Graph Management to Improve Querying of Health and Social Data
Mar
´
ıa Constanza Pab
´
on
1,2
, Claudia Roncancio
3
and Martha Mill
´
an
1
1
Escuela de Ingenier
´
ıa de Sistemas y Computaci
´
on, Universidad del Valle, Cali, Colombia
2
Departamento de Electr
´
onica y Ciencias de la Computaci
´
on, Universidad Javeriana-Cali, Cali, Colombia
3
University of Grenoble, Grenoble Isere, France
Keywords:
Graph Querying, Data Integration, Data Exploration.
Abstract:
Large amount of data related to health care are stored in heterogeneous data sources. Independently, social
media provides information about people’s environment and activities, such as family relationships or patient’s
habits and social interaction. This information could be used to complement patients medical profiles to
improve patient’s care. Providing expert users with mechanisms to integrate and query such sources becomes
crucial to retrieve information allowing to improve the analysis of patient’s situations. This work contributes
to facilitating visualization and querying of data coming from such sources. We adopt a graph data model
at the conceptual level as it facilitates the integration of structured and semi-structured data. Our purpose is
to go a step forward by providing a conceptual query language intended to allow end users, medical domain
experts, to retrieve data from heterogeneous data sources by ad hoc queries. In this paper we introduce a set
of operators to query data by transforming a graph and we analyze how they fulfill some design features of
the conceptual language. These operators allow successive graph transformation to generate subgraphs with
filtered data and to derive new relations representing information that is implicit or that is sparse in the data.
1 INTRODUCTION
The amount of data collected by health information
systems has increased exponentially last years. De-
spite the efforts to provide technologies to integrate
and to improve the access to this information, pa-
tient’s health care data is still distributed in heteroge-
neous data sources. On the other hand, the amount of
available social media data is growing every day. So-
cial media could provide important information about
people’s environment and activities, such as family
relationships or patient’s habits and social interaction.
This information could be used to complement pa-
tients medical profiles, in order to improve patient’s
care. Therefore, a significant potential benefit could
be obtained combining data sources from medical
care systems and social media.
In order to facilitate physicians and medical spe-
cialists access to aforementioned information, we
work on a data integration system and a conceptual
query language
1
. We adopt virtual data integration
based on mediation. At the mediator level, a global
data model provides a view of data available. This
1
This work is supported by the French Government
through the ANR Innoserv project.
view is used to formulate queries. Their evaluation
leads to a distributed execution on the data sources
and final integration by the mediator. In DIG (Data
Integration using Graphs), our data integration sys-
tem, we adopt a graph data model for the global
schema. Due to its expressivity and flexibility, graphs
could represent structured and semi-structured data
and allow the mapping of many other data models.
Therefore, the set of data sources may include both
medical and social data, easily represented by graphs.
Besides, semantic and conceptual models are usually
based on graphs. Therefore, the mediator’s global
graph data model is also the conceptual model under-
lying the conceptual query language.
However, as data and their relations are com-
plex, using a graph query language to express ad hoc
queries may be difficult for end-users and domain ex-
perts —ad hoc end-users queries can not be deter-
mined prior to the moment a query is expressed. To
overcome this difficulty and to facilitate data explo-
ration, this work is a step forward to support a user-
friendly conceptual query language, with a graphi-
cal interface. To support such a query language we
require a set of high-level operators. They facili-
tate query formulation to users who are domain ex-
343
Pabón M., Roncancio C. and Millán M..
Graph Management to Improve Querying of Health and Social Data.
DOI: 10.5220/0004805403430350
In Proceedings of the International Conference on Health Informatics (HEALTHINF-2014), pages 343-350
ISBN: 978-989-758-010-9
Copyright
c
2014 SCITEPRESS (Science and Technology Publications, Lda.)
perts but who have little or no experience with graph
query languages. In this paper we introduce a set of
graph transformation operators as part of the concep-
tual query language. Through successive graph trans-
formations users select filtered data and derive new re-
lations based on paths connecting objects in the graph.
These relations make explicit information that is im-
plicit or sparse in the data. The operators are part of
the query engine in the DIG system. Some benefits
derived from the operators are:
The operators allow users to manipulate objects
maintaining its relationships and attributes, and deriv-
ing new relationships between objects connected by
undirected paths. In this sense, the operators provide
a high level of abstraction.
We use a conceptual schema and take advantage of
it, by, first, bringing users a general vision of the data,
thus allowing better use of information, and second,
guiding users during data exploration. The use of a
data schema is possible since the chosen data model
is flexible.
