=Paper=
{{Paper
|id=Vol-1532/paper2
|storemode=property
|title=Roadmap for a Multilingual BioPortal
|pdfUrl=https://ceur-ws.org/Vol-1532/paper2.pdf
|volume=Vol-1532
|dblpUrl=https://dblp.org/rec/conf/esws/JonquetEM15
}}
==Roadmap for a Multilingual BioPortal==
https://ceur-ws.org/Vol-1532/paper2.pdf
Roadmap for a multilingual BioPortal
Clement Jonquet,1 Vincent Emonet,1 Mark A. Musen2
1
Laboratory of Informatics, Robotics and Microelectronics of Montpellier (LIRMM)
CNRS & University of Montpellier, France
{jonquet,emonet}@lirmm.fr
2
Stanford Center for Biomedical Informatics Research (BMIR)
Stanford University School of Medicine, USA
musen@stanford.edu
Abstract. Ontology indexes and repositories are important in the realization of the
Semantic Web; however, the need has clearly moved to multilingual capabilities
that are hard to offer when dealing with multiple ontologies, originally in different
formats and contributed by an open community. In this paper, we present a roadmap
for addressing the issues of dealing with multilingual or monolingual ontologies in
BioPortal, the reference ontology repository in biomedicine, currently mostly
English-oriented. We propose a set of representations to support multilingualism in
the portal and to enable a complete use of the functionalities and services for any
kind of ontologies and data. While encouraging the community to use the best
available specifications to represent multilingual content e.g., Lemon; our objective
is to handle multilingualism in a proper semantically rich and consistent manner in
the ontology repository. We are currently deploying and implementing these
representations in a local instance of BioPortal for French ontologies.
Keywords: ontology repository, ontology localization, biomedical ontologies,
BioPortal, multilingual Semantic Web, multilingual alignment, ontology relation.
1 Introduction
A key aspect in addressing semantic interoperability for life sciences is the use of
terminologies and ontologies as a common denominator to structure biomedical data and
make them interoperable [4]. For instance, the community has turned toward ontologies to
design semantic indexes of data that leverage the medical knowledge for better
information mining and retrieval. However, ontologies and terminologies in biology and
medicine are originally spread out over the Web and in different formats [9] making their
use often cumbersome. One way to address this issue was by designing ontology indexes
or buy building ontology repositories. For instances, indexes includes Watson [8],
Swoogle [12], or the EBI Ontology Lookup Service [7]; repositories, in the biomedical
domain, includes the NCBO BioPortal [23] or the HeTOP [17]; we may also cite the Open
Ontology Repository [2] or the listing at: http://www.w3.org/wiki/Ontology_repositories.
However, scientific discoveries that could be made with help of ontologies to annotate,
integrate, mine and search data, are often limited by the availability of ontology-based
tools and services only for one natural language, usually English, for which there exist the
most ontologies. Recently, ontology localization, i.e., “the process of adapting and an
ontology to a concrete language and culture community” [6], has become very important
in the ontology development lifecycle, but when efforts are made to properly represent
lexical (e.g., using Lemon [20]) or multilingual information (e.g., using LexOMV [21] or
Lemon translation module [16]) are made, then it is rarely leveraged by ontology indexes
and portals. This situation is clearly a problem for international organizations where
several languages are official e.g., European Union.
In the biomedical domain, the reference platform to host and find ontologies is
BioPortal (http://bioportal.bioontology.org) developed by the National Center for
Biomedical Ontology (NCBO) project. It is an open library of ontologies and
terminologies in biology and medicine [23]. Using the portal, health professionals and
biologists can browse, search, visualize and comment on ontologies both interactively,
through a Web interface, and programmatically, via Web services. Within BioPortal,
ontologies are used to develop a semantic annotation workflow [19] that can be used to
index biomedical text data resources (in English) to provide semantic search features.
In the context of the Semantic Indexing of French Biomedical Data Resources (SIFR)
project (http://www.lirmm.fr/sifr), we are investigating making BioPortal multilingual.
