1. Agro Hackathon Hack 5: AgroPortal and VEST Registry
Agro Hackathon Montpellier, 29/6 – 1/7/2016

2. Team
Antonella Picarella, FAO Sophie Aubin, INRA Anne Toulet, LIRMM Clement Jonquet, LIRMM Valeria Pesce, GFAR

3. Objective of hack n. 5
Analyze the AgroPortal metadata model, coverage, API and registration process
Use the AgroPortal API and the VEST Registry ingestion function to synchronize the content from the AgroPortal to the VEST
 Ingest metadata and links from the AgroPortal to the VEST Registry

4. Hack n. 5: what we did (1)
Analyzed the AgroPortal metadata model, coverage and registration process
Exact mapping of VEST metadata with AgroPortal metadata
Extensive discussion about respective coverage to clarify the scope of the AgroPortal
Review of the ontology registration process to devise best solution for registering non-ontology vocabularies with only metadata (no RDF content)

5. VEST > AgroPortal metadata mapping
CURRENT KOS VEST REGISTRY
AgroPortal mapping (as July 2016)
Name
omv:name
Acronym
omv:acronym
Logo
foaf:logo
Description
omv:description
Languages
omv:naturalLanguage
Owner/Creator
omv:hasCreator
Contact
dcat:contactPoint
URL
schema:url
Contributor
omv:hasContributor
Publisher
dct:publisher
Domain
hasDomain
Other subject (based on the AIMS main taxonomy)
omv:hasDomain
Type
omv:hasFormalityLevel
Format
omv:hasOntologySyntax

6. VEST > AgroPortal metadata mapping
License
omv:hasLicense
Description
omv:description
Endpoint
Dump
sd:endpoint void:dataDump csvDump
Namespace
vann:preferredNamespaceUri
Relationship with other vocabularies (extends, maps, etc.)
voaf:usedBy voaf:metadataVoc omv:useImports door:explanationEvolution voaf:generalizes door:isAlignedTo voaf:hasDisjunctionsWith door:similarTo door:ontologyRelatedTo
omv:conformsToKnowledgeRepresentationParadigm
Creation date
dct:created
Last modification date
omv:modificationDate

7. Main issues with alignments
The necessary metadata elements are all there and there is a general 1-to-1 correspondence
The main issues to solve for a full alignment are around the ranges of recommended values for some key metadata elements (e.g. vocabulary type, domain)
In both systems these values can be modified
>> revision under way

8. Status of Value lists for metadata Domains (VEST) / Category (AgroPortal)
Domain names for English have been updated accordingly to Doc Vocabulary Metadata, KOS taxonomy terms tab.
They have translations (the French one is not up to date, no idea for the others)
It is a non-hierarchical list
Terms allow to categorize resources according to general agriculture, nutrition and environment domains and related human activities
Note : VEST content will most probably be transfered to another portal (different IS)
« Category » is used as a facet for searching resources
Terms are in English only
Category terms have initially been selected from Crop Ontology
There is a possible confusion between « Category » and « Group » (a category named « Crop ontology » corresponds to the initiative)
The coverage is limited to plants
Some resources have no assigned category, thus not accessible through the « Category » facet
Note: AgroPortal currently does NOT handle hierarchical facets nor multilinguism

9. Content of domain / category lists
VEST
AgroPortal
Animal Science and Animal Products
Breeding and Genetic Improvement
Economics, Business and Industry
Education and Extension
Farms and Farming Systems
Fisheries and Aquaculture
Food Security
Food and Human Nutrition
Forest Science and Forest Products
Geographical Locations
Government, Law and Regulations
Health and Pathology
Information Management
Insects and Entomology
Languages
Natural Resources, Earth and Environment
Physical and Chemical Sciences
Plant Science and Plant Products
Research, Technology and Engineering
Rural and Agricultural Sociology
Taxonomic Classification of Organisms
General Germplasm
Plant Anatomy and Development
Phenotype and Trait
Structural and Functional Genomic
Location and Environmental
Crop Ontology
Reference ontologies for plant

10. Agreement
FAO to revise the VEST records to exclude the non domain-specific vocabularies (FAO, INRA)
LIRMM, INRA and FAO to check remaining records for inclusion in the AgroPortal
FAO and LIRMM to contact owners of RDF ontologies for full inclusion in the Portal
FAO to register metadata only for remaining vocabularies

11. What we did (2): the actual hack
2) Ingested some sample metadata from AgroPortal to VEST
Tested a few API calls
Used the /submissions API call as input:
Used the Drupal Feeds module and Json parser plugin to ingest the metadata into the VEST

12. Drupal feeds importer: Json mapping
The Json mapping is based on the previous metadata mapping exercise

13. Main issues with the ingestion
For a quick ingestion, we needed to use the API call that returns all ontologies, which for the moment doesn’t include all the metadata (e.g. logo, owner, category, type) >> will be solved in new API version
The ingestion of the metadata elements using different ranges will be done once the revision of the reference lists is completed

14. Initial ingestion
VEST Registry page with ingested AgroPortal records:

15. How this is useful
It’s an opportunity to increase the coverage of both the AgroPortal and the VEST and promote them as one
It’s the first step in our task of building a global map of standards in a DFID-funded project and in the AgriSemantics RDA group
It’s a first step in our collaboration around the AgroPortal with other partners
It’s a proof of concept for anybody who wants to display metadata from the AgroPortal.
The vocabulary object and the related importer can be made available as a Drupal feature, re-usable in any Drupal website

16. Thank you
Antonella Picarella, Sophie Aubin, Anne Toulet, Clement Jonquet, Valeria Pesce