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.

    FlyBase: 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 Consortium

  • 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 terms.

    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 schema.

  • Schizosaccharomyces pombe

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

  • wFleaBase

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

  • 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 datamodel 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.

    Curation 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 terminology

  • 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.

    The 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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