2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan.

06 – 07, 2017, Coimbatore, INDIA

A Cypher Query based NoSQL Data Mining on

Protein Datasets using Neo4j Graph Database

Johnpaul C I∗ , Tojo Mathew†

∗ Departmentof Information Science & Engineering
† Departmentof Computer Science & Engineering
The National Institute of Engineering, Mysore, India
Affiliated to VTU, Belagavi
Email: johnpaul.ci@gmail.com, tojomathew@gmail.com

Abstract—Graph data analysis is one of the upcoming
methodologies in various niches of computer science.
Traditionally for storing, retrieving and experimenting test
data, researchers start with mysql database which is more
approachable and easier to build their test experimentation
platform. These test bed mysql databases will store data in the
form of rows and columns, over which various SQL queries
are performed. At times when the structure and size of dataset
changed, these traditional mysql databases become inefficient in
storing and retrieving of data. When the structure of dataset
changes from row-column to graph representation, mysql
database based querying and analysis become inefficient. The
internal representation of data is changed to key-value pairs,
more often the data in an unstructured format, which prompted
the researchers to think about other databases which can
achieve faster retrieval and mining over the dataset. This paper
explores the approach of NoSql query design and analysis of
different datasets, particularly a proteome-protein dataset over
a renowned graph database, Neo4j. The mode of experiments
involve the evaluation of NoSql query execution on datasets vary
in the number of nodes and relationships between them. It also
emphasises the process of mining large graphs with meaningful
queries based on a NoSql Query language called Cypher.
Keywords : NoSql, Neo4j, unstructured data, key-value,
graph dataset, datamining.
I. I NTRODUCTION
Data mining is regarded as one of the traditional collection
of methods to formulate meanings of different dimensions
from a given dataset. The success of methods not only de-
pends up on the efficiency of the algorithm, but also on the
structure of the dataset. The dataset can be a physical group of
numbers which are the values of some significant attributes.
Then the aim of any data mining method is to find out the
relation between these bare numbers. Different algorithms,
will consume these numbers, find out various parameters like
mean, median, mode, correlation, variance and coefficients to
establish a relation between these numbers [1]. With the help of
further equational proof and property constants of the dataset,
the algorithms will bring out ample dimensions of conclusion
which will proclaims the relationship of data in the dataset.
These conclusions will finally lead to the identification of new
data, its nature and other prediction properties. This is a general
routine work-flow of any data scientist who works on data
mining. In short, data mining comprises a sequence of steps or
combination of methods or mathematical solutions or machine
learning procedures to establish a relationship between the raw
data (numbers) in a given dataset, with a view to provide a
global meaning to the given dataset.
When a researcher thinks about the relation between the
attributes of a dataset, the most common method he will adopt
is the relational database model, which has significant methods
of establishing relationship between the attributes. In RDBMS
the concept of foreign key will help to link tables of different
attributes [2]. Even the systematic modeling of RDBMS tables
corresponding to a dataset itself requires a disciplined thought
process by adopting different rules of RDBMS including nor-
malization: which will make the table free from the outcomes
of repeated values, partial dependencies: which deals with the
relationship between composite key and other attributes, key
management: which include the possibility of defining super
keys, database schema: which describes the global view of the
table and in turn the database etc. This is the context where
the importance of new family of databases, particularly the
databases which have their base design entirely different from
RDBMS, comes in to picture.
In this new era of data mining, experimentation on
databases other than mysql has a profound significance. The
subject domain of data mining includes key methods of ma-
chine learning, where the training and test datasets have to
be prepared from the original dataset of experimentation. The
proportion of the content of data in test and training dataset
accounts for the accuracy of some algorithms. The relationship
of the values in the dataset has to be established with less
probability of erroneous conclusion. If the database structure
itself helps to establish, relationship between the attributes of
dataset, it will be a major milestone in the efficiency of the
algorithm running over it. The different properties of graph
databases which are of prime focus are listed below. Even
though, one can define a large set of key points, the properties
mentioned below form the major attraction of graph databases.
• Data representation in the form of graph.
• The relationship establishment.
• Simplicity in query formulation.
• Data visualization modules.
• Interoperability.
• Acceptance of different standred forms of data.
• Real programming experience on a conceptual
database design.

