Queries and Query Execution Plans

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Revision as of 22:03, 15 January 2009 by Crk18 (talk | contribs) (→‎Query)

This section describes the queries that have been (or are to be) implemented for the Phenoscape data services, in addition to the execution details of each queries on the PostgreSQL database on Darwin.

Queries for Phenoscape Data Services

Database details

  • Database name: obdphenoscape
  • Database server: Darwin
  • Last updated: Jan 02, 2009
  • Size: Approx. 600 MB

Anatomical Entity Services

This query will return all the PHENOTYPES that inhere in a ANATOMICAL ENTITY* and the subclasses of the ANATOMICAL ENTITY*. In addition, all the QUALITIES that are related to each PHENOTYPE are returned. The SUBSET SLIMS of each QUALITY are returned. Finally, all the TAXA that exhibit the PHENOTYPES are returned.

  • Search Term (The search term in this example is TAO:0000108, which is, you guessed it, a fin!)

Query

<javascript> SELECT DISTINCT taxon_node.uid AS taxon, exhibits_pred_node.uid AS exhibits, phenotype_node.uid AS phenotype, inheres_pred_node.uid AS inheres, anatomy_node.uid AS anatomy, is_a_pred_node.uid AS isA, quality_node.uid AS quality, subset_pred_node.uid AS subset, slim_node.uid AS slim FROM link AS inheres_link, link AS is_a_link, link AS subset_link, link AS exhibits_link, node AS phenotype_node, node AS anatomy_node, node AS inheres_pred_node, node AS is_a_pred_node, node AS quality_node, node AS slim_node, node AS subset_pred_node, node AS taxon_node, node AS exhibits_pred_node WHERE exhibits_pred_node.uid LIKE '%exhibits%' AND subset_pred_node.uid LIKE '%inSubset%' AND is_a_pred_node.uid LIKE '%is_a%' AND inheres_pred_node.uid LIKE '%inheres_in' AND anatomy_node.uid LIKE '%TAO:0000108%' AND exhibits_link.node_id = taxon_node.node_id AND exhibits_link.predicate_id = exhibits_pred_node.node_id AND exhibits_link.object_id = phenotype_node.node_id AND subset_link.node_id = quality_node.node_id AND subset_link.predicate_id = subset_pred_node.node_id AND subset_link.object_id = slim_node.node_id AND is_a_link.node_id = phenotype_node.node_id AND is_a_link.predicate_id = is_a_pred_node.node_id AND is_a_link.object_id = quality_node.node_id AND inheres_link.node_id = phenotype_node.node_id AND inheres_link.predicate_id = inheres_pred_node.node_id AND inheres_link.object_id = anatomy_node.node_id; </javascript>

