AgroPortal: a backbone for data integration and standardization in Agronomy

After having reviewed state of the art of vocabularies and ontologies in agronomy, food, plant sciences, and biodiversity, a recent article in ScienceDirect "AgroPortal: A vocabulary and ontology repository for agronomyhas focused on features, ontology organization and sources in AgroPortal. Below you will find some highlights of the article. 

FROM GAPS ...

Many vocabularies and ontologies are produced to represent and annotate agronomic data.

However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains.

Therefore, there is need for a common platform to receive and host them, and enabling their re-use in agro-informatics applications. To achieve this goal, the vocabularies must be published with respect to open standards and linked/aligned to other existing resources.

…TO SOLUTION

To meet these needs, an ontology repository for the agronomy domain AgroPortal was designed by (the Montpellier scientific community) reusing the National Center for Biomedical Ontologies (NCBO) BioPortal semantic tools and insights.

Besides The UN FAO’s VEST Registry, FAIRSharing, agINFRA linked data vocabularies, the AgroPortal specifically satisfies requirements of agronomy, food, plant, and biodiversity sciences.

As for today (December 2017), AgroPortal features multiple ontology-based services with up to 65 RDF ontologies, in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). 

AgroPortal provides powerful services, open standards, and information that will greatly facilitate the adoption of open data in agriculture and benefit the extended agronomic community, the Semantic Web and data science communities.

AgroPortal & five agronomic use cases : mutual enhancement 

The AgroPortal project was originally driven by five agronomic use cases that were the principal sources of ontologies and vocabularies:

1. Agronomic Linked Data (LD) knowledge base

- a platform to consolidate distributed information and facilitate formulation of research hypotheses.

AgroLD offers information on genes, proteins, Gene Ontology Associations, homology predictions, metabolic pathways, plant traits, and germplasm, on the following species: rice, wheat, arabidopsis, sorghum and maize. 

In the long-term vision for AgroPortal and AgroLD, the former might be an entry point to the knowledge stored in AgroLD, enabling users to easily query and locate data annotated with ontologies.

2. The RDA Wheat Data Interoperability working group

- developed under the umbrella of the International Wheat Initiative

…in order to provide a common framework for describing, linking and publishing wheat data with respect to existing open standards. 

The wheat slice in AgroPortal allows the community to share common definitions for the words they utilize to describe and annotate data, which in turn makes the data more machine-readable and interoperable.

3. Linked Open Vocabularies (LovInra)

- a service offered by the French National Institute for Agricultural Research (INRA) Scientific and Technical Information department …

…to identify and evaluate knowledge organization sources produced by INRA’s scientists, so that the agricultural community and possibly a larger public can benefit from them.

If a semantic resource is declared on the LovInra service, it is immediately uploaded and fully described on AgroPortal. 

4. The Crop Ontology project

- of the Integrated Breeding Platform (IBP) - …

 

… provides 28 crop-specific trait ontologies, in addition to ontologies describing germplasm material and evaluation trials.

Currently, the AgroPortal hosts 19 crop-specific trait ontologies developed within the Crop Ontology project. Hosting ontologies on AgroPortal offers new functionalities to the crop ontology community such as versioning, an open SPARQL endpoint, community notes, and the annotation service, while still supporting the uses of the current web site.

5. GODAN Action VEST / AgroPortal map

-  is the continuation of the FAO VEST Registry (a registry of vocabularies of all types and all formats) under the GODAN Action umbrella.

It's the result of the merging of records from two different sources: the FAO VEST Registry
and the AgroPortal.

The combined system automatically imports resource descriptions from the AgroPortal into the VEST, and links records from the VEST back to the AgroPortal entries, in order to provide access to the AgroPortal content and related services.

The new registry, called Map of Agri-Food Data Standards  leverages the AgroPortal’s new metadata model and application programming interface to populate the entries in the Map using a single web service call.

Towards broad community adoption 

In addition to these five first driving use cases, other projects or organizations have identified AgroPortal as a relevant application to host, share and serve their ontologies:

1.    IRSTEA’s projects, such as the French Crop Usage thesaurus about crops cultivated in France, and the French Agroecology Knowledge Management ontology for design innovative crop systems. These two projects produce ontologies only in French and needed a host for their work.

2.    The AGROVOC thesaurus -  the most worldwide used multilingual vocabulary -  developed by the FAO of the UN. AGROVOC contains more than 34 K concepts covering topics related to food, nutrition, agriculture, fisheries, forestry, environment and other related domains. AGROVOC Linked Data version contains multiple mappings to other vocabularies or resources that a resource hosting AGROVOC incorporates.

3.    The Consortium of Agricultural Biological Databases, - a group of database developers and curators maintaining model organism databases. The group wants to identify which databases use which ontologies, and recommend a list of ontologies based on that information.

Considering the need for a repository of ontologies for agronomy, food, plant sciences, and biodiversity, it is expected broad community adoption of the AgroPortal.

The endorsement of associated partners  illustrates the impact and interest not just in France, but also internationally. More recently, two other RDA working groups (Rice Data Interoperability and AgriSemantics) have expressed interest in using AgroPortal as a backbone for data integration and standardization. Within the RDA AgriSemantics WG, there is an interest in using AgroPortal to host the future Global Agricultural Concept Scheme (GACS),  which will result from the integration and alignment of Agrovoc, NAL Thesaurus and CAB Thesaurus

Moreover, AgroPortal will be offering our common services to these projects:

Fostering AgroPortal community

To foster interest in agronomy and the semantic web and identify potential AgroPortal applications, the AgroPortal Team launched in 2016 a series of AgroHackathons  that focused, among other things, on AgroPortal and AgroLD.  In the next future, it is planned to achieve a community survey evaluation, - to capture the feedback of AgroPortal community, review the requirements, and drive the future directions of the project.

To find out more about the aforementioned use-cases, AgroPortal’s features, requirements and their implementation, you might be interested to read the full article:

AgroPortal: A vocabulary and ontology repository for agronomyby Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande, 

in ScienceDirect, Computers and Electronics in AgricultureVolume 144, January 2018, Pages 126–143: https://doi.org/10.1016/j.compag.2017.10.012 Under a Creative Commons license

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