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

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

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

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)

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 e-mail dcat:contactPoint URL schema:url Contributor omv:hasContributor Publisher dct:publisher Domain hasDomain http://data.agroportal.lirmm.fr/categories Other subject (based on the AIMS main taxonomy) omv:hasDomain Type omv:hasFormalityLevel Format omv:hasOntologySyntax http://www.w3.org/ns/formats/N3 http://www.w3.org/ns/formats/N-Triples http://www.w3.org/ns/formats/RDF_XML http://www.w3.org/ns/formats/RDFa http://www.w3.org/ns/formats/Turtle

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

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

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

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 010-089 General Germplasm 100-299 Plant Anatomy and Development 300-499 Phenotype and Trait 500-699 Structural and Functional Genomic 700-799 Location and Environmental Crop Ontology Reference ontologies for plant

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

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: http://data.stageportal.lirmm.fr/submissions?display=all&display_context=false&display_links=false Used the Drupal Feeds module and Json parser plugin to ingest the metadata into the VEST

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

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

Initial ingestion VEST Registry page with ingested AgroPortal records: http://aims-test.ciard.info/vest-vocabularies​

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

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