Query Execution Plan

<javascript> "Unique (cost=30576.32..30576.35 rows=1 width=243) (actual time=746.269..754.034 rows=2495 loops=1)" " -> Sort (cost=30576.32..30576.33 rows=1 width=243) (actual time=746.265..747.451 rows=4730 loops=1)" " Sort Key: taxon_node.uid, exhibits_pred_node.uid, phenotype_node.uid, inheres_pred_node.uid, anatomy_node.uid, is_a_pred_node.uid, quality_node.uid, subset_pred_node.uid, slim_node.uid" " -> Nested Loop (cost=234.53..30576.31 rows=1 width=243) (actual time=100.128..343.130 rows=4730 loops=1)" " -> Nested Loop (cost=234.53..30554.96 rows=7 width=220) (actual time=76.510..309.103 rows=5084 loops=1)" " -> Nested Loop (cost=234.53..30533.63 rows=7 width=197) (actual time=76.502..278.077 rows=5084 loops=1)" " -> Nested Loop (cost=234.53..30512.30 rows=7 width=178) (actual time=76.494..248.111 rows=5084 loops=1)" " -> Nested Loop (cost=234.53..27963.03 rows=1 width=182) (actual time=76.482..236.770 rows=255 loops=1)" " -> Nested Loop (cost=234.53..27822.74 rows=46 width=159) (actual time=76.469..231.634 rows=898 loops=1)" " -> Nested Loop (cost=234.53..27682.57 rows=46 width=128) (actual time=76.453..226.351 rows=898 loops=1)" " -> Nested Loop (cost=234.53..23794.21 rows=1275 width=105) (actual time=76.129..207.649 rows=3280 loops=1)" " -> Nested Loop (cost=234.53..19909.03 rows=1275 width=82) (actual time=76.116..188.042 rows=3280 loops=1)" " -> Nested Loop (cost=234.53..15182.73 rows=45 width=70) (actual time=76.106..180.003 rows=411 loops=1)" " -> Nested Loop (cost=234.53..15077.70 rows=1 width=58) (actual time=76.093..179.138 rows=17 loops=1)" " -> Nested Loop (cost=234.53..15056.36 rows=7 width=35) (actual time=58.846..141.426 rows=6904 loops=1)" " -> Seq Scan on node inheres_pred_node (cost=0.00..4026.71 rows=1 width=31) (actual time=57.190..128.983 rows=1 loops=1)" " Filter: ((uid)::text ~~ '%inheres_in'::text)" " -> Bitmap Heap Scan on link inheres_link (cost=234.53..10563.47 rows=37294 width=12) (actual time=1.642..7.526 rows=6904 loops=1)" " Recheck Cond: (inheres_link.predicate_id = "outer".node_id)" " -> Bitmap Index Scan on link_predicate_object_indx (cost=0.00..234.53 rows=37294 width=0) (actual time=1.489..1.489 rows=6904 loops=1)" " Index Cond: (inheres_link.predicate_id = "outer".node_id)" " -> Index Scan using node_pkey on node anatomy_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=0 loops=6904)" " Index Cond: ("outer".object_id = anatomy_node.node_id)" " Filter: ((uid)::text ~~ '%TAO:0000108%'::text)" " -> Index Scan using link_node_indx on link is_a_link (cost=0.00..104.68 rows=28 width=12) (actual time=0.006..0.032 rows=24 loops=17)" " Index Cond: ("outer".node_id = is_a_link.node_id)" " -> Index Scan using link_node_indx on link subset_link (cost=0.00..104.68 rows=28 width=12) (actual time=0.005..0.012 rows=8 loops=411)" " Index Cond: ("outer".object_id = subset_link.node_id)" " -> Index Scan using node_pkey on node slim_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=3280)" " Index Cond: ("outer".object_id = slim_node.node_id)" " -> Index Scan using node_pkey on node is_a_pred_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=0 loops=3280)" " Index Cond: ("outer".predicate_id = is_a_pred_node.node_id)" " Filter: ((uid)::text ~~ '%is_a%'::text)" " -> Index Scan using node_pkey on node phenotype_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=898)" " Index Cond: ("outer".node_id = phenotype_node.node_id)" " -> Index Scan using node_pkey on node subset_pred_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=0 loops=898)" " Index Cond: ("outer".predicate_id = subset_pred_node.node_id)" " Filter: ((uid)::text ~~ '%inSubset%'::text)" " -> Index Scan using link_object_indx on link exhibits_link (cost=0.00..2537.96 rows=905 width=12) (actual time=0.005..0.027 rows=20 loops=255)" " Index Cond: (exhibits_link.object_id = "outer".node_id)" " -> Index Scan using node_pkey on node quality_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=5084)" " Index Cond: ("outer".node_id = quality_node.node_id)" " -> Index Scan using node_pkey on node taxon_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.005 rows=1 loops=5084)" " Index Cond: ("outer".node_id = taxon_node.node_id)" " -> Index Scan using node_pkey on node exhibits_pred_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=1 loops=5084)" " Index Cond: ("outer".predicate_id = exhibits_pred_node.node_id)" " Filter: ((uid)::text ~~ '%exhibits%'::text)" </javascript>

Execution Time

  • First run: 349 seconds
  • Subsequent run: 21 seconds

Anatomical Entity Services (with a restriction on Slims returned)

This query will return all the PHENOTYPES that inhere in a ANATOMICAL ENTITY and the subclasses of the ANATOMICAL ENTITY. In addition, all the QUALITIES that are related to each PHENOTYPE are returned. Only those QUALITIES which are either ATTRIBUTE_SLIMS or VALUE_SLIMS are returned. Finally, all the TAXA that exhibit the PHENOTYPES are returned.

