在Neo4j中创建代谢途径 [英] Creating a metabolic pathway in Neo4j

问题描述

我正在尝试使用以下数据在Neo4j中创建此问题底部的图像中所示的糖酵解途径:

I am attempting to create the glycolytic pathway shown in the image at the bottom of this question, in Neo4j, using these data:

glycolysis_bioentities.csv

name
α-D-glucose
glucose 6-phosphate
fructose 6-phosphate
"fructose 1,6-bisphosphate"
dihydroxyacetone phosphate
D-glyceraldehyde 3-phosphate
"1,3-bisphosphoglycerate"
3-phosphoglycerate
2-phosphoglycerate
phosphoenolpyruvate
pyruvate
hexokinase
glucose-6-phosphatase
phosphoglucose isomerase
phosphofructokinase
"fructose-bisphosphate aldolase, class I"
triosephosphate isomerase (TIM)
glyceraldehyde-3-phosphate dehydrogenase
phosphoglycerate kinase
phosphoglycerate mutase
enolase
pyruvate kinase

glycolysis_relations.csv

source,relation,target
α-D-glucose,substrate_of,hexokinase
hexokinase,yields,glucose 6-phosphate
glucose 6-phosphate,substrate_of,glucose-6-phosphatase
glucose-6-phosphatase,yields,α-D-glucose
glucose 6-phosphate,substrate_of,phosphoglucose isomerase
phosphoglucose isomerase,yields,fructose 6-phosphate
fructose 6-phosphate,substrate_of,phosphofructokinase
phosphofructokinase,yields,"fructose 1,6-bisphosphate"
"fructose 1,6-bisphosphate",substrate_of,"fructose-bisphosphate aldolase, class I"
"fructose-bisphosphate aldolase, class I",yields,D-glyceraldehyde 3-phosphate
D-glyceraldehyde 3-phosphate,substrate_of,glyceraldehyde-3-phosphate dehydrogenase
D-glyceraldehyde 3-phosphate,substrate_of,triosephosphate isomerase (TIM)
triosephosphate isomerase (TIM),yields,dihydroxyacetone phosphate
glyceraldehyde-3-phosphate dehydrogenase,yields,"1,3-bisphosphoglycerate"
"1,3-bisphosphoglycerate",substrate_of,phosphoglycerate kinase
phosphoglycerate kinase,yields,3-phosphoglycerate
3-phosphoglycerate,substrate_of,phosphoglycerate mutase
phosphoglycerate mutase,yields,2-phosphoglycerate
2-phosphoglycerate,substrate_of,enolase
enolase,yields,phosphoenolpyruvate
phosphoenolpyruvate,substrate_of,pyruvate kinase
pyruvate kinase,yields,pyruvate

到目前为止，这就是我所拥有的

This is what I have, thus far,

...使用此密码(传递给Cycli或cypher-shell):

... using this cypher code (passed to Cycli or cypher-shell):

LOAD CSV WITH HEADERS FROM "file:/glycolysis_relations.csv" AS row
MERGE (s:Glycolysis {source: row.source})
MERGE (r:Glycolysis {relation: row.relation})
MERGE (t:Glycolysis {target: row.target})
FOREACH (x in case row.relation when "substrate_of" then [1] else [] end |
  MERGE (s)-[r:substrate_of]->(t)
)
FOREACH (x in case row.relation when "yields" then [1] else [] end |
  MERGE (s)-[r:yields]->(t)
  );

我想创建一个全连接的路径，在所有节点上都添加字幕.有什么建议吗?

I'd like to create the fully-connected pathway, with captions on all the nodes. Suggestions?

推荐答案

[更新]

存在多个问题并可能进行改进:

There are multiple issues and possible improvements:

1. 第二个MERGE应该被删除，因为它会创建孤立的节点.关系类型不应调整为Glycolysis节点，并且此类节点永远不会连接到任何其他节点.
2. 第1个和第3个MERGE子句必须对源节点和目标节点使用相同的属性名称(例如，name)，否则相同的化学物质最终可以有2个节点(具有不同的属性密钥).这就是为什么您最终得到的节点没有所有预期的连接.
3. APOC过程 apoc.cypher.doIt 可以是用于简化与动态名称的关系MERGE.
4. 此用例不需要glycolysis_bioentities.csv.

1. The second MERGE should be deleted, since it creates orphaned nodes. A relationship type should not be tuned into a Glycolysis node, and such nodes would never be connected to any other nodes.
2. The 1st and 3rd MERGE clauses must use the same property name (say, name) for source and target nodes, or else the same chemical can end up with 2 nodes (with different property keys). This is why you ended up with nodes that did not have all the expected connections.
3. The APOC procedure apoc.cypher.doIt can be used to simplify somewhat the MERGE of relationships with dynamic names.
4. The glycolysis_bioentities.csv is not needed for this use case.

进行上述更改后，您将得到类似以下的内容，它将生成一个与您的输入数据匹配的连接图:

With the above changes, you end up with something like this, which will generate a connected graph that matches your input data:

LOAD CSV WITH HEADERS FROM "file:/glycolysis_relations.csv" AS row
MERGE (s:Glycolysis {name: row.source})
MERGE (t:Glycolysis {name: row.target})
WITH s, t, row
CALL apoc.cypher.doIt(
  'MERGE (s)-[r:' + row.relation + ']->(t)',
  {s:s, t:t}) YIELD value
RETURN 1;

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