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  description: AggreProt is a web server to predict and engineer protein aggregation.
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    note: null
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  description: APE (the Automated Pipeline Explorer) as a command-line tool and API
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  toolType:
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    metadata:
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    note: null
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    type:
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  relation: []
  toolType:
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  topic:
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  - term: Genomics
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  - term: Proteomics
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    typeEntity: Person
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  description: Freely available electronic database containing detailed information
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    type:
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    note: null
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  biotoolsCURIE: biotools:msnovelist
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  publication:
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    metadata:
      abstract: © 2022, The Author(s).Current methods for structure elucidation of
        small molecules rely on finding similarity with spectra of known compounds,
        but do not predict structures de novo for unknown compound classes. We present
        MSNovelist, which combines fingerprint prediction with an encoder–decoder
        neural network to generate structures de novo solely from tandem mass spectrometry
        (MS2) spectra. In an evaluation with 3,863 MS2 spectra from the Global Natural
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        61% of correct database annotations, without having ever seen the structure
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        suited to complement library-based annotation in the case of poorly represented
        analyte classes and novel compounds.
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      - name: Bocker S.
      - name: Zamboni N.
      citationCount: 1
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      journal: Nature Methods
      title: 'MSNovelist: de novo structure generation from mass spectra'
    note: null
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    type: []
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  - term: Small molecules
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  - term: Machine learning
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  - term: Lipids
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- accessibility: Open access
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    fundrefid: null
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  - email: null
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  - email: null
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    name: François Fenaille
    note: null
    orcidid: null
    rorid: null
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    url: null
  description: A multi-platform digital infrastructure for interoperable metabolite
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      uri: http://edamontology.org/operation_3431
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  homepage: https://peakforest.org
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  language:
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  lastUpdate: '2025-11-03T16:47:12.424836Z'
  license: Other
  link:
  - note: null
    type:
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  name: PeakForest
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  owner: Jennifer
  publication:
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    metadata:
      abstract: '© 2022, The Author(s).Introduction: Accuracy of feature annotation
        and metabolite identification in biological samples is a key element in metabolomics
        research. However, the annotation process is often hampered by the lack of
        spectral reference data in experimental conditions, as well as logistical
        difficulties in the spectral data management and exchange of annotations between
        laboratories. Objectives: To design an open-source infrastructure allowing
        hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with
        an ergonomic Web interface and Web services to support metabolite annotation
        and laboratory data management. Methods: We developed the PeakForest infrastructure,
        an open-source Java tool with automatic programming interfaces that can be
        deployed locally to organize spectral data for metabolome annotation in laboratories.
        Standardized operating procedures and formats were included to ensure data
        quality and interoperability, in line with international recommendations and
        FAIR principles. Results: PeakForest is able to capture and store experimental
        spectral MS and NMR metadata as well as collect and display signal annotations.
        This modular system provides a structured database with inbuilt tools to curate
        information, browse and reuse spectral information in data treatment. PeakForest
        offers data formalization and centralization at the laboratory level, facilitating
        shared spectral data across laboratories and integration into public databases.
        Conclusion: PeakForest is a comprehensive resource which addresses a technical
        bottleneck, namely large-scale spectral data annotation and metabolite identification
        for metabolomics laboratories with multiple instruments. PeakForest databases
        can be used in conjunction with bespoke data analysis pipelines in the Galaxy
        environment, offering the opportunity to meet the evolving needs of metabolomics
        research. Developed and tested by the French metabolomics community, PeakForest
        is freely-available at https://github.com/peakforest.'
      authors:
      - name: Paulhe N.
      - name: Canlet C.
      - name: Damont A.
      - name: Peyriga L.
      - name: Durand S.
      - name: Deborde C.
      - name: Alves S.
      - name: Bernillon S.
      - name: Berton T.
      - name: Bir R.
      - name: Bouville A.
      - name: Cahoreau E.
      - name: Centeno D.
      - name: Costantino R.
      - name: Debrauwer L.
      - name: Delabriere A.
      - name: Duperier C.
      - name: Emery S.
      - name: Flandin A.
      - name: Hohenester U.
      - name: Jacob D.
      - name: Joly C.
      - name: Jousse C.
      - name: Lagree M.
      - name: Lamari N.
      - name: Lefebvre M.
      - name: Lopez-Piffet C.
      - name: Lyan B.
      - name: Maucourt M.
      - name: Migne C.
      - name: Olivier M.-F.
      - name: Rathahao-Paris E.
      - name: Petriacq P.
      - name: Pinelli J.
      - name: Roch L.
      - name: Roger P.
      - name: Roques S.
      - name: Tabet J.-C.
      - name: Tremblay-Franco M.
      - name: Traikia M.
      - name: Warnet A.
      - name: Zhendre V.
      - name: Rolin D.
      - name: Jourdan F.
      - name: Thevenot E.
      - name: Moing A.
      - name: Jamin E.
      - name: Fenaille F.
      - name: Junot C.
      - name: Pujos-Guillot E.