We are currently building a local instance of BioPortal1 to host ontologies and
terminologies with French labels with the goal of designing a semantic annotation
workflow capable of processing French text data. In this paper, we discuss our choices
and propositions to internationalize BioPortal. We distinguish interface
internationalization which consists of displaying static elements of the user interface (e.g.,
menu names, help, etc.) in different languages and enabling to switch from one language
to another; from content internationalization which consists in displaying BioPortal
content (e.g., ontology labels, mappings, etc.) in another language. In the following our
interest goes beyond internationalization (which is mainly related to display) to provide a
full model to support multilingualism in the portal i.e., to enable a complete use of the
functionalities and services of the portal for any kind of multilingual/monolingual
ontologies and data. Our main objective is to handle multilingualism in a proper
semantically rich and consistent manner (i.e., using the appropriate Semantic Web
mechanisms and vocabularies) enabling BioPortal users to use ontologies independently
of the language and therefore enabling cross lingual search or annotation with ontologies
and mining of data indexed with ontologies.
The rest of the paper is organized as follows: Section 2 presents the vocabulary and
definitions we use in the paper. Section 4, presents a brief status of multilingualism in
BioPortal as of today. Section 5 describes in each subsections the propositions to handle
semantic representation of multilingual content as illustrated on an example in Fig. 3.
Then, section 6 establishes the roadmap to implement a future multilingual BioPortal. And
finally, section 7 concludes and presents the perspectives of this work.
1
NCBO technology is open source and available in part on https://github.com/ncbo or as a virtual appliance
http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
2 Related work
Multilingualism became an important issue with the explosion of data being released and
linked over the Web today. Even if today Web content is mainly in English, followed by
Chinese and Spanish,2 the vision of the Semantic Web is to be able to leverage and
interoperate data whatever natural language these data are available into. Within the
Semantic Web community research about multilingualism has gained a lot of interest in
the last years [5]. Several approaches have been proposed to add lexical information to
ontologies such as SKOS-XL, Lexvo [11], Lingvoj, resulting on the proposition of the
Lemon standard [20]. For instance, instead of using rdfs:label or skos:*Label, one can use
the SKOS-XL extension to define labels as classes with property skosxl:literalForm for the
label itself. This reification of the label property allows defining further properties for
labels e.g., acronym, short forms, translations. This solution offers a richer description of
what a label is and support entailment to SKOS. The state-of-the-art for adding complex
lexical information to an ontology is the Lemon (LExical Model for ONtologies) model
done within the Monnet EU project, which is designed to represent lexical information
about words and terms relative to an ontology. Lemon allows for instance, to add part-of-
speech information to terms thanks to a clear separation of the lexicon and ontology layers
in the model. Lemon perfectly defines how to represent translations within a multilingual
ontology3 and making BioPortal multilingual will for sure mean to be able to parse Lemon
translation descriptions when an ontology is uploaded to the portal. A recent extension
offers mechanisms to represent even more precisely multilingual content in ontologies
[16] by reifying the translation relation into a class with specific attributes.
In the biomedical domain, the Unified Medical Language System (UMLS)
Metathesaurus, a set of terminologies which are manually integrated and distributed by
the United States National Library of Medicine [3], does contain terminologies in other
languages than English. In addition, the HeTOP portal [17] also offers translated terms in
multiple languages, especially French, and enables cross lingual search. In both cases, the
underlying approach is one of a common meta-model for all the integrated ontologies
which means that there exists a unique class for concepts (e.g., CUI) and additional label
properties offer translations to multiple languages. This is different from the BioPortal
approach which does not build a global thesaurus but keep each ontologies separated and
use alignments to interconnect them. Another difference with BioPortal, is that neither
UMLS nor HeTOP are built natively with Semantic Web technologies and thus do not
offer semantic representation for ontologies with multilingual content.
We are also interested in the formalization and representation of multilingual ontology
alignments [18, 15], however we do not focus on their creation or extraction [27]. In
addition, a few work has been done about classifications of relations between ontologies
2
Internet World Stats, 2013
3
“A Translation is a special case of SenseVariation involving 2 lexical senses in different languages that stand in
a translation relation in the sense that they can be exchanged for each other without any meaning implications.”
(e.g., [1]), especially related to multilingual aspects, such as [18], where four types of
proximities between the structure of knowledge organization systems are defined.
3 Vocabulary
In the following, we discuss only ontology (thus including the notion of terminology). We
call natural language, the language (French, English, Spanish, etc.) used when defining
the class labels in an ontology. This language property, has not to be confused with the
format language used to describe the ontology (OWL, RDFS, RRF, etc.). We call a
multilingual ontology, an ontology that provides labels or lexicalizations in different
natural languages and uses the standard ways to differentiate them (e.g., rdfs:label et
xmllang property with values in ISO-639-3) or a rich lexical representation (e.g., Lemon).
