Table 1 Glossary

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/

Extended Backus-Naur Form

A notation that expresses the grammar of a computer language.

http://en.wikipedia.org/wiki/Backus-Naur_Form

GEN2PHEN

EU project integrating genotype and phenotype data.

http://www.gen2phen.org

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/

Jackson

Java JSON library

http://wiki.fasterxml.com/JacksonHome

JAVA

General programming language

http://www.java.com

JAXB

Java JSON library

http://jaxb.java.net/

JSON

Javascript Object Notation

http://en.wikipedia.org/wiki/JSON

LSDB

Gene variant database, Locus Specific Database

-

MAGE-TAB

A tab-delimited format for representing functional genomics data.

http://www.mged.org/mage-tab

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/

MOLGENIS

Software generating infrastructure (databases, APIs, GUIs) for life science projects.

http://www.molgenis.org

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

ORCID

Open Researcher and Contributor Identification

http://orcid.org/

PML/DVAR

An implementation of the PaGE-OM object model.

http://www.openpml.org/

RelaxNG

Schema definition language for use with XML.

http://relaxng.org/

RDF

Resource Description Framework

http://www.w3.org/RDF/

Schematron

High-level schema definition language for use with XML.

http://www.ascc.net/xml/resource/schematron/Schematron2000.html

SKOS

Simple Knowledge Organization System

http://www.w3.org/2004/02/skos/

SO

Sequence Ontology

http://www.sequenceontology.org/

UML

Unified Modeling Language

http://en.wikipedia.org/wiki/Unified_Modeling_Language

VariO

Variation Ontology

http://variationontology.org/

VCF

Variant Call Format

http://vcftools.sourceforge.net/specs.html

XGAP

XGAP is an open and flexible object model for xQTL, GWL, GWA and mutagenesis data

http://www.xgap.org

XML

eXtensible Markup Language

http://www.w3.org/XML/