VarioML Schema Reference

For more information, see the GitHub repository, User wiki, and Website.

Contents



acknowledgement (VmlAcknowledgement)

Acknowledgement.

Elements

nametypecardinalitychoice group
namestringmandatory
grant_numberVmlDbXRefoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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age (VmlAge)

text node of type float

Age at the time of observation.

Attributes

nametypecardinalityvalue
codedbooleanoptional
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comment (VmlComment)

Comments are of type Evidence_ontology. The term 'attribute' is optional. See under description of "Evidence_ontology_term data type.

Comments can contain other comments.

Examples:

    <comment>
        <text>simple comment</text>
    </comment>

    <comment source="example_ontology" term="example term">
        <text>my defined comment</text>
    </comment>

    <comment>
        <text>whatever</text>
        <comment>
                <text>my structured comment</text>
        </comment>
    </comment>

    <comment>
        <text>whatever</text>
        <comment>
            <text>my complex structured comment</text>
            <evidence_code term="something"/>
            <db_xref accession="xyz"/>
        </comment>
    </comment> 

    <phenotype term='Autoimmune polyglandular syndrome type 1'>
     <comment term='symptom'><text>Hypoparathyroidism</text></comment>
     <comment term='symptom'><text>Addison's disease</text></comment>
     <comment term='symptom'><text>Mucocutaneous candidiasis</text></comment>
     <comment term='symptom'><text>Malabsorption</text></comment>
     <comment term='symptom'><text>Chronic active hepatitis</text></comment>
    </phenotype>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringoptional

Elements

nametypecardinalitychoice group
textVmlTextzero or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
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consent (VmlConsent)

NOT USED

Database cross-reference for a consent information (not used currently)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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consequence (VmlConsequence)

Consequences of mutation on sequence, structural and molecular levels.

Note: implementation of fixed vocabulary for this element is still pending. Sequence ontology and VariO terms are preferred. See: lsdb-controlled-vocabulary-terms also ClinVarDataDictionary (http://www.ncbi.nlm.nih.gov/projects/clinvar/ClinVarDataDictionary.pdf)

See also documentation under the seq_region and variant_type element

Example:

 <consequence source="SO" accession="1000071" term="mutation affecting splicing" />

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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seq_changes (VmlConsequentVariants)

Related sequence changes on overlapping sequence levels and features.

Element has recursive list of sequence variants of type RNA or AA. The Sub-variant element differ from the main variant element in a following way:

Elements

nametypecardinalitychoice group
variantVmlConsequentVariantone or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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contact (VmlContact)

Attributes

nametypecardinalityvalue
rolestringoptional

Elements

nametypecardinalitychoice group
namestringmandatory
urlstringzero or many
addressstringoptional
phonestringoptional
faxstringoptional
emailstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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creation_date (VmlCreationDate)

Date when submitted information was created

Elements

nametypecardinalitychoice group
choiceoptionalForeign XML nodes
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cultivar (VmlCultivar)

Cultivar

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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db_xref (VmlDbXRef)

Abstract data type for database cross references.

Can include other database cross-references and annotations.

Examples:

  <db_xref source="pubmed" accession="16965330"/>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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description (VmlDescription)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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dob (VmlDobDate)

Date of birth

Elements

nametypecardinalitychoice group
choiceoptionalForeign XML nodes
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embargo_end_date (VmlEmbargo_end_date)

text node of type date

Embargo end date

Attributes

nametypecardinalityvalue
is_undefinedstringoptionaltrue
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evidence_code (VmlEvidenceCode)

Evidence code is an ontology term (i.e. has optional source and accession attributes), which provides information related to the validity or the quality of observation.

dbSNP validation should be used for mutations:

Examples:

 <evidence_code term="inferred"/> 

 <evidence_code term="confirmed" source="obo.vario"/>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
scoreVmlScorezero or many
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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exon (VmlExon)

text node of type string

Exon has optional attributes source, accession, and transcript_ref, which can be used for crossreference purposes. Exon number is given in text node. Element is for legacy exons names

Example:

 <exon>01</exon>   

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
transcript_refstringoptional
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factor (VmlFactor)

Possible factors for pathogenicity (under discussion)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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frequency (VmlFrequency)

Actual frequency is stored in a subelement depending on value type. This type can be: decimal number, number of cases, or categorized value.

Frequency has the optional attribute 'samples', which can hold information on sample size. Typically this is the number of chromosomes.

