Members Organizations
Groups Using or Providing Tools for SO Compliant Data
Genome Databases
All Chado databases employ SO. This is not a comprehensive list.
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SGD
The Saccharomyces Genome Database is annotating with SO terms.
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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
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MGI
The Mouse Genome Informatics are restructuring genome feature objects in their database based on features from SO.
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DictyBase
The online informatics resource for Dictyostelium are using SO terms.
DictyBase have created Modware: An object oriented API for Chado.
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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.
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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
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VectorBase
The online informatics resource uses SO terms via the GMOD Chado schema.
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Schizosaccharomyces pombe
The S. pombe database uses SO terms via the GMOD Chado schema.
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wFleaBase
The water flea genome database uses SO terms via the GMOD Chado schema.
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Tair
The Arabidopsis Information Resource uses SO terms via the GMOD Chado schema.
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Planarian Genome
Coming soon, the Schmidtea mediterranea genome database uses SO terms via the GMOD Chado schema.
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Fishmap
A Chado based zebrafish genomics knowledgebase.
Genome Integration
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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)
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Atlas
The Atlas Integrated Database System is using SO as a mapping to GenBank Features.
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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.
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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.
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Gramene
The gramene resource for comparative grass genomics uses SO to type its sequence features.
Gene Expression
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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
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Royal Society of Chemistry
The RSC have created a semantic enrichment project, with access to 100 articles annotated using OBO ontologies including SO.
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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
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Semi-supervised anaphora resolution in biomedical texts Proceedings of BioNLP in HLT-NAACL, New York, pages 96-103.Caroline Gasperin
Genomic Analysis
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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
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Sybil - Web Based Softwware for Comparative Genomics
Sybil uses SO terms via the Chado schema.
Programming Initiatives
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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
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RedFly
RedFly are working with SO to unify the CIS regulatory region terminology
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PharmGkb
PharmGkb are working with SO to describe sequence variation.
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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
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PRO
PRO (Protein Ontology) are using the SO/biosapiens terms to describe protein features.
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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