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TR: SIFR BioPortal 1.2 beta released - an open platform for French biomedical ontologies and terminologies

From: Clement Jonquet <jonquet@lirmm.fr>
Date: Wed, 22 Feb 2017 14:09:37 -0800
To: "'Clement Jonquet'" <jonquet@lirmm.fr>
Message-ID: <08a301d28d58$5d500750$17f015f0$@lirmm.fr>
(Apologies for multiple postings)

 

---------------------------

 

The  <http://www.lirmm.fr/sifr/> Semantic Indexing of French Biomedical Data
Resources (SIFR) project is pleased to announce the 1.2 release of the SIFR
BioPortal :  <http://bioportal.lirmm.fr> http://bioportal.lirmm.fr

 

Besides the existence of various English tools and platforms, there are
considerably less terminologies and ontologies available in French and there
is a strong lack of easy to use an open related tools and services to
exploit them. This lack does not match the huge amount of biomedical data
produced in French, especially in the clinical world (e.g., electronic
health records).

 

The SIFR BioPortal, is an open semantic web-oriented platform to host French
biomedical ontologies and terminologies based on the technology developed by
the US  <https://www.bioontology.org/> National Center for Biomedical
Ontology and customized for French (BioPortal version 4.24) . The portal
facilitates use and fostering of ontologies by offering a set of services
(search, mappings, metadata, versioning, visualization, recommendation),
including for annotation purposes, which was the original motivation of the
SIFR project as originally supported by French ANR. The SIFR Annotator (
<http://bioportal.lirmm.fr/annotator> http://bioportal.lirmm.fr/annotator)
is a publicly accessible ontology-based annotation tool to index biomedical
French text data with ontologies. 

 

As of today, the portal includes 22 ontologies or terminologies that are
either French “translations” of some English resources, multilingual
ontologies uploaded from the NCBO BioPortal from which the French content
only is parsed, or French specific ontologies that only exists in French.
Ontologies in the SIFR BioPortal are:

*	Extracted from the UMLS Metathesaurus when a French version is
available (4),
*	Pulled automatically from the  <http://bioportal.bioontology.org/>
NCBO BioPortal (8) when French content is available. In that case, the NCBO
BioPortal shall stay the reference hosting repository and the SIFR BioPortal
automatically pulls new versions from the NCBO,
*	Offered by CISMeF (6) that has developed an OWL export tool for the
<http://www.hetop.eu/hetop/> HeTOP platform (if you would like your resource
in the HeTOP platform to be included within the SIFR BioPortal, please
request CISMeF for the OWL version),
*	Uploaded directly by their users (2),
*	A few resources (2) are still accessible on private mode only
(access on request).

 

As the original BioPortal the platform enables to:

*	Store ontology metadata
*	Search within ontologies
*	Store and retrieve mappings between ontologies
*	Visualize ontology content
*	Comment about ontologies, concepts and mappings
*	Annotate text data with ontology concepts
*	Get a recommendation about which ontology to use for a text corpus
or set of keywords
*	Store projects which use ontologies
*	And many other features!!

 

The SIFR BioPortal 1.2 features also a bunch of specific new features: 

Mappings:

*	We have reconciled and stored more than 228K mappings between 10
English ontologies hosted on NCBO BioPortal and their French translations
[WIMS16].
*	We have enabled the storing of: Interportal mappings between an
ontology within the SIFR BioPortal and an ontology in another portal
appliance (typically the NCBO BioPortal itself); External mappings: between
an ontology within the SIFR BioPortal and any other  ontology/vocabulary
for which URIs are available.
*	Multiple relation mappings i.e., the possibility to tag a mapping
with multiple semantic web properties such as skos:exactMatch,
gold:translation, etc.