      - name: Giacomoni F.
      citationCount: 0
      date: '2022-06-01T00:00:00Z'
      journal: Metabolomics
      title: 'PeakForest: a multi-platform digital infrastructure for interoperable
        metabolite spectral data and metadata management'
    note: null
    pmcid: PMC9197906
    pmid: '35699774'
    type: []
    version: null
  relation: []
  toolType:
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  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_3172
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: NMR
    uri: http://edamontology.org/topic_0593
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
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  description: Statistical, functional and integrative analysis of metabolomics data
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    metadata:
      abstract: 'We present a new update to MetaboAnalyst (version 4.0) for comprehensive
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        data. Since the last major update in 2015, MetaboAnalyst has continued to
        evolve based on user feedback and technological advancements in the field.
        For this year''s update, four newkey features have been added to MetaboAnalyst
        4.0, including: (1) real-time R command tracking and display coupled with
        the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways
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      authors:
      - name: Chong J.
      - name: Soufan O.
      - name: Li C.
      - name: Caraus I.
      - name: Li S.
      - name: Bourque G.
      - name: Wishart D.S.
      - name: Xia J.
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        instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC–HRMS
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      - name: Basu N.
      - name: Xia J.
      citationCount: 730
      date: '2022-08-01T00:00:00Z'
      journal: Nature Protocols
      title: Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration
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    note: null
    pmcid: null
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  - term: Small molecules
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  validated: 1
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    metadata: null
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  relation: []
  toolType:
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  topic:
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  - term: Metabolomics
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  additionDate: '2016-10-20T10:31:19Z'
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    typeEntity: Person
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  description: PeptideShaker is a search engine independent platform for interpretation
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  documentation:
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  homepage_status: 0
  language:
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  publication:
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    metadata:
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    note: null
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  - term: Proteome
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    metadata:
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        designed to facilitate common management and productivity tasks for neuroimaging
        and associated data. In particular, XNAT enables qualitycontrol procedures
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        forms. Newly added data are stored in a virtual quarantine until an authorized
        user has validated it. XNAT subsequently maintains a history profile to track
        all changes made to the managed data. User access to the archive is provided
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        explore emergent relations across data types, and to share their data with
        the broader neuroimaging community. © Copyright 2007 by Humana Press Inc.
        All rights of any nature whatsoever are reserved.
      authors:
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      - name: Olsen T.R.
      - name: Ramaratnam M.
      - name: Buckner R.L.
      citationCount: 378
      date: '2007-03-01T00:00:00Z'
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    note: null
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    type:
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  - doi: 10.1162/jocn.2009.21407
    metadata:
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        to 96 years all acquired on the same scanner using identical sequences. Each
        subject was scanned on two or more visits, separated by at least 1 year for
        a total of 373 imaging sessions. Subjects were characterized using the Clinical
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        elsewhere considered to have "mild cognitive impairment." Another 14 subjects
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        (n = 88). For each scanning session, three or four individual T1-weighted
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        high contrast to noise, making the data amenable to a wide range of analytic
        approaches including automated computational analysis. Automated calculation
        of whole-brain volume is presented to demonstrate use of the data for measuring
        differences associated with normal aging and Alzheimer's disease. © 2010 Massachusetts
        Institute of Technology.
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      - name: Marcus D.S.
      - name: Fotenos A.F.
      - name: Csernansky J.G.
      - name: Morris J.C.
      - name: Buckner R.L.
      citationCount: 461
      date: '2010-12-01T00:00:00Z'
      journal: Journal of Cognitive Neuroscience
      title: 'Open access series of imaging studies: Longitudinal MRI data in nondemented
        and demented older adults'
    note: null
    pmcid: PMC2895005
    pmid: '19929323'
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    version: null
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3384
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Bioimaging
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  - term: Tomography
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  - term: Data management
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  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:50:39Z'
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  - note: null
    type: Downloads page
    url: https://openchrom.net/download
    version: null
  - note: null
    type: Source code
    url: https://github.com/OpenChrom/openchrom
    version: null
  editPermission:
    authors:
    - proteomics.bio.tools
    - Mailaender
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  function:
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    input:
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        term: Mass spectrometry spectra
        uri: http://edamontology.org/data_0943
      format:
      - term: dat
        uri: http://edamontology.org/format_1637
      - term: Thermo RAW
        uri: http://edamontology.org/format_3712
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: NetCDF
        uri: http://edamontology.org/format_3650
    note: null
    operation:
    - term: Chromatogram visualisation
      uri: http://edamontology.org/operation_3203
    - term: Spectral analysis
      uri: http://edamontology.org/operation_3214
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    - term: Mass spectrum visualisation
      uri: http://edamontology.org/operation_3694
    output:
    - data:
        term: Peptide mass fingerprint
        uri: http://edamontology.org/data_0944
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: NetCDF
        uri: http://edamontology.org/format_3650
      - term: mzML
        uri: http://edamontology.org/format_3244
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://www.openchrom.net/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-09-24T15:20:41.738330Z'
  license: EPL-1.0
  link:
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: Mature
  name: OpenChrom
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1186/1471-2105-11-405
    metadata:
      abstract: ''
      authors: []
      citationCount: 155
      date: '2010-07-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'OpenChrom: A cross-platform open source software for the mass spectrometric
        analysis of chromatographic data'
    note: null
    pmcid: null
    pmid: '20673335'
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Analytical chemistry
    uri: http://edamontology.org/topic_3370
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-01-21T16:40:38Z'
  biotoolsCURIE: biotools:DataDiscovery
  biotoolsID: DataDiscovery
  collectionID:
  - elixir-fr-sdp-2019
  - URGI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: urgi-support@inrae.fr
    fundrefid: null
    gridid: null
    name: urgi-support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Support
    url: null
  description: 'DataDiscovery aims at providing researchers a simple and fast access
    to relevant biological data using specific keywords and easy to use filters.