For instance, Orphanet ontology [26], that was constructed with labels in 5 languages. We
call a language specific ontology, or a monolingual ontology, an ontology that provides
labels in a unique natural language that usually serves as the basis for conceptualization.
These ontologies are either being originally developed in a given language or are the
result of a translation of an ontology in another language. For instance MeSH-fr, which is
the specific French version of MeSH translated by the French INSERM organization
(http://mesh.inserm.fr). We call partial multilingual ontology, an ontology that contains
labels in multiple language more or less systematically and miss some labels; which
makes them more difficult to use [21]. This is for instance the case of the Foundational
Model of Anatomy (http://fma.biostr.washington.edu).
Fig. 1. Examples of multilingual and monolingual ontologies.
We call a translation, the relation between two monolingual or multilingual ontologies,
in different languages, that represent mainly the same knowledge resource (domain,
topics, classes, relations).4 For instance, MeSH-fr is a translation of MeSH. Other
4
We do not include in this definition of translation, the process of constructing a multilingual ontology by
aggregating several existing monolingual ontologies into a new multilingual one.
relations between ontologies can also be used to be more specific. We call multilingual
mapping, a one-to-one concept mapping (or alignment) between two language specific
ontologies. We call a multilingual translation mapping when additionally the two
concerned language specific ontologies are a translation of one another. A multilingual
mapping states that the terms in the mapped ontologies are a translation of one another
(between the natural languages of the ontologies). For instance, Mesh-fr/mélanome has a
multilingual translation mapping to Mesh/melanoma but only a multilingual mapping to
DOID/melanoma. With those definitions, the notion of translation stays at the ontology
level, while keeping the classic method (mapping) to represent translations between
classes. In the following, we will discuss the best Semantic Web to choose non
exclusively.
4 Status of multilingualism in BioPortal
As of today, BioPortal is not multilingual and hosts mainly English ontologies. The portal
does accept (and parse) both multilingual ontologies and language specific ontologies, but
it is neither capable to leverage the multilingual structure and content of the first ones nor
it is capable to reconcile and deal with the multilingual mappings necessary for the second
ones. As of March 2015, there are 433 ontologies in BioPortal, mostly in English. A few
ontologies (5) are French monolingual ontologies and 1 is in Spanish (cf. Table 1). Some
ontologies are multilingual or partial multilingual, although the exact number can hardly
be determined as they are not uploaded completely or parsed correctly by the portal.
Table 1. Examples of ontologies with multilingual content in the NCBO BioPortal
Ontology Acronym Type Status
International Classification of Primary ICPCFRE French LSO View of ICPC
Care, French translation
Medical Dictionary for Regulatory MDRFRE French LSO View of MEDDRA
Activities Terminology, French edition
Thesaurus Biomedical Francais/Anglais MSHFRE French LSO View of MESH
[French translation of MeSH]s
Minimal Standard Terminology of MSTDE-FRE French LSO Main ontology
Digestive Endoscopy, French
Ontology of Alternative Medicine, French ONTOMA French LSO Main ontology
SNOMED Terminos Clinicos SCTSPA Spanish LSO View of SNOMEDCT
Ontology of Nuclear Toxicity ONTOTOXNUC MO Main ontology
Foundational Model of Anatomy FMA PMO Main ontology
BioPortal neither uses a proper mechanism to identify the language property(ies) of an
ontology nor supports relationships between ontologies in different languages. However,
often, but not systematically, non-English language specific ontologies are available as
views5 of the English version, and in this case the relation between the ontologies is
formal, but not semantically described. The portal model does not semantically represent
5
A view is a subset, a subpart or any other variation of a main ontology explicitly attached to this ontology.
the mapping between e.g., an English term and the French one available in the
corresponding view. Thus, it is impossible to get the French term while browsing the
English one and vice-versa. In addition, when multilingual content is available, the portal
does not appropriately support inclusion/exclusion of labels in different languages in the
use of the services the portal offers. For instance, the Annotator will mix languages when
retrieving concepts from text making the results often incorrect. The historical choice
made during BioPortal design was assuming English as the main and by default language
and considering non English language specific ontologies as specific views of main
English ontologies. However, what to do with language specific ontology not in English,
with no existing translation to English available (or not yet in BioPortal). There would be
no “main” ontology to attach the view. In addition, ontology views are not first class
objects within BioPortal architecture. For instance, they cannot be part of groups, or are
not included in the Annotator.
