Postgres Query

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Query Variation-Phenotype Postgres curation tables from this site:

Postgres query page

Some Queries from Juancarlos:

1) Find number of distinct genes associated with a phenotype via allele (I think it's just allele):

paste :

SELECT COUNT (DISTINCT app_wbgene) FROM app_wbgene;

and click ``Pg !

2) If you want to see them, paste :

SELECT DISTINCT app_wbgene FROM app_wbgene;

3) Find objects where the allele status is populated with a space

SELECT * FROM app_tempname WHERE joinkey IN (SELECT joinkey FROM app_allele_status 

WHERE app_allele_status IS NOT NULL AND app_allele_status != );

4) Find objects that have an allele status value

SELECT * FROM app_tempname WHERE joinkey IN (SELECT joinkey FROM app_allele_status);

5) Find lines where anatomy term field started with a space

SELECT * FROM app_anat_term WHERE app_anat_term ~ ' ';

6) Find lines that have object names with no phenotypes and display the paper info

SELECT * FROM app_paper WHERE joinkey NOT IN (SELECT joinkey FROM app_term);

7) List papers by date they were entered (timestamp), in descending order

SELECT * FROM app_paper ORDER BY app_timestamp DESC;

8) List papers by date they were entered (timestamp), for specific date period

SELECT * FROM app_paper WHERE app_timestamp > '2008-06-06' ORDER BY app_timestamp DESC;

9) Here's a query for characters that exist and have no phenotype entry at all (i.e. never had any kind of phenotype record) :

SELECT * FROM app_tempname WHERE joinkey NOT IN (SELECT joinkey FROM app_term);

10) Here's a query for characters that exist and had a term at some point and it was overwritten with a blank or is also wrong :

SELECT * FROM app_term WHERE app_term !~ '[0-9]';

11) Also, there are some entries from 2:13pm that have just ``WBPhenotype:without numbers, which I hadn't seen before, and possibly is a new problem with the switchover without having changed something or other. (IDs 12809 12811-5 12817-22 &c. To see the whole list:

SELECT * FROM app_term WHERE app_term !~ '[0-9]' AND app_term ~ 'WBPhenotype';

There are 96 results to

SELECT app_paper.joinkey, app_paper.app_paper, app_tempname.app_tempname FROM app_tempname, 

app_paper WHERE app_paper.joinkey = app_tempname.joinkey AND app_paper.joinkey NOT IN (SELECT joinkey FROM app_term) ORDER BY app_paper.app_paper;

There are 225 results to

SELECT app_paper.joinkey, app_paper.app_paper, app_tempname.app_tempname FROM app_term, 

app_tempname, app_paper WHERE app_paper.joinkey = app_tempname.joinkey AND app_term.joinkey = app_paper.joinkey AND app_term.app_term = 'WBPhenotype' ORDER BY app_paper.app_paper;

To not show lines with no data (blank) use:

SELECT app_paper.joinkey, app_paper.app_paper, app_tempname.app_tempname FROM app_tempname, app_paper 

WHERE app_paper.joinkey = app_tempname.joinkey AND app_paper.joinkey NOT IN (SELECT joinkey FROM app_term) AND app_tempname.app_tempname != ORDER BY app_paper.app_paper;