Query

<javascript> SELECT DISTINCT taxon_node.uid AS taxon, exhibits_pred_node.uid AS exhibits, phenotype_node.uid AS phenotype, inheres_pred_node.uid AS inheres, anatomy_node.uid AS anatomy, is_a_pred_node.uid AS isA, quality_node.uid AS quality, subset_pred_node.uid AS subset, slim_node.uid AS slim FROM link AS inheres_link, link AS is_a_link, link AS subset_link, link AS exhibits_link, node AS phenotype_node, node AS anatomy_node, node AS inheres_pred_node, node AS is_a_pred_node, node AS quality_node, node AS slim_node, node AS subset_pred_node, node AS taxon_node, node AS exhibits_pred_node WHERE exhibits_pred_node.uid LIKE '%exhibits%' AND subset_pred_node.uid LIKE '%inSubset%' AND is_a_pred_node.uid LIKE '%is_a%' AND inheres_pred_node.uid LIKE '%inheres_in' AND anatomy_node.uid LIKE '%TAO:0000108%' AND slim_node.uid IN ('attribute_slim', 'value_slim') AND exhibits_link.node_id = taxon_node.node_id AND exhibits_link.predicate_id = exhibits_pred_node.node_id AND exhibits_link.object_id = phenotype_node.node_id AND subset_link.node_id = quality_node.node_id AND subset_link.predicate_id = subset_pred_node.node_id AND subset_link.object_id = slim_node.node_id AND is_a_link.node_id = phenotype_node.node_id AND is_a_link.predicate_id = is_a_pred_node.node_id AND is_a_link.object_id = quality_node.node_id AND inheres_link.node_id = phenotype_node.node_id AND inheres_link.predicate_id = inheres_pred_node.node_id AND inheres_link.object_id = anatomy_node.node_id; </javascript>