978-1-5090-4559-4/17/$31.00©2017IEEE
2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan. 06 – 07, 2017, Coimbatore, INDIA
The first three key points form the major break through
of graph databases compared to traditional mysql databases.
Graph representation of attributes have three major advantages.
Firstly, compared to traditional mysql database design, the
tables should not contain multivalued attributes. But in graph
databases we can have a disciplined number of multivalued
attributes. It can be node name or node number or even an
array of different attributes for a single node. The second
advantage is that each node can have a fixed number of
incoming and outgoing edges, which are otherwise called as
indegree and outdegree. These are analogous to the connec-
tion between different tables in mysql. Third advantage is a
futuristic thought which predicts the possibility of applying
different graph algorithms over the representation, which can
bring unexpected quick convergence to the result for various
experiments in data mining.
The second key point suggests the importance of foreign
key in a native mysql table. The relationships, which can be
established physically between the nodes using typical query
syntax is analogous to the foreign key in mysql. Simplicity in
query formulation helps the database developers, programmers
and academicians to experience the liveliness of their query
thoughts. Graph databases have different plugins for bridging
the gap between a Query based language and traditional
high level programming language. There are different data
visualization modules or packages are available which can be
easily integrated with the work-flow of graph databases. Graph
data visualization is one of the essential properties of a graph
database which will portray the real structure of establishment
of nodes according to the programmers view. It is analogous
to the select * query in mysql database.
The remaining work described in the paper is organized
as follows: Section II contains literature survey remarking the
different graph based frameworks which are used in computing
world. It describes the ideas of graph representation which
are used not only in database domain, but also in distributed
computing, machine learning etc. A significant background
study conducted on programming languages, which are more
compatible for graph like structure programming, is also
included. Section III, comprises of the proposed experiments
carried out over different datasets, proteome-protein datasets,
the query design formulation methods and relationship based
significant queries. Section IV discusses the results of various
experiments done over the above mentioned datasets. Section
V concludes the paper with a vision of future scope on graph
databases.
II. R ELATED W ORK
The ground work conducted to explore graph database
includes the following action plan. Graph theory concepts
helped in mastering and designing queries. With a view to
understand different graph representations, a background study
is performed on various graph theory based computing plat-
forms, a graph theory based in-memory distributed computing
framework called, Spark, Google graph processing framework
Pregel and Neo4j graph database. The end of this base ex-
ploration, includes a description of two co-orporate streams,
which uses Neo4j graph data base in full swing for their mode
of operations related to big data analysis and visualization.
A. Graph Theory Fundamentals and Related Concepts
Graph theory and its associated concepts are assimilated
in designing a graph database for handling data which emphe-
sises on the importance of relationship establishment between
attributes. There are different interesting results from graph
theory which can be extracted to evaluate the graph represen-
tations. Some of the various concepts of interest include the
in degree and out degree count of nodes, the count of cut-
edges, existence of cut-vertices, shortest path algorithms in
database view, network flows and analysis, prominent graph
traversal methods etc. [3][4]. Euler formula, which establishes
a relationship between the number of vertices and edges,
Havel-hakimi theorem of establishing valid graphic sequences,
four coloring theorem, matching property in graphs, sub graph
properties, bipartite and complete bipartite graphs which are
formed by vertex partitioning process, connected components
of a graph, directed acyclic graphs (DAG), finding out centers
and bi-centers of a tree etc are some of the concepts which
are widely used in data representation. Though the results and
concepts seem to be too basic, they have significant impact on
data representation on various graph frameworks, where the
distribution of nodes and processing steps take place across a
network spreading out millions of nodes and edges [5].
B. Spark: Graph theory based In-Memory Cluster Computing
Framework
After the reign of Hadoop [6], which served as one of
the base framework for large number of distributed system
applications, graph theory based frameworks started heading
up for distributed data processing applications. Since the estab-
lishment and other properties are user-friendly, Spark is a well
accepted package for designing clusters with adequate number
of systems. Considering the physical properties of a large
cluster, it is always advisable to consider about disk access. It
is obvious that when the number of worker nodes included in
the cluster grows, the disk access also grows linearly. Rippling
to this, the communication over-head between the systems also
grows drastically. Hence all these post-establishment features
will have an ample impact on the performance and scaling
of the framework. Data scientists thought of different methods
which can also utilize memory space (total RAM) of the cluster
to process, store, retrieve and analyze the data for applications
which works in a strict time bound manner . These aggressive
research gave rise to in-memory cluster computing framework
called Spark [7].
Spark in-memory cluster computing framework is an open
source package that helps in quick data analytics. It evolved
from a group of research scholars from, Berkeley, University
of California under the leadership of Matei Zaharia. When
analytics comes into the scene, it contains both read and
write operations into the data source. To provide a faster
runtime execution environment, Spark makes room for all
the prerequisites to establish an in-memory cluster: The most
striking feature of Spark framework is that the user can load
data directly into memory of the cluster (total RAM space)
and perform queries repeatedly much faster than traditional
disk based systems like hadoop map-reduce [6].
 2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan. 06 – 07, 2017, Coimbatore, INDIA