    This tool is expected to be easily customizable for specific filters, environments,
    or data schemas. Its current implementations supported by URGI are: WheatIS, Plant,
    RARe.'
  documentation:
  - note: General terms of use
    type:
    - Terms of use
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md
  - note: How to contribute
    type:
    - Contributions policy
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute
  - note: How to use
    type:
    - User manual
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md
  - note: How to install
    type:
    - Installation instructions
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup
  download: []
  editPermission:
    authors:
    - urgi-contact
    - cpommier
    - cmichotey
    - erlefloch
    - raphael.flores
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Data
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Relation extraction
      uri: http://edamontology.org/operation_3625
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Information retrieval
      uri: http://edamontology.org/operation_3908
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format: []
    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format: []
    - data:
        term: Identifier
        uri: http://edamontology.org/data_0842
      format: []
  homepage: https://urgi.versailles.inrae.fr/data-discovery/
  homepage_status: 0
  language:
  - JavaScript
  - Java
  - Bash
  lastUpdate: '2025-07-29T13:42:39.375595Z'
  license: BSD-3-Clause
  link:
  - note: GitLab code repository for DataDiscovery
    type:
    - Repository
    url: https://forgemia.inra.fr/urgi-is/data-discovery
  - note: Code repository mirror link for DataDiscovery
    type:
    - Mirror
    url: https://github.com/gnpis/DataDiscovery/
  maturity: Emerging
  name: DataDiscovery
  operatingSystem:
  - Linux
  otherID: []
  owner: nfrancillon
  publication:
  - doi: 10.3835/plantgenome2015.06.0038
    metadata:
      abstract: The genome sequences of many important Triticeae species, including
        bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained
        uncharacterized for a long time because their high repeat content, large sizes,
        and polyploidy. As a result of improvements in sequencing technologies and
        novel analyses strategies, several of these have recently been deciphered.
        These efforts have generated new insights into Triticeae biology and genome
        organization and have important implications for downstream usage by breeders,
        experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu)
        is an EU-funded project aimed at constructing hardware, software, and data
        infrastructure for genome-scale research in the life sciences. Since the Triticeae
        data are intrinsically complex, heterogenous, and distributed, the transPLANT
        consortium has undertaken efforts to develop common data formats and tools
        that enable the exchange and integration of data from distributed resources.
        Here we present an overview of the individual Triticeae genome resources hosted
        by transPLANT partners, introduce the objectives of transPLANT, and outline
        common developments and interfaces supporting integrated data access.
      authors:
      - name: Spannagl M.
      - name: Alaux M.
      - name: Lange M.
      - name: Bolser D.M.
      - name: Bader K.C.
      - name: Letellier T.
      - name: Kimmel E.
      - name: Flores R.
      - name: Pommier C.
      - name: Kerhornou A.
      - name: Walts B.
      - name: Nussbaumer T.
      - name: Grabmuller C.
      - name: Chen J.
      - name: Colmsee C.
      - name: Beier S.
      - name: Mascher M.
      - name: Schmutzer T.
      - name: Arend D.
      - name: Thanki A.
      - name: Ramirez-Gonzalez R.
      - name: Ayling M.
      - name: Ayling S.
      - name: Caccamo M.
      - name: Mayer K.F.X.
      - name: Scholz U.
      - name: Steinbach D.
      - name: Quesneville H.
      - name: Kersey P.J.
      citationCount: 6
      date: '2016-03-01T00:00:00Z'
      journal: Plant Genome
      title: TransPLANT resources for triticeae genomic data
    note: "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier,\
      \ T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer,\
      \ T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer,\
      \ T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo,\
      \ M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P.\
      \ (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1),\
      \ 13 p."
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1038/hortres.2016.56
    metadata:
      abstract: Viticulture, like other fields of agriculture, is currently facing
        important challenges that will be addressed only through sustained, dedicated
        and coordinated research. Although the methods used in biology have evolved
        tremendously in recent years and now involve the routine production of large
        data sets of varied nature, in many domains of study, including grapevine
        research, there is a need to improve the findability, accessibility, interoperability
        and reusability (FAIR-ness) of these data. Considering the heterogeneous nature
        of the data produced, the transnational nature of the scientific community
        and the experience gained elsewhere, we have formed an open working group,
        in the framework of the International Grapevine Genome Program (www.vitaceae.org),
        to construct a coordinated federation of information systems holding grapevine
        data distributed around the world, providing an integrated set of interfaces
        supporting advanced data modeling, rich semantic integration and the next
        generation of data mining tools. To achieve this goal, it will be critical
        to develop, implement and adopt appropriate standards for data annotation
        and formatting. The development of this system, the GrapeIS, linking genotypes
        to phenotypes, and scientific research to agronomical and oeneological data,
        should provide new insights into grape biology, and allow the development
        of new varieties to meet the challenges of biotic and abiotic stress, environmental
        change, and consumer demand.
      authors:
      - name: Adam-Blondon A.-F.
