Postgres Query
Query Variation-Phenotype Postgres curation tables from this site:
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;
12) finding multiallele objects that are called allele
SELECT * FROM app_tempname WHERE app_tempname ~ '[0-9][a-z]';
or multiallele
SELECT * FROM app_tempname WHERE joinkey = '3933';
