HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 211,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=-teams",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=80&ordering=-teams",
"results": [
{
"id": 255,
"name": "Kmerator",
"description": "Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome.",
"homepage": "https://github.com/Transipedia/kmerator",
"biotoolsID": "kmerator",
"biotoolsCURIE": "biotools:kmerator",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_3360"
],
"primary_publication": [
"10.1093/nargab/lqab058"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Thérèse Commes",
"email": "therese.commes@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T16:01:46.602609Z",
"teams": [
"Bio2M"
],
"source_repository": null
},
{
"id": 101,
"name": "Genomicus-plants",
"description": "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "https://www.genomicus.biologie.ens.fr/genomicus-plants",
"biotoolsID": "Genomicus-Plants",
"biotoolsCURIE": "biotools:Genomicus-Plants",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0780"
],
"primary_publication": [
"10.1093/nar/gks1156",
"10.1093/pcp/pcu177"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 98,
"name": "Genomicus-metazoa",
"description": "Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-metazoa/",
"biotoolsID": "Genomicus-metazoa",
"biotoolsCURIE": "biotools:Genomicus-metazoa",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:56:24.333237Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 100,
"name": "Genomicus-fungi",
"description": "Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-fungi/",
"biotoolsID": "Genomicus-fungi",
"biotoolsCURIE": "biotools:Genomicus-fungi",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 107,
"name": "GENOMICUS",
"description": "Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus/",
"biotoolsID": "GENOMICUS",
"biotoolsCURIE": "biotools:GENOMICUS",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/bioinformatics/btq079",
"10.1093/nar/gkab1091"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": "http://www.ibens.ens.fr/?rubrique43&lang=en",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "PB-IBENS",
"email": null,
"url": "https://www.ibens.ens.fr/?rubrique55",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "https://www.youtube.com/watch?v=CokUh3fUbGQ",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-03-06T14:10:23.175189Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 99,
"name": "Genomicus-protists",
"description": "Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-protists/",
"biotoolsID": "Genomicus-protists",
"biotoolsCURIE": "biotools:Genomicus-protists",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 254,
"name": "MOGAMUN",
"description": "A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks.\n\nMOGAMUN is a Multi Objective Genetic Algorithm to find active modules (i.e., highly connected subnetworks with an overall deregulation) in MUltiplex biological Networks. For a detailed description of MOGAMUN check out the preprint https://www.biorxiv.org/content/10.1101/2020.05.25.114215v1. All the expression datasets and networks that we used to obtain the results reported in our preprint are available in the GitHub repository https://github.com/elvanov/MOGAMUN-data.",
"homepage": "https://github.com/elvanov/MOGAMUN",
"biotoolsID": "mogamun",
"biotoolsCURIE": "biotools:mogamun",
"tool_type": [
"Library"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_0121"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": null,
"email": "anais.baudot@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-02-26T09:22:38Z",
"teams": [
"Systems Biomedicine"
],
"source_repository": null
},
{
"id": 94,
"name": "VarAFT",
"description": "VarAFT (Variant Analysis and Filtration Tool) is a standalone and multiplatform tool for annotation and prioritization of potential disease causing genes. With this tool users can annotate variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionally, users can perform a coverage analysis and quality check from any BAM file.",
"homepage": "http://varaft.eu",
"biotoolsID": "varaft",
"biotoolsCURIE": "biotools:varaft",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_3325"
],
"primary_publication": [
"10.1093/nar/gky471"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "http://varaft.eu/#contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Jean-Pierre Desvignes",
"email": "jean-pierre.desvignes@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "Other",
"documentation": "http://varaft.eu/download_files/VarAFT_Documentation_V2.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-04-02T21:35:23.173094Z",
"teams": [
"MMG-GBIT"
],
"source_repository": null
},
{
"id": 140,
"name": "NucleusJ",
"description": "Simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D.",
"homepage": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start",
"biotoolsID": "nucleusj",
"biotoolsCURIE": "biotools:nucleusj",
"tool_type": [
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0097",
"http://edamontology.org/topic_2229",
"http://edamontology.org/topic_3382"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Axel Poulet",
"email": "pouletaxel@gmail.com",
"url": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start#authors",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start#usage",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:54:14.614349Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 141,
"name": "DroPNet",
"description": "DroPNet is a webserver for generating and analyzing Drosophila protein-protein interaction networks. Input data is a list of genes from an experiment such as RNAi screen.",
"homepage": "http://dropnet.isima.fr",
"biotoolsID": "dropnet",
"biotoolsCURIE": "biotools:dropnet",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_3523",
"http://edamontology.org/topic_3678"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "RENAUD Yoan",
"email": "renaud@isima.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://dropnet.gred-clermont.fr/DroPNet_project/UserManual.pdf",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 72000,
"last_update": "2018-12-10T12:58:56Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 126,
"name": "PanGeneHome",
"description": "PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly.",
"homepage": "http://pangenehome.lmge.uca.fr/",
"biotoolsID": "PanGeneHome",
"biotoolsCURIE": "biotools:PanGeneHome",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3407",
