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Copy pathSQL-SRA-QRY-cross-check.txt
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SQL-SRA-QRY-cross-check.txt
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-- Compare the study:study_abstract field annotations (these are scant in frequency)
-- against where they should ideally be documented (i.e. library_construction_protocol)
select 'table: study, field: study_abstract [fragmentation]';
select count(submission_accession) from study where
study_abstract like "% shear%"
or study_abstract like "% restriction%"
or study_abstract like "% digest%"
or study_abstract like "% fragment%"
or study_abstract like "% breaks %"
or study_abstract like "% nebulis%" or study_abstract like "% nebuliz%"
or study_abstract like "% acoustic%"
or study_abstract like "% sonic%"
and submission_accession in
(
select submission_accession from experiment where
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%" or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
);
select 'table: study, field: study_abstract [ligation]';
select count(submission_accession) from study where
study_abstract like "% adapter%"
or study_abstract like "% ligat%"
or study_abstract like "% blunt%"
or study_abstract like "% phosphorylat%"
or study_abstract like "% overhang"
or study_abstract like "% t4-PNK%"
or study_abstract like "% t4%"
or study_abstract like "% pnk%"
or study_abstract like "% kinase%"
or study_abstract like "% a-tail%"
and submission_accession in
(
select submission_accession from experiment where
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
or library_construction_protocol like "% a-tail%"
);
select 'table: study, field: study_abstract [enrichment]';
select count(submission_accession) from study where
study_abstract like "% clone%"
or study_abstract like "% clonin%"
or study_abstract like "% pcr %"
or study_abstract like "% amplif%"
or study_abstract like "% polymerase%"
or study_abstract like "% taq%"
or study_abstract like "% phusion%"
or study_abstract like "% temperat%"
or study_abstract like "% thermal%"
or study_abstract like "% anneal%"
or study_abstract like "% denature%"
and submission_accession in
(
select submission_accession from experiment where
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
);
select 'table: experiment, field: design_description [fragmentation]';
select count(submission_accession) from experiment where
design_description like "% shear%"
or design_description like "% restriction%"
or design_description like "% digest%"
or design_description like "% fragment%"
or design_description like "% breaks %"
or design_description like "% nebulis%" or design_description like "% nebuliz%"
or design_description like "% acoustic%"
or design_description like "% sonic%"
and submission_accession
in
(
select submission_accession from experiment where
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%" or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
);
select 'table: experiment, field: design_description [ligation]';
select count(submission_accession) from experiment where
design_description like "% adapter%"
or design_description like "% ligat%"
or design_description like "% blunt%"
or design_description like "% phosphorylat%"
or design_description like "% overhang"
or design_description like "% t4-PNK"
or design_description like "% t4"
or design_description like "% pnk"
or design_description like "% kinase"
or design_description like "% a-tail"
and submission_accession in
(
select submission_accession from experiment where
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
or library_construction_protocol like "% a-tail%"
);
select 'table: experiment, field: design_description [enrichment]';
select count(submission_accession) from experiment where
design_description like "% clone%"
or design_description like "% clonin%"
or design_description like "% pcr %"
or design_description like "% amplif%"
or design_description like "% polymerase%"
or design_description like "% taq%"
or design_description like "% phusion%"
or design_description like "% temperat%"
or design_description like "% thermal%"
or design_description like "% anneal%"
or design_description like "% denature%"
and submission_accession in
(
select submission_accession from experiment where
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
);