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 | 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/ |