| Language | Full Name | Developer | URL |
| . | Schema Format | Schema | Description |
| BSML | Bioinformatic Sequence Markup Language | LabBook | www.bsml.org |
| . | DTD | www.labbook.com/dtd/bsml2_2_annot.dtd | The Bioinformatic Sequence Markup Language is an open-standard protocol for the encoding and display of graphic genomic displays of DNA, RNA, and protein sequence information. |
| BIOML | BIOpolymer Markup Language | ProteoMetrics | www.bioml.com |
| . | DTD | www.bioml.com/BIOML/bioml.dtd | The BIOpolymer Markup Language (BIOML) is an XML language that is used to describe experimental information about proteins, genes, and other biopolymers. |
| PSDML | Protein Sequence Database Markup Language | National Biomedical Research Foundation | pir.georgetown.edu/pirwww |
| . | DTD | pir.georgetown.edu/pirwww/xml/psdml.dtd | The Protein Sequence Database Markup Language is an open-standard markup language used to store protein information in the Protein Information Resource (PIR) database. |
| AGAVE | Architecture for Genomic Annotation, Visualization and Exchange | DoubleTwist | www.agavexml.org |
| . | XSD | www.agavexml.org/schema/v3_0/agave.xsd | An architecture for genomic annotation, visualization and exchange from the AGAVE Community lead by DuobleTwist. |
| MSAML | Multiple Sequence Alignment Markup Language | Paul Gordon | maggie.cbr.nrc.ca/~gordonp/xml/MSAML |
| . | DTD | maggie.cbr.nrc.ca/~gordonp/xml/MSAML/dtd/msaml.dtd | The Multiple Sequence Alignments Markup Language was developed to make manipulation and extraction of multiple sequence alignment information easier by logically defining the parts of an alignment for use in an XML-based application. |
| GAME | Genome Annotation Markup Elements | BIOXML | www.bioxml.org/Projects/game |
| . | DTD | www.bioxml.org/dtds/game2/game.dtd | Genome Annotation Markup Elements is a markup language used in molecular biology for annotation of a biosequence. |
| MGED-ML | Microarray Gene Expression Database Markup Language | MGED Group/OMG | www.mged.org |
| . | DTD | ftp.omg.org/pub/docs/lifesci/01-11-02.dtd | The Microarray Gene Expression Database (MGED) group is a grass-roots movement to promote the adoption of standards in microarray experiments and data. Subsumes GeneXML, GEML and MAML. |
| CML | Chemical Markup Language | CMl.sourceforge | http://en.wikipedia.org/wiki/Chemical_Markup_Language |
| . | XSD | http://cml.sourceforge.net/schema/cmlCore.xsd | An XML markup language for representing basic chemical structures. |
| SBML | Systems Biology Markup Language | SBML.org | http://sbml.org |
| . | XSD | http://sbml.cvs.sourceforge.net/*checkout*/sbml/ specifications/sbml-level-2/version-3/schema/sbml.xsd | An XML markup language for representing models of biochemical reaction networks. |
| CellML | Cell Markup Language | CellML.org | http://www.cellml.org |
| . | DTD | http://www.cellml.org/specifications/cellml_1.1/#sec_cellml_1_1_dtd | An XML markup language for representing cellular processes. |