By the use of the proposed operators the graphical
interface can avoid unintuitive notions for end users
such as the use of variables, the need of distinguish
output variables, and the need to construct query pat-
terns from scratch by a drag-and-drop approach.
The operators allow incremental query formulation.
A feedback about how the result will be like can be
provided to the user. This helps preventing the execu-
tion of queries that have failed to fulfill the needs of
the user.
This paper is structured as follows. Section 2 in-
troduces conceptual query language features and the
underlying data model. Section 3 introduces the oper-
ators and illustrates their use. Section 4 describes op-
erator implementation DIG system. Related work is
discussed in Section 5. Conclusions and future work
are highlighted in Section 6.
2 DATA MODEL AND QUERY
LANGUAGE FEATURES
Several features are required to provide a concep-
tual query language intended to allow end users to
explore and retrieve data from heterogeneous data
sources. First of all, a flexible underlying conceptual
data model is required. Second, queries should be ex-
pressed on a data schema, navigation should be facil-
itated and incremental query formulation with feed-
back at each step should be possible to guide the user.
Also, as much as possible, variables and specific no-
tions proper to query languages, should be hidden.
These features, intended to ease the query expression,
are described in Sections 2.1 and 2.2.
2.1 Graph Data Model
We use the notation and definitions of GDM (Hidders,
2002). This graph data model allows to define inde-
pendent schema and instance graphs, and the relation
between them. GDM also includes composite values
and n-ary relations. GDM graphs have simple nodes
and edges—they do not include hypernodes, hyper-
edges, nor attributes attached to the nodes and edges.
Nodes represent classes in a schema graph and en-
tities in a instance graph, while edges represent at-
tributes in both graphs. GDM provides three kinds of
classes: objects, composite values and basic values.
In our approach, the data schema is essential and
plays three roles: first, as a conceptual model that uses
concepts easily understandable by users belonging to
the application domain; second, as a mean to spec-
ify the input of the operators; and third, as a mean to
guide users in the query formulation process. Besides,
the data schema gives more expressivity and allows
independence between the definition of the structure
of data and the instance. Also, usually, as the schema
is concise, it is easier to visualize than the instance.
The graphical representation of GDM graphs is
simple. GDM handles two independent graphs rep-
resenting the database schema and the database in-
stance, and the relationship between them. Addition-
ally, the definition of the graph includes functions to
represent the kind of class (object, composite or basic
Figure 1: Clinical record basic schema example. Squares
represent object nodes, small empty circles represent
composite-value nodes, and circles with a basic-type name
inside represent basic-value nodes.
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Figure 2: Clinical record basic instance example (for clarity, values are represented as basic-value nodes).
value) and the class of nodes, and the type of edges.
Therefore, such metadata do not add nodes nor edges
to the graph. Thus, a GDM graph model has less
nodes and edges than, for example, a corresponding
RDF schema. In this sense, GDM schema graph is
easier to navigate and to understand. Besides, the
operators handle in a uniform way entities and their
attributes, since both abstract objects and basic val-
ues are represented with nodes, and neither, nodes nor
edges, has attributes in its internal structure. Further-
more, the representation of basic values as nodes lead
to connections between instance entities (i.e. patients
diagnosed with the same disease are linked to a node
representing that disease). The transformation oper-
ators allow to take advantage of those connections to
find relationships in data.
Figures 1 and 2 illustrate a schema and instance
graphs of basic clinical data. A clinical record has the
patient’s demographic data, such as the date of birth,
birth place, race, and gender. Other data related to
medical care such as reason of the consultation, de-
scription of the illness or diagnoses, are also available.
2.2 Graph Schema and Querying
The interface takes advantage of the graph schema to
help users in query formulation. The schema graph
is displayed and the interface guides users to ex-
plore it. This helps finding the nodes that represent
classes and attributes required for a query and to ap-
ply proper graph transformations. When a transfor-
mation is applied, the transformed schema graph is
displayed. This is done without the execution of the
operator over the data sources. Users can then cor-
roborate the expected query result, and revert or re-
place the transformations applied at any time during
the query formulation process. This prevents execut-
ing queries that have failed to fulfill the needs of the
user. Thus, based on a graphical interface, the schema
graph could be transformed by the user allowing him
to select interest entities, as shown in Figure 3.
The visualization of a schema graph, together with
the user’s knowledge about the domain, allows users
to determine, in a natural way, the information to ac-
cess.
The input of the operators is selected directly over
the schema graph. This avoids dragging (from some
list) class and attribute names to built a query pattern.
