Table 1

Name Definition URL
API Application programming interface -
BSVM Pioneering early LSDB integration standard. See Tyrelle G, King GC, 2003[15]
Café Variome Variation data publishing service webcite
Extended Backus-Naur Form A notation that expresses the grammar of a computer language. webcite
GEN2PHEN EU project integrating genotype and phenotype data. webcite
GSVML Genomic Sequence Variation Markup Language See Nakaya J, Kimura M, et al. 2010[16]
HPO Human Phenotype Ontology webcite
Jackson Java JSON library webcite
JAVA General programming language webcite
JAXB Java JSON library webcite
JSON Javascript Object Notation webcite
LSDB Gene variant database, Locus Specific Database -
MAGE-TAB A tab-delimited format for representing functional genomics data. webcite
MIRIAM The MIRIAM Registry provides a set of online services for the generation of unique and perennial identifiers, in the form of URIs. webcite
MOLGENIS Software generating infrastructure (databases, APIs, GUIs) for life science projects. webcite
Object Model An abstract representation of a domain’s concepts, data, and relationships between these, used to design or generate software. -
Observ-OM A simple system to format and exchange observation data. webcite
ORCID Open Researcher and Contributor Identification webcite
PML/DVAR An implementation of the PaGE-OM object model. webcite
RelaxNG Schema definition language for use with XML. webcite
RDF Resource Description Framework webcite
Schematron High-level schema definition language for use with XML. webcite
SKOS Simple Knowledge Organization System webcite
SO Sequence Ontology webcite
UML Unified Modeling Language webcite
VariO Variation Ontology webcite
VCF Variant Call Format webcite
XGAP XGAP is an open and flexible object model for xQTL, GWL, GWA and mutagenesis data webcite
XML eXtensible Markup Language webcite

Byrne et al.

Byrne et al. BMC Bioinformatics 2012 13:254   doi:10.1186/1471-2105-13-254

Open Data