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The Vitis Ontology: sustainable and FAIR (Findable, Accessible, Interoperable, Reusable) for consistent and complete data description through biologist friendly ontologies

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HAL Id: hal-02947459

https://hal.inrae.fr/hal-02947459

Submitted on 24 Sep 2020

HAL is a multi-disciplinary open access

archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from

L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de

The Vitis Ontology: sustainable and FAIR (Findable,

Accessible, Interoperable, Reusable) for consistent and

complete data description through biologist friendly

ontologies

Eric Duchêne, Cyril Pommier

To cite this version:

(2)

The Vitis Ontology

Sustainable and FAIR (Findable, Accessible, Interoperable, Reusable)

for consistent and complete data description through biologist

friendly ontologies

(3)

What are ontologies?

• Ontology is a data model representative of a set

of concepts in a domain, as well as relationships

between these concepts

• « Ontology is to data what grammar is to

language »

• Concepts are organized in a graph were

relationships can be:

üSemantic relationships

(4)

What are ontologies?

COMPLEXITY

Controlled

Vocabulary

List,

Names,

Definition,

Synonyms,

Taxonomy

Ontology

Adds :

Hierarchical

Structure

Thesaurus

Adds :

Associative

links (« see also »)

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Why to use ontologies?

• To share a common vocabulary among a scientific

community,

• To standardize data description

• Leaf ≠ leaves ≠ L ≠ feuille

• To share information and data,

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How to describe phenotypic data ?

• Describe the experiment,

• Describe the plant material,

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How to describe phenotypic data ?

• Use data standards

• Semantic

• Description of the data

key concepts (the description of the data itself is more

in the metadata)

• Controlled vocabularies: term name and definitions

• Ontologies: semantic links between terms

• Biologist driven

• Reuse

• Formatting and Organizing the data

• Format Standards :

CSV, VCF, GFF,

• Metadata Standards

(about their production): MIAPPE (

www.miappe.org

) ,

etc…

• Biologist & Computer scientist driven

• Technical

infrastructure

• Data integration and sharing

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Describing the experiment

• Who was in charge of the experiment?

• What were the objectives?

• What were the objects to compare ? What kind of

treatments were applied ?

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Describing the experiment: the MIAPPE

project

https://www.miappe.org

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Describing the experiment: the MIAPPE

project

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Describing the experiment: the MIAPPE

project

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Describing the plant material

https://www.bioversityinternational.org/e-

library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/

(14)
(15)

Describing the plant material: exemple for

the grapevine accesion number

258Col1040

Gewurztraminer

Colmar

Clone 1040

23297

Montpellier

Genotype

Code for the variety or

population

Origin of

the

genotype

Accession number

Syrah x Grenache progeny

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Describing a variable: a general approach

(17)

Describing a variable: for the grapevine

http://www.cropontology.org/ontology/CO_356/Vitis

• a trait,

like pruning weight or flowering date,

• a method

that describes how the trait was measured, i.e. with a

scale or computed through image analysis,

• a scale/unit : i.e.

. International system units like centimeter or

meter, or notation scale like late, early, etc...

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The Vitis Ontology: structure

(21)
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The Vitis Ontology: use-case

(24)
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The Vitis Ontology: use-case

Examples for woody plants

https://urgi.versailles.inra.fr/ephesis/ephesis/viewe

r.do#dataResults/trialSetIds=15

https://urgi.versailles.inra.fr/ephesis/ephesis/viewe

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To conclude

• There are existing standards for describing an

experiment, the plant material and phenotyping

variables,

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Thanks to...

• French scientists that helped to build to ontology,

• The URGI Team (Anne-Françoise Adam-Blondon’s

team),

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