Mathématiques et Informatique Appliquées
du Génome à l'Environnement



Bibliome Team

"Extraction and formalization of knowledge from text"


Leader : Claire Nédellec

The Bibliome team develops Natural Language Processing (NLP) and Machine Learning (ML) methods to extract information from text in the biology domain.

We work on a variety information extraction (IE) tasks such as entity recognition, entity normalization, entity linking and relation extraction. We focus on methods that combine linguistic information, ML and domain knowledge (ontologies and taxonomies), for few-shot and zero-shot problems.

We apply our methods to a wide range of biological domains: microbe diversity, plant biology, and epidemiological monitoring.

We promote the development and evaluation of IE systems by organizing Shared Tasks.


On-going projects

FAIROmics H2020 -  FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods (2024-2027)

Omnicrobe : reference database on microbe habitats and phenotypes. CRD ANSES.

HoloOligo Structure diversity, functionality and modulation of milk oligosaccharides in monogastric livestock species: towards optimal development of rabbit and pig holobionts. Project-ANR-21-CE20-0045 - Biologie des animaux, des organismes photosynthétiques et des microorganismes

TyDI Terminology Design Interface. DiBiSO, université Paris-Saclay, INIST-CNRS, BIA-INRAE et MaIAGE-INRAE. 2021-2025.

Beyond - ANR Programme Prioritaire de Recherche Cultiver et protéger autrement. Building epidemiological surveillance and prophylaxis with observations both near and distant Projet IA-20-PCPA-0002

D2KAB Data to Knowledge in Agriculture and Biodiversity. ANR AAPG 2018. Défi : B.7. Axe : axe 4. 

Recent projects

TIERS - ESV. Traitement de l’Information et Expertise des Risques Sanitaires pour l’Epidémiosurveillance en Santé Végétal. IB2021 Departments INRAE MathNum and SPE.

ENovFood Linking a phenotypic and a network food microbe data bases: an application to food microbial ecology and food innovation. Metaprogramme MEM INRA. 2018-2020.

OntoBedding. Amélioration de plongements lexicaux par des ontologies pour leur adaptation aux domaines de spécialité, avec le LIMSI. Projet financé par le DIM RFSI. 2019

Visa TM (Towards an advanced infrastructure in text-mining) CoSO project, (2017-2019)

OpenMinTeD (Open Mining Infrastructure for Text and Data) Infrastructure H2020 project (2015-2018)

D-ONT, Exploitation optimisée des bases de données phénotypiques - Des ontologies pour le partage d’information, ACI Phase 2016-2018.

IMSV, Institut de modélisation des systèmes vivants, Lidex de l'Université Paris-Saclay (2014-2016)

SeeDev, Regulations in the development of Arabidopsis thaliana seed (Challenge Lidex CDS) (2015)

OntoBiotopeMetaprogramme INRA MEM (Metagenomics of microbial ecosystems). (2012-2013).

Triphase: Semantic information system for publications in animal physiology and agricultural systems. PHASE department (2013-2014).

QuaeroAutomatic multimedia content processing. Oséo. (2008-2013).

FSOV SAM BléSelection of wheat by genetic markers. Fond de soutien à l'obtention végétale (2010-2013).

Scientific activities

Workinggroup Labex DigiCosme D2K (from Data to Knowledge)

BioNLP-Open Shared Task 2019: annotated corpora and online evaluation services

BioNLP-Shared Task (201120132016): annotated corpora and online evaluation services

LLL, Learning Language in Logics (2005)



Claire Nédellec

Claire Nédellec

  • Directrice de recherche
  • Responsable de l'équipe Bibliome


Robert Bossy

Robert Bossy

  • Ingénieur de Recherche
  • Responsable de la "Suite Alvis"
Louise Deléger

Louise Deléger

  • Chargée de recherche
 Arnaud Ferré

Arnaud Ferré

  • Chargé de recherche
Mariya Borovikova

Mariya Borovikova

  • Etudiante en thèse

Marine Courtine

  • Ingénieure d'études


Past members

Anfu TangAnfu Tang, étudiant en thèse
Catalina GarciaR&D
Elisa LubriniElisa Lubrini, R&D
Clara SauvionClara Sauvion, R&D
Mouhamadou BaPostdoc, projet OpenMinTeD
Estelle ChaixPostdoc, projet OpenMinTeD
Philippe BessièresDirecteur de recherche
Dialekti ValsamouDoctorante, IDEX IDI


Visit us on GitHub.

