LSDB minimal requirements (D3.4), compared to LOVD and the LSDB XML format

See the current XML format: http://www.gen2phen.org/wiki/lsdb-xml-data-format and workshop notes: http://www.gen2phen.org/post/lsdb-minimal-requirements-johan-discussion-...

See also other LSDB/G2P check list

This list is a mapping between the LSDB minimal data requirements as listed in deliverable 3.4, LOVD 2.0/3.0 and the XML format currently under development (see link above). As the XML format will be developed further, this list will be updated.
Last update: 2010-01-21.

 

Name	D3.4 says	Availability in LOVD 2.0	Availability in LOVD 3.0 (planned)	Cafe Rouge	element or attribute currenly in XML format
Variant/Exon	Recommended	Standard, may be removed	Standard, may be removed	Recommended	variant/exon
Variant/DNA_genomic	Obligatory	Not available, but genomic position can automatically be generated	Always available (generated)	(Obligatory)*	variant/name and scheme attribute = 'HGVS' and variant/type='DNA'
Variant/DNA_coding	Recommended	Always available	Always available	(Obligatory)*	variant/name and scheme='HGVS' and variant/type='cDNA'
Variant/RNA	Obligatory	Always available	Always available	Recommended (might not be available)	variant/seq_change/variant/name
Variant/Protein	Obligatory	Always available	Always available	Recommended (might not be available)	variant/seq_change/variant/name
Variant/DBID	Obligatory	Always available	Always available	Should be generated by LSDB	variant/id
Variant/Reference	Obligatory	Not standard LOVD; can be derived from Patient/Reference	Undecided	Obligatory	variant/ref_seq
Variant/DNA_published	Recommended	Sometimes available	Sometimes available	Recommended	variant/aliases/variant/name
Variant/Detection/Template	Obligatory	Not standard LOVD; can be derived from Patient/Detection/Template	Always available; as Screening/Template	Obligatory	variant/variant_detection/template
Variant/Detection/Technique	Obligatory	Not standard LOVD; can be derived from Patient/Detection/Technique	Always available; as Screening/Technique	Obligatory	variant/variant_detection/technique
Variant/DNA_remark	Recommended	Compatible with Variant/Remarks which is sometimes available	Sometimes available; as Variant/Remarks	Recommended	variant/comment
Variant/Frequency	Recommended	Standard, may be removed	Standard, may be removed	Recommended	variant/frequency
Variant/Origin	Recommended	Not standard LOVD, can only partially be derived from other (optional) columns	Undecided	Recommended	variant/origin
Variant/Restriction_site	Optional	Standard, may be removed	Standard, may be removed	Optional	variant/restriction_site
Variant/Allele	Recommended	Always available	Undecided	Recommended	variant/genetic_origin/source
Variant/Pathogenicity	Recommended	Always available	Undecided	Recommended	variant/pathogenicity
Patient/Patient_ID	Obligatory	Non-public information	Non-public information	Obligatory	patient/original_id
Patient/Phenotype/Disease	Obligatory	Always available	Always available	Obligatory	patient/phenotype
Patient/Remarks	Recommended	Standard, may be removed	Standard, may be removed	Recommended	patient/comment
Patient/Origin/Geographic	Recommended	Sometimes available	Sometimes available	Recommended	patient/population (type="region")
Patient/Origin/Ethnic	Recommended	Sometimes available	Sometimes available	Recommended	patient/population (type="ethnic")
Patient/Gender	Recommended	Sometimes available	Sometimes available	Recommended	patient/gender
ID_submitterid	Obligatory	Sometimes available (field can be empty, which means the curator is the submitter)	Always available	Obligatory	source/id
Variant/HGNC gene Symbol	Obligatory			Obligatory	variant/gene/accession and source="HGNC"
Variant/Sharing policy (public/private)				Obligatory	variant/sharing_policy (since release 1.4)
Variant/Use permission (default Creative Commons 0)				Obligatory	variant/use_permission (since release 1.4)
		Legend
		Always available: Needs modification of LOVD to allow removal
		Standard, may be removed: Is enabled by default but users are allowed to remove these columns
		Sometimes available: Is available in LOVD but not enabled by default; users can activate these columns
		Not standard LOVD: Some LOVD's (especially Leiden-based) have these columns
		Undecided: May be same or similar as in LOVD 2.0, but we haven't decided on the exact implementation yet.
		(Obligatory)*: One of these fields needs to be present.