Table 4 Standardization of data exchange formats and web services.
Domain | Format | Service | Relevant technologies |
|---|---|---|---|
Interaction Network | PSI-MI | PSICQUIC | DIP, STRING, STITCH, IntAct, Cytoscape, Cell Designer |
Glycoinformatics | GlycomicsObject | BioMoby | GLYDE-II, LINUCS, KEGG GLYCAN (KCF), RINGS |
Phyloinformatics | phyloXML, NeXML | PhyloWS | CIPRES, Kepler, BioPerl (Bio::Phylo), NEXUS |
Text-mining | U-Compare type system | U-Compare | UIMA, Whatizit, TerMine, iHOP, Allie |
BioSQL | BioSQL schema | - | BioPerl, BioRuby, BioPython, BioJava |