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Database Schema
If you plan to use the database (especially running SQL queries), it is recommended that you understand the 'Database Schema' section below. You may also find the 'Example Queries' section to be useful.
This section describes the redundancy database tables and their relationships (the schema).
The goals of the schema are:
- to make analysis fast
- to make queries simple
- to provide flexibility to answer a wide range of questions
description: taxon proteome record
columns:
- id
description: canonical protein records
columns:
- id
- sequence (notated as amino acid residues)
- mass
description: records if taxon proteome X contains protein Y
columns:
- id
- taxon_id (foreign key to taxon.id)
- protein_id (foreign key to protein.id)
- metadata (metadata associated with the occurence of the protein, e.g. FASTA headers or NIH IDs)
description: canonical peptide records
columns:
- id
- sequence (in amino acid residues)
- mass
description: protease records
columns:
- id
- cleavage_rule (rule for how this protease cleaves an amino acid sequence. Normally this is a regular expression)
description: digest records columns:
- id
- protease_id (foreign key to protease.id)
- max_missed_cleavages
- min_acids (ignore any peptides with < this many acids)
- max_acids (ignore any peptides with > this many acids)
description: records whether taxon proteome X has been digested with digest Y
columns:
- id
- taxon_id (foreign key to taxon.id)
- digest_id (foreign key to digest.id)
description: records whether protein X has been digested with digest Y
columns:
- id
- protein_id (foreign key to protein.id)
- digest_id (foreign key to digest.id)
description: records if petide X is a product of protein_digest Y
columns:
- id
- peptide_id (foreign key to peptide.id)
- protein_digest_id (foreign key to protein_digest.id)
- count (# of times peptide X appeared in protein_digest Y)
description: records if petide X is a product of taxon_digest Y
columns:
- id
- peptide_id (foreign key to peptide.id)
- taxon_digest_id (foreign key to taxon_digest.id)
- count (# of times peptide X appeared in taxon_digest Y)