2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)
Semantic Data Integration Techniques for
Transforming Big Biomedical Data into Actionable
Knowledge
Maria-Esther Vidal
TIB Leibniz Information Centre
for Science and Technology, Germany
maria.vidal@tib.eu
Abstract—FAIR principles and the Open Data initiatives have
motivated the publication of large volumes of data. Specifically,
in the biomedical domain, the size of the data has increased
exponentially in the last decade, and with the advances in the
technologies to collect and generate data, a faster growth rate is
expected for the next years. The available collections of data are
characterized by the dominant dimensions of big data, i.e., they
are not only large in volume, but they can be also heterogeneous
and present quality issues. These data complexity problems
impact on the typical tasks of data management, and particularly,
in the task of integrating big biomedical data sources. We tackle
the problem of big data integration and present a knowledge-
driven framework able to extract and integrate data collected
from structured and unstructured data sources. The proposed
framework resorts to Natural Language Processing techniques
to extract knowledge from unstructured data and short text.
Furthermore, ontologies and controlled vocabularies, e.g., UMLS,
are utilized to annotate the extracted entities and relations with
terms from the ontology or controlled vocabulary. The annotated
data is integrated into a knowledge graph. A unified schema is
used to describe the meaning of the integrated data as well as the
main properties and relations. As proof of concept, we show the
results of applying the proposed framework to integrate clinical
records from lung cancer patients with data extracted from open
data sources like Drugbank and PubMed. The created knowledge
graph enables the discovery of interactions between drugs in the
treatments prescribed to lung cancer patients.
I. I NTRODUCTION
The amount of publicly available data has experience a
significant growth as the result of initiatives that encourage
the publication of open data following the FAIR principles
[18]. The biomedical domain is an exemplar field where the
number and size of data sources have faced an exponential
increase in the last decade and is projected to grow very
rapidly in the next decade, reaching more than one Zetta bytes
per year by 2025 [17]. In this era, transforming Big Data into
actionable knowledge demands novel and scalable tools for
enabling not only data ingestion and curation, but also for
efficient large-scale knowledge extraction, management, and
analysis. Extracting knowledge from data requires the integra-
tion of data collected from heterogeneous data sources which
can make available the data in structured and unstructured
This work has been supported by the European Union’s Horizon 2020
Research and Innovation Program for the project iASiS with grant agreement
No 727658.
2372-9198/19/$31.00 ©2019 IEEE
DOI 10.1109/CBMS.2019.00116
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Samaneh Jozashoori, Ahmad Sakor
L3S Institute,
Leibniz University of Hannover, Germany
{jozashoori,sakor}@l3s.de
formats. In fact, even structured data sources may comprise
a large number of attributes that include notes, comments,
or descriptions, which encode valuable knowledge about the
entities published by the data source. The integration of the
knowledge encoded in unstructured data sources or attributes
requires the implementation of natural language techniques
able to effectively recognize relevant entities and annotate
them with terms from controlled vocabularies (e.g., SemRep
[14], MetaMap1 , and Sophia [4] ) or from existing knowledge
graphs (e.g., DBpedia Spotlight [10]). Moreover, the problem
of data integration has been also extensively treated in the
literature and several approaches have been proposed to in-
tegrate structured data (e.g., KARMA [7], LDIF [1], LIMES
[13], MINTE [2], Sieve [11], Silk [6], and RapidMiner LOD
Extension [15]). However, none of these approaches is able to
manage the integration of structured and unstructured data.
Our Research Goal: we aim at defining a computational
framework able to exploit knowledge from annotations and
semantic descriptions, and integrate equivalent entities into a
knowledge graph. Formally, the problem of data integration
can be framed as follows. Given a collection of data sets such
as unstructured text or structured databases, the problem of
semantic data integration is to identify if two entities in the
collection of datasets match or do not match the same real-
world entity. An entity in a dataset corresponds to real-world
concept and its properties can be described in structured or
unstructured way. Once equivalent entities have been matched,
different fusion policies need to be performed for merging
them into a single entity [2]. Considering the wide nature of
entities, the state of the art has focused on methods that reduce
manual work and maximize accuracy and precision.
Approach: We propose an approach that relies on both Natural
Language Processing techniques for extracting entities from
unstructured text and ontologies to decide if two or more
entites match to the same real-world entity. As proof of
concept, our annotation techniques utilized UMLS and DB-
pedia as background knowledge. Additionally, the framework
resorts to a knowledge graph to identify when two entities are
connected by relations that indicate that they are equivalent
(e.g., owl:sameAs). We have evaluated our approach on
1 https://metamap.nlm.nih.gov/
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(a) Clinical Records (b) Drug Adverse Events (c) Potential Interactions

Fig. 1: Motivating Example. Heterogeneous sources publishing knowledge about the conditions of a patient and the potential
adverse events. (a) Unstructured clinical records describe a patient medical conditions. (b) Drug interactions and side effects
are the potential adverse events in a treatment. (c) Various biomedical repositories encode knowledge about the potential
interactions between drugs. The integration of all these knowledge is required to determine the effectiveness of a treatment.

heterogeneous datasets collected by the partners of iASiS

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knowledge-driven approach. We also outline the most impor-
tant results that we have obtained so far.
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lows: Section II motivates the data integration problem over 
biomedical data sets. Section III describes our knowledge-
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Section IV concludes and give insights for future work.

