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Special Session on Agricultural Metadata & Semantics 2nd International Conference on Metadata & Semantics Research October 10-11, 2007 - Corfu, Greece. Creating and Querying an Integrated Ontology for Molecular and Phenotypic Cereals Data. Sonia Bergamaschi, Antonio Sala

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creating and querying an integrated ontology for molecular and phenotypic cereals data

Special Session on Agricultural Metadata & Semantics

2nd International Conference on Metadata & Semantics Research

October 10-11, 2007 - Corfu, Greece

Creating and Querying an Integrated Ontology for Molecular and Phenotypic Cereals Data

Sonia Bergamaschi, Antonio Sala

www.dbgroup.unimo.it

DII - Dipartimento di Ingegneria dell’Informazione

Università di Modena e Reggio Emilia, via Vignolese 905, 41100 Modena

Funded by:

FIRB project NeP4B: Networked Peers for Business (www.dbgroup.unimo.it/nep4b) and IST FP6 STREP project STASIS (www.dbgroup.unimo.it/stasis)

motivations
Motivations
  • Numerous public data sources have been realized and are now available for researchers in the field of molecular biology
  • Problem of having access to this great amount of data:
    • Numerous sources
    • Heterogeneous interfaces and structures
    • Low IT skills of the users
  • What is needed:
    • Extracting and fusing information from different data sources
    • Presenting the information according to a unique interface in a transparent and easy way independently from the format of the different sources
cerealab project
CEREALAB project
  • Conducted by the Agrarian faculty of the University of Modena and Reggio Emilia funded by the Regional Government of Emilia Romagna
  • The aim is to perform intelligent data integration of existing databases, i.e. to create a Global Virtual Schema (GVV) for the genotypic selection of cereal cultivars
  • Genotypic selection of cereal cultivars:
    • To extract genotypic data correlated to phenotypic traits
  • 3 species involved:
    • Wheat
    • Barley
    • Rice
the momis system
The MOMIS System

gene

FHB

Wrapper

Wrapper

Wrapper

Wrapper

gene

gene

gene

FHB

FHB

FHB

Wrapper

Wrapper

Graingenes

CEREALAB

Gramene

GRIN

CRA

ERData

MOMIS (Mediator Environment for Multiple Information Sources) (www.dbgroup.unimo.it/Momis) is a framework to perform information extraction and integration from heterogeneous distributed data sources and query management

Global

Virtual

View

(GVV)

integration process overview
Integration Process Overview

COMMON THESAURUSGENERATION

GVV GENERATION

(CEREALAB)

WRAPPING

SYNSET#

SCHEMA DERIVEDRELATIONSHIPS

ODLI3LOCAL SCHEMA 1

GLOBAL CLASSES

SYNSET4

SYNSET1

SYNSET2

LEXICON DERIVEDRELATIONSHIPS

CEREALAB

Common

Thesaurus

Structured

source

clustersgeneration

ODLI3LOCAL SCHEMA 2

OWL

Export

Graingenes

Structured

source

USER SUPPLIEDRELATIONSHIPS

ODLI3

LOCAL SCHEMA 3

MAPPINGTABLES

INFERRED RELATIONSHIPS

GRIN

Structured

source

AUTOMATIC/

MANUALANNOTATION

SEMI-AUTOMATIC

ANNOTATION

data sources
Data Sources
  • Molecular data:
    • Gramene, Relational DB (www.gramene.org)
    • Graingenes, Relational DB (wheat.pw.usda.gov/GG2)
    • CEREALAB experimental data, Relational DB
  • Phenotypic Data:
    • GRIN, Excel Files (www.ars-grin.gov)
    • CEREALAB repository, Relational DB (created collecting data from specific literature for regional germplasms and from the italian National Council of Research in Agriculture (CRA))
  • All these data sources, if considered separately, present incomplete information for the purpose of the CEREALAB project and are sometimes overlapping
local source schemata annotation
Local Source Schemata Annotation

Local Source Annotation

  • To assign meanings (by WordNet) to each local class and attribute name of a local schema
  • Semi-automatically performed
  • a WordNet Editor is available to extend WordNet by adding new domain-dependent terms and synsets
  • This extension step has to be performed just the first time a domain is handled.