Most graphical query interfaces are based on the
construction of search patterns by drawing (or drag-
ging) nodes and edges (Catarci et al., 2003; Gyssens
et al., 1990; Consens and Mendelzon, 1990; San
Mart
´
ın et al., 2011). Some of them offer predefined
graph patterns (Bhowmick et al., 2013). Others al-
low to select in the data graph some interesting pat-
terns and to convert its nodes and edges to variables
GraphManagementtoImproveQueryingofHealthandSocialData
345
(a) Data schema with a subgraph highlighted (b) Extraction from graph (a) (c) Path contraction on graph (b)
Figure 3: Schema transformation example.
or predicates. Therefore, in most cases, users have to
construct the entire query from scratch, and they need
to imagine how to do it mixing the elements of the
language or the graphical interface. In contrast, our
approach is schema based, therefore we provide users
facilities to navigate on the data schema graph and to
select interesting entities by transforming it.
Moreover, graphical interfaces that help users
to formulate formal textual language queries (Smart
et al., 2008; Groppe et al., 2011) usually map
the language elements to a graphical representation.
Thus the interface depends on the language structure.
Therefore, even graphical, the query formulation re-
lies on the language structure. In contrast, our opera-
tors are based on the user interaction with the schema
graph, by navigating and transforming it.
3 GRAPH TRANSFORMATION
OPERATORS
In this section we describe the main graph transfor-
mation operators, we provide examples and highlight
some of their characteristics.
3.1 Description of the Operators
The operators are high-level, in the sense that they al-
low to perform transformations that in current propos-
als would require the execution of several operations.
Each of them takes as input a schema and instance
directed graphs, a set of interest nodes or edges and
other parameters, and returns as output schema and
instance directed graphs.
The subgraph extraction operator allows select-
ing all data that corresponds to a given set of schema
edges. Given the schema graph shown in Figure 3(a),
the subgraph extraction operator can be used to re-
trieve the subgraph that includes patients’ id, first and
last names, the diagnoses they have received and the
diseases in their family history. See Figure 3(b).
The value filtering operator allows selecting the
basic-value nodes of some interest classes. These
nodes are linked to other basic-value nodes that fulfill
a given condition. The value filtering operator returns
the selected nodes and the paths between them. It re-
turns transformed schema and instance graphs. This
operator can be used to find, for example, the id and
names of patients linked by one or several specified
path patterns to a hepatitis B node. These patterns
could be diagnoses or diseases in their family history.
The class filtering operator includes two steps.
First, it selects objects that belong to one interest class
and fulfill a given condition. And second, it retrieves
all data linked to those selected objects by an undi-
rected path that corresponds with a schema path. This
includes not only the selected objects’ attributes, but
also their relationships with other objects or compos-
ite values and their attributes, provided that they are
covered by an undirected path of the schema. Class
filtering does not change the schema graph but selects
data associated with subsets of objects of the interest
class. It is useful to retrieve, for example, information
of female patients born in 2005 who have been diag-
nosed with diabetes. In this case, the interest class is
patient, the operator retrieves each patient that fulfills
the given condition. Then, retrieves the data linked
to those patients by some undirected path that cor-
responds with a schema path. In the schema given
in Figure 3(a) each patient selected will have the pa-
tient’s attributes (idNumber, firstName, etc.) plus en-
counters, physician and diseases related to the patient,
and their attributes.
The path contraction operator changes both the
schema and the instance, to generate graphs that
make explicit relations that are implicit in the origi-
nal graph. The path contraction operator replaces in-
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Figure 4: Subgraph extraction resulting schema.
Figure 5: Subgraph extraction resulting instance.
ner nodes and edges of a given schema’s path with a
new node connected to the path’s initial and terminal
nodes. It is useful, for example, to establish a more di-
rect relationship between patient and disease descrip-
tion nodes, so an user can easily see diagnoses given
to patients. See Figures 3(b) and 3(c).
Finally, to accomplish specific domain query re-
quirements, specific transformations be defined com-
bining several operations. As an example, we de-
fine the co-occurrence operator. Given two classes
A and B, this operator allows to find pairs of objects
belonging to class A that are related to the same ob-
ject of class B. The relationship is established by a
path that corresponds with a given schema undirected
path. The co-occurrence operator materializes a rela-
tionship inverse to the given path, then it applies con-
traction of the path plus its inverse. For example, this
operator can be used to identify pairs of diseases that
appear on the same patient.
