=Paper=
{{Paper
|id=Vol-1741/paos2016_paper5
|storemode=property
|title=Data Integration Framework of Pharmacology Databases Using Ontology
|pdfUrl=https://ceur-ws.org/Vol-1741/paos2016_paper5.pdf
|volume=Vol-1741
|authors=Phimphan Thipphayasaeng,Poonpong Boonbrahm,Marut Buranarach,Anunchai Assawamakin
|dblpUrl=https://dblp.org/rec/conf/jist/ThipphayasaengB16
}}
==Data Integration Framework of Pharmacology Databases Using Ontology==
https://ceur-ws.org/Vol-1741/paos2016_paper5.pdf
Data Integration Framework of Pharmacology Databases
Using Ontology
Phimphan Thipphayasaeng 1, Poonpong Boonbrahm 1, Marut Buranarach2
and Anunchai Assawamakin3
1 School of Informatics, Walailak University, NakornsiThammarat, Thailand
2 National Electronics and Computer Technology Center (NECTEC), Pathumthani, Thailand
3Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
Abstract. This paper presents linked data of pharmacology domain generated
with ontology as central schema. To link data from several formats, data are
transformed into database format, and they are mapped to ontology. The ontology
is developed with concepts provided in the dataset. Mainly, the developed ontol-
ogy contains a concept of drug, disease, genetic and drug-gene interaction with
their details. The ontology is used as central schema to link concepts together;
thus, linked data are created. Within the linked data, we found three types of
links, i.e. addition of instances, addition of attributes and changing of variable
data field to a link to another table. In this paper, actual scenarios of the found
links with exemplified data are explained.
Keywords: Linked data; Ontology; Pharmacological data; Data integration
1 Introduction
In pharmacology field, data of drugs, their usage, study, and description have been dig-
italized and provided on many sites. Those data give different characteristics of drugs;
hence, a schema of the databases was designed specifically for their purpose. Addition-
ally, these data are live data that have regularly been updated for experts to reference.
These data sources are open to use and are important for experts in the field to consult
for a case result and lengthen their researches.
These databases apparently contain a large amount of data, and their schema is com-
plex. Users are needed to understand database schema and have pharmacological back-
ground to read through the data. In fact, provided data have been gathered based on a
ground from where they are designed. Every database has its own strength and specified
to their locality. In usage, experts commonly require searching through many databases
to assure correctness and coverage of data, and they need to be aware of different ap-
pearance terms referring to a same concept or instance (synonymy) or a same term with
many definitions (polysemy).
To support users of the data, this work aims to link those open pharmaco-genetic
data together using Resource Description Framework (RDF) standard. RDF standard
[1] is often used as the metadata interchange format since its expression was designed
to represent as a model of information using a variety of syntax notations and data se-
rialization formats. This work proposes a method for interoperability between the da-
tasets from different formats and schema using Linked Data framework. Moreover, a
method for integration of data is designed to recognize an overlapping of data and ex-
tend range of data with other data sources. A complete data integration solution should
provide data influent to be trusted by within crosschecking from a variety of sources
since a volume of data will be increased and coverage of scope will be extended.
2 Background
Pharmacology is the study of drug action and effects of the drug on biological sys-
tems. Nowadays, available linked data were created and distributed as accessible data
for experts in the field. In this work, we review some of the well-known linked data in
pharmacology and summarized them as follows.
ChEMBL[2] provides chemical entities of biological activities against drug targets.
That could be used as a reference for drug researchers. DrugBank [3] gathers infor-
mation on drugs and their targets that include in drug target discovery, drug design,
drug screening or docking, interaction prediction, metabolism prediction and pharma-
ceutical education. Diseasome [4] provides a resource for biomedical researchers that
include disease-gene associations using network maps and understanding of the genetic
origins of disease. DisGeNET [5] representation knowledge in the molecular mecha-
nisms that combines detailed gene data with disease and calculate a score in order to
rank of these associations for support research in the biomedical science. The Linking
Open Drug Data project focuses on linking various sources of drug data to answer sci-
entific questions [6].
3 Methodology
This work aims to combine provided pharmacological data from several sources into
linked information. Ontology is chosen as an intermediate schema to relate data into
uniform concepts. The method involves with four processes as summarized in Fig. 1.
