Difference between revisions of "Manual Phenotyping Database"

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(Added example row to column query for phenotype table.)
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[[File:phenotyping.png]]
 
[[File:phenotyping.png]]
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Example Queries
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The query below is an example of how to generate a monthly report of the PCTHEAD (percent heading) trait.
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SET SESSION group_concat_max_len = 10000;
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SET @sql = NULL;
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SELECT
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  GROUP_CONCAT(DISTINCT
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    CONCAT(
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      'MAX(IF(phenotype_date = ''', `phenotype_date`, ''',phenotype_value,NULL)) AS ''', `phenotype_date`,'''')
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  ) INTO @sql
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FROM phenotype WHERE YEAR(phenotype_date) = 2016;
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SET @sql = CONCAT('SELECT  entity_id, ', @sql, '
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                  FROM    phenotype WHERE phenotype.entity_id LIKE ''%16ASH0%'' AND phenotype.trait_id LIKE ''%PCTHEAD%''
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                  GROUP  BY entity_id');
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PREPARE stmt FROM @sql;
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EXECUTE stmt;
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DEALLOCATE PREPARE stmt;

Revision as of 08:29, 5 October 2016

The manual phenotyping database contains phenotypic field data that was collected by hand.

The main tables in the manual phenotyping database are shown in the figure below.


Phenotyping.png

Example Queries

The query below is an example of how to generate a monthly report of the PCTHEAD (percent heading) trait.

SET SESSION group_concat_max_len = 10000; SET @sql = NULL; SELECT

 GROUP_CONCAT(DISTINCT
   CONCAT(
     'MAX(IF(phenotype_date = , `phenotype_date`, ,phenotype_value,NULL)) AS , `phenotype_date`,')
 ) INTO @sql

FROM phenotype WHERE YEAR(phenotype_date) = 2016; SET @sql = CONCAT('SELECT entity_id, ', @sql, '

                 FROM    phenotype WHERE phenotype.entity_id LIKE %16ASH0% AND phenotype.trait_id LIKE %PCTHEAD%
                 GROUP   BY entity_id');

PREPARE stmt FROM @sql; EXECUTE stmt; DEALLOCATE PREPARE stmt;