3.2 Examples of Queries
Let us consider other examples of queries using suc-
cessive transformations on the graph. Based on Fig-
ure 1, consider the query Find pairs of diseases di-
agnosed by endocrinologist on patients previously di-
agnosed with diabetes. It can be calculated as fol-
lows: First, extract the subgraph including Patient,
disDescription (disease description) and phySpecialty
(physician specialty) classes, and the path between
them that represents a diagnosis (see Figures 4 and
5). Second, apply a class filter on the subgraph to
obtain patients having a Diabetes diagnosis. The
schema is maintained, and Figure 6 shows an ex-
ample of the answer instance graph. Third, apply a
class filter on the previous result to obtain all data
linked to physicians with a “endocrinology” specialty.
Again, the schema is maintained. Finally, apply a co-
occurrence operator to create a direct relationship be-
tween pairs of diseases diagnosed to the same patient.
The schema and instance result are shown in Figure
7.
Enterprise social media may provide information
about employees, their contacts, activities, interest,
and participations in work teams, as shown in Figure
8(a). When such a data source is integrated in the me-
diation system, the global schema includes part of its
information (Figure 8(b)). Consider the case where
we need ID and last name of patients who work at
the same building (same address) and have been diag-
nosed with “whooping cough” since October, 2013.
Based on the given schema, a value filter could be
used to obtain these data from patients related to an
encounter that took place after “2013/10/01”, along
with the diagnoses given in those encounters. Then, a
Figure 6: Class filtering result.
(a) Schema (b) Instance
Figure 7: Co-occurrence result.
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(a) Social Media Data Schema (b) Global Schema
Figure 8: Schema graph including a social media source.
second value filter is used to extract same data from
patients with a “whooping cough” diagnosis. Finally,
a path contraction operator allows to show a direct
relationship between patients and their work address.
The answer includes several subgraphs like the one
shown in Figure 9.
3.3 Operator Characteristics
In order to accomplish the conceptual language de-
sign features, the proposed graph transformation op-
erators have the following characteristics.
First, the input for the operators are specified by
the nodes and edges in the graph. This allows to hide
the notion of variable, since users manipulate only
objects, its attributes and relationships. This also al-
lows to avoid the construction of query patterns from
Figure 9: Query result.
scratch.
Second, the output schema is defined according
to the semantics of each operator. Then, the input of
the operators does not require the specification of the
structure (or pattern) of the output graph. Besides,
our operators graphical interface may visualize the
schema result before the execution of the query, in or-
der to allow users to better understand the result. The
operators are compositional since both the input and
the output are graphs.
Third, the operators mix the concept of subgraph
and pattern matching. Subgraphs allow to select
objects with incomplete information, while pattern
matching is used to identify objects that exhibit spe-
cific characteristics.
Fourth, languages that offer direct transforma-
tions of the graph (Gyssens et al., 1990; Hidders and
Paredaens, 1993) usually provide basic operations for
adding and deleting nodes and edges, and abstrac-
tion (abstraction allows grouping nodes with common
characteristics (Gyssens et al., 1990)). In contrast, our
operators encapsulate several basic operations. This
characteristic facilitates the graphical interface func-
tionality with respect to the incremental query con-
struction and the capacity to go forward and backward
during the query formulation. Besides, this character-
istic opens optimization opportunities.
Fifth, the operators could be executed generat-
ing the corresponding queries in other languages as
SPARQL (Harris and Seaborne, 2013) or GraphLog
(Consens and Mendelzon, 1990), or can be imple-
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Figure 10: DIG System Architecture.
mented directly in a query engine.
4 DIG SYSTEM
We implemented DIG, Data Integration using Graphs,
as a proof of concept for our proposal. DIG follows
a mediation approach (Figure 10). The mediator uses
a graph data model to represent the data available in
several heterogeneous data sources. Each data source
has its own data model and query language. In DIG
their database schema is also represented by a local
graph. DIG uses a GAV (Global As a View) approach
to map the global graph with the local ones. The user
interface captures the queries and express them by
means of the proposed operators. The mediator gen-
erates subqueries in SPARQL (Harris and Seaborne,
2013), which are sent to each data source for exe-
cution. Data sources which cannot be accessed by a
SPARQL query require a wrapper.
A set of metadata associated to wrappers and data
sources is a distinguish component of DIG. The in-
clusion of metadata responds to a feature frequently
presented in patients medical data in which is com-
mon to find unstructured data. As examples, we find
free description texts referring the patient condition,
or medical images. In this case, metadata is composed
of semantic descriptors (i.e. concepts of one or sev-
eral ontologies) associated to unstructured attributes.
The DIG prototype has been implemented in Java.
