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docs/extending.md

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+# Extending the database
+
+A key advantage of graph database over relational databases, is that adding additional nodes, attributes or relationships can be done on the fly without redesigning the schema.
+If a user wants to specify new relationship or node types, then the most straightforward appraoch is to use the Cypher LOAD_CSV functionality, as follows. 
+
+## Loading new relationships: kinship example
+
+Kinship are person-to-person relationships which give an estimate of how related people are.
+The relationship inference software KING (http://people.virginia.edu/~wc9c/KING/) ran on a VCF
+file of genotypes produces a tab delimited file showing the kinship relation between the different individuals.
+
+
+The Cypher query language can then be used to directly load this file as relationships between persons. The “Relatedness” relationships are annotated with the following attributes N_SNP, HetHet, IBS0 and Kinship.
+Here is the Cypher command to do the import:
+
+``cypher
+USING PERIODIC COMMIT 500
+LOAD CSV WITH HEADERS FROM "file://<absolute_path_to_file/relatedness.txt>" AS csvLine FIELDTERMINATOR '\t'
+MATCH (person1:Person { personId: csvLine.ID1}),(person2:Person { personId: csvLine.ID2})
+CREATE (person1)-[:Relatedness { N_SNP: csvLine.N_SNP, HetHet: csvLine.HetHet, IBS0: csvLine.IBS0, Kinship: csvLine.Kinship }]->(person2)
+```
+
+## Loading new nodes and relationships: transcript to tissue expression example
+ 
+It also possible to create new node types and link them to existing nodes.
+For example tissue expression data can be downloaded from Gene tissue expression database (GTEx) (https://www.gtexportal.org) in order to link a new Tissue type node to existing Transcript nodes on TranscriptReads relationship.
+
+ 
+The data can be integrated using the following commands.
+Load the Tissue Nodes:
+ 
+ ``cypher
+USING PERIODIC COMMIT 500
+LOAD CSV WITH HEADERS FROM "file://<absolute_path_to_file/Transcript2Tissue.csv>" AS csvLine 
+MERGE (tissue:Tissue { name: csvLine.Tissue })
+ ```
+
+Load the TranscriptToTissue relationships:
+ ``cypher
+USING PERIODIC COMMIT 500
+LOAD CSV WITH HEADERS FROM "file://<absolute_path_to_file/Transcript2Tissue.csv>" AS csvLine 
+MATCH (transcript:Transcript { transcript_id: csvLine.Transcript}),(tissue:Tissue { name: csvLine.Tissue})
+CREATE (transcript)-[:TranscriptReads { Value: csvLine.Value }]->(tissue)
+```