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.

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