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FAIR data requires FAIR ontologies, how do we do?

EUDAT Porto January 2018

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FAIR data requires FAIR ontologies, how do we do?

  1. 1. FAIR data requires FAIR ontologies, how do we do? Clement Jonquet, PhD Assistant Professor – LIRMM, University of Montpellier Visiting Scholar at Stanford University EUDAT Semantics Services in EOSC meeting
  2. 2. 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. 2
  3. 3. Ontology repositories help to make ontologies FAIR 3
  4. 4. 4
  5. 5. 5
  6. 6. Linked Open Data cloud in 2017 ( 6 NCBO BioPortal data as of 2013
  7. 7. Ontology repositories help to make ontologies FAIR 7 Interoperable Findable Accessible Re-usable
  8. 8. Ontology libraries, registries, 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 Metadata Vocabulary. 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] 8
  9. 9. What are the ontology libraries out there? • Ontology repositories / portal • NCBO BioPortal • Ontobee • AberOWL • EBI Ontology Lookup Service • OKFN Linked Open Vocabularies • 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 • FAO VEST Registry • BioSharing • DERI Vocabularies , OntologyDesignPatterns,, W3C Good ontologies • Platform technology • Mondeca ITM, LexEVS • Abandoned projects • Cubboard, Knoodl, Schemapedia, SchemaWeb, OntoSelect, OntoSearch, TONES 9
  10. 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. 10
  11. 11. 11 • 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
  12. 12. 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 12
  13. 13. Who has been reusing NCBO technology so far? • Recently • AgroPortal ( – agronomy, food, plant sciences, biodiveristy • SIFR/French BioPortal ( – French biomedical ontologies & terminologies • BiblioPortal ( – libraries and metadata standards • EcoPortal – ongoing discussion with the Lifewatch/LTER projects for a more focused portal on ecology & biodiversity • Historically • NCI term browser ( – BioPortal first, then LexEVS • Open Ontology Repository (OOR) Initiative ( – Now stopped. Looked also at OntoHub • Marine Metadata Interoperability Ontology Registry and Repository ( • ESIPPortal (Earth Science Information Partners - ) • And a few hospitals, research labs, with private data and specific needs (often in-house annotation) 13
  14. 14. 2 collaborative projects reusing NCBO technology 14
  15. 15. SIFR: Semantic Indexing of French Biomedical Data Resources • Ontology-based services to index, mine and retrieve French biomedical data • In France, there is already a reference repository for medical terminologies but nothing public for annotation • Crucial need for tools & services for French biomedical data 15
  16. 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 26 monolingual ontologies/terminologies • From the UMLS or EHTOP • Cleaned and checked for the Annotator purpose 16 A. Tchechmedjiev, ..., C. Jonquet. Enhanced Functionalities for Annotating and Indexing Clinical Text with the NCBO Annotator+, Bioinformatics, January 2018.
  17. 17. AgroPortal: ontology repository for the agronomic domain • Develop and support a reference ontology repository • Primary focus on the agronomy & close related domains (food, plant sciences and biodiversity) • Reusing the NCBO BioPortal technology • Avoid to re-implement what has been done, facilitate interoperability • Reusing the scientific outcomes, experience & methods of the biomedical domain • Enable straightforward use of agronomy ontologies • Respect the requirements & specificities of the agronomic community • Fully semantic web compliant infrastructure • Enable new science Jonquet, C., Toulet, A., Arnaud, E., Aubin, S., DzaléYeumo, E., Emonet, V., Graybeal, J., Laporte, M.-A., Musen, M.A., Pesce, V., Larmande, P., AgroPortal: A vocabulary and ontology repository for agronomy. Comput. Electron. Agric. 144, (Jan 2018). 17
  18. 18. AgroPortal an ontology repository for agronomy, food, plant sciences & biodiversity Publish, search, download Browse, visualize Peer review Versioning Annotation Recommendatio n Mapping Notes Projects 80 ontologies, 95 candidates 5 driving use cases ~90 registered users http://agroportal. 18
