TABLE 1
FROM:
Life Sciences and the web: a new era for collaboration
Jonathan A Sagotsky, Le Zhang, Zhihui Wang, Sean Martin & Thomas S Deisboeck
doi:10.1038/msb.2008.39
BACK TO ARTICLETable 1: A table of commonly used bioinformatics data standards
| Examples of Web 2.0 applications data standards and semantic web projects | |
|---|---|
| Web 2.0 | |
| OpenWetWare (http://openwetware.org) | A wiki for the synthetic biology and biological engineering community |
| YeastPheromoneModel.org (http://yeastpheromonemodel.org/wiki/Main_Page) | A wiki used as a modeling resource for the Saccharomyces cerevisiae mating pathway |
| UsefulChem (http://usefulchem.wikispaces.com) | An example of OpenNotebook science |
| Nature Network (http://network.nature.com) | A web 2.0 platform facilitating scientific networking |
| SciVee (http://scivee.tv) | A site for sharing science videos |
| Standards | |
| BioPax (http://biopax.org) | Open source data exchange ontology and format for biological pathways |
| CellML (http://www.cellml.org/) | XML-based open standard for storing and exchanging computer-based mathematical models; utilizes MathML and RDF |
| FuGE (http://fuge.sf.net) | XML-based model for shared components in different functional genomics domains |
| LSID (http://lsids.sf.net) | Life Science Identifier is a unique and persistent ID for naming documents and objects |
| Mage-ML (http://www.mged.org/Workgroups/MAGE/mage.html) | Language based on XML for representing gene expression |
| mzXML (http://tools.proteomecenter.org/mzXMLschema.php) | Mass spectrometry representation based on XML |
| SBML (http://sbml.org) | Machine-readable format for representing quantitative models |
| Semantic Web | |
| YeastHub (http://yeasthub.gersteinlab.org) | Integration of diverse types of biological data stored in a variety of formats |
| CViT (http://www.cvit.org) | Computational and mathematical cancer modeling community; includes a semantic RDF-based repository |
| WikiProfessional (http://www.wikiprofessional.org) | Web-based environment that combines wiki functionalities with semantic navigation capabilities |
| Freebase (http://www.freebase.com) | Free online database for structured information |
