=Paper=
{{Paper
|id=Vol-1546/poster_55
|storemode=property
|title=Exposing French Agronomic Resources as Linked Open Data
|pdfUrl=https://ceur-ws.org/Vol-1546/poster_55.pdf
|volume=Vol-1546
|authors=Aravind Venkatesan,Nordine El Hassouni,Florian Philippe,Cyril Pommier,Hadi Quesneville,Manuel Ruiz,Pierre Larmande
|dblpUrl=https://dblp.org/rec/conf/swat4ls/VenkatesanHPPQR15
}}
==Exposing French Agronomic Resources as Linked Open Data==
https://ceur-ws.org/Vol-1546/poster_55.pdf
Exposing French agronomic resources as Linked Open
Data
Aravind Venkatesan 1 , Nordine El Hassouni2 , Florian Phillipe3 , Cyril Pommier3 , Hadi
Quesneville3 , Manuel Ruiz12 , Pierre Larmande145
1
Institut de biologie Computationelle, M ontpellier, France
Aravind.Venkatesan@lirmm.fr
2
UM R AGAP, CIRAD, M ontpellier, France
{nordine.el_hassouni,manuel.ruiz}@cirad.fr
3
URGI, INRA, Versailles, France
{fphilippe,Cyril.pommier,hadi.quesneville}@versailles.inra.fr
4
UM R DIADE, IRD, M ontpellier, France
5
Equipe Zenith, INRIA et LIRM M , M ontpellier, France
pierre.larmande@ird.fr
Abstract. The advancements in empirical technologies has generated vast
amounts of heterogeneous data. This situation has created a need to integrate
the data to understand the system of interest in its entirety. Therefore, infor-
mation systems play a crucial role in managing these data, enabling the biolo-
gists in the extraction of new knowledge. The plant bioinformatics node of the
Institut Français de Bioinformatique (IFB) maintains public information sys-
tems that houses domain specific data. Currently, efforts are being taken to ex-
pose the IFB plant bioinformatics resources as Linked Open Data, utilising do-
main specific ontologies and metadata. Here, we present the overview and the
initial results of the project.
Keywords: Data integration, Data interoperability, Knowledge management,
Linked Data, RDF, Bioinformatics application, Agronomic research
1 Introduction
Agronomy is an overarching field that encompasses various research areas such as
genetics, plant molecular b iology, and agro-ecology. The last several decades has
seen the successful imp lementation of high-throughput technologies that have revolu-
tionised research in agronomy. These technological advancements have resulted in a
number of init iatives been taken to systematically store and share information over
the web. A mong others, the Institut Français de Bioinformatique (IFB) is a French-
ELIXIR node (http://www.elixir-europe.org/about/elixir-france) that is focused on
providing integrated services for the life science co mmunity. The plant research wing
of the IFB p latform prov ides access to a number of databases and tools distributed
across six regional bioin formatics portals. Data in these portals ranges fro m ‘o mics’ to
genetics (genetic markers, maps and phenotypes) for various crop species. The objec-
tive of the current effort is to develop RDF knowledge bases that integrates existing
domain specific ontologies and data fro m the respective regional portals, pro moting
data interoperability between the resources. To this end, we have developed the Ag-
ronomic Linked Data knowledge base (www.agrold.org) that is representative of the
data housed in the southern region portal o f France, the South Green Bioinfo rmatics
platform (SG) (http://www.southgreen.fr/).
2 AgroLD for SG resources
Currently, SG consists of 12 databases covering various plant species such as Banana,
Cocoa, Maize and Rice. AgroLD is being developed in phases to expose all of these
databases as Linked Data. Currently, Phase I of AgroLD includes data from:
1. Trop GeneDB (Hamelin et al. 2013), a database that hosts genetic, mo lecular and
phenotypic information on tropical crop species.
2. Ory GenesDB (Droc et al. 2006), a database that serves as a repository on function-
al genomics for rice.
3. Ory za Tag Line (Larmande et al. 2008), a database that contains sequence infor-
mat ion (Flan king Sequence Tags) that are based on molecu lar categorisation of
mutagen insertion sites for rice.
4. GreenPhylDB (Conte et al. 2008), provides sequence homology information for the
members of kingdom plantae.
Additionally, do main specific ontologies, ontology annotations, proteomics and
genomics informat ion fro m a variety of publically availab le data sources have been
integrated, this includes Gene Ontology, Plant Ontology, UniprotKB, Gramene
(Gene, ontology annotation, gene, Quantitative Trait Loci (QTL) and Metabolic
Pathway informat ion) (Monaco et al. 2014). The objective of this is to provide the
critical mass required to imp lement real world use cases. Currently, Agro LD includes
data pertaining to selected species namely, Oryza species (O.sativa, O.barthii,
O.brachyantha, O. glaberimma and O.meridionalis), Arabidopsis thaliana, Sorghum
bicolor, Zea mays and Triticum species (T.aestivum and T. uraruta). In the subsequent
phases informat ion pertaining to other species and SG databases will be considered.
The AgroLD effort will be further extended set-up RDF knowledge bases to host data
from other regional portals.
References
Barrell, D. et al., 2009. The GOA database in 2009 - An integrated Gene Ontology
Annotation resource. Nucleic Acids Research, 37(SUPPL. 1).
Conte, M.G. et al., 2008. GreenPhylDB: A database for plant comparative genomics.
Nucleic Acids Research, 36(SUPPL. 1).
Droc, G. et al., 2006. Ory GenesDB: a database for rice reverse genetics. Nucleic acids
research, 34(Database issue), pp.D736–D740.
Hamelin, C. et al., 2013. Trop GeneDB, the mu lti-tropical crop informat ion system
updated and extended. Nucleic Acids Research, 41(D1).
Larmande, P. et al., 2008. Ory za Tag Line, a phenotypic mutant database for the
Génoplante rice insertion line library. Nucleic Acids Research, 36(SUPPL. 1).
Monaco, M.K. et al., 2014. Gramene 2013: Co mparative plant genomics resources.
Nucleic Acids Research, 42(D1).