Vfrdtyky

I have an XML file that looks like this:

<rebase>

   <Organism>

     <Name>Aminomonas paucivorans</Name>

       <Enzyme>M1.Apa12260I</Enzyme>

         <Motif>GGAGNNNNNGGC</Motif>

       <Enzyme>M2.Apa12260I</Enzyme>

         <Motif>GGAGNNNNNGGC</Motif>

   </Organism>

   <Organism>

    <Name>Bacillus cellulosilyticus</Name>

       <Enzyme>M1.BceNI</Enzyme>

         <Motif>CCCNNNNNCTC</Motif>

       <Enzyme>M2.BceNI</Enzyme>

         <Motif>CCCNNNNNCTC</Motif>

   </Organism>

</rebase>

I want to visualize this XML data into a graphical format. The connectivity is such that a lot of enzymes can contain common motifs but no organims can have similar enzymes. I looked at d3.js but I dont think it has what im looking for. I was really excited with the visualization neo4j seems to provide but i will need to learn it from scratch. However I havent come across any good tutorials for importing or creating a graph in neo4j via XML datasets. I know in the world of programming anything is possible so I wanted to know the possible ways I could import my data (preferably using python) to a neo4j database to visualize it.

UPDATE

I tried following this answer (second answer under this question). I created the 2 CSV files that he suggested. However the query has a lot of syntax errors , such as :

1. Invalid input 'S': expected 'n/N' (line 6, column 2)
"USING PERIODIC COMMIT"


2. WITH is required between CREATE and LOAD CSV (line 6, column 1)
"MATCH (o:Organism { name: csvLine.name}),(m:Motif { name: csvLine.motif})"

My cypher query skill are extremely limited and i couldnt get any imports to work so fixing the query by myself is proving to be really difficult. Any help will be greately appreciated

There is also a series of posts how to import XML into Neo4j.

• http://supercompiler.wordpress.com/2014/07/22/navigating-xml-graph-using-cypher/


• http://supercompiler.wordpress.com/2014/04/06/visualizing-an-xml-as-a-graph-neo4j-101/

First you should model how your data should look like as a graph, which entities do you need for your use-cases and which semantic connections.

In general if you can load the data in python, you can use py2neo or neo4jrestclient (see http://neo4j.org/develop/python) to import your data into your model.

for this i would suggest to use directly gephi . at least a year ago it worked flawlessly, it supports xml/csv data format import directly and there is no need to use neo4j as pre-processor.

edit

oh, i see now, i though the connections are already included. in this case, you must create all the data from xml as a separate node - new node for each enzyme and motif and also for each organism(with a parameter name). those enzyme nad motif nodes must be unique - i.e. no duplicates. when creating an organism node, you connect the organism to its enzyme and motif nodes by a relationship. after this is done, querying/visualizing similar nodes is no problem, since common nodes share at least one of the enzyme/motif.

i don't know any smart way to import data xml to neo4j, but you should have no problem to convert it into two csv files. the format of that csv would than be:

first file:

name,enzyme

Aminomonas paucivorans,M1.Apa12260I

Aminomonas paucivorans,M2.Apa12260I

Bacillus cellulosilyticus,M1.BceNI

Bacillus cellulosilyticus,M2.BceNI

second file (i don't understand why the motif is duplicite thought):

name,motif

Aminomonas paucivorans,GGAGNNNNNGGC

Aminomonas paucivorans,GGAGNNNNNGGC

Bacillus cellulosilyticus,CCCNNNNNCTC

Bacillus cellulosilyticus,CCCNNNNNCTC

now we are going to do the import, which creates unique nodes and relationships (thus the above duplicite motifs would transfer just into 1 unique relation) (if neccessary, it is possible to have multiple relationships to the same motif node, too):

(i'm not sure with this import but it should work):

USING PERIODIC COMMIT

LOAD CSV WITH HEADERS FROM "file1.csv" AS csvLine

MATCH (o:Organism { name: csvLine.name}),(e:Enzyme { name: csvLine.enzyme})

CREATE (o)-[:has_enzyme]->(e) //or maybe CREATE UNIQUE?



USING PERIODIC COMMIT

LOAD CSV WITH HEADERS FROM "file2.csv" AS csvLine

MATCH (o:Organism { name: csvLine.name}),(m:Motif { name: csvLine.motif})

CREATE (o)-[:has_motif]->(m) //or maybe CREATE UNIQUE?

this shall create th graph with 2 organism nodes, 4 enzyme nodes and 2 motif nodes. each organism node should than have a relationship to its enzymes and motifs. after this is done, you can move forward to the visualization part described at the beginning.