src/README.md

In cycle20/scancer: Harvest drug compound data

scancer/src: file list of script folder

• src/load_uniprot_ids.bash: loads STRING-UniProtKB mapping table from a TSV file into the database. TSV structure: first column: STRING external identifier; second column: UniProtKB identifier. The script transforms lines to SQL UPDATE-statements and UNIPROT_KB_ID of the extended ITEMS_PROTEINS table gets its value based on the PROTEIN_EXTERNAL_ID attribute.
• string_db_on_the_fly_scan.bash: script to download (with no saving), extract and filter the very large network_schema.v11.0.sql.gz file.
• string_db_subset.bash: build SQLite3 DB file from TSV files. It is just a subset of the whole STRING database.
• uniprot2string_network.bash: download STRING translation of its UniProt Id list.

Prototype files of network extractions

These files will be renamed and be more general to work with a list of identifiers.

• network_associations.bash: execute query to collect connections of items in table uniprot2string.
• network_associations.sql: SQL SELECT statement to get some demo data.

cycle20/scancer documentation built on Jan. 10, 2023, 11:21 a.m.