Annotation Mapping

From BioSQL

This page documents the recommended BioSQL-standard of mapping sequence annotations (through Bio* object models) to the BioSQL relational model.

GenBank

DIVISION	column division in table bioentry
accession numbers	secondary accession numbers go into bioentry qualifier value table. Primary accession maps to column accession in table bioentry
TITLE	this is part of a publication reference, and should map to column title in table reference
VERSION	in BioPerl we parse this apart into a version for the accession (which is column version in table bioentry) and the GI number, which maps to column identifier in table bioentry
REFERENCE	table reference (and bioentry_reference for association with the bioentry)
KEYWORDS	map to bioentry_qualifier_value
GI	column identifier in table bioentry
SIZE	if it is the length of the sequence, it should map to column length in table biosequence
DEFINITION	column description in table bioentry
ORGANISM	this is the organism and maps to the table taxon (and taxon_name), with a foreign key in bioentry pointing to the taxon
JOURNAL	this is part of a reference, see 'references'
ACCESSION	the primary accession, maps to column accession in table bioentry
LOCUS	in the file itself this is an entire line consisting of multiple fields; BioPerl/bioperl-db maps the locus name (the first token after the literal token LOCUS) to column name in table bioentry
SOURCE	this is the organism, see 'ORGANISM'
PUBMED	this is part of a literature reference, and maps to a foreign key in the reference table (reference.dbxref) to a dbxref entry with PUBMED or PMID as the database and the pubmed ID as the accession
AUTHORS	part of a literature reference, maps to column authors in table reference
TYPE	if this is the alphabet, it maps to table biosequence, column alphabet
CIRCULAR	this at present maps to bioentry_qualifier_value, though there are plans to make it a column in table biosequence.