Groups Using or Providing Tools for SO Compliant Data
All Chado databases employ SO. This is not a comprehensive list.
The Saccharomyces Genome Database is annotating with SO terms.
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
The Mouse Genome Informatics are restructuring genome feature
objects in their database based on features from SO.
The online informatics resource for Dictyostelium are using SO
DictyBase have created Modware: An object
oriented API for Chado.
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 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
The online informatics resource uses SO terms via the GMOD Chado
The S. pombe database uses SO terms via the GMOD Chado
The water flea genome database uses SO terms via the GMOD Chado
The Arabidopsis Information Resource uses SO terms via the GMOD
Coming soon, the Schmidtea mediterranea genome database
uses SO terms via the GMOD Chado schema.
A Chado based zebrafish genomics knowledgebase.
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)
The Atlas Integrated Database System is using SO as a mapping to
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.
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.
The gramene resource for comparative grass genomics uses SO to
type its sequence features.
The MGED (Microarray Gene Expression Data) Ontology is using SO
terms for sequence annotation.
MGED Ontology: a resource for semantics-based description of
microarray experiments Bioinformatics 2006 22(7):866-873;
Natural Language Processing and Text Mining
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.
the Recognition and Anaphoric Linking of Named Entities in
Drosophila Pacific Symposium on Biocomputing
11:100-111(2006) Andreas Vlachos, Caroline Gasperin, Ian Lewin,
anaphora resolution in biomedical texts Proceedings of
BioNLP in HLT-NAACL, New York, pages 96-103.Caroline Gasperin
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
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 uses SO terms via the Chado schema.
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 are working with SO to unify the CIS regulatory region
PharmGkb are working with SO to describe sequence variation.
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 (Protein Ontology) are using the SO/biosapiens terms to describe
Biosapiens joined forces with SO to catalogue polypeptide features.
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