C. Graph Processing Frameworks

Graphs gather attention from research community when
they project real-world data. They are intuitive and flexible in
terms of elementary data operations. Supporting graph theory
forms a strong basement in nurturing of graph processing
Fig. 1: Visualization of a Neo4j nodes and Relationship
frameworks. There are various standard algorithms in graph
between them
theory: shortest path, finding the route, detection of loop in a
network, matching and subgraph generation etc are some of
them [8].
Problems arise when very large graph representation are form of queries, written in Cypher programming language. It
required. The communication overhead is large when visiting is famous for its simplicity in writing the queries for retrieving
highly connected vertices. Considering this scenario graph and declaring relationships between the nodes.
cannot accommodate on a single physical machine, and the
Another striking feature of Neo4j is the availability of
implementation spreads over a cluster of machines. Algorithms
a graphical user interface to track down all the nodes, re-
typically trace the vertices through edges of graph. This
lationships, queries and performance. It provides the user
will increase the communication overhead due to machine-
a well organized GUI for declaring nodes and relationship
to-machine communication. For dividing the graph optimally
between the nodes graphically. It is also equipped with a
on the cluster, Bluk-Synchronous Parallel (BSP) algorithm is
performance analysis graph which will update in every three
commonly used [8][9].
seconds with the recent details of data. More than that there
1) Pregel: Google Graph Processing System: Processing is no much hurdle to establish a Neo4j database in a server,
a massive graph, with the help of an algorithm that explores there by increased users trust and acceptance. Neo4j can also
the graph along its edges. Originating from an set of vertices, be integrated with Python using Py2neo plugin, where all the
one can travel from one vertex to another and transmit the queries can be written as programming statements. Thus the
execution of algorithm, across a group of active vertices. emerging graph database had a commendable acceptance in
This is the BSP model of running an algorithm iteratively by developer community [13][14].
transferring messages [10]. The pregel system proceeds further
in a master-slave mode of graph processing.
III. P ROPOSED W ORK
2) Apache Giraph: Giraph is yet another graph processing
package from Apache foundation following the development This quarter of the paper contains the in-depth description
Pregel. It is still undergoing research to modify its capabilities. of the experiments conducted over datasets on Neo4j. It
Fault tolerance is one of the major issues taken care by Giraph starts with a basic modeling of the data set parsing methods,
[11]. proceeds further to Neo4j and reaches the query formulation.
The whole process of experiments can be inferred from Figure
3) Apache HAMA: HAMA was originated by inspiring 2
ideas from Google Pregel. The source of data to HAMA is
through HDFS APIs, in the form of adjacency lists stored in
text files with every line starts with a vertex ID, followed by the
list of IDs of vertices connected to the former by its outgoing
edges. Synchronization is performed by Zookeeper, which is
the most widely used synchronization component in distributed
system frameworks [12].