"http://edamontology.org/topic_0154"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:48:31.897688Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 258,
"name": "FAIR-Checker",
"description": "FAIR-Checker is a tool aimed at assessing FAIR principles and empowering data provider to enhance the quality of their digital resources. Data providers and consumers can check how FAIR are web resources. Developers can explore and inspect metadata exposed in web resources.",
"homepage": "https://fair-checker.france-bioinformatique.fr",
"biotoolsID": "fair-checker",
"biotoolsCURIE": "biotools:fair-checker",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3316",
"http://edamontology.org/topic_0089"
],
"primary_publication": [
"10.1186/s13326-023-00289-5"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:45:19.260708Z",
"teams": [
"IFB Core"
],
"source_repository": null
},
{
"id": 156,
"name": "ORDO",
"description": "The Orphanet Rare Disease Ontology (ORDO) - structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features. It integrates a classification of rare diseases, relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).",
"homepage": "http://www.ebi.ac.uk/ols/ontologies/ordo",
"biotoolsID": "ordo",
"biotoolsCURIE": "biotools:ordo",
"tool_type": [
"Ontology",
"Web application",
"Database portal"
],
"collection": [
"RD-connect",
"Rare Disease"
],
"scientific_topics": [
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3307",
"http://edamontology.org/topic_3572",
"http://edamontology.org/topic_3325"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://www.ebi.ac.uk/support/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Inserm US14",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "ols-submission@ebi.ac.uk",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Apache-2.0",
"documentation": "https://www.ebi.ac.uk/ols/docs/index",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-09-16T07:06:49Z",
"teams": [
"Orphanet"
],
"source_repository": null
},
{
"id": 70,
"name": "GnplS",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": null,
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 87,
"name": "Genetic and Genomic Information System (GnpIS)",
"description": "A multispecies integrative information system dedicated to plant and fungi pests.. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment",
"homepage": "https://urgi.versailles.inrae.fr/gnpis",
"biotoolsID": "gnpis",
"biotoolsCURIE": "biotools:gnpis",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_0625"
],
"primary_publication": [
"10.1093/database/bat058",
"10.1007/978-1-4939-6658-5_5",
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "urgi-contact@versailles.inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": "https://urgi.versailles.inra.fr/gnpis/",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:38.871501Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 92,
"name": "RARe",
"description": "RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms.\nThe purpose of this web portal is to facilitate the discoverability of these data. \nRARe search is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/rare/",
"biotoolsID": "RARe",
"biotoolsCURIE": "biotools:RARe",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "Support service",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inrae.fr/rare/about",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:40.608985Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 90,
"name": "FAIDARE",
"description": "FAIDARE: FAIR Data-finder for Agronomic Research. \nThe purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.\n\nIt is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services.\n\nIt is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.",
"homepage": "https://urgi.versailles.inrae.fr/faidare/",
"biotoolsID": "faidare",
"biotoolsCURIE": "biotools:faidare",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "URGI support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inrae.fr/faidare/help",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-09-02T05:04:34.812991Z",
"teams": [
"URGI"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/faidare"
},
{
"id": 69,
"name": "WheatIS",
"description": "This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. \nThe WheatIS search is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/wheatis/",
"biotoolsID": "WheatIS",
"biotoolsCURIE": "biotools:WheatIS",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.1186/s13059-018-1491-4"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "Support service",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inra.fr/wheatis/about",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-02-15T15:54:13Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 105,
"name": "REPET",
"description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.",
"homepage": "https://urgi.versailles.inrae.fr/Tools/REPET",
"biotoolsID": "repet",
"biotoolsCURIE": "biotools:repet",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"REPET",
"PlantBioinfoPF"
],
"scientific_topics": [
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0097"
],
"primary_publication": [
"10.1371/journal.pone.0091929",
"10.1371/journal.pone.0016526",
"10.1371/journal.pcbi.0010022",
"10.1007/s00239-003-0007-2"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Documentor",
"Maintainer",
"Contributor",
"Support",
"Developer",
"Provider"
],
"name": "URGI",
"email": "urgi-repet@versailles.inra.fr",
"url": "http://urgi.versailles.inra.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
},
{
"type_role": [
"Developer",
"Contributor",
"Maintainer",
"Provider",
"Support",
"Documentor"
],
"name": "URGI",
"email": "urgi-repet@versailles.inrae.fr",
"url": "http://urgi.versailles.inrae.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
}
],
"tool_licence": "CECILL-2.0",
"documentation": "https://urgi.versailles.inrae.fr/Tools/REPET",
"maturity": "Legacy",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-09-09T08:10:41.737859Z",
"teams": [
"URGI"
],
"source_repository": "https://urgi.versailles.inrae.fr/download/repet/"
},
{
"id": 91,
"name": "DataDiscovery",
"description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "DataDiscovery",
"biotoolsCURIE": "biotools:DataDiscovery",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "urgi-support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:39.375595Z",
"teams": [
"URGI"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/data-discovery"
}
]
}