Mastering an ontology & vocabulary management technology in France ?
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This document discusses ontology and vocabulary management technologies in France. It describes challenges for ontology repositories, including metadata, evaluation, multilingual support, ontology alignment, scalability and interoperability. Two collaborative projects are highlighted that reuse NCBO ontology repository technology: SIFR BioPortal for French biomedical ontologies and AgroPortal for agronomy. Shared technology visions are proposed, with ontology repositories working together through a unified open source platform to support multiple domains. Open questions remain around long-term support, the European Open Science Cloud, and France's role in this area.
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Mastering an ontology & vocabulary management technology in France ?
- 1. M A S T E R I N G A N O N T O L O G Y & V O C A B U L A R Y M A N A G E M E N T T E C H N O L O G Y I N F R A N C E ? C l e m e n t J o n q u e t — j o n q u e t @ l i r m m . f r A s s i t . P r o f e s s o r, U n i v. d e M o n t p e l l i e r Paris, November 2018
- 2. M A I T R I S E R U N E T E C H N O L O G I E D E G E S T I O N D E S O N T O L O G I E S E T V O C A B U L A I R E S E N F R A N C E ? C l e m e n t J o n q u e t — j o n q u e t @ l i r m m . f r M a i t r e d e C o n f é r e n c e s , U n i v. d e M o n t p e l l i e r Paris, Novembre 2018
- 3. WHY ONTOLOGY REPOSITORIES ARE IMPORTANT? • 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 resources that are relevant to the domain of the ontology (or to specific terms)? • How could you leverage your ontology to enable new science? • How could you use ontologies without managing them ? C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 3
- 4. AS ANY DATA, ONTOLOGIES NEED TO BE FAIR • The FAIR principles have established the importance of using standards vocabularies or ontologies to describe FAIR data and to facilitate interoperability and reuse… • Explosion of the number of ontologies/vocabularies • Cumbersome to identify the ontologies we need and manage their overlap C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 4
- 5. ONTOLOGY REPOSITORIES HELP TO MAKE ONTOLOGIES FAIR C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 5
- 6. ONTOLOGY REPOSITORIES HELP TO MAKE ONTOLOGIES FAIR C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 InteroperableFindable Accessible Re-usable 6
- 7. L I N K E D O P E N DATA C L O U D I N 2 0 1 7 ( H T T P : / / L O D - C L O U D. N E T ) C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 NCBO BioPortal data as of 2013 7
- 8. ONTOLOGY LIBRARIES & REPOSITORIES • Ontology libraries defined as – “a library system that offers various functions for managing, adapting and standardizing groups of ontologies. It should fulfill the needs for re-use of ontologies. In this sense, an ontology library system should be easily accessible and offer efficient support for re-using existing relevant ontologies and standardizing them based on upper-level ontologies and ontology representation languages.” [Ding & Fensel, 2001] • Ontology repositories defined as – “a structured collection of ontologies (…) by using an Ontology MetadataVocabulary. References and relations between ontologies and their modules build the semantic model of an ontology repository.Access to resources is realized through semantically-enabled interfaces applicable for humans and machines.Therefore a repository provides a formal query language” [Hartmann, Palma, Gomez-Perez, 2009] C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 8
- 9. WHAT ARE THE ONTOLOGY LIBRARIES OUT THERE? • Ontology repositories / portal – NCBO BioPortal – Ontobee – AberOWL – EBI Ontology Lookup Service – OKFN Linked OpenVocabularies – ONKI Ontology Library Service – MMI Ontology Registry and Repository – ESIPportal – AgroPortal – SIFR BioPortal – CISMEF HeTOP – OntoHub • Web indexes – Watson, Swoogle, Sindice, Falcons • Ontology libraries / listings (more or less updated) – OBO Foundry – WebProtégé – Romulus – DAML ontology library – Colore – FAOVEST Registry – FAIRSharing – DERIVocabularies , OntologyDesignPatterns, Semanticweb.org,W3C Good ontologies – ANDS – BARTOC • Platform technology – Mondeca ITM, LexEVS, SKOSMOS, SissVoc • Abandoned projects – Cubboard, Knoodl, Schemapedia, SchemaWeb, OntoSelect, OntoSearch,TONESC. Jonquet – SemWeb.Pro – Paris, Nov. 2018 9
- 10. FOCUS ON NCBO BIOPORTAL : A “ONE STOP SHOP” FOR BIOMEDICAL ONTOLOGIES • Web repository for biomedical ontologies – Make ontologies accessible and usable – abstraction on format, locations, structure, etc. – Users can publish, download, browse, search, comment, align ontologies and use them for annotations both online and via a web services API. C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 10
- 11. C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 • Online support for ontology • Peer review & notes • Versioning • Mapping • Search • Resources • Annotation • Open source technology • Packaged in a “virtual appliance” • Set up your own “bioportal” in a few hours 11
- 12. http://bioportal.bioontology.org Ontology Services • Search • Traverse • Comment • Download Widgets • Tree-view • Auto-complete • Graph-view Annotation Data Access Mapping Services • Create • Upload • Download Term recognition Search data annotated with a given term http://data.bioontology.org C.Jonquet–SemWeb.Pro–Paris,Nov.2018 12
- 13. WHO HAS BEEN REUSING NCBO TECHNOLOGY SO FAR? • Recently – AgroPortal (http://agroportal.lirmm.fr) – agronomy, food, plant sciences, biodiveristy – SIFR/French BioPortal (http://bioportal.lirmm.fr) – French biomedical ontologies & terminologies – BiblioPortal (http://biblio.ontoportal.org) – libraries and metadata standards – EcoPortal – ongoing discussion with the Lifewatch/LTER projects for a more focused portal on ecology & biodiversity • Historically – NCI term browser (https://nciterms.nci.nih.gov) – BioPortal first, then LexEVS – Open Ontology Repository (OOR) Initiative (http://www.oor.net) – Now stopped. Looked also at OntoHub – Marine Metadata Interoperability Ontology Registry and Repository (http://mmisw.org) – ESIPPortal (Earth Science Information Partners - http://semanticportal.esipfed.org ) – Recently move to ORR branch • And a few hospitals, research labs, with private data and specific needs (often in-house annotation) C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 13
- 14. C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 14
- 15. 2 COLLABORATIVE PROJECTS REUSING NCBO TECHNOLOGY C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 15
- 16. C. Jonquet, et al.. SIFR BioPortal: French biomedical ontologies and terminologies available for semantic annotation, In 16th Journées Francophones d'Informatique Médicale, JFIM'16. Geneva, Switzerland, July 2016. A DEDICATED VERSION OF BIOPORTAL FOR FRENCH ONTOLOGIES http://bioportal.lirmm.fr 28 monolingual ontologies/terminologies • From the UMLS or EHTOP or other SIFR Annotator • Annotation of biomedical/clinical text data in French 16 C.Jonquet–SemWeb.Pro–Paris,Nov.2018 A. Tchechmedjiev, ..., C. Jonquet. Ontology-Based Semantic Annotation of French Biomedical Text and Clinical Notes BMC Bioinformatics, In PRESS, 2018.
