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Roadmap for a multilingual BioPortal

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Clement Jonquet's Presentation Multilignual Semantic Web Workshop, MSW4 2015

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Roadmap for a multilingual BioPortal

  1. 1. Roadmap for a multilingual BioPortal Clement Jonquet (jonquet@lirmm.fr), Vincent Emonet (emonet@lirmm.fr) & Mark A. Musen (musen@stanford.edu) 4th workshop on the Multilingual Semantic Web Portoroz, Slovenia – June 1st 2015
  2. 2. A few introduction words 4th workshop on the Multilingual Semantic Web
  3. 3. Context: increasing number of biomedical data + multilingualism  Limits of keyword-based indexing  Biomedical community has turned to ontologies to describe their data and turn them into structured and formalized knowledge  Using ontologies is by means of creating semantic annotations  Crucial need for tools & services for French biomedical data  Biomedical data integration challenge  New potential sceintific discoveries hidden in data  Translational research 4th workshop on the Multilingual Semantic Web
  4. 4. Biologist have adopted ontologies  To provide canonical representation of scientific knowledge  To annotate experimental data to enable interpretation, comparison, and discovery across databases  To facilitate knowledge-based applications for  Decision support  Natural language-processing  Data integration  But ontologies are: spread out, in different formats, of different size, with different structures  In different “languages” 4th workshop on the Multilingual Semantic Web
  5. 5. Working with terminologies & ontologies – a portal please!  You’ve built an ontology, how do you let the world know?  You need an ontology, where do you go o get it?  How do you know whether an ontology is any good?  How do you find 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 ? 4th workshop on the Multilingual Semantic Web
  6. 6. A few words about BioPortal 4th workshop on the Multilingual Semantic Web
  7. 7. 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.  Online support for ontology  Peer review  Notes (comments and discussion)  Versioning  Mapping  Search  Resources 4th workshop on the Multilingual Semantic Web
  8. 8. http://bioportal.bioontology.org BioPortal Ontology Repository
  9. 9. http://data.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://bioportal.bioontology.org 4th workshop on the Multilingual Semantic Web
  10. 10. Status of multilingualism in BioPortal  Does accept (and parse) both multilingual ontologies and monolingual ontologies  sometime represented as views  No leveraging of multilingual structure and content  inclusion/exclusion of labels in different languages in the use of the services the portal offers e.g., Annotator  No t capable to reconcile and deal with the multilingual mappings  Not use a proper mechanism to identify the language property(ies) of an ontology  Not support relationships between ontologies in different languages (or in general)  Does not support any internationalization.  whole UI exists only in English 4th workshop on the Multilingual Semantic Web
  11. 11. A few words about words 4th workshop on the Multilingual Semantic Web
  12. 12. multilingual ontology 4th workshop on the Multilingual Semantic Web en:disease fr:maladie ... en:cancer fr:cancer en:spindel cell sarcome fr:sarcome à cellules fusiformes en:melanoma fr:mélanome disease ... cancer spindle cell sarcome melanoma maladie ... cancer sarcome à cellules fusiformes mélanome language specific ontology (monolingual)
  13. 13. Ontology language & translation  Natural language = the language (French, English, Spanish, etc.) used when building a language specific ontology  Format language = used to describe the ontology (OWL, RDFS, RRF, etc.)  Translation = relation between two language specific ontologies that represent mainly the same object (domain, topics, set of concepts and relations) 4th workshop on the Multilingual Semantic Web
  14. 14. Multilingual mappings  Mapping (or alignment) = a correspondence between concepts in different ontologies  Multilingual mapping = a concept mapping between 2 language specific ontologies  Multilingual translation mapping = additionally the 2 concerned language specific ontologies are a translation of one another  For instance,  Mesh/melanoma has a mapping to DOID/melanoma  Mesh-fr/mélanome has multilingual mapping to DOID/melanoma  Mesh/melanoma has a multilingual translation mapping to Mesh- fr/mélanome 4th workshop on the Multilingual Semantic Web
  15. 15. What is being multilingual?  Interface internationalization = displaying static elements of the user interface (e.g., menu names, help, etc.) in different languages  Content internationalization = displaying BioPortal content (e.g., ontology labels, mappings, etc.) in different languages  Multilingual = internationalization (display) + to enabling a complete use of the functionalities and services of BioPortal for multilingual ontologies or monolingual ontologies  completely and properly addressed (languages, translations, multilingual mappings, etc.)  rich semantic description 4th workshop on the Multilingual Semantic Web
