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<bridge_layer schema="gadfly">
<notes>
Bridge layer for GadFly Database schema - allows chado to "masquerade"
as a GadFly Schema, which means we can use (legacy) GadFly software;
GadFly is still in use at the BDGP/DHGP
Activate this to make this bridge take precedence
SET SEARCH_PATH TO gadfly,public;
(note that placing gadfly first in the search path means
that gadfly.dbxref takes precedence over public.dbxref)
</notes>
<relation id="seq_feature">
<sql>
<![CDATA[
SELECT
feature_id AS id,
feature.name AS name,
0 AS created,
CASE WHEN strand<0 THEN fmax ELSE fmin END AS "start",
CASE WHEN strand<0 THEN fmin ELSE fmax END AS "end",
0 AS major_version,
0 AS minor_version,
NULL AS primary_acc,
NULL AS primary_dbname,
t.name AS type,
organism_id AS species_id,
NULL AS annotation_id,
feature_id AS seq_id,
srcfeature_id AS src_seq_id
FROM feature INNER JOIN featureloc USING (feature_id)
INNER JOIN cvterm AS t ON (type_id=cvterm_id);
]]>
</sql>
</relation>
<relation id="seq">
<sql>SELECT
feature_id AS id,
0 AS created,
feature.name AS name,
NULL AS molecule_type,
NULL AS last_modified,
residues,
NULL AS description,
seqlen AS length,
0 AS major_version,
md5checksum
FROM feature;
</sql>
</relation>
<relation id="sf_produces_sf">
<sql>SELECT
produced_by_sf_id AS subject_id,
produces_sf_id AS object_id
FROM feature_relationship;
</sql>
</relation>
<relation id="exon_rank">
<sql>SELECT
exon_sf_id AS subject_id,
transcript_sf_id AS object_id,
rank
FROM feature_relationship;
</sql>
</relation>
<relation id="analysis">
<sql>SELECT
analysis_id AS id,
name,
program,
sourcename AS dbname,
NULL AS descrption,
0 AS created,
0 AS last_modified
FROM analysis;
</sql>
</relation>
<relation id="sf_analysis">
<sql>SELECT
analysis_id,
feature_id AS seq_feature_id,
0 AS job_id
FROM analysisfeature;
</sql>
</relation>
<relation id="result_span">
<sql>
<![CDATA[
SELECT
f.feature_id AS id,
CASE WHEN fl1.strand<0 THEN fl1.fmax ELSE fl1.fmin END AS "start1",
CASE WHEN fl1.strand<0 THEN fl1.fmin ELSE fl1.fmax END AS "end1",
CASE WHEN fl2.strand<0 THEN fl2.fmax ELSE fl2.fmin END AS "start1",
CASE WHEN fl2.strand<0 THEN fl2.fmin ELSE fl2.fmax END AS "end1",
t.name AS type,
NULL AS annotation_id,
fr.object_id AS rset_sf_id,
0 AS analysis_id,
fl1.srcfeature_id AS seq1_id,
fl2.srcfeature_id AS seq2_id,
0 AS expect_mantissa,
0 AS expect_exponent,
fl1.phase AS query_frame,
fl2.phase AS subject_frame,
rawscore AS score,
identity AS percent_identity
FROM featyre AS f
INNER JOIN featureloc AS fl1 ON (fl1.feature_id=f.feature_id)
INNER JOIN featureloc AS fl2 ON (fl2.feature_id=f.feature_id)
INNER JOIN cvterm AS t ON (type_id=cvterm_id)
INNER JOIN feature_relationship AS fr ON (f.feature_id=fr.subject_id)
]]>
</sql>
</relation>
<relation id="sf_property">
<sql>SELECT
feature_id AS seq_feature_id,
t.name AS p_key,
value AS p_val
FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id);
</sql>
</relation>
<relation id="sf_comment">
<sql>SELECT
feature_id AS seq_feature_id,
0 AS is_internal,
value AS comment
FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id)
WHERE t.name='comment';
</sql>
</relation>
<relation id="sf_description">
<sql>SELECT
feature_id AS seq_feature_id,
0 AS is_internal,
value AS comment
FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id)
WHERE t.name='description';
</sql>
</relation>
<relation id="result_span_data">
<sql>SELECT
result_span_id AS seq_feature_id,
t.name AS param_key,
value AS param_value
FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id)
</sql>
</relation>
<relation id="seq2dbxref">
<sql>SELECT
feature_id AS seq_id,
dbxref_id
FROM feature_dbxref;
</sql>
</relation>
<relation id="seq2taxon">
<sql>SELECT
feature_id AS seq_id,
organism_id
FROM feature;
</sql>
</relation>
<relation id="seq_feature2dbxref">
<sql>SELECT
feature_id AS feature_id,
dbxref_id
FROM feature_dbxref;
</sql>
</relation>
<relation id="feature2taxon">
<sql>SELECT
feature_id AS feature_id,
organism_id
FROM feature;
</sql>
</relation>
<relation id="dbxref">
<notes>table name clash - be sure to prefix with schema name</notes>
<sql>
SELECT
dbxref_id AS id,
db.name AS dbname,
dbxref.accession AS accession,
CAST(NULL AS VARCHAR) AS accessiontype,
dbxref.description AS description
FROM public.dbxref
INNER JOIN public.db USING (db_id);
</sql>
<index>
CREATE INDEX dbxref_idx1 ON gadfly.dbxref (id);
CREATE INDEX dbxref_idx2 ON gadfly.dbxref (dbname);
CREATE INDEX dbxref_idx3 ON gadfly.dbxref (accession);
CREATE INDEX dbxref_idx4 ON gadfly.dbxref (accessiontype);
CREATE INDEX dbxref_idx5 ON gadfly.dbxref (description);
</index>
</relation>
<relation id="taxon">
<sql>SELECT
organism_id AS id,
0 AS parent_taxon_id,
genus,
species,
common_name,
'' AS taxon_code,
'' AS embl_code
FROM organism;
</sql>
</relation>
</bridge_layer>
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