Finally, BioPortal does not support any interface internationalization. The whole user
interface exists only in English.
5 Representation of multilingual content in BioPortal
5.1. Representation of natural language property for an ontology
We need a way to represent the natural language(s) of an ontology. We propose to use the
property omv:naturalLanguage because OMV (http://omv2.sourceforge.net) [25] is already
used within BioPortal Metadata ontology, which represents metadata about ontologies,
projects, mappings, etc. [24].
omv:
omv:naturalLanguage (with values in ISO-639-3)6
Note that this is not a functional property, therefore it can be used multiple times in the
case of multilingual ontologies. In the case of partial multilingual ontologies we propose
to assign values for each language possibly available in the ontology.
5.2. Representation of relations between ontologies
We need a way to represent the translation relation between ontologies and more
generally any relationships between ontologies. We suggest to use and extend the DOOR
ontology [1] which is the state-of-the-art about ontology relationships. We need to extend
the DOOR ontology (Fig. 2) with a new relation to represent ontology translation i.e., a
translated ontology is a specific evolution of the ontology with an equivalent syntax but in
another language; this can also be done in BioPortal Metadata.
6
Note that as of the latest version of OMV, omv:naturalLanguage is a data property which range is String.
However, Lexvo does now provides URIs for ISO-639-3 values that would be better to use.
meta:
door:
meta:isTranslationOf
subPropertyOf door:explanationEvolutionOf
subPropertyOf door:syntacticallyEquivalentTo
Fig. 2. Extension of DOOR ontology.
5.3. Representation of the distinction between ontologies with multilingual content
Optionally, we can also extend OMV within BioPortal Metadata to include and formalize
the distinction between multilingual ontology and language specific ontology. Then create
the following classes and relations.
meta:MultilingualOntology
rdfs:subClassOf omv:Ontology
omv:naturalLanguage some Literal
meta:LanguageSpecificOntology
rdfs:subClassOf omv:Ontology
omv:naturalLanguage exactly 1 literal
However, this solution does not allows to represent partial multilingual ontologies.
Fig. 3. Representations of multilingual content in BioPortal. New elements in orange.
5.4. Representation of multilingual mappings
We need a way to represent multilingual translation mappings between concepts (mostly
from monolingual ontologies). Considering that multilingual mappings could be as
complex to extract and represent than others mappings, we suggest to keep a single and
simple model as the one BioPortal already provides to represent any mappings. Therefore,
we propose to represent multilingual mappings (i.e., one-to-one mappings) between
concepts from ontologies in different languages as any other BioPortal mapping, but with
a specific relation. We currently suggest to represent translations with the GOLD ontology
(http://linguistics-ontology.org/) [14] and the gold:translation property when mappings
explicitly connect terms with a different ‘orthographic expression’.
gold:
gold:translation //both expression have the same or roughly the same meaning
gold:freeTranslation //both expressions have exactly the same meaning
subPropertyOf gold:translation
gold:literalTranslation //translation word-by-word
subPropertyOf gold:translation
Other vocabularies or classification may also be used, such as Chen & Chen’s one [18]:
equivalence (exact, inexact, partial) and non-equivalence (cultural or scope) assuming
they are described in an available ontology or vocabulary. Depending on the types of
translation to represent, GOLD might not be appropriate and we suggest to represent
translations with other specifications such as the Lemon translation module [16].
trcat:
trcat:Translation
trcat:translationCategory trcat:directEquivalent // semantically equivalent
entities that refer to entities that exist in both cultures and languages
trcat:translationCategory trcat:culturalEquivalent // entities that are not
semantically but pragmatically equivalent
trcat:translationCategory trcat:lexicalEquivalent // point to the same entity,
but one of them verbalizes the original term by using target language words
This approach avoid to create specific relations per languages e.g.,
frenchToEnglishTranslationOf. Indeed, using omv:naturalLanguage property will provide
the information about which language are concerned.7 In addition, those representations
are not exclusives: other mapping relations already used in BioPortal can also be used
(owl:sameAs, skos:*Match). For instance, Mesh-fr/mélanome, and Mesh/melanoma, can be
linked by two mappings skos:exactMatch and gold:freeTranslation.
