This document explains the relevant tables and fields in the database of DNAse I footprints in Bergman, Carlson and Celniker (2005) Bioinformatics; see paper or email <casey.bergman[at]manchester.ac.uk> for further details. The database was derived from the Gadfly schema developed for the re-annotation of the Drosophila melanogaster genome, and therefore has a similar table.field structure, though most of the tables are unused and therefore dropped from our database.  The relevant tables.fields that hold the footprint data are as follows.

seq - contains sequences of fragments and footprints.
seq.id		
seq.residues - sequence of fragments and footprints.	

seq_feature - contains Release 4 coordinates of fragments and footprints.
seq_feature.id
seq_feature.name - name of fragment (e.g. CE1000) or footprint (e.g. Trl:1).
seq_feature.start - start position on source sequence identified by src_seq_id; the source sequence is a chromosome arm for a fragment, or a fragment for a footprint.
seq_feature.end - end position on source sequence identified by src_seq_id; the source sequence is a chromosome arm for a fragment, or a fragment for a footprint.
seq_feature.type - "Enhancer region" (= fragment) or "transcription factor site" (= footprint).
seq_feature.seq_id - id of the sequence in the "seq" table of this feature.
seq_feature.src_seq_id - id of the source sequence in "seq" table from which feature was derived (e.g. id of chromosome arm 3L for CE1000 or id of fragment CE1000 for Trl:1); the mapping to chromosome arms is as follows:

src_seq_id   R3 chromosome arm
    1                X
    2                2L
    3                2R
    4                3L
    5                3R
    6                4
    7                U

sf_property - contains names of fragments and associated target genes.
sf_property.seq_feature_id - id of the feature in the "seq_feature" table.
sf_property.p_key - "Associated Gene" or "symbol" of fragment.
sf_property.p_val - value of associated target gene (e.g. CG1000) or symbol of fragment (e.g. "e74 promoter")

dbxref - contains PubMed unique identifiers (PMIDs) of papers annotated.
dbxref.id
dbxref.accession - accession pointed to by the database cross-reference; in this case the PubMed unique identifier (PMID).
dbxref.dbname - name of database cross-referenced; in this case PubMed.

seq_featre2dbxref - contains keys to link seq_features to dbxrefs.
seq_featre2dbxref.seq_feature_id - id of the feature in the "seq_feature" table.
seq_featre2dbxref.dbxref_id - id of the reference in the "dbxref" table.