Frequency type can be either "allele" or "carrier", with optional subelements:

Examples:

 <frequency samples="1000" >
    <population type="nationality" term="Finnish"/>
    <freq>0.2</freq>
 </frequency> 

 <frequency><freq>0.1</freq></frequency>

 <frequency samples="1000">
    <cases>11</cases>
 </frequency>

 <frequency>
    <population type="region" term="Sweden"/>
    <category term="exist"/>
 </frequency>      

 <frequency samples="1111">
    <population type="ethnic" term="Caucasian"/>
    <freq>0.12</freq>
    <evidence_code source="sampling_ontology" accession="abcd" term="random"/>
 </frequency>

Attributes

nametypecardinalityvalue
samplesintoptional
typestringoptionalallele | carrier | genotype

Elements

nametypecardinalitychoice group
populationVmlPopulationoptional
choiceoptionalfreq|counts|category
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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gender (VmlGender)

Gender of individual. Gender code is stored in the attribute 'code'. Possible values are iso5218 codes: 0,1,2 and 9 ('unknown','male','female' and 'not applicable').

Description of gender (code: 9) can be stored into optional 'description' sub-element, which is of type #type_LSDB.Evidence_ontology_term" Evidence_ontology_term.

Example:

<gender code='9'>
    <description term="XX-male"/>
</gender>

Attributes

nametypecardinalityvalue
codestringmandatory0 | 1 | 2 | 9

Elements

nametypecardinalitychoice group
descriptionVmlDescriptionoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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gene (VmlGene)

Database cross reference where 'source' is the name of the database or system (e.g. HUGO) and 'accession' is the gene name (e.g.AGA).

HGNC names (symbols) should be used to name genes.

Can include other database cross-references and annotations.

Example source: * HGNC

Example accession: * BRCA2

Example:

 <gene source="HGNC" accession="BRCA2" />

 <gene source="HGNC" accession="BRCA2">
    <db_xref accession="7581463" uri="http://identifiers.org/pubmed/600185" source="pubmed"/>
    <db_xref accession="BRCA2" source="hgnc.symbol" uri="http://www.identifiers.org/hgnc.symbol/BRCA2"/>
 </gene>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

observation (VmlGenericObservation)

Abstract type. See subtypes for the documentation. Observation which has evidence code and observation protocol (dbxref).

Example:

 <genetic_origin term="paternal">
   <evidence_code term="inferred"/>            
 </genetic_origin>

 <phenotype term="Osteogenesis Imperfecta" >
   <evidence_code term="assessed by clinician"/>
   <protocol_id source="protocoldb_xyz" accession="XYZ0001"/>
 </phenotype>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory
typestringoptionallifestyle | environment | relationship

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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source (VmlGeneticSource)

Source of variant (paternal, maternal). See genetic_origin for more information.

Controlled vocabulary terms for genetic source:

N.B: Standardization of this list is pending. See: lsdb-controlled-vocabulary-terms

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
populationVmlPopulationzero or many
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
[ top ]

genetic_origin (VmlGenetic_origin)

Genetic origin of variation.

Genetic origin corresponds to the Sequence Ontology's variant_origin.

Genetic origin and source are evidence ontology terms.

Genetic origin documents the following information:

Controlled vocabulary terms for genetic origin:

N.B: Standardization of this list is pending. See: lsdb-controlled-vocabulary-terms

Example:

 <genetic_origin term="inherited">
    <source term="paternal"/>
    <evidence_code term="inferred"/>                                
 </genetic_origin>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
sourceVmlGeneticSourceoptional
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

genotype (VmlGenotype)

Genotype

Orginal genotype call e.g. A/T

Elements

nametypecardinalitychoice group
callstringmandatory
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

group_type (VmlGroupType)

Group type (NOT USED)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

haplotype (VmlHaplotype)

Haplotypes. Complex variants can be given as a list of phased variants. This element still in testing.

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
alleleintoptional

Elements

nametypecardinalitychoice group
nameVmlNameoptional
variantVmlVariantEventone or many
sequenceVmlSequenceoptional
consequenceVmlConsequencezero or many
pathogenicityVmlPathogenicityzero or many
frequencyVmlFrequencyzero or many
seq_changesVmlConsequentVariantsoptional
aliasesVmlRelatedVariantsoptional
sourceVmlSourceoptional
locationVmlLocationzero or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

individual (VmlIndividual)

Individual or patient

Example:

    <individual>
         <gender code="2" />
         <phenotype term="Osteogenesis Imperfecta" >
         </phenotype>
         <variant type="cDNA">
             <gene source="HGNC" accession="COL1A1" />
             <ref_seq accession="NG_007400.1" />
             <name scheme="HGVS">c.579delT</name>
             <genetic_origin term="paternal">
                 <evidence_code term="inferred"/>            
             </genetic_origin>
             <sharing_policy type="openAccess">
                 <embargo_end_date>2002-12-12</embargo_end_date>
                 <use_permission accession="CC0" uri="http://creativecommons.org/publicdomain/zero/1.0/" term="Creative commons"/>
             </sharing_policy>

