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2017-08-17T18:53:28Z

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← Older revision		Revision as of 18:53, 17 August 2017
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	This is the curator page for clinical trials curation.		This is the curator page for clinical trials curation.

			It would be a good idea to update drugbank and HMDB and their synonyms before updating CT.

			= curating subname, the basis for joining CT to substance =
			These are examples. look closely before executing.
	update subname set name=regexp_replace(name, ' .inn.$','') where name like '%[inn%';		update subname set name=regexp_replace(name, ' .inn.$','') where name like '%[inn%';

	begin; delete from subname where length(name) < 10 and name like '% %';		begin; delete from subname where length(name) < 10 and name like '% %';
	begin; delete from subname where length(name) < 7 and name like '9%'; 1-9		begin; delete from subname where length(name) < 7 and name like '9%'; 1-9
			# update after editing subname table
	begin; update subname set terms=to_tsvector('english',name),query=plainto_tsquery(name);		begin; update subname set terms=to_tsvector('english',name),query=plainto_tsquery(name);
			# to solve the no lexemees problem
	# to solve the no lexemees
	select * from subname where numnode(plainto_tsquery(name))=0 limit 10;		select * from subname where numnode(plainto_tsquery(name))=0 limit 10;

	# create the mapping table between them~~....~~		= create the mapping table between them =
			Do this after updating subname
	insert into clinical1.ct2subint (sub_id_fk, ct2int_fk)		insert into clinical1.ct2subint (sub_id_fk, ct2int_fk)
	select distinct sub_id_fk, ct2int_id from ctinttemp as ct		select distinct sub_id_fk, ct2int_id from ctinttemp as ct
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	join subname on ct.terms@@subname.query		join subname on ct.terms@@subname.query
	where not exists(select 1 from clinical1.ct2subint as e where e.sub_id_fk=subname.sub_id_fk and e.ct2int_fk=cti.ct2int_id);		where not exists(select 1 from clinical1.ct2subint as e where e.sub_id_fk=subname.sub_id_fk and e.ct2int_fk=cti.ct2int_id);

			= History =
			Some history about how the tables were originally created.
			[[Creating clinical name mappings]]. Note that this page should be obsoleted by the current page.


	[[Category:Curator]]		[[Category:Curator]]

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2017-08-17T17:41:45Z

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New page

This is the curator page for clinical trials curation.

update subname set name=regexp_replace(name, ' *.inn.*$','') where name like '%[inn%';

begin; delete from subname where length(name) < 10 and name like '% %';
begin; delete from subname where length(name) < 7 and name like '9%'; 1-9

begin; update subname set terms=to_tsvector('english',name),query=plainto_tsquery(name);

# to solve the no lexemees
select * from subname where numnode(plainto_tsquery(name))=0 limit 10;

# create the mapping table between them....

insert into clinical1.ct2subint (sub_id_fk, ct2int_fk)
select distinct sub_id_fk, ct2int_id from ctinttemp as ct
join clinical1.ct2 on ct.code=ct_code
join clinical1.ct2int as cti on ct2_id=cti.ct2_fk and cti.name=ct.name
join subname on ct.terms@@subname.query
where not exists(select 1 from clinical1.ct2subint as e where e.sub_id_fk=subname.sub_id_fk and e.ct2int_fk=cti.ct2int_id);

[[Category:Curator]]

Clinical trials curation - Revision history

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