- 17. AGROPORTAL AN ONTOLOGY REPOSITORY FOR AGRONOMY, FOOD, PLANT SCIENCES & BIODIVERSITY Publish, search, download Browse, visualize Peer review Versioning Annotation Recommendation Mapping Notes Projects C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 101 ontologies, 80 candidates 5 driving use cases ~90 registered users http://agroport al.lirmm.fr 17
- 18. CHALLENGES FOR ONTOLOGY / VOCABULARY REPOSITORIES C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 18
- 19. Metadata, evaluation and selection Multilingualism Ontology alignment (creation & use) Generic ontology-based services (especially for free text data) Annotations and linked data Scalability & interoperability (to multiple domain and to the number/variety of ontologies) CHALLENGESFOR ONTOLOGYREPOSITORIES C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 19 C. Jonquet. Challenges for ontology repositories and applications to biomedicine & agronomy, Keynote at SIMBig: Symposium on Information Management and Big Data, Sep 2017, Lima, Peru.
- 20. Metadata, evaluation and selection Multilingualism Ontology alignment (creation & use) Generic ontology-based services (especially for free text data) Annotations and linked data Scalability & interoperability (to multiple domain and to the number/variety of ontologies) CHALLENGESFOR ONTOLOGYREPOSITORIES C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 20 C. Jonquet. Challenges for ontology repositories and applications to biomedicine & agronomy, Keynote at SIMBig: Symposium on Information Management and Big Data, Sep 2017, Lima, Peru.
- 21. PROJECT D2KAB (2019-2023) • Data to Knowledge in Agronomy and Biodiversity – Partnership with UM-LIRMM, CNRS-I3S, CNRS-CEFE, INRA, IRSTEA,ACTA/API-AGRO, Stanford • 2 work-packages on ontology services and alignment – Development of AgroPortal and extended services • 1 work-package on building and harnessing knowledge graphs • 2 work-packages of driving ag & biodiv projects (food packaging, agro-agri linked data, wheat phenotype, ecosystems & plant biogeography) C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 21
- 22. SHARED TECHNOLOGY VISION O N TO L O G Y R E P O S I TO R I E S WO R K I N G TO G E T H E R C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 22
- 23. CURRENT ISSUES • With the increasing demand of FAIR data, other scientific communities need similar portals or services – e.g., ongoing discussion on EcoPortal (ecology, biodiversity, environment) – Geosciences?, social sciences & humanities, etc… • Explosion of Data Science – Not just knowledge engineers are interested in ontologies/vocabularies anymore • Long term support of any data infrastructure – Adopt a shared open source technology approach • Connection with the European Open Science Cloud roadmap – Cross-disciplinary open science services for European scientists in the next 10-15 years C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 23
- 24. biomedicine biology healthbiomedicine biology health agronomy agriculture food sciences plant sciences ecology biodiversity environment EcoPortal marine oceanography ?? ?Portal Shared open source technology for multiple distributed ontology repositories Domain specific repository with unified APIs and similar user interfaces Scientificadvisory board Specific community driven easy deployable “slices” with ontologies from multiple repositories and selected servicesDeveloper community Specificgroupor community http://umls.bioportal.bioontology.org http://limics.bioportal.lirmm.fr/ http://obo-foundry.agroportal.lirmm.fr/ http://agbiodata.agroportal.lirmm.fr/ … Whichgroup/feature isneeded? Whichontologygoes where? Howthisneedis implemented? metadata libraries standards Ontology repositories working together
- 25. CONCLUSION & OPEN QUESTIONS • Good ontologies are required for FAIR data and ontology repositories are important to FAIR ontologies – Continue our work to ease the sharing of FAIR ontologies and vocabularies • Possible industrial (non academics) valorization of the technology… while keeping an open model and foster scientific discoveries?Which industrial partners? • How to support FAIRification of data on the long term? • What role can France play in this area? – French Minister Open Science Roadmap and participation within EOSC – GO-FAIR initiative C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 25
- 26. THANK YOU! jonquet@lirmm.fr @jonquet_lirmm C. Jonquet – SemWeb.Pro – Paris, Nov. 2018 26