Participating Groups

Members Organizations

• WormBase
• Berkeley Drosophila Genome Project
• FlyBase
• Mouse Genome Informatics
• Sanger Institute

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 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.

  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

• MGED Ontology

  The MGED (Microarray Gene Expression Data) Ontology is using SO
  terms for sequence annotation.

  The
  MGED Ontology: a resource for semantics-based description of
  microarray experiments Bioinformatics 2006 22(7):866-873;
  doi:10.1093/bioinformatics/btl005

Natural Language Processing and Text Mining

• Royal Society of Chemistry

  The RSC have created a semantic enrichment
  project, with access to 100 articles annotated using OBO
  ontologies including SO.

• NLIP group at the University of Cambridge

  Members of this group are using SO to aid anaphora resolution in
  NLP of biomedical texts and have created a tool for FlyBase
  annotators to identify salient entities within papers.

  Bootstrapping
  the Recognition and Anaphoric Linking of Named Entities in
  Drosophila Pacific Symposium on Biocomputing
  11:100-111(2006) Andreas Vlachos, Caroline Gasperin, Ian Lewin,
  Ted Briscoe

• Semi-supervised
  anaphora resolution in biomedical texts Proceedings of
  BioNLP in HLT-NAACL, New York, pages 96-103.Caroline Gasperin

Genomic Analysis

• Comparative Genomics Library

  The Yandell Lab developed CGL, a perl library that parses SO
  annotated genomes and uses the ontology to traverse the contents
  of annotations. They have used library in the analysis of
  several genomes.

  Large-Scale
  Trends in the Evolution of Gene Structures within 11 Animal
  Genomes Mark Yandell, Chris J. Mungall, Chris Smith, Simon
  Prochnik, Joshua Kaminker, George Hartzell, Suzanna Lewis and
  Gerald M. Rubin

• Sybil – Web Based Softwware for Comparative Genomics

  Sybil uses SO terms via the Chado schema.

Programming Initiatives

• BioPerl

  BioPerl is SO aware.

  Open source tools and toolkits for bioinformatics: significance, and where are we? Briefings in Bioinformatics 2006 7(3):287-296 Jason E. Stajich and Hilmar Lapp

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

To get your project listed here, please email
keilbeck AT genetics.utah.edu