INTEGRATION OF DATA SOURCES FOR PLANT GENOMICS

P. Larmande, C. Tranchant-Dubreuil, L. Regnier, I. Mougenot, T. Libourel

CIRAD, IRD, CINES, LIRMM, CNRS

UMR PIA, TA 40/03, av Agropolis Montpellier cedex 5, 34389, France

Keywords:

Plant genomics, interoperability, integration, mediator.

Abstract:

The study of the function of genes, or functional genomics, is today one of the most active disciplines in the life

sciences and requires effective integration and processing of related information. Today’s biologist has access

to bioinformatics resources to help him in his experimental research. In genomics, several tens of public data

sources can be of interest to him, each source contributing a part of the useful information. The difﬁculty lies

in the integration of this information, often semantically inconsistent or expressing differing viewpoints, and,

very often, only available in heterogenous formats. In this context, informatics has a role to play in the design

of systems that are ﬂexible and adaptable to signiﬁcant changes in biological data and formats. It is within

this framework that this paper presents the design and implementation of an integrated environment strongly

supported by knowledge-representation and problem-solving tools.

1 INTRODUCTION

The study of the function of genes, or functional ge-

nomics, is today one of the most active disciplines

in the life sciences. Researchers in the domain have

to manage a constant ﬂow of voluminous information

originating from:

• experimental data,

• data that is structured or semi-structured according

to pre-existing adapted schemas (databases),

• analysis results,

• annotations,

• output from models, etc.

For example, research into mutations in an organism

is one of the study techniques of functional genomics.

To identify a mutation in a gene and the consequences

it can lead to, the biologist researcher has to consult

and compare several information sources such as bi-

ological sequencing data obtained from public or pri-

vate resources. He has also to compare experimen-

tal data and data that has undergone diverse proce-

dures to be able to reﬁne and perfect his analyses.

Functional genomics is a research subject that there-

fore relies on several tools, expertise and resources to

process and produce information on the function of

genes. To this end, access to different necessary re-

sources and services is imperative. However, there

exist few integrating solutions for plant genomics and

this lack is as much felt here as it is within the bio-

medical community, whose situation is very similar

(Davidson et al., 1995).

One has to admit that the difﬁculties are many. To

identify, sort and annotate sources is a task that is be-

coming more and more difﬁcult. From a biological

point of view, there is need (i) to identify the relevant

sources for an analysis from a catalogue that does not

stop growing in size (Galperin, 2004), (ii) to confer a

degree of conﬁdence to a source and to possibly anno-

tate it, (iii) to keep track of regular updates and to pos-

sibly rerun one’s own analyses. From an informatics

point of view, one is faced with a diversity of formats

because, depending on the need and the concerned ex-

periments, the biological sources can have very het-

erogeneous structures. For example, data is often in

a ﬂat ﬁle (e.g., Format GenBank, EMBL, ASN1) but

could also be in an XML ﬁle or in the form of tabu-

lated data. The structures of the sources also undergo

changes and can present variations.

Any attempt to integrate diverse data, procedures, ex-

pertise and resources leads to problems of syntactic

and semantic interoperabilities in the informatics do-

main. To these problems must be added the factor

that this information is often sensitive (even conﬁden-

tial) and highly variable and subject to change. The

goal of the present work is to present an integrated

environment for knowledge representation that per-

mits interoperability between different data sources

by overcoming problems of heterogeneity . The in-

314

Larmande P., Tranchant-Dubreuil C., Regnier L., Mougenot I. and Libourel T. (2006).

INTEGRATION OF DATA SOURCES FOR PLANT GENOMICS.

In Proceedings of the Eighth International Conference on Enterprise Information Systems - DISI, pages 314-318

DOI: 10.5220/0002455103140318

 SciTePress

tegration of data sources can be approached from dif-

ferent angles, each with its own advantages and draw-

backs (Karp, 2003); we present a brief state of the art

in the following section 2. Section 3 will be dedicated

to an operational mediation system: Le Select. In the

rest of the article, we will show how our exploratory

approach is based on the contextualization of this sys-

tem for use in the plant genomics domain.

2 STATE OF THE ART

The integration of heterogeneous data is a question

that has occupied the information-systems scientiﬁc

community for many years now. And the commu-

nity has responded in many ways with various solu-

tions. Within the conﬁnes of the database domain, the

approach has gone from the distributed perspective

to the federated databases perspective to the media-

tion perspective. The arrival of Web technologies has

also strongly inﬂuenced this concept of integration by

offering ’light’ integration solutions as well as more

complex solutions based on integrators of Web ser-

vices. Within the genomics context, the solution that

is the most handy is the light integration of sources

in their original formats. References cross-coded us-

ing hypertext links are now found in a large number

of biological sources (e.g., GenBank, SWISS-PROT)

and searching them by browsing allows fast access to

information.

