# Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform

Mouhamadou Ba, Véronique Martin, Olivier Rué, Sophie Schbath, Valérie Vidal, Valentin Loux

► To cite this version:

Mouhamadou Ba, Véronique Martin, Olivier Rué, Sophie Schbath, Valérie Vidal, et al. Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022. [hal-04176740](https://hal.inrae.fr/hal-04176740)

HAL Id: hal-04176740

https://hal.inrae.fr/hal-04176740

Submitted on 3 Aug 2023

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution - ShareAlike 4.0 International License
INRAE

Mouhamadou Ba
Véronique Martin
Olivier Rué
Sophie Schbath
Valérie Vidal
Valentin Loux

<figure><img src="image_2.png" /></figure>

# Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform

Migale, as a collective scientific infrastructure of INRAE, is building a text mining service offer to enable the bioinformatics community to more easily exploit and extract the information contained in the scientific literature.

<figure><img src="image_3.png" /></figure>

ifb
INSTITUT FRANÇAIS
DE BIOINFORMATIQUE

<figure><img src="image_4.png" /></figure>

FRANCE
GENOMIQUE

**BioinfOmics**
INRAE RESEARCH INFRASTRUCTURE

<figure><img src="image_5.png" /></figure>

## As part of the platform missions

<figure><img src="image_6.png" /></figure>

**Provision on the platform of data and software for text mining**

<figure><img src="image_7.png" /></figure>

**Textual data analysis (text mining)**

<figure><img src="image_8.png" /></figure>

**Design and development of applications**

<figure><img src="image_9.png" /></figure>

**Training of users in text mining methods and tools**

→ https://migale.inrae.fr/

## Reinforce the integration and use of text mining in bioinformatics

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

## Data and Tools

* **Provision** of ~ 15 instances of text mining tools developed by partners

- AlvisIR: generic semantic search engine

- Tydi: terminology editor

- AlvisAE: text annotation editor

* Regular updating of PubMed local databank

* Packaging, deployment and management of text mining tools

AlvisNLP/ML
corpus processing engine

fastText

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

BIOCONDA®

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

Centre
Île-de-France - Jouy-en-Josas-Antony

## Data Analysis

**Expertise Area:**

- Text and data mining

**Applications:**

- Creation of thematic corpora

- Extraction of named entities

- Classification of texts

**Application Domain:**

- Microbiologie

**Example of projet << TDM4AnimalPhysiology >>**

- Extraction of genes, pesticides, polyphenols using thematic corpora collected from PubMed

- Study of male and female fertility and energy metabolism of different organisms (mammals, fish, c elegans, drosophila, plants, etc.)

<figure><img src="image_17.png" /></figure>

## Design and Development

* **Text Mining APIs:** development of APIs wrapping text mining processes based on specialized uses

* **Tydi+:** deployment and management of instances of a new application for terminology edition

* **Omnicrobe:** management and evolution of the information extraction workflow that implements the text mining process of the Omnicrobe Information System

<figure><img src="image_18.png" /></figure>

## Trainings

* **A text mining module** in the << Bioinformatics by practicing >> cycle of Migale

* Entitled: << **Introduction au text mining avec AlvisNLP** >>

* Target audience: (Bio-)informaticians

* Contents:

- Techniques for Named **Entity Recognition** (NER)

- Use cases in biology (recognition of genes, proteins, habitats of bacteria, etc.)

- Practice with **AlvisNLP**, a corpus processing engine developed by the Bibliome team at INRAE

<figure><img src="image_19.png" /></figure>

Université Paris-Saclay, INRAE, MaiAGE, 78350, Jouy-en-Josas, France

Université Paris-Saclay, INRAE, BioinfOmics, Migale, 78350, Jouy-en-Josas, France

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

MaiAGE

<figure><img src="image_22.png" /></figure>

CERTIFIED

<figure><img src="image_23.png" /></figure>

ISO 9001