Variable not defined but the variable already exists

Neo4j Graph Platform Cypher
1

Hi,

I am trying to bulid the relationship between my nodes.

However, the "variable not defined "error messages keep pop up in my neo4j browser, even though the variable existed.

When I run this

LOAD CSV WITH HEADERS FROM 'file:///genes2hallmark.csv' AS link
MATCH (g:gene{ENS_ID: topTable.ID}),(hmgs:HMGS{hallmark_gene_sets: hmgenesets.hallmark_genesets})
WITH g, hmgs
MERGE (g)-[r:BELONG]->(hmgs)

Gives me the error message:

Variable topTable not defined (line 2, column 23 (offset: 86))
"MATCH (g:gene{ENS_ID: topTable.ID}),(hmgs:HMGS{hallmark_gene_sets: hmgenesets.hallmark_genesets})"

Anyone can give me a hints about this?

Thank you so much.



My code and data --------------------------------------------------------------------------------------------------------------------------- - neo4j version 3.5.14, browser version 3.2.26 - API / driver: I am using neo4j browser
My cypher query as following (I run them in order): > USING PERIODIC COMMIT 1000 > LOAD CSV WITH HEADERS FROM 'file:///hmgs.csv' AS hmgenesets > MERGE (hmgs:HMGS{hallmark_gene_sets: hmgenesets.hallmark_genesets}) > WITH hmgs > MATCH (hmgs) > RETURN (hmgs)

USING PERIODIC COMMIT 500
LOAD CSV WITH HEADERS FROM 'file:///topTable.csv' AS topTable
MERGE (g:gene
{ENS_ID: topTable.ID,
log_FG: topTable.logFC,
Average_Expression: topTable.AveExpr,
t_test: topTable.t,
P_value: topTable.P_Value,
Adjusted_P_value: topTable.adj_P_Val,
entrez_id: topTable.entrezid,
gene_name: topTable.gene_name})
WITH (g)
MATCH (g)
RETURN (g)

LOAD CSV WITH HEADERS FROM 'file:///genes2hallmark.csv' AS link
MATCH (g:gene{ENS_ID: topTable.ID}),(hmgs:HMGS{hallmark_gene_sets: hmgenesets.hallmark_genesets})
WITH g, hmgs
MERGE (g)-[r:BELONG]->(hmgs)


The topTable.csv looks like this:

ID,logFC,AveExpr,t,P_Value,adj_P_Val,entrezid,gene_name
E971,3,8,3,8,1,5,FO
E938,3,8,3,8,1,5,F

The geneshallmark.csv looks like this:

gene_id,geneset
E938,HALLMARK_A
E971,HALLMARK_C
E971,HALLMARK_C

The hmgs.csv looks like this:

hallmark_genesets
HALLMARK_A
HALLMARK_C

2

Where exactly are you getting the variable does not exist error?

3

Hi,

Thank you for your reply.
The error message is

Variable topTable not defined (line 2, column 23 (offset: 86))
"MATCH (g:gene{ENS_ID: topTable.ID}),(hmgs:HMGS{hallmark_gene_sets: hmgenesets.hallmark_genesets})"

So the I think it stands for the variable topTable is not defined. But I defined it in

USING PERIODIC COMMIT 500
LOAD CSV WITH HEADERS FROM 'file:///topTable.csv' AS topTable

4

Ok, it looks like the problem is you're calling that topTable, without providing the ID. Yes you've created it, but you would need to provide the ID again as a parameter. You can't simply just call it again. You need to have a list of the IDs you're trying to call and match to the links. You could probably collect the ids before hand and loop through them like:

MATCH (g:gene)
with COLLECT(g.ENS_ID) as ids
......

Then you'd be able to match them correctly and go on.

5

Hi, you are referring to a variable defined in another query.

Here the variable available for you is "link"

gene_id,geneset
E938,HALLMARK_A
E971,HALLMARK_C
E971,HALLMARK_C

Based on this data set change the code to

LOAD CSV WITH HEADERS FROM 'file:///genes2hallmark.csv' AS link
MATCH (g:gene{ENS_ID: link.gene_id}),(hmgs:HMGS{hallmark_gene_sets: link.geneset})
WITH g, hmgs
MERGE (g)-[r:BELONG]->(hmgs)

This should work.

7

Thank you so much for your reply.

It works!