Table 1 XML languages for the representation of biological data types
From: XML-based approaches for the integration of heterogeneous bio-molecular data
Type of Data | Format | Concrete Scope | Version | Comments |
|---|---|---|---|---|
Molecular entities | BSML [57] | Biological sequences and sequence annotation | v.3.1/2005 | Uses DTD. Included in EMBLxml. |
| Â | ProXML [58] | Protein sequences, structures and families | v.1.0/2006 | Uses XSD. Included within HOBIT formats |
| Â | RNAML [59] | RNA sequence, structure and experimental data | v.1.1/2002 | Uses XSD |
| Â | AGAVE [16] | Biological sequences and sequence annotation | 2003 | XSD Included in EMBLxml |
| Â | Uniprot XSD [121] | Representation of UniProt Records | 2004 | XSD, Successor of SP (SwissProt) ML format |
| Â | EMBLxml [17] | Biological sequences and sequence annotation | v.1.1./2007 | Uses XSD. Currently includes BSML and AGAVE. |
| Â | GAME [18] | Genome and Sequence | v.0.3/1999 | Uses DTD |
| Â | SequenceML | Sequence Information | v.2.1 2006 | Designed to replace FASTA. Belongs to HOBIT XML formats. |
Biological Expression | GeneXML [122] | Gene expression data | - | Uses DTD |
| Â | MAGE-ML [123] | Microarray expression data | v.1.0/2006 | Uses DTD |
System Biology | CellML [124] | Models of biochemical reaction networks | v.1.1/2006 | Uses DTD. Available conversion to BioPAX. |
| Â | SBML [57] | Models of biochemical reaction networks | Lev. 2/2007 | Uses XSD. Available conversion to BioPAX. |
| Â | PSI-MI [125] | Protein Interactions | v.2.5/2005 | Uses XSD and OBO. Linked with OBO vocabularies. |
| Â | BioPAX [60] | Metabolic pathways, molecular interactions | Lev. 3/2008 | Uses OWL. Linked to OBO vocabularies. |
| Â | CML [126] | Description of Molecules and Reactions | v.2.1./2003 | Uses XSD |