From Schemalet Wiki

Contents 1 Description 2 Class diagram 2.1 Documentation of classes, attributes and associations 3 Comments 3.1 Relation to other LSDBs 3.2 Extensions 3.2.1 Genotype and Genomic observations 4 Data formats 4.1 XML 5 Mappings 5.1 PaGE-OM Mapping 5.2 MAGE-TAB Mapping

Description

Consensus object model for locus specific databases, based on the LSDB:Checklist, data modelling workshop report. Note: Newer work and version(s) is available on gen2phen knowledge center site

Class diagram

Documentation of classes, attributes and associations

• aliases - Aliases of variant (typically alternative or older (legacy named) versions)
• author - Author of publication (Identified by name and optional affiliation
• consequence - Consequences of variation. For example see variation effect in [http://www.sequenceontology.org sequence ontology}: alters splicing, alters transcription..
• contact - Contact details of source system/site.
• doi - Digital object identifier of publication
• ethnicity - Ethnicity of Patient, coded using specific ontology terms/standards
• frequency - Frequency of variation in optional population. Is either number of cases or categorized frequency: at least once, once, 2-10 times, 11-99 times, >100 times.
• exon - Number/code of exon or "sub"-exon (see http://www.lrg-sequence.org/docs/LRG.pdf for more information)
• geographical_region - Geographical region of Patient.
• lsdb - Container for data submission information. Root element of XML document.
• name (identifiable) - Optional display name (user readable name of object)
• name (variant) - Name of variant using specific naming scheme (typically HGVS). Type defines sequence context (DNA,RNA and AA) where name is given.
• ontology_term - Ontology term as defined in FuGE. Provides name of ontology source and accession number of term.
• origin - Origin of variation (cv term). Example values from LOVD:

in vitro (cloned)
familial
familial, consanguineous parents
sporadic
sporadic, consanguineous parents
sporadic, non-consanguineous parents
sporadic, consanguinity parents? 
uniparental disomy
de novo
de novo, somatic mosaicism
de novo, germline mosaicism
de novo, germline and somatic mosaicism
de novo, in patient
de novo, in patient (maternal allele)
de novo, in patient (paternal allele)
de novo, in mother
de novo, in mother (grandmaternal allele)
de novo, in mother (grandpaternal allele)
de novo, in father
de novo, in father (grandmaternal allele)
de novo, in father (grandpaternal allele

• parental_origin - Parental origin of variation (controlled vocabulary (ontology) term)). Codes from LOVD:

Parent #1
Parent #2 
Paternal (inferred)
Paternal (confirmed)
Maternal (inferred)
Maternal (confirmed)
de novo
de novo, on paternal allele 
de novo, maternal allele

• pathogenicity - Pathogenicity of variant using ontology term.
• phenotype - Phenotype of patient (as ontology term). Can be also outcome of diagnose (have specific disease)
• population - Name of population (optional) where frequency is observed. (Is an ontology term)
• publication - Publication
• pubmed_id - Pubmed id of publication
• ref_seq - Cross-reference for reference sequence
• reference - Database cross-references
• restriction_site - Restriction enzyme cut site for example -RsaI.
• remark - Remarks or annotations using controlled vocabulary terms.
• seq_changes - Related sequence variants on RNA and AA levels
• source - Information on source system, identified by name and list of URLs
• submitter_id - Local identifier of identifiable (variant and patient) as used by submitter
• variant_detection - Detection template (DNA,RNA,AA) and technique of detection like DHPLC

Comments

Relation to other LSDBs

• Sample level is needed in diagnostic databases
• Population (national mutation) databases databases do not have patient information (disease association must be done directly or to generalized super class (like Observation_target in PaGE-OM)

Extensions

Genotype and Genomic observations

Data formats

XML

• XML schema implementation based on the model (pre-alpha version)
• XML schema

Mappings

PaGE-OM Mapping

• DNA_variation - Genomic_allele
• Phenotype - Phenotype_feature and Observed_value, with more detailed info how measurement is done (Observation_method)
• Frequency - Frequency
• Patient - Individual
• Population - Panel
• Alignment to PAGE-OM

MAGE-TAB Mapping

• Object model (the core lsdb model + MAGE investigation framework)