# OpenMinTeD: Text mining services for e-infrastructures

Sophie Aubin

► To cite this version:

Sophie Aubin. OpenMinTeD: Text mining services for e-infrastructures. Open Harvest, May 2017, Chania, Greece. pp.15. hal-01543468

HAL Id: hal-01543468

https://hal.science/hal-01543468v1

Submitted on 4 Jun 2020

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publics ou privés.

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openM1N7E2D

Sophie Aubin - INRA

OpenMinTeD

Text mining services for
e-infrastructures

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Amounts of scientific texts...

1 paper/sec

120,000 papers
published on a single
taxon "Zea mays"

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Publications

90% of papers
**never** cited

50% of papers
**never** read by
anyone than its
authors, referees,
journal editors

+ reports, patents, books,
surveys, news, etc.

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# TDM services

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Indexing documents and
datasets

Entities identification and
normalisation against
reference data

Information extraction: from
semi-structured to structured

Semantic/lexical resource
acquisition from texts

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However, ...

Multitude of solutions catering for different

Text Types

Newswire

Scientific Literature

Tweets/blogs

Patents

Clinical/medical records

Textbooks, monographs

Online forums

Domains

Agriculture

Health

Biology

Social Sciences

Environment

....

Tasks

Translation

Knowledge acquisition

Semantic Search

Question Answering

Sentiment Analysis

Summarization

Knowledge Discovery

....

Languages

English

French

German

Spanish

Portuguese

Italian

Polish

....

Creating a fragmented landscape
Then comes openM1N7ED

• Started: June 2015 , Duration: 3 years

• 16 Partners:

- research groups in
text-mining

- content providers

- a data center

- a library association

- legal experts

- community related partners

- SMEs

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## What is openM1N7ED?

openM1N7ED is a platform that works as an **infrastructural service** of the wider **research ecosystem**

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Our Services

1. Discover TDM Services and tools

2. Feed with home content or easily get texts from (OA) content hubs

3. Pick adequate knowledge resources

4. Build your own service/applications – Combine components into a Workflow

5. Share and Re-Use

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# How does all this bind together?

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Open Harvest, Chania, 3 June 2017
# OpenMinTeD Scientific/Business Applications

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**Data & content repositories/registries**

For Data analysts, Scientists

**Curation tools**

For Data providers

**Analytical tools**

For Scientists-policy makers

**Decision tools**

For Farmers, SMEs

**Knowledge acquisition tools**

For Scientists, Ontologists

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# Example: WheatIS / gnpIS

**Application:** federated search of genomic and genetic data for wheat

**Added value:** direct access from data to related scientific articles

**Objects:** taxa, genes, markers, phenotypes and varieties

**Challenges:** naming heterogeneity & scale variety between textual and experimental data

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open

MIN7ED

Open Harvest, Chania, 3 June 2017

This is where the footer goes

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data - text interoperability

experimental data

Knowledge

300,000 genes

30,000 markers

220 taxa

208 phenotypes

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web services

semantic
交互.

INRA
SCIENCE & IMPACT
bib

openM1N7ED
Open Mining Infrastructure for Text & Data

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textual
data

>18,000 articles

WHEAT
INITIATIVE

Search in all WheatIS nodes...

Examples: fhb, wmc430, Triticum, TRAES3BF001000010CFD
# Example: living conditions of food-related micro-organisms

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**Application:** study and characterize the microbial biodiversity of food ecosystems (dairy or meat products, fish, wine, etc.)

- risk management

- food quality improvement

**Added value:** completion of knowledge databases with info from the literature

**Objects:** bacteria, habitats and phenotypes

**Challenges:** heterogeneous data integration, object identity

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ifb

French Institute of
Bioinformatics

misole

open

MIN7ED

Open Harvest, Chania, 3 June 2017

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# OpenMinTeD for agriculture

Data/Content

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Semantics

openM1N7ED

Open Mining Infrastructure for Text & Data

AgroPortal

LIRMM

GACS
landvoc
Agrovoc
PO...

End-user

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WHEAT
INITIATIVE

Search in all WheatIS nodes...

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Examples: fgb, wmc430, Trifikum, TRAES3BF001000010CF0

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landportal.info

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Food and Agriculture Organisation
of the United Nations

English | French | Turkish | عربي | 日本語

AGRIC

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Looking for Agricultural Science and Technology Information?
Papers, data, statistics, and multimedia material, you get it with AGRIC all on one
page!

SEARCH

Find Resources

Search on AgriS

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My decision app
# Text mining

- creates value from texts

- creates even more value if the results are linked to other data

This relies on shared semantics, standards & protocols

This requires less tech competencies & resources thanks
to the common e-infra openM1N7ED

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THANK YOU!

Sophie Aubin

sophie.aubin@inra.fr

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