D. Neo4j: The emerging graph data base

Neo4j is one of the emerging and most used graph
databases in this computing era. There is a wide acceptance
to Neo4j apart from mysql due to various reasons. For a
quite long time, the database world enjoyed all the privileges
of mysql, row based data storage. For software applications,
academics and research, mysql paved an immense role of Fig. 2: Work-flow Diagram of Query Formulation of Graph
establishing trust on data storage. In course of time, the data-sets
structure and scale of data also changed. It turned out to be
inefficient to store data in the form of rows and columns. As a
result, people started thinking of migrating to other databases
[13]. The parser program is written in Perl which contains specific
functions to identify the source and destination node and
Neo4j provides a convenient way to visualize data with its formulate the necessary queries. To generate a basic graph
inherent graph structure. The users can declare data attributes model it is essential to define two type of queries, viz. create
in the form of nodes and relationships between these nodes and relationship. A general description of the algorithm for
as edges during the declaration itself. Querying is another generating these queries is shown in the below mentioned
property of all databases. In Neo4j the data is retrieved in the algorithm 1.
2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan. 06 – 07, 2017, Coimbatore, INDIA
Algorithm 1 Query Generation Algorithm
Data: Graph Dataset
Result: Create queries, Relationship queries
initialize file descriptor FILEDES as null;
while FILEDES != null do
line = String FILEDES
Array(output) = split(line)
source = output[0]
createquery(source,nodename,properties)
destination = output[1]
destinationcount = length(output[1])
iter = null
while iter != destinationcount do
relationquery(source,output[1].iter)
iter = iter + 1
end
FILEDES = FILEDES + 1
end
The algorithm depends directly on the count of lines or
source nodes. We can trace these count with the help of file
descriptor, FILEDES. Consider there are m nodes in a graph
dataset. Hence the maximum value of FILEDES is m. Looking
forward to the algorithm mentioned above it is clear that for
each source node say, i there can be an arbitrary number of
destination nodes, say n. In general, if we consider the running
time of this algorithm it can found that it will attain close to
O(mn), keeping the assumption that the average out-degree of
any node will not scale up to m.
Fig. 3: Generation of Node Creation Queries
As an initial step towards the formulation of create and
relationship queries, the graph dataset selected contains 20000
nodes and 100000 edges, with an average degree 5, for each
node. The whole dataset is of the form, sourcenode dest1,
dest2, dest3 ... and so on. On running the query formulation
algorithm for neo4j the query for create node as shown in fig-
ure 3 and the queries for establishing the relationship between
the nodes can be viewed from figure 4. Taking the first create
query from the figure 3, it tells that a node of name node0
and type largenode has to be created as n0. Here nodename is
property of the node n0. Considering the first relation query
from figure 4, it advances as a combination of match and create
queries [15][16]. With the help of node creation queries, all
the respective nodes would have been created and with that
existing nodes, relationship queries are formulated. The first
step in creating the relationship is matching. The match sub-
query will identify the nodes for establishing the relationship
between them. This will be in accordance with specification
of the datasets. The match query will find out two nodes viz.
n1 and n3255 and it will create relationships between n1 and
Fig. 4: Generation of Relationship Queries
n3255 with the relationship construct -[:connectedto]− >, the
term connectedto is the type of relationship. The meaning of
this query formulation is left to the designer.
Various experiments conducted over yeast dataset and
other datasets are basically different in query formulation. An
instance of match query is as follows
match (a)-[:connectedto]− >(b) return a,b limit 200
This query will return the nodes named as a and b
with the relationship connectedto. Since the result set contains
as many 20000 nodes, we can limit the result for 200.
match(n0:yeastnode)-[link:linkedproteinto]− >(n1:yeastnode)
where link.edgeweight = 0.003721 return link limit 40
This query will result in the retrieval of yeastnode having an
edgeweight greater than 0.003721 in blocks of 40. The query
formulation gives rise to different meanings which can be
utilized for complex graph data analysis.
match testnode =(begin)−[link : linkedproteinto]− >(end)
where begin.yeastlabel=’ylow34’ and end.name=’ylowe43’
foreach (n in yeastnodes(link)|set n.edgeweight = n.edgeweight
+ 1)
The above complex query help the programmer to find
path from the starting yeast node labeled ylow34 and ending
at node labeled ylowe43. After finding the path using the
existing linkedproteinto relationship, it will increment the
current edgeweight by one.
match testnode = (a)−[∗1..3]− > (b) where a.yeastlabel =
’y0w5rt’ and b.yeastlabel =’ymly98’ and all (x in yeastnode
(testnode) where x.edgeweight > 0.001675) return p
This query will return all the nodes starting from the
yeastnode labeled y0w5rt through the yeastnode labeled
ymly98 and all the other nodes having a relationship
edgeweight greater than 001675.
match p=(a)−− >(b)−− >(c) where a.yeastlabel=’ylwdd43’
and b.yeastlabel=’ywerll3’ and c.yeastlabel = ’yylw3c’ return
extract(n in yeastnode(p)|n.yeastlabel) as extracted
The graph framework, neo4j also contains inbuilt functions
for processing the output of match statements [16]. The above
Cypher query is one of the instances where the functions
2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan. 06 – 07, 2017, Coimbatore, INDIA

are used. Here the inbuilt function extract is used to filter

out only the labels from the path specified by the match
query. The function extract works with the help of an iterator
variable over the result of match function and filters off the
required result by the user.

