diff --git a/petagraph/data_dict.md b/petagraph/data_dict.md index 7e6dacd..0c01772 100644 --- a/petagraph/data_dict.md +++ b/petagraph/data_dict.md @@ -233,19 +233,19 @@ return * limit 1 **Preproccessing**: The dataset relationships as well as nodes use HSCLO as their SAB. HSCLO nodes are defined at 5 resolution levels; chromosomes, 1 Mbp, 100 kbp, 10 kbp and 1kbp with each level connecting to lower levels with `above_(resolution level)_band` (e.g. "above_1Mbp_band", "above 1_kbp_band") and nodes at the same resolution level are connected through `precedes_(resolution level)_band` (e.g. "precedes_10kbp_band"). The dataset contains 3,431,155 nodes and 6,862,195 relationships. -### NEED BETTER HSCLO FIGURE -drawing +drawing **Schema Description**: ```cypher // Cypher query to reproduce the schema figure -match (a:Code {SAB:'HSCLO'})-[r0:CODE]-(b:Concept)-[r1]-(c:Concept)-[r2:CODE]-(d:Code) -MATCH (b)-[r3:loop_ds_end]-(c:Concept)-[:CODE]-(e:Code {SAB:'4DNL'}) -MATCH (b)-[r4:located_in]-(c2:Concept)-[:CODE]-(f:Code {SAB:'GTEXEQTL'}) -return * limit 1 +MATCH (c1:Concept)-[:contains_chromosome{SAB:'HSCLO'}]->(c2:Concept)-[:above_1Mbp_band {SAB:'HSCLO'}]->(c3:Concept)-[:above_100kbp_band {SAB:'HSCLO'}]->(c4:Concept)-[:above_10kbp_band {SAB:'HSCLO'}]->(c5:Concept)-[:above_1kbp_band {SAB:'HSCLO'}]->(c6:Concept), +(c3:Concept)-[:precedes_1Mbp_band {SAB:'HSCLO'}]->(c7:Concept), +(c4:Concept)-[:precedes_100kbp_band {SAB:'HSCLO'}]->(c8:Concept), +(c5:Concept)-[:precedes_10kbp_band {SAB:'HSCLO'}]->(c9:Concept), +(c6:Concept)-[:precedes_1kbp_band {SAB:'HSCLO'}]->(c10:Concept), +(c1)-[:CODE]->(o1:Code),(c2)-[:CODE]->(o2:Code),(c3)-[:CODE]->(o3:Code),(c4)-[:CODE]->(o4:Code),(c5)-[:CODE]->(o5:Code),(c6)-[:CODE]->(o6:Code),(c7)-[:CODE]->(o7:Code),(c8)-[:CODE]->(o8:Code),(c9)-[:CODE]->(o9:Code),(c10)-[:CODE]->(o10:Code) +RETURN * LIMIT 1 ``` --- @@ -276,7 +276,10 @@ return * limit 1 ```cypher // Cypher query to reproduce the schema figure -match (a:Code {SAB:'UBERON'})-[r0:CODE]-(b:Concept)-[r1 {SAB:'CLINVAR'}]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'HGNC'}) +match (a:Code {SAB:'HPO'})<-[r0:CODE]-(b:Concept)-[r1 {SAB:'CLINVAR'}]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'HGNC'}) +where id(r1) = 29001875 +match (a:Code {SAB:'HPO'})-[r0:CODE]-(b:Concept)-[r3 {SAB:'CLINVAR'}]->(c:Concept)-[r2:CODE]-(d:Code {SAB:'HGNC'}) +where id(r3) = 52494094 return * limit 1 ``` @@ -298,6 +301,13 @@ return * limit 1 // Cypher query to reproduce the schema figure match (a:Code {SAB:'AZ'})-[r0:CODE]-(b:Concept)-[r1]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'HGNC'}) return * limit 1 + + + +match (a:Code {SAB:'AZ'})-[r0:CODE]-(b:Concept)-[r1]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'HGNC'}) +match (b)-[r3 {SAB:'AZ'}]-(e:Concept)-[:CODE]-(f:Code) + +return distinct f.SAB ``` --- @@ -353,9 +363,7 @@ return * limit 1 ```cypher // Cypher query to reproduce the schema figure -match (a:Code {SAB:'GLY.TYPE.SITE'})-[r0:CODE]-(b:Concept)-[r1]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'GLYTOUCAN'}) -match (b)-[r3]-(e:Concept)-[:CODE]-(f:Code {SAB:'UNIPROTKB.ISOFORM'}) -return * limit 1 +MATCH (o0)<-[:CODE]-(g:Concept)-[:has_gene_product]->(u:Concept)-[:has_isoform]-(i:Concept)-[:has_type_site]-(s:Concept)<-[:binds_site]-(l:Concept),(g)-[:PREF_TERM]->(t1:Term),(u)-[:CODE]->(o2:Code),(u)-[PREF_TERM]->(t2:Term),(s)-[:CODE]->(o3:Code), (l)-[:CODE]->(o4:Code),(i)-[:CODE]->(o5:Code) RETURN * LIMIT 1 ``` --- @@ -392,12 +400,15 @@ return * LIMIT 1 ```cypher // Cypher query to reproduce the schema figure -match (a:Code {SAB:'4DNF'})-[r0:CODE]-(b:Concept)-[r1]-(c:Concept)-[r2:CODE]-(d:Code {SAB:'4DNL'}) -match (b)-[r3]-(e:Concept)-[:CODE]-(f:Code {SAB:'4DND'}) -match (c)-[:loop_ds_end]-(g:Concept)-[:CODE]-(h:Code {SAB:'HSCLO'}) -match (c)-[r4]-(i:Concept)-[:CODE]-(j:Code {SAB:'4DNQ'}) -//match (j)-[r5]-(k:Concept)-[:CODE]-(l:Code {SAB:'UBERON'}) -return * limit 1 +MATCH (loop_concept:Concept)-[r2:loop_us_end {SAB:'4DN'}]->(us_end_concept:Concept)-[:CODE]->(us_end_code:Code) +MATCH (loop_concept:Concept)-[r3:loop_ds_start {SAB:'4DN'}]->(ds_start_concept:Concept)-[:CODE]->(ds_start_code:Code) +MATCH (loop_concept:Concept)-[r4:loop_ds_end {SAB:'4DN'}]->(ds_end_concept:Concept)-[:CODE]->(ds_end_code:Code) +MATCH (loop_code:Code {SAB:'4DNL'})<-[:CODE]-(loop_concept:Concept)-[r5:loop_has_qvalue_bin {SAB:'4DN'} +]->(qvalue_bin_concept:Concept)-[:CODE]->(qvalue_bin_code:Code {SAB:'4DNQ'}) +MATCH (file_code:Code {SAB:'4DNF'})<-[:CODE]-(file_concept:Concept)-[r6:file_has_loop {SAB:'4DN'}]->(loop_concept:Concept) +MATCH (dataset_code:Code {SAB:'4DND'})<-[:CODE]-(dataset_concept:Concept)-[r7:dataset_has_file {SAB:'4DN'}]->(file_concept:Concept) +MATCH (dataset_concept:Concept)-[r8:dataset_involves_cell_type {SAB:'4DN'}]->(cell_type_concept:Concept)-[:PREF_TERM]->(cell_type_term:Term ) +RETURN * LIMIT 1 ```