cui, id_p1, id_p2 );

-- Suma de interaccion proteinas por enfermedad
DROP TABLE IF EXISTS tmp_disppitot;
CREATE TABLE tmp_disppitot AS
SELECT disease_cui, COUNT(*) AS ppitot
  FROM tmp_disppi
 GROUP BY disease_cui;
CREATE INDEX ix_tmp_disppitot ON tmp_disppitot ( disease_cui );

-- Combinaciones de enfermedades con interaccion proteinas coincidentes sin agrupar
DROP TABLE IF EXISTS tmp_disppicomb;
CREATE TABLE tmp_disppicomb AS
SELECT dp1.disease_cui AS id_dis1, dp2.disease_cui AS id_dis2
  FROM tmp_disppi dp1 INNER JOIN tmp_disppi dp2
    ON ( dp1.id_p1 = dp2.id_p1 AND dp1.id_p2 = dp2.id_p2 AND dp2.disease_cui > dp1.disease_cui );
CREATE INDEX ix_tmp_disppicomb ON tmp_disppicomb ( id_dis1, id_dis2 );

-- Coeficientes de los vectores de enfermedades relacionadas por interaccion proteinas
DROP TABLE IF EXISTS tmp_disppicoef;
CREATE TABLE tmp_disppicoef
       ( id_dis1 CHAR(8)
        ,id_dis2 CHAR(8)
        ,ppi_cos FLOAT
        ,ppi_jac FLOAT
        ,ppi_dic FLOAT )
    AS
SELECT dpvc.id_dis1
      ,dpvc.id_dis2
      ,dpvc.ppitot / (SQRT(dpv1.ppitot) * SQRT(dpv2.ppitot)) AS ppi_cos
      ,dpvc.ppitot / (dpv1.ppitot + dpv2.ppitot - dpvc.ppitot) AS ppi_jac
      ,dpvc.ppitot * 2 / (dpv1.ppitot + dpv2.ppitot) AS ppi_dic
  FROM (SELECT id_dis1, id_dis2, count(*) AS ppitot
          FROM tmp_disppicomb
         GROUP BY id_dis1, id_dis2 ) AS dpvc
       ,tmp_disppitot AS dpv1
       ,tmp_disppitot AS dpv2
 WHERE dpvc.id_dis1 = dpv1.disease_cui
   AND dpvc.id_dis2 = dpv2.disease_cui;
CREATE INDEX ix_tmp_disppicoef ON tmp_disppicoef ( id_dis1, id_dis2 );

-- ----------------------------------------------------------------
-- -- BioSimilarity                                              --
-- ----------------------------------------------------------------

DROP TABLE IF EXISTS bio_similarity;
CREATE TABLE bio_similarity (
           id_dis1 char(8) NOT NULL
          ,id_dis2 char(8) NOT NULL
          ,S_gen_cos float DEFAULT 0
          ,S_gen_jaccard float DEFAULT 0
          ,S_gen_dice float DEFAULT 0
          ,S_prot_cos float DEFAULT 0
          ,S_prot_jaccard float DEFAULT 0
          ,S_prot_dice float DEFAULT 0
          ,S_path_cos float DEFAULT 0
          ,S_path_jaccard float DEFAULT 0
          ,S_path_dice float DEFAULT 0
          ,S_ppi_cos float DEFAULT 0
          ,S_ppi_jaccard float DEFAULT 0
          ,S_ppi_dice float DEFAULT 0  )
    AS
SELECT  comb.id_dis1 AS id_dis1
       ,comb.id_dis2 AS id_dis2
       ,COALESCE(gen.gen_cos,0) AS S_gen_cos
       ,COALESCE(gen.gen_jac,0) AS S_gen_jaccard
       ,COALESCE(gen.gen_dic,0) AS S_gen_dice
       ,COALESCE(prot.prot_cos,0) AS S_prot_cos
       ,COALESCE(prot.prot_jac,0) AS S_prot_jaccard
       ,COALESCE(prot.prot_dic,0) AS S_prot_dice
       ,COALESCE(path.path_cos,0) AS S_path_cos
       ,COALESCE(path.path_jac,0) AS S_path_jaccard
       ,COALESCE(path.path_dic,0) AS S_path_dice
       ,COALESCE(ppi.ppi_cos,0) AS S_ppi_cos
       ,COALESCE(ppi.ppi_jac,0) AS S_ppi_jaccard
       ,COALESCE(ppi.ppi_dic,0) AS S_ppi_dice
  FROM ( SELECT a.cui AS id_dis1, b.cui AS id_dis2
           FROM (SELECT DISTINCT cui AS cui FROM edsssdb.has_biological_info) a,
                (SELECT DISTINCT cui AS cui FROM edsssdb.has_biological_info) b
          WHERE b.cui > a.cui ) comb
       LEFT JOIN tmp_disgencoef AS gen
         ON (comb.id_dis1 = gen.id_dis1 AND comb.id_dis2 = gen.id_dis2)
       LEFT JOIN tmp_disprotcoef AS prot
         ON (comb.id_dis1 = prot.id_dis1 AND comb.id_dis2 = prot.id_dis2)
       LEFT JOIN tmp_dispathcoef AS path
         ON (comb.id_dis1 = path.id_dis1 AND comb.id_dis2 = path.id_dis2)
       LEFT JOIN tmp_disppicoef AS ppi
         ON (comb.id_dis1 = ppi.id_dis1 AND comb.id_dis2 = ppi.id_dis2);
ALTER TABLE bio_similarity
ADD PRIMARY KEY (id_dis1, id_dis2);

-- ----------------------------------------------------------------
-- -- Housekeeping                                               --
-- ----------------------------------------------------------------

DROP TABLE IF EXISTS tmp_disgentot;
DROP TABLE IF EXISTS tmp_disgencomb;
DROP TABLE IF EXISTS tmp_disgencoef;
DROP TABLE IF EXISTS tmp_disprot;
DROP TABLE IF EXISTS tmp_disprottot;
DROP TABLE IF EXISTS tmp_disprotcomb;
DROP TABLE IF EXISTS tmp_disprotcoef;
DROP TABLE IF EXISTS tmp_dispath;
DROP TABLE IF EXISTS tmp_dispathtot;
DROP TABLE IF EXISTS tmp_dispathcomb;
DROP TABLE IF EXISTS tmp_dispathcoef;
DROP TABLE IF EXISTS tmp_disppi;
DROP TABLE IF EXISTS tmp_disppitot;
DROP TABLE IF EXISTS tmp_disppicomb;
DROP TABLE IF EXISTS tmp_disppicoef;


END;

@@

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