      - name: Alaux M.
      - name: Pommier C.
      - name: Cantu D.
      - name: Cheng Z.-M.
      - name: Cramer G.
      - name: Davies C.
      - name: Delrot S.
      - name: Deluc L.
      - name: Di Gaspero G.
      - name: Grimplet J.
      - name: Fennell A.
      - name: Londo J.
      - name: Kersey P.
      - name: Mattivi F.
      - name: Naithani S.
      - name: Neveu P.
      - name: Nikolski M.
      - name: Pezzotti M.
      - name: Reisch B.
      - name: Topfer R.
      - name: Vivier M.
      - name: Ware D.
      - name: Quesneville H.
      citationCount: 37
      date: '2016-11-23T00:00:00Z'
      journal: Horticulture Research
      title: Towards an open grapevine information system
    note: "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M.,\
      \ Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet,\
      \ J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu,\
      \ P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware,\
      \ D., Quesneville, H. (2016). Towards an open grapevine information system.\
      \ Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56"
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1186/s13059-018-1491-4
    metadata:
      abstract: The Wheat@URGI portal has been developed to provide the international
        community of researchers and breeders with access to the bread wheat reference
        genome sequence produced by the International Wheat Genome Sequencing Consortium.
        Genome browsers, BLAST, and InterMine tools have been established for in-depth
        exploration of the genome sequence together with additional linked datasets
        including physical maps, sequence variations, gene expression, and genetic
        and phenomic data from other international collaborative projects already
        stored in the GnpIS information system. The portal provides enhanced search
        and browser features that will facilitate the deployment of the latest genomics
        resources in wheat improvement.
      authors:
      - name: Alaux M.
      - name: Rogers J.
      - name: Letellier T.
      - name: Flores R.
      - name: Alfama F.
      - name: Pommier C.
      - name: Mohellibi N.
      - name: Durand S.
      - name: Kimmel E.
      - name: Michotey C.
      - name: Guerche C.
      - name: Loaec M.
      - name: Laine M.
      - name: Steinbach D.
      - name: Choulet F.
      - name: Rimbert H.
      - name: Leroy P.
      - name: Guilhot N.
      - name: Salse J.
      - name: Feuillet C.
      - name: Paux E.
      - name: Eversole K.
      - name: Adam-Blondon A.-F.
      - name: Quesneville H.
      citationCount: 181
      date: '2018-08-17T00:00:00Z'
      journal: Genome Biology
      title: Linking the International Wheat Genome Sequencing Consortium bread wheat
        reference genome sequence to wheat genetic and phenomic data
    note: "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama  F, Pommier C, Mohellibi\
      \ N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach\
      \ D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International\
      \ Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F,\
      \ Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium\
      \ bread wheat reference genome sequence to wheat genetic and phenomic data.\
      \ Genome Biology, 19:111."
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: wheatis
    type: usedBy
  - biotoolsID: RARe
    type: usedBy
  - biotoolsID: Plant_DataDiscovery
    type: usedBy
  toolType:
  - Web API
  - Web application
  - Web service
  - Database portal
  topic:
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 1
  version: []
- accessibility: null
  additionDate: '2019-11-27T10:47:08Z'
  biotoolsCURIE: biotools:OakMine
  biotoolsID: OakMine
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Quercus robur annotation database
  documentation:
  - note: null
    type:
    - API documentation
    url: http://intermine.readthedocs.org/en/latest/web-services/
  - note: null
    type:
    - User manual
    url: https://flymine.readthedocs.io/en/latest/
  download: []
  editPermission:
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    - cmichotey
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Over-representation data
        uri: http://edamontology.org/data_3753
      format: []
    - data:
        term: Query script
        uri: http://edamontology.org/data_3786
      format: []
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
  homepage: https://urgi.versailles.inra.fr/OakMine_PM1N
  homepage_status: 0
  language:
  - R
  - Ruby
  - Java
  - Python
  - JavaScript
  - Perl
  lastUpdate: '2025-07-29T13:42:35.424110Z'
  license: LGPL-2.1
  link:
  - note: null
    type:
    - Software catalogue
    url: https://registry.intermine.org
  - note: null
    type:
    - Other
    url: http://intermine.org
  maturity: Mature
  name: OakMine
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: InterMine
  publication:
  - doi: 10.1093/bioinformatics/bts577
    metadata:
      abstract: InterMine is an open-source data warehouse system that facilitates
        the building of databases with complex data integration requirements and a
        need for a fast customizable query facility. Using InterMine, large biological
        databases can be created from a range of heterogeneous data sources, and the
        extensible data model allows for easy integration of new data types. The analysis
        tools include a flexible query builder, genomic region search and a library
        of 'widgets' performing various statistical analyses. The results can be exported
        in many commonly used formats. InterMine is a fully extensible framework where
        developers can add new tools and functionality. Additionally, there is a comprehensive
        set of web services, for which client libraries are provided in five commonly
        used programming languages. © The Author 2012. Published by Oxford University
        Press. All rights reserved.
      authors:
      - name: Smith R.N.
      - name: Aleksic J.
      - name: Butano D.
      - name: Carr A.
      - name: Contrino S.
      - name: Hu F.
      - name: Lyne M.
      - name: Lyne R.
      - name: Kalderimis A.
      - name: Rutherford K.
      - name: Stepan R.
      - name: Sullivan J.
      - name: Wakeling M.
      - name: Watkins X.
      - name: Micklem G.
      citationCount: 202
      date: '2012-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'InterMine: A flexible data warehouse system for the integration and
        analysis of heterogeneous biological data'
    note: null
    pmcid: PMC3516146
    pmid: '23023984'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  - Web service
  - Database portal
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 1
  version:
  - '2.3'
- accessibility: null
  additionDate: '2019-11-27T10:47:40Z'
  biotoolsCURIE: biotools:WheatMine
  biotoolsID: WheatMine
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Wheat IWGSC RefSeq v1.0
  documentation:
  - note: null
    type:
    - API documentation
    url: http://intermine.readthedocs.org/en/latest/web-services/
  - note: null
    type:
    - User manual
    url: https://flymine.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors:
    - cmichotey
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Over-representation data
        uri: http://edamontology.org/data_3753
      format: []
    - data:
        term: Query script
        uri: http://edamontology.org/data_3786
      format: []
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
  homepage: https://urgi.versailles.inra.fr/WheatMine
  homepage_status: 0
  language:
  - R
  - Ruby
  - Java
  - Python
  - JavaScript
  - Perl
  lastUpdate: '2025-07-29T13:42:33.209390Z'
  license: LGPL-2.1
  link:
  - note: null
    type:
    - Software catalogue
    url: https://registry.intermine.org
  - note: null
    type:
    - Other
    url: http://intermine.org
  maturity: Mature
  name: WheatMine
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: InterMine
  publication:
  - doi: 10.1093/bioinformatics/bts577
    metadata:
      abstract: InterMine is an open-source data warehouse system that facilitates
        the building of databases with complex data integration requirements and a
        need for a fast customizable query facility. Using InterMine, large biological
        databases can be created from a range of heterogeneous data sources, and the
        extensible data model allows for easy integration of new data types. The analysis
        tools include a flexible query builder, genomic region search and a library
        of 'widgets' performing various statistical analyses. The results can be exported
        in many commonly used formats. InterMine is a fully extensible framework where
        developers can add new tools and functionality. Additionally, there is a comprehensive
        set of web services, for which client libraries are provided in five commonly
        used programming languages. © The Author 2012. Published by Oxford University
        Press. All rights reserved.
      authors:
      - name: Smith R.N.
      - name: Aleksic J.
      - name: Butano D.
      - name: Carr A.
      - name: Contrino S.
      - name: Hu F.
      - name: Lyne M.
      - name: Lyne R.
      - name: Kalderimis A.
      - name: Rutherford K.
      - name: Stepan R.
      - name: Sullivan J.
      - name: Wakeling M.
      - name: Watkins X.
      - name: Micklem G.
      citationCount: 202
      date: '2012-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'InterMine: A flexible data warehouse system for the integration and
        analysis of heterogeneous biological data'
    note: null
    pmcid: PMC3516146
    pmid: '23023984'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  - Web service
  - Database portal
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2015-08-03T09:36:21Z'
  biotoolsCURIE: biotools:online_sbml_validator
  biotoolsID: online_sbml_validator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Frank Bergmann
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
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    url: https://www.biocatalogue.org
  - email: frank.bergmann@bioquant.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Frank Bergmann
    note: null
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  description: Check the syntax and internal consistency of files in SBML (The Systems
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      - term: SBML
        uri: http://edamontology.org/format_2585
    note: null
    operation:
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      uri: http://edamontology.org/operation_2422
    - term: Format validation
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    output: []
  homepage: https://sbml.bioquant.uni-heidelberg.de/validator_servlet/
  homepage_status: 0
  language:
  - Java
  - Python
  lastUpdate: '2025-07-07T11:10:03.422874Z'
  license: LGPL-2.0
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  - note: null
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    - Service
    url: https://sbml.org/facilities/
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  name: Online SBML Validator
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  otherID: []
  owner: frankbergmann
  publication: []
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2023-06-14T13:47:49.064543Z'
  biotoolsCURIE: biotools:virtual_imaging_platform
  biotoolsID: virtual_imaging_platform
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: VIP is a web portal for medical imaging applications. It allows users
    to access scientific applications as a service (directly through the web browser
    with no installation required), as well as distributed computing resources in
    a transparent manner. It exploits the resources available in the biomed virtual
    organization of the EGI e-infrastructure to offer an open service to researchers
    worldwide.
  documentation:
  - note: null
    type:
    - Other
    url: https://github.com/virtual-imaging-platform/VIP-portal/wiki
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  - note: null
    type: Source code
    url: https://github.com/virtual-imaging-platform/
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    input:
    - data:
        term: Image
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      format:
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        uri: http://edamontology.org/format_2333
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://vip.creatis.insa-lyon.fr
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-06-06T11:51:24.125664Z'
  license: CECILL-B
  link:
  - note: null
    type:
    - Service
    url: https://vip.creatis.insa-lyon.fr/
  maturity: Mature
  name: Virtual Imaging Platform
  operatingSystem: []
  otherID: []
  owner: sorina.pop
  publication:
  - doi: 10.1109/tmi.2012.2220154
    metadata:
      abstract: This paper presents the Virtual Imaging Platform (VIP), a platform
        accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of
        object models and medical image simulators, and to provide access to distributed
        computing and storage resources. A complete overview is presented, describing
        the ontologies designed to share models in a common repository, the workflow
        template used to integrate simulators, and the tools and strategies used to
        exploit computing and storage resources. Simulation results obtained in four
        image modalities and with different models show that VIP is versatile and
        robust enough to support large simulations. The platform currently has 200
        registered users who consumed 33 years of CPU time in 2011. © 1982-2012 IEEE.
      authors:
      - name: Glatard T.
      - name: Lartizien C.
      - name: Gibaud B.
      - name: Da Silva R.F.
      - name: Forestier G.
      - name: Cervenansky F.
      - name: Alessandrini M.
      - name: Benoit-Cattin H.
      - name: Bernard O.
      - name: Camarasu-Pop S.
      - name: Cerezo N.
      - name: Clarysse P.
      - name: Gaignard A.
      - name: Hugonnard P.
      - name: Liebgott H.
      - name: Marache S.
      - name: Marion A.
      - name: Montagnat J.
      - name: Tabary J.
      - name: Friboulet D.
      citationCount: 88
      date: '2013-01-10T00:00:00Z'
      journal: IEEE Transactions on Medical Imaging
      title: A virtual imaging platform for multi-modality medical image simulation
    note: null
    pmcid: null
    pmid: '23014715'
    type: []
    version: null
  relation: []
  toolType:
  - Bioinformatics portal
  topic: []
  validated: 0
  version:
  - 3.0.1
- accessibility: null
  additionDate: '2025-05-23T06:39:06.695509Z'
  biotoolsCURIE: biotools:rspace
  biotoolsID: rspace
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'RSpace is an open-source platform that orchestrates research workflows
    into FAIR data management ecosystems.

    RSpace is a continuously evolving community-inspired open-source research data
    management platform for research organizations and cloud/commons providers compliant
    with regulatory standards by design. Researchers and Research Data Managers create
    FAIR data workflows through a modern and user-centric research data management
    frontend with electronic laboratory notebook, intuitive research sample management,
    and file management solutions integrated seamlessly with research data management
    tools and infrastructure researchers and their organizations already use.'
  documentation:
  - note: null
    type:
    - General
    url: https://documentation.researchspace.com/
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  homepage: https://www.researchspace.com
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2025-05-23T06:39:06.698074Z'
  license: AGPL-3.0
  link:
  - note: ResearchSpace provides services and support around RSpace
    type:
    - Service
    url: https://www.researchspace.com
  - note: GitHub organisation page with all relevant repositories for RSpace
    type:
    - Repository
    url: https://github.com/rspace-os
  - note: null
    type:
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    url: https://bsky.app/profile/researchspace.com
  maturity: Mature
  name: RSpace
  operatingSystem: []
  otherID: []
  owner: tilomat
  publication: []
  relation: []
  toolType:
  - Web application
  - Web API
  - Command-line tool
  - Web service
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  - term: Chemistry
    uri: http://edamontology.org/topic_3314
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Laboratory information management
    uri: http://edamontology.org/topic_0607
  - term: Physics
    uri: http://edamontology.org/topic_3318
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 0
  version:
  - '2.1'
- accessibility: null
  additionDate: '2016-05-17T10:18:56Z'
  biotoolsCURIE: biotools:splicemachine
  biotoolsID: splicemachine
  collectionID:
  - BIG N2N
  - VIB
  - Plant Systems Biology
  - UGent
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ugent.be
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: yves.vandepeer@psb.vib-ugent.be
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Splice site prediction.