Fig. 1. An overview of Data Integration of Pharmacology Databases Using Ontology
3.1 Data preparation
In this paper, five pharmacological datasets, i.e. KEGG Disease [7, 8, 9], ThaiSNP
[10], Comparative Toxicogenomics Database [11], Drugbank [3] and MeSH [12], are
chosen as input data for integration. The details of the dataset are given in Table 1.
Table 1. Details of the chosen pharmacological datasets
Dataset name About Format Concepts
KEGG Dis- disease entry knowledge on genetic relational Drug,
ease and other relevant database Disease
ThaiSNPs Single Nucleotide Polymorphisms relational Gene,
(SNPs) and Copy Number Variations database SNPs
(CNVs) in genetic of Thai population
CTD chemical–gene/protein interactions, CSV, TSV, Gene,
chemical–disease and gene–disease re- XML Disease
lationships
Drugbank bioinformatics and cheminformatics XML Drug,
resource including detailed drug data Pharmacology
with their drug target
MeSH mapping drug-disease relationships in XML Drug,
research Disease
The commonness of data in these dataset in Table 1 is about drug, gene, and disease.
All datasets represent in several data formats such as database and XML. Please be
noted that these datasets contain some data tags involving in data management and re-
ferring, such as sorting key and ID for their related application, in which we will ignore
in data integration since they are not semantically important. To combine these data
together, we need to uniform data format to database format. These databases will be
mapped to ontology in later process.
3.2 Ontology design
Since the core of the aforementioned data is about drug, we decide to initiate with drug
concept as a main class and expand relations from this concept. Our ontology was de-
signed on and created by Hozo ontology editor [13] following the development guide-
line by Mizucuchi [14].
Firstly, terms in these datasets were gathered from the table heads and fields. With
the gathered terms, concepts of terms were recognized and relations to link concepts
were decided. Relations of concepts were decided based on following criteria:
is-a relation : forming superclass-subclass relation in which the concepts must
be the same kind, and all properties of superclass inherit to its subclass
object property : forming belonging relation of two concepts in which repre-
senting of a part in another concept
data property : forming concept-data type relation to signify a concept con-
taining a value such as number or string
instance of : providing a relation to link a concept to real data or instance, this
relation is to link ontology class to real data in database
Regarding to data in dataset, our ontology is designed to gather all the concepts. The
major concepts are Drug, Gene, Disease, interaction and SNP, and their properties are
the fields of their dataset. Some parts of the ontology are demonstrated in Fig. 2.
Fig. 2. Some parts of the designed ontology using Hozo Editor
3.3 Schema mapping
With ontology as a schema to gather and relate concepts from the datasets, the ontology
can be mapped to all data in the datasets. An ontology mapping from Ontology Appli-
cation Management (OAM) [15] tool is chosen to help us in mapping. The mapping of
ontology class and dataset field was exemplified in Table 2.
Table 2. Examples of an ontology-data mapping table
Ontology Data Field
property DB1 DB2 DB3 DB4
Drug name Drug name - - name
Drug Chemical Structure Structure - - chemical
structure
Drug Indication Indication - - indication
Genotype Gene gene genotype -
Disease Description - indication description -
3.4 Data Linking
To combine these data, we have to focus on commonness of data and concepts. In this
work, we found three types of integration of different dataset as 1. Same head concept,
different data, 2. Same head concept, different properties and 3. One of the concept is
a property of another.
For the first integration, this results in gaining more instances. This helps in expand-
ing a variety of data. It should benefit users in giving more data to look through. The
second integration is about linking more data attributes for the same data. This widens
more aspects of data and includes more relevant information to the concepts. This type
gives users for more broad view of data properties. Last, the integration of different
tables. This is to give in-depth details of the information since the information will be
added with information of whole table. This is a change of single value or text of one
attribute to more details. The three types of integration are summarized in Table 3.
Table 3. A summary of data linking from different datasets
Data Integration Type Linking Ontology Representation
1 Same head concept, Adding of instance roll none
different data
2 Same head concept, Adding of attributes to data More properties of a concept
different properties table
3 one of the concept is a Changing from value re- Changing of attribute-of
property of another quired field to foreign key property to part-of property
for linking to another table
4 Usage Scenario
In this section, we demonstrate a case scenario of the data linking types to exemplify
actual cases with the dataset chosen for integration in this work.