Gene: a segment of DNA that is involved in producing a polypeptide chain; it can include regions preceding and following the coding DNA as well as introns between the exons; it is considered a unit of heredity) "genes were formerly called factors"

Automatic Annotation

(Present in WordNet)

Marker: A segment of DNA with an identifiable physical location on a chromosome for any feature that has been genetically mapped

Marker: some conspicuous object used to distinguish or mark something "the buoys were markers for the channel"

Manual Annotation

(Not present in WordNet)

common thesaurus generation
Common Thesaurus Generation
  • MOMIS constructs a Common Thesaurus including SYN, BT/NT, and RT relationships among schema elements.
  • The Common Thesaurus is constructed through an incremental process in which the following relationships are added:
    • schema-derived relationships
    • lexicon-derived relationship
    • designer-supplied relationships
    • inferred relationships
  • As an example:

gene is identified as a BT of allele (as gene is a direct hypernym of allele)

marker is identified as a NT of gene (as genetic marker as been added as a direct hyponym of gene)

global virtual schema generation
Global Virtual Schema Generation

Mappings are generated among global and local classes in the cluster (according to a GAV approach)

A Mapping Table (MT) is automatically generated for each global class of a GVV

MOMISidentifies and groups classes that describe the same or semantically related concept in different sources into clusters (global classes)

  • The designer may interactively refine and complete the proposed integration by adding
  • Data Conversion Functions from local to global attributes or Resolution Functions for global attributes to solve data conflicts of local attribute values

Source, Reference: a publication (or a passage from a publication that is referred to

join conditions
Join Conditions
  • Object identification: merging data from different sources requires different instantiations of the same real world object to be identified
  • Join Conditions among pairs of local classes belonging to the same global class allow to identify instances of the same object and fuse them.

(CEREALAB.gene.name) = (gramene.gene.name)

the global virtual schema gvv
The Global Virtual Schema (GVV)
  • Each GVV element is automatically annotated w.r.t. WordNet and can be exported in OWL
  • The GVV can be seen as an Ontology of the underlying sources
  • This Ontology correlates the molecular data of Gramene, Graingenes and the CEREALAB project with the phenotypic data of the GRIN database and those collected by the CEREALAB project
the integrated ontology
The Integrated Ontology
  • Molecular data associated with germplasms and phenotypic evaluations
the integrated ontology1
The Integrated Ontology

Phenotypic data are divided into six categories chosen among those of major interest for the cereal breeders:

  • Abiotic Stress
  • Biotic Stress
  • Growth and Development related traits
  • Quality traits
  • Yield traits.
the integrated ontology2
The Integrated Ontology
  • For each trait the specific evaluation of a germplasm for that trait is available
the integrated ontology3
The Integrated Ontology
  • Molecular data are related to phenotypic data indicating their presence in a germplasm for which a quantitative phenotypic evaluation is available
  • Information about specific molecular markers that can identify genes or QTLs that express a particular phenotypic trait.
  • In this way genotypic selection of cereals cultivars can be performed starting from phenotypic data
querying the integrated ontology
Querying the Integrated Ontology

The MOMIS Query Manager is the coordinated set of functions which takes an incoming query (say global query) and performs the following steps:

  • Query rewriting
    • to rewrite a global query as an equivalent set of queries expressed on the local sources (local queries)
  • Local queries execution
    • the local queries are sent and executed on local sources
  • Fusion and Reconciliation
    • The local answers are fused into the global answer
  • A Graphical User Interface has been developed to compose queries over the GVV regardless of the specific languages of the source databases.
example
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example1
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example2
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example3
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example4
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example5
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

example6
Example

“Find information about wheat QTLs that express resistance to the Fusarium fungus”

conclusions
Conclusions
  • The MOMIS system allows a straightforward creation of a Global Virtual Schema to integrate data from the CEREALAB research project with data coming from the databases Gramene, Graingenes and GRIN
  • The integration process provides a unique interface for the 3 sources according to a common ontology
  • Querying the 3 sources results completely transparent and easy to the user through a GUI
  • A unique answer is obtained
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