6 Roadmap for making BioPortal multilingual
6.1. Reconciliation of multilingual mappings
Language specific ontologies that have been produced by translating another ontology
will not always precisely describe a way to resolve translations between concepts. If the
two ontologies do not use the same URIs, then a one-to-one multilingual mapping need to
be reconcile between the ontologies. BioPortal does not extract or generate mappings
when an ontology is uploaded and parsed by the portal. But it offers a batch or API8
access to the mappings store enabling to add mappings connecting ontologies as a side
7
Note that in the case of a translation multilingual mappings between multilingual ontologies (with multiple
omv:naturalLanguage values) we assume the labels will themselves by tagged with their language (xmllang).
8
http://data.bioontology.org/documentation#Mapping. Eventually, multilingual mapping extraction and
reconciliation should happen automatically when an ontology is uploaded to BioPortal.
process after uploading the ontologies in the portal. Therefore, we need to implement
several methods to extract multilingual translation mappings between translated
ontologies and then reconcile them into BioPortal mapping repositories. We have
identified several approaches (sorted hereafter from simplest to harder):
Directly using the concept codes (or any other local class identifier) if they are the
same in the translated ontologies. For instance, both Mesh/melanoma
(http://purl.bioontology.org/ontology/MSH/D008545) and Mesh-fr/mélanome
(http://purl.bioontology.org/ontology/MSHFRE/D008545) share the same code.
Using a federated database such as the UMLS Metathesaurus [3] which offer a few
terminologies in other languages than English and link terms to one another using CUI
identifiers. Or using the CISMEF information system [10] and the HeTOP portal which
is the biggest source of French-English alignments for biomedical terms.
From other mappings existing between ontologies (eng-eng or fr-fr). Indeed, BioPortal
include large number of mappings between the ontologies. However, one need to make
sure that mappings (that are not multilingual) are not automatically transposed to
multilingual mappings because it could lead to irrelevant results.
From external multilingual dictionary or lexicalized semantic network publicly
available such as BabelNet [22].
From data resources available in multiple languages and that can be used for translation
e.g., Health Canada (http://www.hc-sc.gc.ca).
From adapting any complex alignment generation process to be multilingual [13, 27].
6.2. Internationalization of the portal
Once multilingual mappings are reconciled within BioPortal, and multilingual ontologies
are properly handled, content internationalization of the portal becomes possible. One can
switch from a user interface display to another using a contextual link (e.g., clicking on a
language flag): in the case of a multilingual ontology a simple change of the label
displayed is necessary whereas in the case of a monolingual ontology the concept being
displayed has to change using the multilingual translation mapping if exists. Services,
such as the Annotator can be use with a language parameter for the language of the given
text data. In addition, we will have to translate the user interface (menu, help) and make
sure the portal can switch from one language to the other (as any other web application).
7 Conclusion and future work
In this paper we have presented propositions to make BioPortal multilingual. We believe
the challenge of managing multilingualism within biomedical ontologies repository is
important and exceeds the linguistic aspects. Multilingual data sets integration will permit
translational discoveries by merging not only data in other natural languages but data
relating to different populations and/or culture. In biomedicine, considering the enormous
results obtained in mining & analysis of clinical data one maybe motivated by the
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. For instance, multilingual crossing of genotype-
phenotype distinction studies will certainly help understanding better the role of the
environment on the expression of genes.
We have seen that even if some mechanisms exist to semantically describe lexical or
multilingual content within an ontology, it has to be completed with solutions for an open
platform like BioPortal that do not edit the ontologies uploaded directly by their
developers. In the future, this will be interesting to make the portal fully compliant with
specifications like LexOMV or Lemon, in order to encourage ontology developers to
adopt and uses those specifications to encode multilingual ontologies. In addition, we
envision potential new applications for multilingual content in BioPortal such as
automated translation of free text, or automatic query expansion for multilingual search.
The SIFR project currently works on implementing the propositions in a local instance
of BioPortal. In the future, we will push those modifications back into the main BioPortal,
while taking into account that multiple instances may have to be interoperable.
Acknowledgements
This work was supported in part by the French National Research Agency under JCJC
program, grant ANR-12-JS02-01001, as well as by University of Montpellier, CNRS and
the Computational Biology Institute (IBC) of Montpellier. We thanks the National Center
for Biomedical Ontology (NCBO) for latest information about BioPortal.
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