AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

AgroPortal
a vocabulary and ontology
repository for agronomy, plant
sciences, biodiversity and nutrition
Clément Jonquet, Anne Toulet
jonquet@lirmm.fr
SemanDiv
Montpellier, July 11th 2017
http://agroportal.lirmm.fr

Clement Jonquet
Anne Toulet
Vincent Emonet
Pierre Larmande
Marie-Angélique Laporte
Elizabeth Arnaud
Valeria Pesce
Esther Dzalé-Yeumo
Sophie Aubin
and
Cyril Pommier (URGI)
Pascal Neveu (MISTEA)
Patrice Buche (DIADE)
Odile Hologne (DIST)
Mark Musen
John Graybeal
AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th 2017

Biologist have adopted ontologies
• To provide canonical representation of scientific knowledge
• To annotate experimental data to enable interpretation, comparison, and
discovery across databases
• To facilitate knowledge-based applications for
• Decision support
• Natural language-processing
• Data integration
But ontologies are: spread out, in different
formats, of different size, with different structures

Working with vocabularies & ontologies
– a portal please!
• You’ve built an ontology, how do you let the world know?
• You need an ontology, where do you go to get it?
• How do you know whether an ontology is any good?
• How do you find data that are relevant to the domain of the
ontology (or to specific terms)?
• How could you use ontologies without managing them ?

Why don’t have a portal like the NCBO
BioPortal for agronomy?
• The is definitively such a need in the
community
• We listed 120+ candidate vocabularies/
ontologies
• Maybe listed in OBO Foundry or not
• NCBO BioPortal is specific for health and
biomedical ontologies
• Overlap exists
• Some ontologies are not really biomedical ones
• But many plant/agro related ontologies are not covered
• NCBO technology is domain-independent and open
source

Two years ago
• Mid 2014, we started the AgroPortal project with the vision of
offering a vocabulary & ontology repository for agronomy and related
domains such as biodiversity, plant sciences and nutrition
• The prototype found a good adoption and growing interest
• Advanced prototype platform
• v1.4 was released in June 2017
• Hosts 64 public ontologies or vocabularies including 38 not present in any
such ontology repository
• We have identified around 90 candidates (still some work to do!)

Objectives of AgroPortal project
• Develop and support a reference ontology repository for agronomy
• Primary focus on agronomy
• One-stop-shop for agronomical ontologies & services
• Reusing the NCBO BioPortal technology
• Avoid to re-implement what has been done, facilitate interoperability
• Reusing the scientific outcomes, experience & methods of biomedicine
• Enable cross domain interaction
• Enable straightforward use of agronomical ontologies
• Respect the requirements of the agronomic community
• Fully semantic web compliant infrastructure
• Focus on new enabled science

5 Driving Agronomic Use Cases
➢ IBC Rice Genomics & AgroLD project
➢ Data integration and knowledge management related to rice (P. Larmande)
➢ RDA Wheat Data Interoperability working group
➢ Common framework for publishing wheat data (E. Dzalé-Yeumo)
➢ LovInra : INRA Linked Open Vocabularies
➢ Vocabularies produced by INRA scientists (S. Aubin)
➢ Crop Ontology project
➢ Ontologies for describing crop germplasm & traits (E. Arnaud)
➢ GODAN global map of agri-food data standards
➢ VEST/AgroPortal MAP of standards (V. Pesce)

Examples of
ontologies
uploaded in
AgroPortal
Title Format Groups Size
IBP Rice Trait Ontology (CO_320) OWL CROP, RICE ~2K
IBP Wheat Trait Ontology (CO_321) OWL CROP, WHEAT ~1K
IBP Wheat Anatomy Ontology (CO_121) OBO CROP, WHEAT ~80
IBP Crop Research (CO_715) OBO CROP ~250
Multi-Crop Passport Ontology (CO_020) OBO CROP ~90
Biorefinery (BIOREFINERY) OWL LOVINRA ~300
Matter Transfer (TRANSMAT) OWL LOVINRA ~1.1K
Plant Ontology (PO) OWL WHEAT, RICE, OBOF ~2K
Plant Trait Ontology (TO) OWL WHEAT, RICE, OBOF ~4.4K
Durum Wheat (DURUM_WHEAT) OWL LOVINRA ~130
Agricultural Experiments (AEO) OWL LOVINRA ~60
Environment Ontology (ENVO) OWL WHEAT, OBOF ~6.3K
NCBI Organismal Classification (NCBITAXON) RRF WHEAT ~900K
AnaEE Thesaurus (ANAEE) SKOS LOVINRA ~3.3K
French Crop Usage (CROPUSAGE) SKOS none ~300
Agrovoc (AGROVOC) SKOS none ~32K
Food Ontology (FOODON) OWL OBOF ~10K
National Agriculture Library Thesaurus (NALT) SKOS none ~67K
Global Agricultural Concept Scheme (GACS) SKOS none ~585K
Potential interest
for biodiversity:
ENVO
PATO
ANAEE
TO
PO
… soon
BCO
TDWG
TAXREF
TOP
…