IV. R ESULTS AND A NALYSIS

The experiments performed over neo4j can be broadly
classified into to two sections. Firstly, the aim of the
experiments involves the design of various queries using
Cypher language. In the previous section different use case
queries are discussed. The results of such queries have to
go in pace with programmers view. For each query the
output is recorded in terms of the number of nodes and
relationships. This data is taken by executing the query under Fig. 7: The Webadmin Window which gives the Accurate
a threshold limit to restrict the number of nodes appearing in Statistics of neo4j Contents
the webadmin of neo4j. Some of the prominent query result
visuals obtained can be viewed from the figures 5, 6, 7.
The figure 5 was produced as a result of match query on
properties of the infrastructure. The activity graph shows the
progress of node, relation and property creation at specific
times.

The following table 1 gives the various values of the

nodes and relationship retrieved when the match query was
executed. The match query was performed over the 20000
node, 100000 edge dataset with a check of discrete limit
intervals.
Limit Number of Nodes Number of Relationships
50 39 86
100 73 166
Fig. 5: Match Query Visualization on connectedto Relationship 150 105 253
200 126 299
250 184 355
300 241 417
20000 node and 100000 edges dataset on the relationship 350 300 474
connectedto. The query returns large number of nodes. To 400 359 529
450 417 588
have a better visualization the view is limited to 200 nodes. 500 476 654
Figure 6, is formed as a result of the match query on yeast
TABLE I: Node and Relationship Count based on Limit based
Match Query Execution

The statistical details of match query experiments over the

yeast dataset under descrete limit can be viewed from table 2.

Limit Number of Nodes Number of Relationships

50 59 66
100 108 133
150 155 233
200 196 302
250 250 388
300 280 492
Fig. 6: Match Query Visualization on Yeast Dataset based on 350 330 583
linkedproteinto relationship 400 364 700
450 398 792
500 433 894
protein dataset. The protein nodes of this dataset are linked TABLE II: Node and Relationship Count of Yeast Dataset
with the linkedproteinto relationship. Each link is associated based on Limit based Match Query Execution
with an edgeweight. The query returns the nodes having
relationship equal to the given edge weight. Figure 7 reveals
the capacity of the neo4j database during various experiments.
It gives an accurate statistics of nodes, relationships and The two graphs represented by figures 8, 9 throw light to
2017 International Conference on Advanced Computing and Communication Systems (ICACCS -2017), Jan. 06 – 07, 2017, Coimbatore, INDIA
Fig. 8: Node and Relationship Graph of Limit based Match
Query Execution
Fig. 9: Node and Relationship Graph of Limit based Match
Query Execution on Yeast Dataset
following conclusions. From the figure 8, it is obvious that the
nodes and relationships keep a safe distance between them
in their growth. It is because of the nature of 20000 node
100000 edge dataset. The dataset contains nodes on an average
outdegree of five, where as in the graph represented by the
figure 9, the internal structure of the dataset in not known until
the graphs are created using create and relationship queries.
It can be noticed that when the nodes increase, the growth of
relationship tends to increase tremendously and it is attaining
an exponential curve.
V. C ONCLUSION AND F UTURE S COPE
Experiments of graph-database neo4j reveals a new dimen-
sion of data mining research. In this modern times, the dataset
format changes and mysql database experiments seems to be
inadequate, when the data cannot be represented in the form
of rows and columns. The NoSql queries are more powerful in
performing retrieval from a graph database without the hurdles
of constraints. Moreover graph database also supports the
storage of unstructured data in the form of defined properties
and relationships. It can be also integrated with modern forms
of data interchange using JSON an REST interfaces. The only
challenge on using the graph database is the design of efficient
queries using Cypher language. Programmers, developers have
to invest their effort to design meaningful queries on the dataset
based on the existing properties of the dataset. Successful de-
sign of queries will provide new dimension of research results
which can be scaled over to a vast number of datasets, there
by drilling out various meaningful conclusions and predictions
from that dataset. The neo4j graph database is widely accepted
by research community and corporate world. In this era of
unformatted data and methods like big data analytics, neo4j
will be one of the base platform to provide solutions to various
data mining requirements.
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