  • Alvis NLP/ML is a pipeline that annotates text documents for the semantic annotation of textual documents. It integrates Natural Language Processing (NLP) tools for sentence and word segmentation, named-entity recognition, term analysis, semantic typing and relation extraction. These tools rely on resources such as terminologies or ontologies for the adaptation to the application domain. Alvis NLP/ML contains several tools for (semi)-automatic acquisition of these resources, using Machine Learning (ML) techniques. New components can be easily integrated into the pipeline. Part of this work has been funded by the European project Alvis and the French project Quaero. (See the paper by Nedellec et al. In Handbook on Ontologies 2009 for an overview)

  • AlvisAE (Alvis Annotation Editor) is an on-line annotation editor for the collective edition and the visualisation of annotations of entities, relations and groups. It includes a workflow for annotation campaign management. The annotations of the text entities are defined in an ontology that can be revised in parallel. AlvisAE also includes a tool for detection and resolution of annotation conflicts. Part of this work has been funded by the European project Alvis and the French project Quaero. See Bossy et al., LAW VI 2012 for more details.

  • AlvisIR (Alvis Information Retrieval) is an on-line generic semantic search engine ; only few hours are needed to create a a new instance for a given document collection and an ontology. A user query with the ontology concepts retrieves all documents that contain the concepts, in the form of specific concepts, or synonyms. AlvisIR semantic search engine also handles relational queries. See for example search on biotopes of microorganisms . Part of this work has been funded by the European project Alvis and the French project Quaero.

  • BioYaTeA is an extension of the YaTeA term extractor that deals with prepositional attachments and adjectival participle. It extracts terms from documents in French and in English. Its distribution includes post-filtering of irrelevant terms. It is publicly available as CPAN module. Part of this work has been funded by the European project Alvis and the French project Quaero. See (Golik et al., CiCLING'2013) for more details.

  • TyDI (Terminology Design Interface) is a collaborative tool for the manual validation and structuring of terms either originating from terminologies or extracted from training corpus of textual documents. It is used on the output of so-called term extractor programs (like BioYatea), which are used to identify candidates terms (e.g. compound nouns). With TyDI, a user can validate candidate terms and specify synonymy/hyperonymy relations. These annotations can then be exported in several formats, and used in other natural language processing tools. Part of this work has been funded by the French project Quaero. More details (Golik et al., Ekaw 2010 ).

Online Services

Semantic search engines based on the AlvisIR technology

  • Biotope relational search engine indexes all PubMed references on habitats of microorganisms and phenotypes (2,3 millions references) with Alvis Suite technology and OntoBiotope Ontology. Funded by OpenMinTeD, Quaero project and MEM metaprogramme.

  • SamBlé indexes a large set of references on genetic markers and phentoypes in bread wheat with Alvis Suite technology and Wheat Trait Ontology. FSOV SamBlé Project and OpenMinTeD

  • SeeDev indexes a large set of references on molecular mechanism involved in seed development using Alvis Suite technology. Supported by UPSay CDS&IMSV projects and OpenMinTeD.

  • TriPhas’IR indexes the publications of the PHASE scientific department (2010-2014) with the TriPhase termino-ontology.

  • AnimalIR indexes Animal Journal articles with the ATOL ontology


  • Omnicrobe is an online database that integrates information on microbe habitats and phenotypes from articles and databases, BRC, and genetic databases.

Shared Tasks, Ontologies and Corpora