  19. 19. AgroPortal Annotator identifies ontology concepts within plain text for semantic indexing 19
  20. 20. Harnessing the power of metadata to facilitate the comprehension of the agronomical ontology landscape 20
  21. 21. A new metadata model to better support description of ontologies and their relations • Building a list of properties to describe ontologies • Pickup properties and relations from 23 existing vocabularies • Existing properties in ontology repositories (especially BioPortal) • Non specific properties that “belong to the ontology” 346 relevant properties that could be used to described ontologies 127 used to build a new metadata model inside AgroPortal Ontology repositories metadata Other Interesting vocabularies (e.g., IDOT, PAV, SD, DOAP, …) Standards & Relevant (e.g., DC, DCAT, SKOS, OWL, PROV, OMV, VOID, VOAF, MOD …) 21
  22. 22. AgroPortal landscape page Display “per property” • Global presentation of the properties • Synthesis diagrams & listing • Metadata automatically extracted from the files and authored by us and the ontology developpers • Allows to explore the agronomical ontology landscape by automatically aggregating the metadata fields of each ontologies in explicit vizualizations (charts, term cloud and graphs). 22 Jonquet, C., Toulet, A., Dutta, B., Emonet, V.: Harnessing the power of unified metadata in an ontology repository: the case of AgroPortal. Data Semant. UNDER REVIEW.
  23. 23. • Metadata vocabulary for Ontology Description and publication • 88 properties • Ontology • To be discussed within the RDA Vocabulary and Semantic Services Interest Group (VSSIG) 23 Generalizing this with MOD Dutta, B., … Jonquet, C.: New Generation Metadata vocabulary for Ontolog yDescription and Publication. 11th Metadata and Semantics Research Conference, MTSR’17. , Tallinn, Estonia (2017).
  24. 24. Better ontology identification & selection (via ontology metadata) Multilingualism Ontology alignment (creation & use) Catching up with relevant data: annotations and linked data Generalized ontology-based services (keep quality while enabling horizontal studies) Scale to multiple domain and to the number/variety of ontologies Challenges for ontology repositories 24 Jonquet, C.: Challenges for ontology repositories and applications to biomedicine & agronomy. Keynote at 4th Annual International Symposium on Information Management and Big Data, SIMBig’17. pp. 25–37, Lima, Peru (2017).
  25. 25. Scale to multiple domain and to the number/variety of ontologies • There are +600 ontologies and +110 ontology views in BioPortal right now • Mostly biology and medicine • Overlaps with other domains • Lots of upper level ontologies • Lots of vocabularies • Swoogle in 2007: “Search over 10.000 ontologies” • Today a Google Search for “filetype:owl” returns around 34K results 25
  26. 26. Mutualize efforts, harmonize, enhance robustness • No repository (except the web itself) will handle them all, while keeping the level of features (and curation!) • Avoid duplicating ontologies • Connect repositories one another • Sharing the technology is the best way to guaranty long term support and future development (more interoperability) • Developers all around the world, different funders & support • We should be able to make a new portal for another community in minutes • What matters is the motivation of a community • Technology must follow and make this easy 26
  27. 27. Conclusion 27
  28. 28. FAIR ontologies are needed for the European Open Science Cloud • What’s needed • Standardization of ontologies (OWL, RDF and SKOS) • Strong community to develop good quality ontologies • Standardization of Ontology Repositories • Next • Semantic Lookup Services prototype (project with Yann Le Franc) • Convergence with B2NOTE (annotation of chunk of texts inside Web pages with the Annotators) • Possible work with EU project OpenMinTeD to make our ontologies accessible to their research infrastructure • Collaboration on EcoPortal • Toward a new standard for ontology metadata with the VSSIG Will EU take the lead on developing and maintaining ontology repositories for Open Science in any domain ? 28
  29. 29. Thank you! 29 @jonquet_lirmm