Participating Groups

Members Organizations


Groups Using or Providing Tools for SO Compliant Data

Genome Databases

All Chado databases employ SO. This is not a comprehensive list.

  • SGD

    The Saccharomyces Genome Database is annotating with SO terms.

  • FlyBase

    FlyBase is using SO terms to annotate features.

    genomes by the dozen
    Nucleic Acids Research 2007 35(Database
    issue):D486-D491;Madeline A. Crosby, Joshua L. Goodman, Victor
    B.Strelets, Peili Zhang, William M. Gelbart and The FlyBase

  • MGI

    The Mouse Genome Informatics are restructuring genome feature
    objects in their database based on features from SO.

  • DictyBase

    The online informatics resource for Dictyostelium are using SO

    DictyBase have created Modware: An object
    oriented API for Chado.

  • WormBase

    WormBase are creating SO compliant annotations.

    WormBase: a comprehensive data resource for Caenorhabditis
    biology and genomics
    Nucleic Acids Research, 2005, Vol. 33,
    Database issue D383-D389 Nansheng Chen, Todd W. Harris, Igor
    Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar,
    Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen,
    Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana
    Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller,
    Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei
    Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz,
    Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth,
    Paul W. Sternberg and Lincoln D. Stein

    WormBase are building ZMap; a replacement for Acedb as a
    sequence viewer for vertebrate annotation groups. ZMap uses SO
    to describe input data.

  • ParameciumDB

    ParameciumDB are creating SO compliant annotations using CHADO.

    ParameciumDB: a community resource that integrates the
    Paramecium tetraurelia genome sequence with genetic data

    Nucleic Acids Res. 2007 January; 35(Database issue): D439
    D444. Olivier Arnaiz, Scott Cain, Jean Cohen, and Linda Sperling

  • VectorBase

    The online informatics resource uses SO terms via the GMOD Chado

  • Schizosaccharomyces pombe

    The S. pombe database uses SO terms via the GMOD Chado

  • wFleaBase

    The water flea genome database uses SO terms via the GMOD Chado

  • Tair

    The Arabidopsis Information Resource uses SO terms via the GMOD
    Chado schema.

  • Planarian Genome

    Coming soon, the Schmidtea mediterranea genome database
    uses SO terms via the GMOD Chado schema.

  • Fishmap

    A Chado based zebrafish genomics knowledgebase.


Genome Integration

  • FlyMine

    FlyMine use SOFA to define the data model for annotations they import from FlyBase and Ensembl.

    Coming soon: accepted Genome Biology 2007 publication (Lyne et al)

  • Atlas

    The Atlas Integrated Database System is using SO as a mapping to
    GenBank Features.

  • VirGen

    VirGen uses SO to make a dictionary of synonyms to enhance
    keyword searching of viral genomes.

    of viral genomes: challenges, applications and the way forward
    BMC Bioinformatics. 2006; 7(Suppl 5): S12.Urmila
    Kulkarni-Kale, Shriram G Bhosle, G Sunitha Manjari, Manali
    Joshi, Sandeep Bansode, and Ashok S Kolaskar.

  • Bioinformatics Resource Center

    The BRC is composed of 8 individual bioinformatics resource
    centers sponsored by the NIAID to maintain data repositories for
    pathogen data. The BRC is SO compliant.

  • Gramene

    The gramene resource for comparative grass genomics uses SO to
    type its sequence features.


Gene Expression


Natural Language Processing and Text Mining


Genomic Analysis


Programming Initiatives


Working with SO

  • RedFly

    RedFly are working with SO to unify the CIS regulatory region

  • PharmGkb

    PharmGkb are working with SO to describe sequence variation.

  • RNA Ontology Consortium

    The RNA Ontology Consortium is working with SO to develop
    terminology to describe RNA.

    RNA Ontology Consortium: An open invitation to the RNA community
    RNA (2006), 12:533-541. Neocles B. Leontis, Russ B. Altman,
    Helen M. Berman, Steven E. Brenner, James W. Brown, David
    R. Engelke, Stephen C. Harvey, Stephen R. Holbrook, Fabrice
    Jossinet, Suzanna E. Lewis, Francois Major, David H. Mathews,
    Jane Richardson, James R. Williamson and Eric Westhof

  • PRO

    PRO (Protein Ontology) are using the SO/biosapiens terms to describe
    protein features.

  • Biosapiens

    Biosapiens joined forces with SO to catalogue polypeptide features.

Add Your Group to This List

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