Repository details
GnpIS
Name of repository
GnpIS
Additional name(s)
- Genetic and Genomic Information System for Plants
Repository URL
Subject(s)
- Engineering Sciences
- Computer Science, Systems and Electrical Engineering
- Computer Science
- Agriculture, Forestry and Veterinary Medicine
- Life Sciences
- Biology
- Basic Research in Biology and Medicine
- Security and Dependability, Operating, Communication and Distributed Systems
- Agriculture, Forestry and Veterinary Medicine
- Forestry
- Plant Cultivation, Plant Nutrition, Agricultural Technology
- Plant Breeding and Plant Pathology
- Evolution and Systematics of Plants and Fungi
- Plant Genetics and Genomics
- Plant Sciences
- Bioinformatics and Theoretical Biology
Description
GnpIS is an integrative and multi-species information system dedicated to plants, including forest trees. It handles various types of data, focusing on genetic resources and phenomics. It allows researchers from the Plant community to access and cross-reference genetic data (accessions, phenotypes, polymorphisms, markers and QTLs) and genomic data (sequences, physical maps, genome annotations) for species of agronomic and forestry interest.
Accessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services. Data hosted in GnpIS is also indexed in FAIDARE and WheatIS Data Discovery. GnpIS curates and adds value its datasets by enabling their interoperability and reusability through the use of internationally agreed standards and ontologies (MIAPPE and Crop Ontology for phenotyping data, MultiCropPassportData for genetic resources, NCBI/EMBL recommendations for genomic data). It is continuously improving its compliance with the FAIR principles (Findable, Accessible, Interoperable, Reusable). To enhance the findability and accessibility of the submitted datasets, we collaborate with Data INRAE to assign a DOI (Digital Object Identifier) to your dataset and integrate it into GnpIS. Finally, GnpIS gives access to curated genome annotations, with a strong expertise of URGI’s staff on transposable elements annotation.
GnpIS is used by INRAE and its partners in major national and international projects. For instance, GnpIS is the repository for the global community working on wheat genomics (International Wheat Genome Sequencing Consortium; IWGSC; https://wheat-urgi.versailles.inra.fr ). GnpIS is also INRAE’s repository for crops and forest trees catalogs of genetic resources, their phenotyping data and genetic data, as no central archive exists for such data, and support their linkage with genomic data, feed the catalog of the French infrastructure of Resources for Research in Agriculture ( www.agrobrc-rare.org ). It is a major player for data management of the French national node of the ESFRI EMPHASIS for plant phenotyping and its staff has been very active in linking the ELIXIR and EMPHASIS European infrastructures ( https://www.elixir-europe.org/use-cases/plant-sciences ).
Contact(s)
- administrative: urgi-contact@inrae.fr
- support: urgi-support@inrae.fr
Keyword(s)
Repository type(s)
- disciplinary
Mission statement for designated community
Research data repository language(s)
- French
- English
Data and/or service provider
- dataProvider
Dates
Started
2001
Institutions (1)
Institution name
Additional name(s)
- INRAE - URGI
Country
Type(s) of responsibility
- funding
- technical
- general
Type of institution
non-profit
Policies (1)
Policy name
Database access
Type of access to research data repository
open
Data access (3)
Type of access to data
restricted
Data access restriction type(s)
- institutional membership
- registration
Type of access to data
embargoed
Type of access to data
open
Data licenses (1)
Data license
Data upload (1)
Type of data upload
restricted
Data upload restriction type(s)
- institutional membership
Data upload license (1)
Data upload license name
Persistent identifier system(s)
- DOI
Versioning
yes
Data citation guideline
Application programming interfaces (1)
Metadata standards (1)
Metadata standard
Remarks
Remarks
GnpIS use internationally agreed standards and ontologies: Minimun Information About Plant Phenotyping Experiments - MIAPPE (https://www.miappe.org/) and Crop Ontology (https://www.cropontology.org) for phenotyping data, MultiCropPassportData (https://hdl.handle.net/10568/69166) for genetic resources, NCBI/EMBL recommendations for genomic data
Publications:
Mining Plant Genomic and Genetic Data Using the GnpIS Information System, https://doi.org/10.1007/978-1-4939-6658-5_5
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data, https://doi.org/10.1186/s13059-018-1491-4
Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS, https://doi.org/10.34133/2019/1671403
Entry date
2018-04-19
Last update
2026-09-11
Cite this re3data.org record:
re3data.org: GnpIS; editing status 2026-09-11; re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3RF6C last accessed: 2026-09-18-
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- Cite this service: re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3D last accessed: 2026-09-18