The scenario is an integration of Drugbank and CTD. In these datasets, they have
common data about a drug. Both of these datasets are about drug. For Drugbank, given
data are relevant to drug chemical compound and affected organ. Pharmaceutical action
of drug, however, is mentioned in CTD. These attributes do not exist in another set, and
it is recognized as the second type mentioned in Table 3. With ontology mapped to
these data, we realize that the table is the same concept since they are both mapped to
the same ontology class although table labels are different. After integration, we ob-
tained a combination of more properties to widen more aspects of the same data.
5 Conclusion and Future Work
This paper presents a data integration of pharmacology data from several sources using
ontology as a central schema. Five datasets are gathered in which provides data about
drug, disease, gene and interaction. To integrate data, cleaning process and uniform of
data format are initiated. Ontology is created with concepts given in datasets and is
mapped to the data via OAM framework. With ontology mapped to data, data from
those five sources are linked with semantic. In this work, the linked data contain three
types of links that are addition of instances, addition of attributes and changing of var-
iable data field to a link to another table. In the future, we plan to include more relevant
dataset to link more pharmacology data. An automatic method to map data to ontology
class will be researched to reduce human burden and time consuming in mapping pro-
cess. Lastly, we will apply semantic search with the obtained linked data.
References
[1] Bruijn, J., Welty, C., RIF RDF and OWL Compatibility: available online at
https://www.w3.org/TR/2013/REC-rif-rdf-owl-20130205/
[2] Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings
J, Chen B and DJ Wild DJ.: The ChEMBL database as linked open data. Journal of
cheminformatics. 5(1), 1–12 (2013).
[3] Wishart, D., Knox, C., Guo, A., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z.,
Woolsey J.: DrugBank: a comprehensive resource for in silico drug discovery and explora-
tion. Nucleic Acids Res. 34, D668-D672 (2006).
[4] Wysocki K, Ritter L.: Diseasome: an approach to understanding gene-disease interactions.
Annu Rev Nurs Res. 29, 55–72 (2011).
[5] Piñero J, Queralt-Rosinach N, Bravo À, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F,
Furlong LI.: DisGeNET: a discovery platform for the dynamical exploration of human dis-
eases and their genes. The journal of biological Database and Curation. 2015, 1-17 (2015).
[6] Samwald M., Jentzsch A., Bouton C., Kallesøe CS., Willighagen E., Hajagos J., Marshall
MS., Prud'hommeaux E., Hassenzadeh O., Pichler E., Stephens S.: Linked open drug data for
pharmaceutical research and development. J Cheminform. 3, (2011).
[7] Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.: KEGG for represen-
tation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res.
38, D355-D360 (2010).
[8] Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.: KEGG as a refer-
ence resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
[9] Kanehisa, M. and Goto, S.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic
Acids Res. 28, 27-30 (2000).
[10] Hattirat, S., Ngamphiw, C., Assawamakin, A., Chan, J., and Tongsima, S.: Catalog of Ge-
netic Variations (SNPs and CNVs) and Analysis Tools for Thai Genetic Studies. Computa-
tional Systems-Biology and Bioinformatics. 115, 130-140 (2010).
[11] Davis, A., Grondin, C., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B.,
Wiegers, T, Mattingly, C.: The Comparative Toxicogenomics Database's 10th year anniver-
sary: Update 2015. Nucleic Acids Res. 43, D914-D920 (2015).
[12] Rogers, Frank B.: “Communications to the Editor.” Bulletin of the Medical Library Asso-
ciation. 70, 5131–5136 (1963).
[13] Hozo Ontology Editor: available online at http://www.hozo.jp
[14] Mizuguchi, R.: Tutorial on ontological engineering - part 1: Introduction to ontological en-
gineering. In: New Generation Computing. 21, 365–384 (2003).
[15] Buranarach, M., Thein, Y., Supnithi, T.: A Community-Driven Approach to Development
of an Ontology-Based Application Management Framework. Semantic Technology. 7774,
306–312 (2013).