Ontology groups
and categories
Category Number
Plant Phenotypes and Traits 18
Plant Anatomy and Development 3
Natural Resources, Earth and Environment 2
Animal Science and Animal Products 6
Agricultural Research, Technology and Engineering 9
Breeding and Genetic Improvement 1
Plant Science and Plant Products 4
Plant Genetic Resources 2
Food and Human Nutrition 4
Taxonomic Classifications of Organisms 2
Farms and Farming Systems 3
Specific slices display to use only the
ontologies of a group
http://inra.agroportal.lirmm.fr/

AgroPortal: an
ontology repository
for agronomy
Publish, search,
download
Browse, visualize
Peer review
Versioning
Annotation
Recommendation
Mapping
Notes
Projects
64 ontologies, 95 candidates
5 driving use cases
~60 registered users
http://agroportal.
lirmm.fr

Browse and select
ontologies
• Allows to search, order and select
ontologies using a facetted search
approach, based on the metadata
• 4 additional ways to filter ontologies in the
list
• 2 new options to sort this list (name,
released date).
AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th
2017

Align ontologies one
another
concept
by
concept

AgroPortal
Annotator
identifies ontology
concepts within plain
text for semantic
indexing

AgroPortal Recommender
get the most relevant
ontologies for your data

AgroPortal landscape page
Display “per property”
• Global presentation of the properties
• Synthesis diagrams & listing
• Allows to explore the agronomical ontology
landscape by automatically aggregating the
metadata fields of each ontologies in explicit
vizualizations (charts, term cloud and graphs).

Structural information about ontologies
AgroPortal - C. Jonquet - GDR SemanDiv - Montpellier, July 11th
2017

Information about the community

Information about the
ontology network

Future
ontologies
on the list
AgroPortal - C. Jonquet - GDR SemanDiv -
Montpellier, July 11th 2017
Title Organization
CAB Thesaurus CABI
Wine Ontology INRA
Oat, Barley, Brachiaria, Potato (etc.) trait ontologies Crop Ontology
Agronomy Ontology CGIAR
Agriculture Activity Ontology CAVOC
IC-FOODS Ontologies (12) UC Davis
agINFRA Soil Vocabulary FAO, GFAR
Plant-Pathogen Interactions Ontology CBGP
Biological Collections Ontology OBO Foundry
Plant Phenology Ontology OBO Foundry
Thesaurus Of Plant characteristics CEFE

Postdoc LINGUA

LINGUA 12-month postdoc (NUMEV)
• One of the challenges when dealing with multiple ontologies is the
overlap and mappings between these ontologies. Within the LINGUA
project, we will address specifically this aspect by developing ontology
mapping capabilities to align AgroPortal ontologies and define a lingua
franca for the domain. We will make AgroPortal a state-of-the-art platform
for mapping extraction, generation, validation, evaluation, storage and
retrieval by adopting a complete semantic web and open linked data
approach and engaging the community for curation. We will first focus on
the research topics of the Montpellier community (agronomy, food,
biodiversity) and second join the international Global Agricultural Concept
Scheme (GACS) project (integration of Agrovoc, NALt & CABt) to integrate
the 3 main vocabularies to help build the new concept scheme and align
GACS to other vocabularies & ontologies in AgroPortal.

AgroPortal mapping life cycle
• align the ontologies within
AgroPortal with one another
and with the GACS
• make YAM++/AgroPortal the
reference platform to extract,
generate, validate, evaluate,
store and retrieve ontology
alignments by developing a
state-of-the-art ontology
alignment framework

AgroPortal
• A platform for ontology publication (≠edition or curation)
• Need for the biodiversity community?
• We expect it to become a reference platform
• Reuse NCBO technology and focus on customization and new science
Sign up and join us with your ontologies, feedback!
http://agroportal.lirmm.fr

Conclusion
• The first 2 years of the project have been very productive
• Analysis of the portal content helps to figure out what are some of the
main domain of interests as well as common development practices when
creating an ontology in agronomy
• Continue our metadata edition and curation effort to be sure to provide
the community with the best descriptions for ontologies available
• Converge with the Map of standards for food and agriculture effort (Godan
Action)

AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

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AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition