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  additionDate: '2024-03-12T10:56:44.977314Z'
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  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
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  download: []
  editPermission:
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    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
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    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output: []
  homepage: https://github.com/AbeelLab/lorikeet
  homepage_status: 0
  language:
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  lastUpdate: '2024-03-12T10:56:44.980036Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: lorikeet
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Genotype and phenotype
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2024-03-12T09:39:30.275596Z'
  biotoolsCURIE: biotools:bbtools
  biotoolsID: bbtools
  collectionID: []
  community: null
  confidence_flag: null
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  description: 'BBTools is a suite of fast, multithreaded bioinformatics tools designed
    for analysis of DNA and RNA sequence data. BBTools can handle common sequencing
    file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,
    with autodetection of quality encoding and interleaving. It is written in Java
    and works on any platform supporting Java, including Linux, MacOS, and Microsoft
    Windows and Linux; there are no dependencies other than Java (version 7 or higher).
    Program descriptions and options are shown when running the shell scripts with
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    BBTools is open source and free for unlimited use, and is used regularly by DOE
    JGI and other institutions around the world.'
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    output: []
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  homepage_status: 0
  language: []
  lastUpdate: '2024-03-12T09:39:30.279447Z'
  license: null
  link: []
  maturity: null
  name: BBTools
  operatingSystem: []
  otherID: []
  owner: paulzierep
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-03-11T16:40:14.136794Z'
  biotoolsCURIE: biotools:legsta
  biotoolsID: legsta
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Performs in silico Legionella pneumophila sequence based typing
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/tseemann/legsta
  homepage_status: 0
  language: []
  lastUpdate: '2024-03-11T16:40:14.139298Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: legsta
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  - Command-line tool
  topic:
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  validated: 0
  version:
  - 0.5.1
  - 0.3.7
  - 0.3.2
  - '0.2'
- accessibility: Open access
  additionDate: '2024-03-11T15:00:11.214878Z'
  biotoolsCURIE: biotools:kofamscan
  biotoolsID: kofamscan
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: KofamScan is a gene function annotation tool based on KEGG Orthology
    and hidden Markov model. You need KOfam database to use this tool.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence analysis
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    - term: Gene functional annotation
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    output: []
  homepage: https://github.com/takaram/kofam_scan
  homepage_status: 0
  language: []
  lastUpdate: '2024-03-11T15:00:11.219298Z'
  license: MIT
  link: []
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  name: kofamscan
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  owner: rlibouban
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  relation: []
  toolType:
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  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 1.3.0
- accessibility: Open access
  additionDate: '2024-03-11T13:25:13.344697Z'
  biotoolsCURIE: biotools:plasflow
  biotoolsID: plasflow
  collectionID: []
  community: null
  confidence_flag: tool
  cost: null
  credit: []
  description: PlasFlow is a set of scripts used for prediction of plasmid sequences
    in metagenomic contigs.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
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    output: []
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  link: []
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  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - '1.1'
- accessibility: null
  additionDate: '2015-08-03T09:35:17Z'
  biotoolsCURIE: biotools:infernal_cmscan
  biotoolsID: infernal_cmscan
  collectionID:
  - EBI Tools
  - Job Dispatcher Tools
  community: null
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sean Eddy
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
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    gridid: null
    name: EMBL-EBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Job Dispatcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: http://www.ebi.ac.uk/jdispatcher
  description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
    databases (e.g. Rfam) for RNA structure and sequence similarities.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: https://www.ebi.ac.uk/jdispatcher/help
  - note: null
    type:
    - General
    url: http://eddylab.org/infernal/
  download:
  - note: null
    type: Downloads page
    url: http://eddylab.org/infernal/
    version: null
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  language: []
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  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: Infernal cmscan (EBI)
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1093/bioinformatics/btt509
    metadata:
      abstract: 'Summary: Infernal builds probabilistic profiles of the sequence and
        secondary structure of an RNA family called covariance models (CMs) from structurally
        annotated multiple sequence alignments given as input. Infernal uses CMs to
        search for new family members in sequence databases and to create potentially
        large multiple sequence alignments. Version 1.1 of Infernal introduces a new
        filter pipeline for RNA homology search based on accelerated profile hidden
        Markov model (HMM) methods and HMM-banded CM alignment methods. This enables
        ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration
        over exhaustive non-filtered CM searches. © The Author 2013. Published by
        Oxford University Press. All rights reserved.'
      authors:
      - name: Nawrocki E.P.
      - name: Eddy S.R.
      citationCount: 1686
      date: '2013-11-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Infernal 1.1: 100-fold faster RNA homology searches'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac240
    metadata:
      abstract: The EMBL-EBI search and sequence analysis tools frameworks provide
        integrated access to EMBL-EBI's data resources and core bioinformatics analytical
        tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search
        engine across nearly 5 billion entries, while the Job Dispatcher tools framework
        (https://www.ebi.ac.uk/services) enables the scientific community to perform
        a diverse range of sequence analysis using popular bioinformatics applications.
        Both allow users to interact through user-friendly web applications, as well
        as via RESTful and SOAP-based APIs. Here, we describe recent improvements
        to these services and updates made to accommodate the increasing data requirements
        during the COVID-19 pandemic.
      authors:
      - name: Madeira F.
      - name: Pearce M.
      - name: Tivey A.R.N.
      - name: Basutkar P.
      - name: Lee J.
      - name: Edbali O.
      - name: Madhusoodanan N.
      - name: Kolesnikov A.
      - name: Lopez R.
      citationCount: 699
      date: '2022-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: Search and sequence analysis tools services from EMBL-EBI in 2022
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation:
  - biotoolsID: infernal
    type: uses
  toolType:
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  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2015-01-29T15:47:33Z'
  biotoolsCURIE: biotools:TCoffee_EBI
  biotoolsID: TCoffee_EBI
  collectionID:
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  - EBI Tools
  - Job Dispatcher Tools
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Cedric Notredame
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: CRG
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Job Dispatcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
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  description: Multiple sequence alignment that combines several alignment methods.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: https://www.ebi.ac.uk/jdispatcher/help
  - note: null
    type:
    - General
    url: https://tcoffee.org/Projects/tcoffee/index.html
  download:
  - note: null
    type: Downloads page
    url: https://tcoffee.org/Projects/tcoffee/index.html
    version: null
  editPermission:
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    - biomadeira
    type: group
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment
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      format: []
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  homepage_status: 0
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  lastUpdate: '2024-01-12T16:33:19.565882Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: Mature
  name: T-Coffee (EBI)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1006/jmbi.2000.4042
    metadata:
      abstract: We describe a new method (T-Coffee) for multiple sequence alignment
        that provides a dramatic improvement in accuracy with a modest sacrifice in
        speed as compared to the most commonly used alternatives. The method is broadly
        based on the popular progressive approach to multiple alignment but avoids
        the most serious pitfalls caused by the greedy nature of this algorithm. With
        T-Coffee we pre-process a data set of all pair-wise alignments between the
        sequences. This provides us with a library of alignment information that can
        be used to guide the progressive alignment. Intermediate alignments are then
        based not only on the sequences to be aligned next but also on how all of
        the sequences align with each other. This alignment information can be derived
        from heterogeneous sources such as a mixture of alignment programs and/or
        structure superposition. Here, we illustrate the power of the approach by
        using a combination of local and global pair-wise alignments to generate the
        library. The resulting alignments are significantly more reliable, as determined
        by comparison with a set of 141 test cases, than any of the popular alternatives
        that we tried. The improvement, especially clear with the more difficult test
        cases, is always visible, regardless of the phylogenetic spread of the sequences
        in the tests. (C) 2000 Academic Press.
      authors:
      - name: Notredame C.
      - name: Higgins D.G.
      - name: Heringa J.
      citationCount: 5641
      date: '2000-09-08T00:00:00Z'
      journal: Journal of Molecular Biology
      title: 'T-coffee: A novel method for fast and accurate multiple sequence alignment'
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  - doi: 10.1093/nar/gkac240
    metadata:
      abstract: The EMBL-EBI search and sequence analysis tools frameworks provide
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        engine across nearly 5 billion entries, while the Job Dispatcher tools framework
        (https://www.ebi.ac.uk/services) enables the scientific community to perform
        a diverse range of sequence analysis using popular bioinformatics applications.
        Both allow users to interact through user-friendly web applications, as well
        as via RESTful and SOAP-based APIs. Here, we describe recent improvements
        to these services and updates made to accommodate the increasing data requirements
        during the COVID-19 pandemic.
      authors:
      - name: Madeira F.
      - name: Pearce M.
      - name: Tivey A.R.N.
      - name: Basutkar P.
      - name: Lee J.
      - name: Edbali O.
      - name: Madhusoodanan N.
      - name: Kolesnikov A.
      - name: Lopez R.
      citationCount: 651
      date: '2022-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: Search and sequence analysis tools services from EMBL-EBI in 2022
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation:
  - biotoolsID: tcoffee
    type: uses
  toolType:
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  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - '1'
- accessibility: Open access
  additionDate: '2023-12-13T14:54:35.138186Z'
  biotoolsCURIE: biotools:altair
  biotoolsID: altair
  collectionID:
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  - Rare Disease
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  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jorge.miguel.ferreira.silva@ua.pt
    fundrefid: null
    gridid: null
    name: Jorge M. Silva
    note: Researcher at IEETA. J.M.S. has received funding from the EC under grant
      agreement 101081813, Genomic Data Infrastructure.
    orcidid: http://orcid.org/0000-0002-6331-6091
    rorid: null
    typeEntity: Project
    typeRole:
    - Contributor
    url: null
  - email: pratas@ua.pt
    fundrefid: null
    gridid: null
    name: Diogo Pratas
    note: Researcher at IEETA. D.P. is funded by national funds through FCT – Fundação
      para a Ciência e a Tecnologia, I.P., under the Scientific Employment Stimulus
      - Institutional Call - reference CEECINST/00026/2018.
    orcidid: http://orcid.org/0000-0003-1176-552X
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  description: 'AltaiR is a C toolkit for alignment-free and spatial-temporal analysis
    of multi-FASTA data.


    This method provides alignment-free and spatial-temporal analysis of multi-FASTA
    data through the implementation of a C toolkit that is highly flexible and with
    characteristics covering large-scale data, namely extensive collections of genomes/proteomes.
    This toolkit is ideal for scenarios entangling the presence of multiple sequences
    from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading
    to increase the computational speed, is flexible for multiple applications, and
    does not contain external dependencies. The tool accepts any sequence(s) in (multi-)
    FASTA format.'
  documentation: []
  download: []
  editPermission:
    authors:
    - pratas
    type: group
  elixirCommunity: []
  elixirNode:
  - Portugal
  elixirPlatform:
  - Tools
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/cobilab/altair
  homepage_status: 0
  language:
  - C
  lastUpdate: '2023-12-13T14:54:35.146893Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/cobilab/altair
  maturity: Mature
  name: AltaiR
  operatingSystem:
  - Linux
  otherID: []
  owner: jorgeMFS
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Medicine
    uri: http://edamontology.org/topic_3303
  validated: 0
  version:
  - 1.0.1
- accessibility: Open access
  additionDate: '2021-01-18T10:20:32Z'
  biotoolsCURIE: biotools:virusurf
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  community: null
  confidence_flag: tool
  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: Stefano Ceri
    note: Professor of Database Systems at Politecnico di Milano
    orcidid: https://orcid.org/0000-0003-0671-2415
    rorid: null
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    typeRole:
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    url: https://ceri.faculty.polimi.it/
  - email: arif.canakoglu@polimi.it
    fundrefid: null
    gridid: null
    name: Arif Canakoglu
    note: Research assistant at Politecnico di Milano
    orcidid: https://orcid.org/0000-0003-4528-6586
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://www.deib.polimi.it/eng/people/details/626632
  - email: pietro.pinoli@polimi.it
    fundrefid: null
    gridid: null
    name: Pietro Pinoli
    note: Researcher at Politecnico di Milano
    orcidid: https://orcid.org/0000-0001-9786-2851
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: https://www.deib.polimi.it/ita/personale/dettagli/585322
  - email: anna.bernasconi@polimi.it
    fundrefid: null
    gridid: null
    name: Anna Bernasconi
    note: Research assistant at Politecnico di Milano
    orcidid: https://orcid.org/0000-0001-8016-5750
    rorid: null
    typeEntity: Person
    typeRole:
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  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole: []
    url: https://elixir-italy.org/
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-POLIMI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole: []
    url: https://www.deib.polimi.it/eng/elixir-iib
  description: "ViruSurf, available at http://gmql.eu/virusurf/, is a large public\
    \ database of viral sequences and integrated and curated metadata from heterogeneous\
    \ sources (RefSeq, GenBank, COG-UK, and NMDC); it also exposes computed nucleotide\
    \ and amino acid variants, called from original sequences. A GISAID-specific ViruSurf\
    \ database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these\
    \ functionalities. \n\nThe database is centered on sequences, described from their\
    \ biological, technological, and organizational dimensions. In addition, the analytical\
    \ dimension characterizes the sequence in terms of its annotations and variants.\
    \ The web interface enables expressing complex search queries in a simple way;\
    \ arbitrary search queries can freely combine conditions on attributes from the\
    \ four dimensions, extracting the resulting sequences."
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/DEIB-GECO/vue-metadata/wiki
  download: []
  editPermission:
    authors:
    - abernasconi
    - arif.canakoglu@polimi.it
    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
  homepage: http://gmql.eu/virusurf/
  homepage_status: 0
  language: []
  lastUpdate: '2023-12-03T20:55:22.756702Z'
  license: null
  link:
  - note: GISAID-specific ViruSurf database
    type:
    - Other
    url: http://gmql.eu/virusurf_gisaid/
  maturity: null
  name: ViruSurf
  operatingSystem: []
  otherID: []
  owner: abernasconi
  publication:
  - doi: 10.1093/nar/gkaa846
    metadata:
      abstract: ViruSurf, available at http://gmql.eu/virusurf/, is a large public
        database of viral sequences and integrated and curated metadata from heterogeneous
        sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide
        and amino acid variants, called from original sequences. A GISAID-specific
        ViruSurf database, available at http://gmql.eu/virusurf gisaid/, offers a
        subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2
        data are collected from the four sources; but ViruSurf contains other virus
        species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue.
        The database is centered on sequences, described from their biological, technological
        and organizational dimensions. In addition, the analytical dimension characterizes
        the sequence in terms of its annotations and variants. The web interface enables
        expressing complex search queries in a simple way; arbitrary search queries
        can freely combine conditions on attributes from the four dimensions, extracting
        the resulting sequences. Several example queries on the database confirm and
        possibly improve results from recent research papers; results can be recomputed
        over time and upon selected populations. Effective search over large and curated
        sequence data may enable faster responses to future threats that could arise
        from new viruses.
      authors:
      - name: Canakoglu A.
      - name: Pinoli P.
      - name: Bernasconi A.
      - name: Alfonsi T.
      - name: Melidis D.P.
      - name: Ceri S.
      citationCount: 32
      date: '2021-01-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'ViruSurf: An integrated database to investigate viral sequences'
    note: null
    pmcid: PMC7778888
    pmid: '33045721'
    type:
    - Primary
    version: null
  - doi: 10.1186/s12859-022-05022-0
    metadata:
      abstract: 'Background: Genomics and virology are unquestionably important, but
        complex, domains being investigated by a large number of scientists. The need
        to facilitate and support work within these domains requires sharing of databases,
        although it is often difficult to do so because of the different ways in which
        data is represented across the databases. To foster semantic interoperability,
        models are needed that provide a deep understanding and interpretation of
        the concepts in a domain, so that the data can be consistently interpreted
        among researchers. Results: In this research, we propose the use of conceptual
        models to support semantic interoperability among databases and assess their
        ontological clarity to support their effective use. This modeling effort is
        illustrated by its application to the Viral Conceptual Model (VCM) that captures
        and represents the sequencing of viruses, inspired by the need to understand
        the genomic aspects of the virus responsible for COVID-19. For achieving semantic
        clarity on the VCM, we leverage the “ontological unpacking” method, a process
        of ontological analysis that reveals the ontological foundation of the information
        that is represented in a conceptual model. This is accomplished by applying
        the stereotypes of the OntoUML ontology-driven conceptual modeling language.As
        a result, we propose a new OntoVCM, an ontologically grounded model, based
        on the initial VCM, but with guaranteed interoperability among the data sources
        that employ it. Conclusions: We propose and illustrate how the unpacking of
        the Viral Conceptual Model resolves several issues related to semantic interoperability,
        the importance of which is recognized by the “I” in FAIR principles. The research
        addresses conceptual uncertainty within the domain of SARS-CoV-2 data and
        knowledge.The method employed provides the basis for further analyses of complex
        models currently used in life science applications, but lacking ontological
        grounding, subsequently hindering the interoperability needed for scientists
        to progress their research.'
      authors:
      - name: Bernasconi A.
      - name: Guizzardi G.
      - name: Pastor O.
      - name: Storey V.C.
      citationCount: 6
      date: '2022-11-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'Semantic interoperability: ontological unpacking of a viral conceptual
        model'
    note: Description of the Viral Conceptual Model (VCM) used by ViruSurf
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: genosurf
    type: uses
  toolType:
  - Database portal
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Virology
    uri: http://edamontology.org/topic_0781
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-11-06T09:29:56.888140Z'
  biotoolsCURIE: biotools:genespace
  biotoolsID: genespace
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: 'GENESPACE: an R package for synteny- and orthology-constrained comparative
    genomics'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome alignment
      uri: http://edamontology.org/operation_3182
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/jtlovell/GENESPACE
  homepage_status: 0
  language:
  - R
  lastUpdate: '2023-11-06T09:31:59.658628Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/jtlovell/GENESPACE
  maturity: null
  name: GENESPACE
  operatingSystem: []
  otherID: []
  owner: alexcorm
  publication:
  - doi: 10.7554/eLife.78526
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version: []
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