             <comment>
                 <text>Variant inherited from affected father</text>
             </comment>

         </variant>
     </individual>

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
genderVmlGenderoptional
dobVmlDobDateoptional
ageVmlAgeoptional
original_idVmlOriginalIdoptional
roleVmlRoleTypeoptional
relationshipVmlRelationshipzero or many
organismVmlOrganismoptional
strainVmlStrainoptional
cultivarVmlCultivaroptional
phenotypeVmlPhenotypezero or many
observationVmlGenericObservationzero or many
populationVmlPopulationzero or many
variantVmlVariantzero or many
variant_groupVmlVariantGroupzero or many
sourceVmlSourceoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
sharing_policyVmlSharingPolicyoptional
creation_dateVmlCreationDateoptional
modification_dateVmlModificationDateoptional
choicezero or manyForeign XML nodes
[ top ]

inheritance_pattern (VmlInheritancePattern)

Inheritance pattern of the phenotype. Possible values for the term:

See: lsdb-controlled-vocabulary-terms

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

location (VmlLocation)

Location of variant on a reference sequence/genomic build.

Example:

 <location>
   <ref_seq source="embl" accession="ABC1023345"/>
   <start>111111</start>
   <end>111112</end>
 </location>



 <location>
    <ref_seq source="refseq" accession="NC_000001.10"/>
    <start>100315752</ns2:start>
    <end>100315752</ns2:end>
 </location>

Attributes

nametypecardinalityvalue
unitstringoptionalfeature | residue

Elements

nametypecardinalitychoice group
ref_seqVmlRefSeqoptional
chrstringoptional
startstringmandatory
endstringoptional
choicezero or manyForeign XML nodes
[ top ]

lsdb (VmlLsdb)

Single data submission batch element for individual data. The batch contains:

Example:

 <lsdb xmlns="http://gen2phen.org/varioml/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xmlns:dc="example.org" xsi:noNamespaceSchemaLocation="lsdb.xsd">
     <created>2000-01-12T12:13:14Z</created>
     <source id="AIREbase" version="1.2" uri="http://www.uta.fi/imt/bioinfo/AIREbase/">
         <name>DatabaseXYZ</name>
         <url>http://www.uta.fi/imt/bioinfo/AIREbase/</url>
         <contact>
             <name>Matti Meikäläinen</name>
             <address>Institute for Molecular Medicine</address>
         </contact>
         <acknowledgement>
             <name>European Union</name>
             <grant_number accession="23230001"/>
         </acknowledgement>
     </source>

     <individual id="xyz">
         <gender code="2"/>
         <variant>
             <ref_seq accession="xyz"></ref_seq>
             <name scheme="HGVS">c.1343GT</name>
         </variant>
     </individual>

     <individual id="abce">
         <gender code="2"/>
         <variant>
             <ref_seq accession="xyz"></ref_seq>
             <name scheme="HGVS">c.1343GC</name>
         </variant>
     </individual>

 </lsdb>

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
schema_versiondecimaloptional
submissionid_typestringoptional

Elements

nametypecardinalitychoice group
createdstringoptional
sourceVmlSourcezero or many
individualVmlIndividualzero or many
panelVmlPanelzero or many
variantVmlVariantzero or many
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

modification_date (VmlModificationDate)

Date when submitted information was modified.

Example:

 <modification_date>2001</modification_date>
 <modification_date>2001-09</modification_date>
 <modification_date>2001-09-10</modification_date>

Elements

nametypecardinalitychoice group
choiceoptionalForeign XML nodes
[ top ]

name (VmlName)

text node of type string

Name of variant

Element has following optional attributes: scheme - naming scheme, which should typically be HGVS.

Example:

 <name type="DNA" scheme="HGVS">
      c.755G\A
 </name>

Attributes

nametypecardinalityvalue
schemestringoptional
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observations (VmlObservationCombo)

Abstract type. See subtypes for the documentation. Observation which has evidence code and observation protocol (dbxref).

Example:

 <genetic_origin term="paternal">
   <evidence_code term="inferred"/>            
 </genetic_origin>

 <phenotype term="Osteogenesis Imperfecta" >
   <evidence_code term="assessed by clinician"/>
   <protocol_id source="protocoldb_xyz" accession="XYZ0001"/>
 </phenotype>

Elements

nametypecardinalitychoice group
choiceoptionalpanel|individual
phenotypeVmlPhenotypezero or many
variantVmlVariantzero or many
observationVmlGenericObservationzero or many
variant_groupVmlVariantGroupzero or many
sharing_policyVmlSharingPolicyoptional
creation_dateVmlCreationDateoptional
modification_dateVmlModificationDateoptional
choicezero or manyForeign XML nodes
[ top ]

observation_date (VmlObservationDate)

Observation_date captures the date of an observation. A boolean attribute can be used when an exact date cannot be given. An age attribute captures the age of the subject at the time of observation.

