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Leiden Open Variation Database

Abbreviation:LOVD

Recommended

General Information

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

Homepage https://www.lovd.nl/3.0/home

Countries that developed this resource Netherlands

Created in 2004

Taxonomic range

Homo sapiens

Knowledge Domains

Subjects

User-defined Tags

Functional impact of genetic variants

In the following recommendations:

Advanced Genetics

How to cite this record FAIRsharing.org: LOVD; Leiden Open Variation Database; DOI: https://doi.org/10.25504/FAIRsharing.21tjj7; Last edited: March 18, 2021, 10:22 a.m.; Last accessed: Oct 20 2021 1:49 a.m.

Publication for citation LOVD v.2.0: the next generation in gene variant databases. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT; Human Mutation ; 2011; 10.1002/humu.21438;

This record is maintained by ifokkema ORCID

Record added: April 22, 2017, 10:41 p.m.
Record updated: March 18, 2021, 10:22 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.21tjj7' by 'The FAIRsharing Team' at 10:22, 18 Mar 2021 (approved):

	'contact' has been modified:
		Before: 
		After: General Contact

	'contactORCID' has been modified:
		Before: 0000-0002-1368-1939
		After:

Edits to 'https://fairsharing.org/FAIRsharing.21tjj7' by 'The FAIRsharing Team' at 10:21, 18 Mar 2021 (approved):

	'standardsImplemented' has been modified:
		Before:
		After:
			HGNC Gene Symbols, Gene Names and IDs
		Added:
			HGNC Gene Symbols, Gene Names and IDs
		Removed:

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.lovd.nl/3.0/faq
			contact form|http://www.lovd.nl/3.0/contact
			online documentation|http://www.lovd.nl/3.0/docs/
			twitter|@LOVD
		After:
			FAQ|https://www.lovd.nl/3.0/faq
			blog|https://www.lovd.nl/3.0/news
			contact form|https://www.lovd.nl/3.0/contact
			help|https://www.lovd.nl/3.0/docs/manual.html
			twitter|@LOVD
			wikipedia|https://en.wikipedia.org/wiki/Leiden_Open_Variation_Database
		Added:
			FAQ|https://www.lovd.nl/3.0/faq
			blog|https://www.lovd.nl/3.0/news
			contact form|https://www.lovd.nl/3.0/contact
			help|https://www.lovd.nl/3.0/docs/manual.html
			wikipedia|https://en.wikipedia.org/wiki/Leiden_Open_Variation_Database
		Removed:
			FAQ|http://www.lovd.nl/3.0/faq
			contact form|http://www.lovd.nl/3.0/contact
			online documentation|http://www.lovd.nl/3.0/docs/

	'description' has been modified:
		Before: The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also provides patient-centered data storage and storage of NGS data, also of variants outside of genes. LOVD is open source, released under the GPL license, and is actively being improved.
		After: The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes. 

	'onto_disciplines' has been modified:
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			Biomedical Science
			Human Genetics
			Life Science
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			Biomedical Science
			Human Genetics
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		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			Genetic Polymorphism
			deoxyribonucleic acid
			variant
		After:
			Genetic Polymorphism
			deoxyribonucleic acid
			disease
			gene
			genetic disorder
			phenotype
			variant
		Added:
			disease
			gene
			genetic disorder
			phenotype
		Removed:

	'miriam_id' has been modified:
		Before: None
		After: 

	'dataProcesses' has been modified:
		Before:
		After:
			Search All Installations, data access, https://www.lovd.nl/3.0/search
			Search and Browse All Installation Locations, data access, https://www.lovd.nl/3.0/public_list
			Download Gene List, data release, https://www.lovd.nl/3.0/public_list?format=text/plain
			Search and Browse Gene List by Location, data access, https://grenada.lumc.nl/LSDB_list/lsdbs
			Browse Genes, data access, https://databases.lovd.nl/shared/genes
			Browse Transcripts, data access, https://databases.lovd.nl/whole_genome/transcripts
			Browse Variants, data access, https://databases.lovd.nl/whole_genome/variants
		Added:
			Search All Installations, data access, https://www.lovd.nl/3.0/search
			Search and Browse All Installation Locations, data access, https://www.lovd.nl/3.0/public_list
			Download Gene List, data release, https://www.lovd.nl/3.0/public_list?format=text/plain
			Search and Browse Gene List by Location, data access, https://grenada.lumc.nl/LSDB_list/lsdbs
			Browse Genes, data access, https://databases.lovd.nl/shared/genes
			Browse Transcripts, data access, https://databases.lovd.nl/whole_genome/transcripts
			Browse Variants, data access, https://databases.lovd.nl/whole_genome/variants
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://www.lovd.nl/3.0/docs/manual.html|Data Retrieval API Documentation (Section 11.1)
			REST|https://www.lovd.nl/3.0/docs/manual.html|Data Submision API Documentation (Section 11.2)
		Added:
			REST|https://www.lovd.nl/3.0/docs/manual.html|Data Retrieval API Documentation (Section 11.1)
			REST|https://www.lovd.nl/3.0/docs/manual.html|Data Submision API Documentation (Section 11.2)
		Removed:

	'homepage' has been modified:
		Before: http://www.lovd.nl/
		After: https://www.lovd.nl/3.0/home

Edits to 'https://fairsharing.org/FAIRsharing.21tjj7' by 'ifokkema' at 19:28, 15 May 2017 (approved):

	'description' has been modified:
		Before: Leiden Open Variation Database. (LOVD) provides a flexible|freely available tool for Gene-centered collection and display of DNA variations. 
		After: The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also provides patient-centered data storage and storage of NGS data, also of variants outside of genes. LOVD is open source, released under the GPL license, and is actively being improved.

Support

General

FAQ	FAQ
blog	News
contact form	Contact Form
help	User Guide
twitter	@LOVD
wikipedia	LOVD Wikipedia Page

Additional Information

Contact

General Contact

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Database software

GNU General Public License (GPL) 3.0

Data Release

Download Gene List

https://www.lovd.nl/3.0/public_list?format=text/plain

Data Access

Search All Installations	https://www.lovd.nl/3.0/search
Search and Browse All Installation Locations	https://www.lovd.nl/3.0/public_list
Search and Browse Gene List by Location	https://grenada.lumc.nl/LSDB_list/lsdbs
Browse Genes	https://databases.lovd.nl/shared/genes
Browse Transcripts	https://databases.lovd.nl/whole_genome/transcripts
Browse Variants	https://databases.lovd.nl/whole_genome/variants

REST Web Services

Data Retrieval API Documentation (Section 11.1)	https://www.lovd.nl/3.0/docs/manual.html
Data Submision API Documentation (Section 11.2)	https://www.lovd.nl/3.0/docs/manual.html

Publications

LOVD v.2.0: the next generation in gene variant databases.

Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT
Human Mutation 2011

View Paper (PubMed) View Publication

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

Fokkema IF, den Dunnen JT, Taschner PE
Human Mutation 2005

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

HGNC Gene Symbols, Gene Names and IDs

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

European Variation Archive

Implementing Policies

Credit

Record Maintainer

This record is maintained by ifokkema ORCID

Funds

European Commission FP7 (Government body)

Maintains

Leiden University Medical Center (LUMC), Leiden, The Netherlands (University) Lead

Grant Number(s)

200754 (European Commission FP7)

Leiden Open Variation Database

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