Table 1

Glossary
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 http://cafevariome.org/ webcite
Extended Backus-Naur Form A notation that expresses the grammar of a computer language. http://en.wikipedia.org/wiki/Backus-Naur_Form webcite
GEN2PHEN EU project integrating genotype and phenotype data. http://www.gen2phen.org webcite
GSVML Genomic Sequence Variation Markup Language See Nakaya J, Kimura M, et al. 2010[16]
HPO Human Phenotype Ontology http://www.human-phenotype-ontology.org/ webcite
Jackson Java JSON library http://wiki.fasterxml.com/JacksonHome webcite
JAVA General programming language http://www.java.com webcite
JAXB Java JSON library http://jaxb.java.net/ webcite
JSON Javascript Object Notation http://en.wikipedia.org/wiki/JSON webcite
LSDB Gene variant database, Locus Specific Database -
MAGE-TAB A tab-delimited format for representing functional genomics data. http://www.mged.org/mage-tab webcite
MIRIAM The MIRIAM Registry provides a set of online services for the generation of unique and perennial identifiers, in the form of URIs. http://www.ebi.ac.uk/miriam/main/ webcite
MOLGENIS Software generating infrastructure (databases, APIs, GUIs) for life science projects. http://www.molgenis.org 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. http://www.molgenis.org/wiki/ObservStart webcite
ORCID Open Researcher and Contributor Identification http://orcid.org/ webcite
PML/DVAR An implementation of the PaGE-OM object model. http://www.openpml.org/ webcite
RelaxNG Schema definition language for use with XML. http://relaxng.org/ webcite
RDF Resource Description Framework http://www.w3.org/RDF/ webcite
Schematron High-level schema definition language for use with XML. http://www.ascc.net/xml/resource/schematron/Schematron2000.html webcite
SKOS Simple Knowledge Organization System http://www.w3.org/2004/02/skos/ webcite
SO Sequence Ontology http://www.sequenceontology.org/ webcite
UML Unified Modeling Language http://en.wikipedia.org/wiki/Unified_Modeling_Language webcite
VariO Variation Ontology http://variationontology.org/ webcite
VCF Variant Call Format http://vcftools.sourceforge.net/specs.html webcite
XGAP XGAP is an open and flexible object model for xQTL, GWL, GWA and mutagenesis data http://www.xgap.org webcite
XML eXtensible Markup Language http://www.w3.org/XML/ webcite

Byrne et al.

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

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