The mediator uses Neo4j
2
to manage the graph
database schema. A wrapper to access a DICOM
3
repository has also been developed. Metadata is man-
aged in RDF repositories. In particular, DICOM im-
ages are annotated with SMITag (L
´
opez et al., 2012).
2
http://www.neo4j.org/
3
http://medical.nema.org/standard.html
SMITag allows to select regions of interest (ROI) in
the images and annotate them with concepts belong-
ing to multiple ontologies (i.e. ICD-10, RadLex,
FMA, and ontologies in the Bioportal repository).
These annotations are stored in a Jena triple store. Ac-
cess to relational databases will be done by the use
of a SPARQL endpoint, such as DARQ (Quilitz and
Leser, 2008) or fedX (Schwarte et al., 2011).
5 RELATED WORK
In order to facilitate the access to graph based data,
several query languages have been proposed (Gyssens
et al., 1990; Consens and Mendelzon, 1990; Blau
et al., 2002; Chau et al., 2008; San Mart
´
ın et al.,
2011). Also, since RDF and OWL models are nat-
urally represented with graphs, we consider visual
query languages and graphical interfaces proposed
to retrieve RDF or OWL data, (Catarci et al., 2003;
Smart et al., 2008; Groppe et al., 2011). All of
them use graph patterns to specify the query and
their graphical interface —when it is described— ask
users to construct the pattern. Among its distinctive
characteristics, we highlight the ones more related to
our work: GOOD (Gyssens et al., 1990) makes use
of the database schema to define the graph patterns
and propose ve operators to transform a graph. In
GraphLog (Consens and Mendelzon, 1990), NITE-
LIGHT (Smart et al., 2008) and Gruff
4
the nodes are
labeled with variables, besides in GraphLog (Consens
and Mendelzon, 1990) the edges are labeled with reg-
ular expressions. Both notions, variables and regular
expressions, are unintuitive. An SNQL (San Mart
´
ın
et al., 2011) query is defined by two patterns, an ex-
traction and a construction pattern. The last one de-
fines the output graph. NITELIGHT (Smart et al.,
2008) proposes graphical notation to represent the el-
ements of a triple pattern. Most of these proposals
allow to place boolean conditions on the attribute val-
ues and global constraints in the edges. Users have to
mark out in some way the output variables.
Regarding graph transformations, SPARQL (Har-
ris and Seaborne, 2013), GraphLog (Consens and
Mendelzon, 1990), the language for GOOD (Gyssens
et al., 1990) and SNQL (San Mart
´
ın et al., 2011) are
languages that allow to have a graph as query output.
However, only GMOD and GOOD are based on direct
graph transformations, in the sense that they do not
require the specification of two patterns, one for se-
lection and the other for output construction. GOOD
has operators for abstraction and for the addition and
4
http://www.franz.com/agraph/gruff/
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349
deletion of nodes and edges. Since these are basic
operators, a query is expressed by long and complex
patterns. GMOD provides a unique operation that in-
cludes three patterns: selection, addition, and dele-
tion patterns. Addition patterns modify the database
schema. In contrast, we propose operations that en-
capsulate several basic operations (addition of nodes
and edges), offering a higher level of abstraction.
6 CONCLUSIONS AND FUTURE
RESEARCH
This paper reports work to improve data exploration
in heterogeneous data sources. We consider that join
querying of health related data and social informa-
tion can be helpful in understanding patient situa-
tions. Considering the characteristics of such sources,
we use a conceptual data model, GDM, a graph data
model, at the mediator level, and propose a set of op-
erators to query data by transforming the graph. The
operators are proposed to support a conceptual query
language (with a graphical interface) intended to al-
low end users, medical domain experts, to retrieve
data from the heterogeneous sources.
We followed a design approach in which opera-
tors emerge from the desired interface features. We
exploit a global graph schema to help users in ex-
pressing and incrementally refine their queries. We
introduced high-level graph transformation operators
which allow expressive querying.
A first version of the DIG system uses Neo4J
at the mediation level. The mediator process im-
plements subgraph extraction and value filter opera-
tors and generates subqueries in SPARQL (Harris and
Seaborne, 2013). Class filter and path contraction
operators do not generate subqueries, because their
processing will be based in a subgraph extraction re-
sults. The completion of the prototype and perfor-
mance evaluation is future work.
Research perspectives mainly concern optimiza-
tion and visualization issues. Optimization of the
distributed execution plan for graph exploration and,
visualization to provide adequate representation of
queries and data graphs to be well accepted by end-
users.
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