WP3 - Standard Data Models and Terminologies

WP Resources

• Completed Deliverables
• Pending Deliverables
• All Documents

Title	Work Package	Lead benneficiary	Dissemination level		Due delivery date
D3.1 - Identification of Consortium Use Cases	WP3	EMBL	Public		Sep 2008
D3.2 - Development of High-Level Domain Model Version 1	WP3	EMBL	Public		Dec 2008
D3.3 - Standard Reference Sequences, Made Available from Ensembl	WP3	EMBL	Public		Jun 2009
D3.4 - Scope and Range Requirements of Specialized Domain Models.	WP3	EMBL	Public		Jun 2009
D3.5 - A High-Level Domain Model Version 2, with Sample/Phenotype Focus	WP3	EMBL	Public		Jun 2009
D3.6 - A High-Level Domain Model Version 3	WP3	EMBL	Public		Dec 2009
D3.7 - Derivation and Specification of Exchange Format	WP3	EMBL	Public		Dec 2009
D3.8 - DAS Implementation for GEN2PHEN Data	WP3	EMBL	Public		Dec 2009

Title	Work Package	Lead benneficiary	Dissemination level		Due delivery date
D3.9 - Iterative Specialized Domain Modelling Complete	WP3	EMBL	Public		Dec 2011

	Title	Work Package	Resource Type	Post date
	MOLGENIS and D2R	WP3, WP6	Other	21 Oct 2010 - 09:18
	New variation XML version (v1.2) is made available	WP3		9 May 2010 - 06:11
	LSDB object model	WP3, WP4		3 May 2010 - 13:40
	RDFization of exchange formats	WP3		18 Apr 2010 - 09:40
	GEN2PHEN Phenotype file format reference	WP3	Working document	8 Feb 2010 - 18:37
	LSDB - Controlled vocabulary terms	WP3		8 Jan 2010 - 11:01
	LSDB minimal requirements (D3.4), compared to LOVD and the LSDB XML format	WP3, WP4		4 Dec 2009 - 14:18
	Exchange format for LSDBs	WP3		29 Oct 2009 - 15:37
	Findis Prototype Web Service	WP3, WP6		21 Oct 2009 - 19:11
	Exchange format	WP3		12 Oct 2009 - 10:23
	Ontologies	WP3		9 Oct 2009 - 11:47
	Standards	WP3		9 Oct 2009 - 08:35
	Genotype data models	WP3		9 Oct 2009 - 08:34
	Modeling resources	WP2, WP3		5 Oct 2009 - 14:51
	D3.5 High-Level Domain Model Version 2, with Sample/Phenotype Focus	WP3	Deliverable	19 Aug 2009 - 10:54
	D3.4 Scope and Range Requirements of Specialized Domain Models	WP3	Deliverable	19 Aug 2009 - 10:51
	D3.3 Standard Reference Sequences, Made Available from Ensembl	WP3	Deliverable	19 Aug 2009 - 10:46
	Web Service Interfaces to LSDBs - Browser Point of View	WP3, WP4, WP6, WP7	Other	29 May 2009 - 13:26
	D3.2 - Development of High Level Domain Model version 1	WP3	Deliverable	7 May 2009 - 15:52
	D3.1 - Identification of Consortium Use Cases	WP3	Deliverable	7 May 2009 - 15:37
	Web services and exchange formats wiki	WP3, WP4, WP6, WP7		29 Apr 2009 - 22:36

• View all deliverables for all WPs

Description

This work package will take the domain analysis documents and priority use cases produced by WP2, and build on these to create reference data models upon which all our subsequent database development and implementation work will be based. Inter-compatible data models will be devised that will support each type of G2P database and data exchange. These data models will also be aligned with genomics data standards being developed in the clinical domain, for example by HL7. The model(s) will be formalized via submission to standards organisation(s). Subsequently, as new scientific issues arise, the models will be enhanced accordingly via a rolling review process. A similar standardisation path will be followed with mutation nomenclatures. However, for the complex field of G2P ontologies, this work package will not undertake direct ontology development work. It will instead devise a plan for precisely incorporating suitable ontologies into G2P databases. WP3 will thus provide mission-critical ‘blue-prints’ upon which all our database development work will be based. By standardising the data models and terminologies from an early stage, and registering these as official global standards, this work package will ensure that the databases and other deliverables from all subsequent work packages are maximally interoperable.