  documentation:
  - note: null
    type:
    - General
    url: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Splice site prediction
      uri: http://edamontology.org/operation_0433
    output:
    - data:
        term: Sequence motif (nucleic acid)
        uri: http://edamontology.org/data_2070
      format: []
  homepage: http://bioinformatics.psb.ugent.be/software/details/SpliceMachine
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-05-13T13:36:17.236762Z'
  license: null
  link: []
  maturity: null
  name: SpliceMachine
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Katrijn.Vannerum@ugent.be
  publication:
  - doi: 10.1093/bioinformatics/bti166
    metadata: null
    note: null
    pmcid: null
    pmid: '15564294'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2016-07-12T10:54:05Z'
  biotoolsCURIE: biotools:pia
  biotoolsID: pia
  collectionID:
  - KNIME
  - de.NBI
  - Proteomics
  - BioInfra.Prot
  - CUBiMed.RUB
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: julian.uszkoreit@rub.de
    fundrefid: null
    gridid: null
    name: Julian Uszkoreit
    note: null
    orcidid: http://orcid.org/0000-0001-7522-4007
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: cubimed@rub.de
    fundrefid: null
    gridid: null
    name: CUBiMed.RUB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  description: The main focus lays on the integrated inference algorithms, concluding
    the proteins from a set of identified spectra. But it also allows you to integrate
    results of various search engines, inspect your peptide spectrum matches, calculate
    FDR values across different results and visualize the correspondence between PSMs,
    peptides and proteins.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/medbioinf/pia/wiki
  download:
  - note: null
    type: Source code
    url: https://github.com/mpc-bioinformatics/pia
    version: null
  - note: null
    type: Software package
    url: http://bioconda.github.io/recipes/pia/README.html
    version: null
  - note: null
    type: Binaries
    url: https://github.com/mpc-bioinformatics/pia/releases
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/julianusz/pia
    version: null
  editPermission:
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  elixirCommunity:
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  elixirNode:
  - Germany
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry spectra
        uri: http://edamontology.org/data_0943
      format:
      - term: Mascot .dat file
        uri: http://edamontology.org/format_3713
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: PRIDE XML
        uri: http://edamontology.org/format_3684
      - term: X!Tandem XML
        uri: http://edamontology.org/format_3711
      - term: MSF
        uri: http://edamontology.org/format_3702
      - term: mzTab
        uri: http://edamontology.org/format_3681
    note: PIA allows you to inspect the results of common proteomics spectrum identification
      search engines, combine them seamlessly and conduct statistical analyses. The
      main focus of PIA lays on the integrated inference algorithms, i.e. concluding
      the proteins from a set of identified spectra. But it also allows you to inspect
      your peptide spectrum matches, calculate FDR values across different search
      engine results and visualize the correspondence between PSMs, peptides and proteins.
      Search engine results in several formats peptide spectrum matches (PSMs) and
      peptides Inferred Proteins
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Target-Decoy
      uri: http://edamontology.org/operation_3649
    output:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: Sequence feature table format (text)
        uri: http://edamontology.org/format_2206
      - term: KNIME datatable format
        uri: http://edamontology.org/format_3765
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: mzTab
        uri: http://edamontology.org/format_3681
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
    - data:
        term: Protein identifier
        uri: http://edamontology.org/data_0989
      format:
      - term: Sequence feature table format (text)
        uri: http://edamontology.org/format_2206
      - term: KNIME datatable format
        uri: http://edamontology.org/format_3765
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: mzTab
        uri: http://edamontology.org/format_3681
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
  homepage: https://github.com/medbioinf/pia
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-05-02T13:15:26.717477Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/medbioinf/pia
  maturity: Mature
  name: PIA - Protein Inference Algorithms
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: julianu
  publication:
  - doi: 10.1021/acs.jproteome.5b00121
    metadata:
      abstract: Protein inference connects the peptide spectrum matches (PSMs) obtained
        from database search engines back to proteins, which are typically at the
        heart of most proteomics studies. Different search engines yield different
        PSMs and thus different protein lists. Analysis of results from one or multiple
        search engines is often hampered by different data exchange formats and lack
        of convenient and intuitive user interfaces. We present PIA, a flexible software
        suite for combining PSMs from different search engine runs and turning these
        into consistent results. PIA can be integrated into proteomics data analysis
        workflows in several ways. A user-friendly graphical user interface can be
        run either locally or (e.g., for larger core facilities) from a central server.
        For automated data processing, stand-alone tools are available. PIA implements
        several established protein inference algorithms and can combine results from
        different search engines seamlessly. On several benchmark data sets, we show
        that PIA can identify a larger number of proteins at the same protein FDR
        when compared to that using inference based on a single search engine. PIA
        supports the majority of established search engines and data in the mzIdentML
        standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.
      authors:
      - name: Uszkoreit J.
      - name: Maerkens A.
      - name: Perez-Riverol Y.
      - name: Meyer H.E.
      - name: Marcus K.
      - name: Stephan C.
      - name: Kohlbacher O.
      - name: Eisenacher M.
      citationCount: 57
      date: '2015-07-02T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface'
    note: null
    pmcid: null
    pmid: '25938255'
    type:
    - Primary
    version: null
  - doi: 10.1021/acs.jproteome.8b00723
    metadata:
      abstract: Proteomics using LC-MS/MS has become one of the main methods to analyze
        the proteins in biological samples in high-throughput. But the existing mass-spectrometry
        instruments are still limited with respect to resolution and measurable mass
        ranges, which is one of the main reasons why shotgun proteomics is the major
        approach. Here proteins are digested, which leads to the identification and
        quantification of peptides instead. While often neglected, the important step
        of protein inference needs to be conducted to infer from the identified peptides
        to the actual proteins in the original sample. In this work, we highlight
        some of the previously published and newly added features of the tool PIA
        - Protein Inference Algorithms, which helps the user with the protein inference
        of measured samples. We also highlight the importance of the usage of PSI
        standard file formats, as PIA is the only current software supporting all
        available standards used for spectrum identification and protein inference.