Annotator:

*	We have introduced several possible annotation scores (based on
frequency) [SWAT4LS14].
*	Results available in RDF format using the Annotation Ontology
[SWAT4LSp].
*	We have developed a proxy service, the NCBO Annotator +,  that offer
new developed features to the original web service developed by the NCBO
(this service consumes English biomedical text data):
<http://bioportal.lirmm.fr/ncbo_annotatorplus>
http://bioportal.lirmm.fr/ncbo_annotatorplus 

Ontologies:

*	We have organized ontologies in groups and categories to reflect the
French context.
*	We have made several subset user interfaces (called slices), for
instance to see the ontologies developed by the LIMICS one can browse:
<http://limics.bioportal.lirmm.fr/> http://limics.bioportal.lirmm.fr/ 
*	A new model for ontology metadata. We have reviewed 350 properties
from the most standard and relevant vocabularies out-there (21 totals) to
describe metadata for ontologies (such as Dublin Core, OMV, DCAT, VOID,
etc.) and selected 124 properties implemented in the SIFR BioPortal (
<http://bit.ly/2aCuSWi> http://bit.ly/2aCuSWi). Now, when an ontology is
uploaded, metadata is directly extracted from the original file and used to
populate the model. Then the API can be used to edit the metadata and add
information (the UI are under development). The current metadata appears on
each ontology page e.g.,  <http://bioportal.lirmm.fr/ontologies/HRDO>
http://bioportal.lirmm.fr/ontologies/HRDO

 

The content of the platform is accessible via REST API (that returns
JSON-LD) and SPARQL endpoint:

 <http://data.bioportal.lirmm.fr/documentation>
http://data.bioportal.lirmm.fr/documentation (being updated)

 <http://sparql.bioportal.lirmm.fr/test/>
http://sparql.bioportal.lirmm.fr/test/

 

The SIFR BioPortal is the result of a collaboration between: LIRMM (Univ. of
Montpellier) and the NCBO (Stanford). We acknowledge the support of the EU
H2020 (MSCA No 701771), French ANR (grant ANR-12-JS02-01001) as well as by
University of Montpellier and the CNRS. We thanks CISMeF and the other labs
for sharing their ontologies.

 

Please, refer to the project with: [JFIM16]

 

The SIFR BioPortal is an open source project:
<https://github.com/sifrproject> https://github.com/sifrproject 

 

Please contact us at sifrportal-support@lirmm.fr
<mailto:sifrportal-support@lirmm.fr> 


See all release notes:
https://github.com/sifrproject/bioportal_web_ui/wiki/Release-notes 

 


References


[JFIM16] C. Jonquet, A. Annane, K. Bouarech, V. Emonet & S. Melzi. SIFR
BioPortal : Un portail ouvert et générique d’ontologies et de terminologies
biomédicales françaises au service de l’annotation sémantique, In 16th
Journées Francophones d'Informatique Médicale, JFIM'16. Genève, Suisse, July
2016. pp. 16.
<http://www.lirmm.fr/~jonquet/publications/documents/Article_JFIM2016_SIFR_J
onquet.pdf> [PDF]

 

[WIMS16] A. Annane, V. Emonet, F. Azouaou & C. Jonquet. Multilingual Mapping
Reconciliation between English-French Biomedical Ontologies, In 6th
International Conference on Web Intelligence, Mining and Semantics, WIMS'16.
Nimes, France, June 2016. (13), pp. 12. ACM.
<http://www.lirmm.fr/~jonquet/publications/documents/Article_WIMS2016_Reconc
iliation_Annane.pdf> [PDF]

 

[SWAT4LS] S. Melzi & C. Jonquet. Scoring semantic annotations returned by
the NCBO Annotator, In 7th International Semantic Web Applications and Tools
for Life Sciences, SWAT4LS'14. Berlin, Germany, December 2014. CEUR Workshop
Proceedings, Vol. 1320 pp. 15. CEUR-WS.org.
<http://www.lirmm.fr/~jonquet/publications/documents/Article-SWAT4LS_2014.pd
f> [PDF]

 

[SWAT4LSp] S. Melzi & C. Jonquet. Representing NCBO Annotator results in
standard RDF with the Annotation Ontology, In 7th International Semantic Web
Applications and Tools for Life Sciences - poster session, SWAT4LS'14.
Berlin, Germany, December 2014. CEUR Workshop Proceedings, Vol. 1320 pp. 5.
CEUR-WS.org.
<http://www.lirmm.fr/~jonquet/publications/documents/Article-SWAT4LS_2014-po
ster.pdf>  [PDF]

 

 

Regards, 

Clement Jonquet

 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet@lirmm.fr> jonquet@lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 
Received on Wednesday, 22 February 2017 22:10:14 UTC

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