Florilege, a new database of habitats and phenotypes of food microbe flora

Key Info
Description - a brief synopsis, abstract or summary of what the learning resource is about: 

This tutorial explains how to use the “Habitat-Phenotype Relation Extractor for Microbes” application available from the OpenMinTeD platform. It also explains the scientific issues it addresses, and how the results of the TDM process can be queried and exploited by researchers through the Florilège application.  

In recent years, developments in molecular technologies have led to an exponential growth of experimental data and publications, many of which are open, however accessible separately. Therefore, it is now crucial for researchers to have bioinformatics infrastructures at their disposal, that propose unified access to both data and related scientific articles. With the right text mining infrastructures and tools, application developers and data managers can rapidly access and process textual data, link them with other data and make the results available for scientists.

The text-mining process behind Florilege has been set up by INRA using the OpenMinTeD environment. It consists in extracting the relevant information, mostly textual, from scientific literature and databases. Words or word groups are identified and assigned a type, like  “habitat” or “taxon”.

Sections of the tutorial:
1. Biological motivation of the Florilege database
2. Florilège Use-Case on OpenMinTeD (includes a description of how to access the Habitat-Phenotype Relation Extractor for Microbes application)
3. Florilege backstage: how is it build?
4. Florilège description
5. How to use Florilege ?

 

Authoring Organization(s) Name: 
Facilitate Open Science Training for European Research (FOSTER)
Access Cost: 
No fee
Primary language(s) in which the learning resource was originally published or made available: 
English
More info about
Keywords - short phrases describing what the learning resource is about: 
Data access
Data access methods
Data wrangling
Linked data
Open access
Text and data mining
Subject Discipline - subject domain(s) toward which the learning resource is targeted: 
Life Sciences: Microbiology
Publisher - organization credited with publishing or broadcasting the learning resource: 
Facilitate Open Science Training for European Research (FOSTER)
Media Type - designation of the form in which the content of the learning resource is represented, e.g., moving image: 
Text - an explanation of a concept or a story using human readable characters formed into words, usually distinguished from graphical images.
Contributor Organization(s): 
Name: 
INRA Science and Impact
Type: 
Collaborator
Educational Info
Purpose - primary educational reason for which the learning resource was created: 
Professional Development - increasing knowledge and capabilities related to managing the data produced, used or re-used, curated and/or archived.
Learning Resource Type - category of the learning resource from the point of view of a professional educator: 
Lesson - detailed description of an element of instruction in a course, [could be] contained in a unit of one or more lessons, and used by a teacher to guide class instruction. Example: presentation slides on a topic.
Target Audience - intended audience for which the learning resource was created: 
Data policymaker
Research scientist
Software engineer
Mid-career research scientist
Early-career research scientist
Research faculty
Graduate student
Intended time to complete - approximate amount of time the average student will take to complete the learning resource: 
Up to 1 hour
Framework - A community-based organization plan or set of steps for education or training: 
FAIR Data Principles
Framework Node: FAIR: 
Findable
Interoperable