Query Execution Plan

<javascript> "Unique (cost=27033.30..27033.32 rows=1 width=243) (actual time=95708.710..95715.120 rows=2070 loops=1)" " -> Sort (cost=27033.30..27033.30 rows=1 width=243) (actual time=95708.707..95709.717 rows=3887 loops=1)" " Sort Key: taxon_node.uid, exhibits_pred_node.uid, phenotype_node.uid, inheres_pred_node.uid, anatomy_node.uid, is_a_pred_node.uid, quality_node.uid, subset_pred_node.uid, slim_node.uid" " -> Nested Loop (cost=9416.69..27033.29 rows=1 width=243) (actual time=70172.832..95404.139 rows=3887 loops=1)" " -> Nested Loop (cost=9416.69..27030.24 rows=1 width=220) (actual time=227.929..79578.381 rows=2919406 loops=1)" " -> Nested Loop (cost=9416.69..27027.19 rows=1 width=197) (actual time=227.919..62509.808 rows=2919406 loops=1)" " -> Nested Loop (cost=9416.69..27024.14 rows=1 width=174) (actual time=227.903..38352.678 rows=4115922 loops=1)" " -> Nested Loop (cost=9416.69..27021.09 rows=1 width=151) (actual time=227.885..12271.892 rows=4115922 loops=1)" " -> Hash Join (cost=9414.52..26907.04 rows=1 width=163) (actual time=227.752..2896.269 rows=114658 loops=1)" " Hash Cond: ("outer".object_id = "inner".node_id)" " -> Nested Loop (cost=4261.24..21750.61 rows=630 width=109) (actual time=86.733..2633.493 rows=252348 loops=1)" " -> Nested Loop (cost=4261.24..19830.87 rows=630 width=78) (actual time=86.711..1176.546 rows=252348 loops=1)" " -> Nested Loop (cost=234.53..15791.56 rows=315 width=47) (actual time=58.083..587.038 rows=252348 loops=1)" " -> Nested Loop (cost=234.53..15056.36 rows=7 width=35) (actual time=58.071..136.526 rows=6904 loops=1)" " -> Seq Scan on node inheres_pred_node (cost=0.00..4026.71 rows=1 width=31) (actual time=56.524..124.720 rows=1 loops=1)" " Filter: ((uid)::text ~~ '%inheres_in'::text)" " -> Bitmap Heap Scan on link inheres_link (cost=234.53..10563.47 rows=37294 width=12) (actual time=1.531..6.138 rows=6904 loops=1)" " Recheck Cond: (inheres_link.predicate_id = "outer".node_id)" " -> Bitmap Index Scan on link_predicate_object_indx (cost=0.00..234.53 rows=37294 width=0) (actual time=1.379..1.379 rows=6904 loops=1)" " Index Cond: (inheres_link.predicate_id = "outer".node_id)" " -> Index Scan using link_node_indx on link is_a_link (cost=0.00..104.68 rows=28 width=12) (actual time=0.005..0.037 rows=37 loops=6904)" " Index Cond: ("outer".node_id = is_a_link.node_id)" " -> Materialize (cost=4026.71..4026.73 rows=2 width=31) (actual time=0.000..0.001 rows=1 loops=252348)" " -> Seq Scan on node exhibits_pred_node (cost=0.00..4026.71 rows=2 width=31) (actual time=28.608..132.502 rows=1 loops=1)" " Filter: ((uid)::text ~~ '%exhibits%'::text)" " -> Index Scan using node_pkey on node phenotype_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=252348)" " Index Cond: ("outer".node_id = phenotype_node.node_id)" " -> Hash (cost=5153.24..5153.24 rows=14 width=66) (actual time=37.026..37.026 rows=4413 loops=1)" " -> Nested Loop (cost=4.01..5153.24 rows=14 width=66) (actual time=0.067..32.679 rows=4413 loops=1)" " -> Nested Loop (cost=4.01..5110.58 rows=14 width=35) (actual time=0.058..6.879 rows=4413 loops=1)" " -> Bitmap Heap Scan on node slim_node (cost=4.01..12.03 rows=2 width=31) (actual time=0.044..0.046 rows=2 loops=1)" " Recheck Cond: (((uid)::text = 'attribute_slim'::text) OR ((uid)::text = 'value_slim'::text))" " -> BitmapOr (cost=4.01..4.01 rows=2 width=0) (actual time=0.040..0.040 rows=0 loops=1)" " -> Bitmap Index Scan on node_uid_key (cost=0.00..2.00 rows=1 width=0) (actual time=0.026..0.026 rows=1 loops=1)" " Index Cond: ((uid)::text = 'attribute_slim'::text)" " -> Bitmap Index Scan on node_uid_key (cost=0.00..2.00 rows=1 width=0) (actual time=0.013..0.013 rows=1 loops=1)" " Index Cond: ((uid)::text = 'value_slim'::text)" " -> Index Scan using link_object_indx on link subset_link (cost=0.00..2537.96 rows=905 width=12) (actual time=0.013..1.901 rows=2206 loops=2)" " Index Cond: (subset_link.object_id = "outer".node_id)" " -> Index Scan using node_pkey on node quality_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=4413)" " Index Cond: ("outer".node_id = quality_node.node_id)" " -> Bitmap Heap Scan on link exhibits_link (cost=2.18..113.61 rows=29 width=12) (actual time=0.021..0.052 rows=36 loops=114658)" " Recheck Cond: ((exhibits_link.predicate_id = "outer".node_id) AND (exhibits_link.object_id = "outer".node_id))" " -> Bitmap Index Scan on link_predicate_object_indx (cost=0.00..2.18 rows=29 width=0) (actual time=0.016..0.016 rows=36 loops=114658)" " Index Cond: ((exhibits_link.predicate_id = "outer".node_id) AND (exhibits_link.object_id = "outer".node_id))" " -> Index Scan using node_pkey on node subset_pred_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=1 loops=4115922)" " Index Cond: ("outer".predicate_id = subset_pred_node.node_id)" " Filter: ((uid)::text ~~ '%inSubset%'::text)" " -> Index Scan using node_pkey on node is_a_pred_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.004..0.005 rows=1 loops=4115922)" " Index Cond: ("outer".predicate_id = is_a_pred_node.node_id)" " Filter: ((uid)::text ~~ '%is_a%'::text)" " -> Index Scan using node_pkey on node taxon_node (cost=0.00..3.03 rows=1 width=31) (actual time=0.004..0.004 rows=1 loops=2919406)" " Index Cond: ("outer".node_id = taxon_node.node_id)" " -> Index Scan using node_pkey on node anatomy_node (cost=0.00..3.04 rows=1 width=31) (actual time=0.005..0.005 rows=0 loops=2919406)" " Index Cond: ("outer".object_id = anatomy_node.node_id)" " Filter: ((uid)::text ~~ '%TAO:0000108%'::text)" </javascript>

Execution Details

  • Rows returned: 2070
  • First run: 116 seconds
  • Sunsequent run: 1.13 seconds
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