Source files from Al-Nasir and Shanahan, (2015) Investigation into the annotation of protocol sequencing steps in the Sequence Read Archive.
DOI:10.5524/100142
The Bioconductor SRAdb.sqlite database used in the publication had a timestamp of [2013-12-03 08:29:26] and is available from:
The latest version can be downloaded from the Bioconductor consortium's SRAdb page:
http://www.bioconductor.org/packages/release/bioc/html/SRAdb.html
Timestamp of the Bioconductor SQLite database can be obtained from the database using the following SQL:
$> sqlite3 SRAmetadb.sqlite [to load the database]
sqlite> Select * from metaInfo;
The SQL master scripts can be run using the following command, the individual scripts they contain can also be copied/pasted:
$> sqlite3 SRAmetadb.sqlite < scriptname.txt
SQL-SRA-QRY-all-field-anno-check.txt SQL-SRA-QRY-anno-counts.txt SQL-SRA-QRY-anno-distribution2.txt SQL-SRA-QRY-anno-distribution.txt SQL-SRA-QRY-anno-proportions.txt SQL-SRA-QRY-cross-check.txt SQL-SRA-QRY-date-checks.txt SQL-SRA-QRY-lib-cons-prot-venn.txt SQL-SRA-QRY-null.txt SQL-SRA-QRY-reagent-kits.txt SQL-SRA-QRY-submission-joined-anno-report.txt SQL-SRA-QRY-submission-joined-count.txt SQL-SRA-QRY-submission-joined-unannotated-count.txt SQL-SRA-QRY-unjoined-anno-counts-by-type.txt SQL-SRA-QRY-url-only-lib-cons-prot.txt SQL-SRA-QRY-url.txt SQL-SRA-QRY-wordlists_study-joined-by-year.txt SQL-SRA-QRY-wordlists_study-joined-lib-cons-prot.txt SQL-SRA-QRY-wordlists_submission-joined-lib-cons-prot.txt SQL-SRA-QRY-wordlists_submission-joined.txt SQL-SRA-QRY-wordlists-unjoined.txt SQL-SRA-to-Graph.txt
Diagram-ALL-FIELDS-Check-annotation.jpg - Diagram-SRA-Study-Experiment-Joined-probing.jpg -
Additional documentation on the SRA can be found at http://www.ncbi.nlm.nih.gov/books/NBK47528/ http://www.ebi.ac.uk/ena/submit/read-submission http://trace.ddbj.nig.ac.jp/dra/submission_e.html