Skip to main content

Table 1 Glossary

From: VarioML framework for comprehensive variation data representation and exchange

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
Extended Backus-Naur Form A notation that expresses the grammar of a computer language.
GEN2PHEN EU project integrating genotype and phenotype data.
GSVML Genomic Sequence Variation Markup Language See Nakaya J, Kimura M, et al. 2010[16]
HPO Human Phenotype Ontology
Jackson Java JSON library
JAVA General programming language
JAXB Java JSON library
JSON Javascript Object Notation
LSDB Gene variant database, Locus Specific Database -
MAGE-TAB A tab-delimited format for representing functional genomics data.
MIRIAM The MIRIAM Registry provides a set of online services for the generation of unique and perennial identifiers, in the form of URIs.
MOLGENIS Software generating infrastructure (databases, APIs, GUIs) for life science projects.
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.
ORCID Open Researcher and Contributor Identification
PML/DVAR An implementation of the PaGE-OM object model.
RelaxNG Schema definition language for use with XML.
RDF Resource Description Framework
Schematron High-level schema definition language for use with XML.
SKOS Simple Knowledge Organization System
SO Sequence Ontology
UML Unified Modeling Language
VariO Variation Ontology
VCF Variant Call Format
XGAP XGAP is an open and flexible object model for xQTL, GWL, GWA and mutagenesis data
XML eXtensible Markup Language