Other, more complex, solutions integrate the sources

by offering a common interface and query language to

users. Several such systems have been implemented,

for example, SRS

, the Entrez

system developed at

NCBI, DBGet

in Japan or even the French ACNUC

system (Gouy et al., 1985). In all these examples,

the systems are analogous to huge access catalogues:

the user selects the sources he want to query from

amongst those already indexed.

Recently, proposals for stronger integration have been

put forward. Architectures that allow transparent ac-

cess to the user and the location of data sources by

integrating their schemas have been proposed. Sev-

eral solutions have emerged:

• non-materialized integration offered by mediation

architectures, most often designed around a single

representation model and a high-level query lan-

guage,

• ’materialized’ integration requiring the pre-

integration of the various data in data warehouses

whose schema is designed using the schemas of the

Sequence Retrieval System, www.infobiogen.fr/srs/

www.ncbi.nlm.nih.gov/Entrez/

www.genome.ad.jp/dbget/

pbil.univ-lyon1.fr/search/query.html

concerned sources and depending on the analyses

to be conducted.

In mediation systems, a mediator module manages ac-

cess to distributed sources. It breaks down the user’s

global query into elementary queries, assigning each

to a distributed source that can respond to it. It then

recomposes the response to the global query from re-

sponses to the elementary queries. Adaptors or ’wrap-

pers’ interpose themselves between each source and

the mediator. Systems developed according to this

architecture include K2/Kleisli, DiscoveryLink and

TAMBIS (Eckman et al., 2001). Access to biological

resources by these systems however remains limited

and does not fully satisfy scientists’ requirements.

On the other hand, in the materialized approach,

the data warehouses import locally the sources in

one same schema and the user’s global request is

processed directly. In France, in the plant genomics

domain, the bioinformatics platform G

enoplante-

info

uses this approach for integration (Samson et al.,

2003; D. Samson et al, 2005; A. Duclert et al, 2005).

This type of solution permits cleanup and annotations

of imported data (Susan B. Davidson et al, 2001).

Thanks to the rapid evolution of Web technologies,

applications can now develop Web-based services (re-

sponding, for example, to a speciﬁc query). These

Web services have the advantage of homogenizing the

data exchange format, thus facilitating interaction be-

tween applications. Moreover, they can be included

within a repository. This is the case with the Bio-

Moby repository project which implements a service

for locating resources based on a service ontology (P.

Lord et al, 2004). Another project, myGRID, helps

the user locate a sequence of services appropriate for

any one analysis.

In the following sections, we will describe the media-

tion system that we have used and the stages involved

in integrating the sources.

3 LE SELECT

Le Select is an integration system of type mediator

(Manolescu et al., 2002; Cavalcanti et al., 2002) de-

veloped at INRIA at Rocquencourt within the frame-

work of the Caravel project

. This system provides

uniform access for integrating, publishing and interro-

gating distributed heterogeneous sources by support-

ing several data types: structured and semi-structured

data, ﬂat ﬁles, images, etc. It also handles programs

that use this data in the same manner. Le Select is a

mediator for access to distributed and heterogeneous

resources. A Le Select server authorizes the publica-

genoplante-info.infobiogen.fr

http://www-caravel.inria.fr/LeSelect/

INTEGRATION OF DATA SOURCES FOR PLANT GENOMICS

315

tion of a resource (data or program), while preserv-

ing the sources’ independence and format. It allows a

certain amount of ﬂexibility of use since the resources

can be published incrementally in the system.

Before a resource can be published, an adaptor (wrap-

per) speciﬁc to the resource has to be designed (Fig.

1.). The creation of wrappers is the responsibility

of the administrator of the concerned resource but a

wrapper library dedicated to standard resource types

is slowly growing. Wrappers play multiple roles:

as translators between the mediator and the resource

by offering a homogenous representation based on

the relational model and as exporters of statistical

metadata on the resources they publish, such as the

resource’s availabilty, the query execution time, the

ability to execute a query (ability to join two resources

or to test them for equality).

As for the mediator, it offers a pivot language for

querying (close to the SQL standard). It includes a

query management and optimization program which

uses meta-information supplied by the wrappers to es-

tablish the execution plan of every query. At a general

level, it breaks down the global query into elementary

queries, assigning each elementary query to a source

that can respond to it, submits the queries, then recon-

structs the complete response from the elementary re-

sponses.