II. M OTIVATING E XAMPLE

We motivate the problem of data integration by presenting
a set of heterogeneous biomedical data sources (Figure 1).
The health conditions of a lung patient are described in a
clinical note; this note corresponds to unstructured data that
encodes valuable knowledge for understanding the diagnostic,
comorbidities, familial antecedents, and treatments of the
patient. Albeit informative, the clinical notes are presented
in a form that cannot be directly processed during data
integration. Contrary, Natural Language Processing techniques
are required in order to extract relevant entities that describe
the principal characteristics of a patient– for example, words
highlighted in bold in the text in Figure 1a. Then, as shown
in Figure 1b, adverse events or side effects may occur as a
consequence of interactions among of prescribed drugs. How-
ever, the information about interactions is usually represented
in unstructured formats, e.g., as short text in DrugBank or
in scientific publications from PubMed (See Figure 1c). The
problem is how to extract all the relevant data from the myriad
data sources, e.g., clinical notes, Drugbank, and PubMed, and
2 http://project-iasis.eu/
Fig. 2: Knowledge-driven Framework. Data is collected
from structured and unstructured data sources. (1) Knowledge
extraction methods transform unstructured data and describe
the extracted facts using ontologies. (2) Semantic data in-
tegration rely on annotations and semantic descriptions to
integrate the data into a knowledge graph. (3) Federated query
processing enables the exploration of the knowledge graph. (4)
Knowledge discovery facilitates the uncovering of patterns.
integrate the extracted entities in a way that useful insights
can be discovered, e.g., drug interactions and side effects.
III. O UR A PPROACH
We present a knowledge-driven framework that resorts to a
knowledge graph for describing and integrating data collected
from heterogeneous data sources. A knowledge graph corre-
sponds to a data structure that represents data, knowledge, and
actionable insights using a graph data model. Figure 2 presents

564

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Fig. 3: An Example for KG Creation. Entity and predicate linking extracts relevant facts from clinical notes and short text
describing drug interactions. Mapping rules and semantic enrichment create entities for (1) a patient, and (2) drug interactions.
an overview of the proposed knowledge-driven framework.
The framework comprises four components: 1) Knowledge
extraction; 2) Semantic data integration; 3) Exploration and
traversal; 4) Knowledge discovery. In the first component, facts
from unstructured data sources are extracted and represented
in the form of triples, i.e., subject, predicates, and objects [12].
Ontologies and controlled vocabularies are used to guide the
extraction process as well as to annotate the extracted facts
with the terms, e.g., terms from UMLS are utilized to represent
medical concepts and their meaning in a standard way. Once
relevant entities are extracted and annotated with ontologies,
semantic data integration methods are utilized to decide when
two entities are equivalent entities based on their annotations
and to integrate these entities in the knowledge graph. Figure
3 depicts an example of the steps followed for knowledge
extraction and knowledge graph creation. First, NLP methods
(e.g., Menasalvas et al. [9] and Sakor et al. [16]) able to solve
the problem of named entity recognition are used to extract rel-
evant entities from unstructured clinical notes and to annotate
the extracted concepts with terms from UMLS. The annotated
entities are semantically described using a unified schema and
represented as triples by the means of executing a set of
mappings rules. These mappings rules are expressed using the
RDF Mapping Language (RML) [3] and allow for the creation
of entities and all their properties in the knowledge graph (e.g.,
a patient entity in Figure 3). Additionally, short texts included
as attributes in structured data sources, e.g., in the description
of the drug interactions in DrugBank, are processed in order
to perform entity and predicate linking. Then, mapping rules
are also executed to represent as triples the extracted entities
and predicates. Step 2 in Figure 3 illustrates the portion of
the knowledge graph that represents the interactions between
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drugs Carboplatin and Fingolimod. The DrugBank identifiers
are utilized in the knowledge graph to identify the drugs
and their relationship. Moreover, equivalences between terms
in different vocabularies are maintained in the knowledge
graph; Figure 4 illustrates an example of the portion of the
knowledge graph that maintains the equivalences between the
identifiers of DrugBank and UMLS for the drugs Carboplatin
and Fingolimod (step 3 in the figure). These alignments are
utilized during semantic data integration to create the portion
of the knowledge graph that relates the drugs identifies with
the identifiers from UMLS (step 4 in Figure 4). This rewriting
allows for linking the drugs and their interactions with the
drugs that have been prescribed to a patient (step 5 in Figure
4). Thus, the identifiers from UMLS are used not only to
annotate all the entities in the knowledge graph, but also
to match equivalent entities and integrate them. Once the
knowledge graph is created, techniques by Sakor et al. [16]
are used to link entities in the knowledge graph to entities
in other knowledge graphs (e.g., DBpedia [8] and Bio2RDF
[5]). This framework has been used in the context of the EU
H2020 project iASiS in order to transform biomedical data into
actionable knowledge for the support of precision medicine.
The current version of the iASiS knowledge graph has 1,3
Billion triples, 46 RDF classes, in average 6.98 relations per
entity, and each class is connected in average to 2.87 classes.
Classes include drugs, publications, lung cancer patients, side
effects, and drug interactions. In addition, each patient is
associated (in average) with four drugs, 20 side effects, 42
scientific publications, and 2 pairs of drug interactions. Thus,
the clinicians can traverse the knowledge graph and identify
not only potential drug interactions, but also the scientific
publications that support their diagnostics and treatments.
565
 
Fig. 4: An Example for Data Integration. Alignments between drug identifiers in UMLS and DrugBank enable the integration
of drug interactions (3 and 4). A portion of graph representing a patient and the interactions of his prescribed drugs (5).
IV. C ONCLUSIONS AND F UTURE W ORK
We present a knowledge-driven framework able to integrate
heterogeneous data into a knowledge graph. In the knowledge
graph, the integrated data is described in terms of a unified
schema and ontologies. Alignments between terms enable the
matching and integration of equivalent entities. The framework
is part of the iASiS platform, and clinicians are starting the
process of evaluation of outcomes. In the future, we plan to
develop curation techniques to allow clinicians to evaluate the
knowledge represented in the knowledge graph.
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