This document outlines a roadmap for making BioPortal, an ontology repository, more multilingual. It proposes representing the natural language of ontologies, distinguishing between monolingual and multilingual ontologies, and representing relations between translated ontologies. It also discusses reconciling multilingual mappings and representing multilingual content overall. Making BioPortal multilingual could enable new discoveries by connecting data in different languages and addressing cultural differences reflected in language. Some challenges include dealing with partial multilingual ontologies and multiple mappings between terms. The proposals aim to better support multilingual ontologies, translations, and mappings within BioPortal.

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. A few introduction words
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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
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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”
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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 ?
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6. A few words about
BioPortal
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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
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8. http://bioportal.bioontology.org
BioPortal Ontology Repository

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
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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
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11. A few words about words
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12. multilingual
ontology
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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. 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)
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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
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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
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16. A few propositions for
multilingual BioPortal
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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
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18. Representation of the distinction
between ontologies
 Extend OMV within BioPortal Metadata to include and
formalize the distinction
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meta:MultilingualOntology
rdfs:subClassOf omv:Ontology
omv:naturalLanguage some Literal
meta:LanguageSpecificOntology
rdfs:subClassOf omv:Ontology
omv:naturalLanguage exactly 1 literal

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
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20. 4th workshop on the Multilingual
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meta:isTranslationOf

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)
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disease
... cancer
spindle cell sarcome melanoma
maladie
... cancer
sarcome à cellules
fusiformes
mélanome
gold:freeTranslation
gold:literalTranslation

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.
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23. Overall representation of
multilingual content
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24. A few elements of
discussion
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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
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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
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traitement de
données
transfer de
données
téléchargement
data
process
data
transfer
upload download sideload

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
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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)
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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
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Thank you.
Any questions?