  16. 16. A few propositions for multilingual BioPortal 4th workshop on the Multilingual Semantic Web
  17. 17. Representation of natural language property for an ontology  Reuse the OMV (http://omv2.sourceforge.net) is already imported and used in BioPortal Metadata ontology (http://bioportal.bioontology.org/ontologies/BP-METADATA)  omv:naturalLanguage 4th workshop on the Multilingual Semantic Web
  18. 18. Representation of the distinction between ontologies  Extend OMV within BioPortal Metadata to include and formalize the distinction 4th workshop on the Multilingual Semantic Web meta:MultilingualOntology rdfs:subClassOf omv:Ontology omv:naturalLanguage some Literal meta:LanguageSpecificOntology rdfs:subClassOf omv:Ontology omv:naturalLanguage exactly 1 literal
  19. 19. Representation of relation between ontologies  Extend the DOOR ontology (http://kannel.kmi.open.ac.uk)  A translated ontology is a specific evolution of the ontology with a different syntax (an equivalent ontology but in another language)  new property in BioPortal metadata 4th workshop on the Multilingual Semantic Web
  20. 20. 4th workshop on the Multilingual Semantic Web meta:isTranslationOf
  21. 21. Representation of multilingual mappings  Keep a single and simple model as the one BioPortal already provides to represent any mappings  as any other mapping, but with a specific relation (non exclusive)  Reuse standard properties to represent translations  the LEMON translation module (direct|cultural|lexicalEquivalent)  the GOLD ontology (free|literalTranslation) 4th workshop on the Multilingual Semantic Web disease ... cancer spindle cell sarcome melanoma maladie ... cancer sarcome à cellules fusiformes mélanome gold:freeTranslation gold:literalTranslation
  22. 22. Reconciliation of multilingual mappings  Methods to extract multilingual (translation) mappings between (translated) ontologies and then reconcile them into BioPortal mapping repository  Approaches  Via term code when they are the same  Extraction from a meta-thesaurus such as UMLS  Extraction from external mapping databases e.g. CISMEF  Using existing monolingual mappings  Using language parallel data resources  Etc. 4th workshop on the Multilingual Semantic Web
  23. 23. Overall representation of multilingual content 4th workshop on the Multilingual Semantic Web
  24. 24. A few elements of discussion 4th workshop on the Multilingual Semantic Web
  25. 25. Important for the Web of tomorrow  Multilingualism is an important issue in the explosion of data being released and linked over the Web today  The vision of the semantic web is to be able to leverage and interoperate data whatever natural language these data is available into  Make ontology repository multilingual and thus making ontologies inside the repositories multilingual 4th workshop on the Multilingual Semantic Web
  26. 26. Language reflects cultural difference  An ontology corresponds to an interpretation of a certain reality done by a group of people at a certain time  Language => cultural differences => conceptual differences  When the sociological and cultural differences are important, the effect on the knowledge formalized is also important 4th workshop on the Multilingual Semantic Web traitement de données transfer de données téléchargement data process data transfer upload download sideload
  27. 27. What is the challenge?  Multilingual translational discoveries  Potential discoveries that would become possible by crossing large amount of (clinical) data about population of different ethnics and continental origins currently expressed and limited to a unique natural language  e.g. multilingual crossing of genotype-phenotype distinction studies to help understanding better the role of the environment on gene expression 4th workshop on the Multilingual Semantic Web
  28. 28. Remaining open questions  How to deal with partial multilingual ontology?  How to deal more than one-to-one mapping?  download/upload vs. télecharger  Formalize entailment of these new classes and properties  e.g., a multilingual translation mapping is a multilingual mapping connecting 2 ontologies that are a translation one of the other  Make BioPortal ontology parser deals with lexical enrichment vocabularies  SKOS-XL, LIR, LexINfo, Lexvo, Lingvoj => LEMON  LEMON translation module (Jan 2014) 4th workshop on the Multilingual Semantic Web
  29. 29. Conclusions  Multilingual semantic Web is crucial  Propositions to manage multilingualism in an ontology repository such like BioPortal  Deal with monolingual ontologies and translation mappings  Deal with multilingual ontologies (from xmllang to LEMON)  Within the SIFR project, we are implementing and test those propositions in a local instance of BioPortal deployed at LIRMM 4th workshop on the Multilingual Semantic Web Thank you. Any questions?

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