Finally, since the Le Select server is installed on a

Web server, it possesses an interface which can be ac-

cessed by a Web browser. Published resources are

thus accessible by simple browsing (access by links)

or by the intermediary of SQL queries.

The fact that Le Select communicates using SQL is

of great interest because existing applications can be

reused to connect to sources. For example, an applica-

tion can be connected to the server network and com-

municate with a mediator via a JDBC bridge (Fig. 1).

At the same time, several servers can be installed

within the network (specially P2P peer-to-peer net-

works) and can co-operate to provide access to data

and services.

Figure 1: Diversity of resources that can be published.

3.1 Contextualization of Le Select

In our context, the exchange and distribution of

information for the purposes of sharing it is of the

utmost importance. Not only does data exchange

allow the validation of data by other scientists

running identical analyses, but data sharing also leads

to generation of new data. Within the framework of a

functional genomics project whose goal is to generate

a collection of rice insertion lines (Oryza sativa)

(Sallaud et al., 2004), a database has been created to

store experimental data: Oryza Tag Line (OTL)

.In

addition, another database, Rice BRC-db (BRC-db),

has been developed for consolidating information on

genetic and genomic rice resources.

The short term objective is to bring closer together

the correlated information in these two databases,

indeed to migrate part of the information from OTL

to BRC-db, within the strict condition that the two

databases should remain independent (DBMS and

interface). In such a scenario, using a mediator

approach seemed of interest to us.

Before publishing the two information systems,

we designed a virtual global conceptual model to

solve the problems of semantic heterogeneity and

to deﬁne correspondences between the entities. We

encountered, for example, a case of homonymy

(Karp, 1995): the class ’plant’. In the OTL model,

this referred to ’mutant’ plants whereas in BRC-db

they were ’wild’. In this case, a new ’plant’ class

was created in the global schema to correspond to

the ’mutant’ individuals. To help limit problems of

this nature, we referred to shared deﬁnitions within

the domain: the ontologies (Gruber, 1993). The

ones that are most commonly used in plant genomics

are Gene Ontology (M.A. Harris et al, 2004) and

Plant Ontology (The Plant OntologyTM Consortium,

2002).

Figure 2 shows the publication of OTL via Le Se-

lect’s interface. As can be seen, the page is divided

into four parts. On the left are displayed the wrappers

corresponding to the published sources. At the top,

one can select the types of wrappers (wrappers & ta-

bles, views and programs). In the central part of the

screen is displayed the data corresponding to a query

posed in the Query area at the bottom. In the example

shown, data is displayed from the TRAIT

VIEW ta-

ble corresponding to the phenotypical characters ob-

served in the collection of mutants. Data is directly

extracted from the database, the table structure is not

modiﬁed. The wrapper created for publishing this re-

source uses Java drivers (JDBC).

As we wanted to bring together data from the two

databases in conformance with the studied virtual

http://genoplante-info.infobiogen.fr/OryzaTagLine

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Figure 2: Oryza Tag Line published by Le Select.

global conceptual model, we would have had to trans-

form the schema of the sources before publication.

But Le Select also offers a mechanism for viewing

published sources. For the mediator, the views are

also wrappers that execute a query on an already-

published source. It is this feature that we have used

by creating views of tables that have to be trans-

formed. This establishes, in a simple manner, the cor-

respondences between the OTL and BRC-db database

schemas.

4 CONCLUSION

The information systems that researchers in func-

tional genomics have to put together to fulﬁl their re-

quirements need to preserve the resources’ indepen-

dence and, very often, the conﬁdentiality of at least a

part of their information.

The mediation solution is thus of relevance; it con-

serves the resources’ independence while allowing

their distribution and it provides uniform access to in-

formation. In fact, even though the materialized ap-

proach is also a robust one, it does not handle well the

changing character of genomic sources. Unavoidable

changes in both systems, OTL and BRC-db, would

entail numerous changes to the schema of the data

warehouse and, subsequently, to the procedures for

loading the underlying data.

The solution implemented using Le Select takes

changes in the Oryza Tag Line schema in stride; they

are incorporated directly by the mediator. And, by

using the intermediary of views, the establishment of

new correspondences with BRC-db is also relatively

easy. We can thus think that the approach we propose

is transferable to other functional genomics applica-

tions. On the longer term, aside from incorporating

the integration of programs, the systems should allow

researchers to conduct online analyses by authorizing

procedures on the data (access to both types of re-

sources having been made transparent).

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