        Additionally, we briefly describe the benefits of working with workflow environments
        for proteomics analyses and show the new features of the PIA nodes for the
        KNIME Analytics Platform. Finally, we benchmark PIA against a recently published
        data set for isoform detection. PIA is open source and available for download
        on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the
        community extensions inside the KNIME analytics platform.
      authors:
      - name: Uszkoreit J.
      - name: Perez-Riverol Y.
      - name: Eggers B.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 30
      date: '2019-02-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: Protein Inference Using PIA Workflows and PSI Standard File Formats
    note: null
    pmcid: null
    pmid: '30474983'
    type: []
    version: null
  relation:
  - biotoolsID: knime
    type: uses
  toolType:
  - Command-line tool
  - Library
  - Desktop application
  - Workflow
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Protein variants
    uri: http://edamontology.org/topic_3120
  validated: 1
  version:
  - '1.5'
- accessibility: Open access (with restrictions)
  additionDate: '2017-04-22T17:35:18Z'
  biotoolsCURIE: biotools:gemma
  biotoolsID: gemma
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: pavlab-support@msl.ubc.ca
    fundrefid: null
    gridid: null
    name: Pavlidis Lab Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://pavlab.msl.ubc.ca/
  description: Gemma provides data, experimental design annotations, and differential
    expression analysis results for thousands of microarray and RNA-seq experiments.
    We re-analyze raw data from public sources (primarily NCBI GEO), annotate experimental
    conditions, conduct quality control and compute differential expression using
    standardized procedures. We have especially good coverage of experiments relevant
    to the nervous system.
  documentation:
  - note: null
    type:
    - General
    url: https://pavlidislab.github.io/Gemma/
  - note: Documentation for the Gemma REST API.
    type:
    - API documentation
    url: https://gemma.msl.ubc.ca/resources/restapidocs/
  download:
  - note: null
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    url: https://github.com/PavlidisLab/Gemma/releases
    version: null
  editPermission:
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    type: group
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  function:
  - cmd: null
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    - data:
        term: Raw microarray data
        uri: http://edamontology.org/data_3110
      format: []
    note: null
    operation:
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    output:
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format: []
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format: []
  homepage: https://gemma.msl.ubc.ca/
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2025-04-22T22:09:03.811075Z'
  license: CC-BY-NC-4.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    url: https://github.com/PavlidisLab/Gemma
  maturity: Mature
  name: Gemma
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: artrymix
  publication:
  - doi: 10.1093/bioinformatics/btp259
    metadata:
      abstract: 'Motivation: Many microarray datasets are available online with formalized
        standards describing the probe sequences and expression values. Unfortunately,
        the description, conditions and parameters of the experiments are less commonly
        formalized and often occur as natural language text. This hinders searching,
        high-throughput analysis, organization and integration of the datasets. Results:
        We use the lexical resources and software tools from the Unified Medical Language
        System (UMLS) to extract concepts from text. We then link the UMLS concepts
        to classes in open biomedical ontologies. The result is accessible and clear
        semantic annotations of gene expression experiments. We applied the method
        to 595 expression experiments from Gemma, a resource for re-use and meta-analysis
        of gene expression profiling data. We evaluated and corrected all stages of
        the annotation process. The majority of missed annotations were due to a lack
        of cross-references. The most error-prone stage was the extraction of concepts
        from phrases. Final review of the annotations in context of the experiments
        revealed 89% precision. A naive system, lacking the phrase to concept corrections
        is 68% precise. We have integrated this annotation pipeline into Gemma. ©
        2009 The Author(s).'
      authors:
      - name: French L.
      - name: Lane S.
      - name: Law T.
      - name: Xu L.
      - name: Pavlidis P.
      citationCount: 9
      date: '2009-06-09T00:00:00Z'
      journal: Bioinformatics
      title: Application and evaluation of automated semantic annotation of gene expression
        experiments
    note: null
    pmcid: PMC2687992
    pmid: '19376825'
    type:
    - Primary
    version: null
  - doi: 10.1093/database/baab006
    metadata:
      abstract: 'Vast amounts of transcriptomic data reside in public repositories,
        but effective reuse remains challenging. Issues include unstructured dataset
        metadata, inconsistent data processing and quality control, and inconsistent
        probe-gene mappings across microarray technologies. Thus, extensive curation
        and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics
        system was created to help address these issues. Gemma consists of a database
        of curated transcriptomic datasets, analytical software, a web interface and
        web services. Here we present an update on Gemma''s holdings, data processing
        and analysis pipelines, our curation guidelines, and software features. As
        of June 2020, Gemma contains 10 811 manually curated datasets (primarily human,
        mouse and rat), over 395 000 samples and hundreds of curated transcriptomic
        platforms (both microarray and RNA sequencing). Dataset topics were represented
        with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic
        annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of
        conditions and tissues, it captures a large majority of available brain-related
        datasets, accounting for 34% of its holdings. Users can access the curated
        data and differential expression analyses through the Gemma website, RESTful
        service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html'
      authors:
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