Attributes

nametypecardinalityvalue
codedbooleanoptional
datestringoptional
agefloatoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

category (VmlOntologyTerm)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
[ top ]

organism (VmlOrganism)

Organism

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

original_id (VmlOriginalId)

Identifier used by the submitter.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

panel (VmlPanel)

Panel. Unspecified group of individuals. Has following information besides properties inherited from AbstractObservation target:

*individuals - list of individuals beloning to the panel

Example:

Frequency for existence of two alleles.

    <panel>
         <frequency samples="224" type="allele">
             <freq>0.763</freq>
         </frequency>
         <population type="group" term="El Salvadorans"/>
         <population type="ethnic" term="Mestizo">
             <comment><text>Amerindian and European descent</text></comment>
         </population>
         <variant>
             <ref_seq accession="NM_000777"/>
             <name>g.6986AG</name>                                    
         </variant>
         <variant>
             <ref_seq accession="NM_000777"/>
             <name>g.1289TG</name>                                    
         </variant>
     </panel>

Note also that also variant specific frequency can be given as usual:

     <panel>      
         <population type="group" term="Yorubans"/>
         <population type="region" term="Nigeria"/>
         <variant>
             <ref_seq accession="NM_000777"/>
             <name>g.6986AG</name>                                                
             <frequency samples="50" type="allele"> 
                 <freq>0.06</freq>
             </frequency>
         </variant>
     </panel>

Usage of the format must be agreed on separately.

Attributes

nametypecardinalityvalue
sizeintegeroptional
typestringoptionalfamily | extended family | population
idstringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
individualVmlIndividualzero or many
genderVmlGenderoptional
dobVmlDobDateoptional
ageVmlAgeoptional
original_idVmlOriginalIdoptional
roleVmlRoleTypeoptional
relationshipVmlRelationshipzero or many
organismVmlOrganismoptional
strainVmlStrainoptional
cultivarVmlCultivaroptional
phenotypeVmlPhenotypezero or many
observationVmlGenericObservationzero or many
populationVmlPopulationzero or many
variantVmlVariantzero or many
variant_groupVmlVariantGroupzero or many
sourceVmlSourceoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
sharing_policyVmlSharingPolicyoptional
creation_dateVmlCreationDateoptional
modification_dateVmlModificationDateoptional
choicezero or manyForeign XML nodes
[ top ]

pathogenicity (VmlPathogenicity)

Pathogenicity of variant.

Controlled vocabulary for pathogenicity is sourced from the GEN2PHEN project. See: VarioML - Pathogenicity.

SKOS terms are preferred: http://purl.org/varioml/pathogenicity/skos/1.0/

Note that g2p is always used as a source

Examples of the terms:

  • Non-pathogenic
  • Not known
  • Pathogenic
  • Probably not pathogenic
  • Probably pathogenic
  • Unclassified

Pathogenicity has new attributes: phenotype, scope (individual, family, population) and score.

CMGS/VKGL suggested classification

Via Alamut:

The Practice guidelines for the Interpretation and Reporting of Unclassified Variants (UVs) in Clinical Molecular Genetics suggest the following classification system:

Class 1 – Certainly not pathogenic Class 2 – Unlikely to be pathogenic but cannot be formally proven Class 3 – Likely to be pathogenic but cannot be formally proven Class 4 - Certainly pathogenic


Note [1]: implementation of fixed vocabulary for this element is still pending. See: lsdb-controlled-vocabulary-terms

*Note [2]: Textual values will likely be changing to "Affects function" to cover non-disease implications such as Eye color.

Attributes

nametypecardinalityvalue
scopestringoptionalindividual | family | population
panel_refstringoptional
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
phenotypeVmlPhenotypezero or many
factorVmlFactorzero or many
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

phenotype (VmlPhenotype)

Phenotype of individual. Phenotype is evidence ontology term (see evidence_ontology)

Example:

 <phenotype term='Autoimmune polyglandular syndrome type 1'/>

 <phenotype term='Autoimmune polyglandular syndrome type 1' accession='240300' source='omim'>
     <evidence_code term="confirmed" source="vario"/>
     <protocol_id accession="observation_method_xyz" source="protocol_database"/>
    <db_xref accession="12345" source="pubmed"/>
     <comment term='symptom'><text>Hypoparathyroidism</text></comment>
     <comment term='symptom'><text>Addison's disease</text></comment>
     <comment term='symptom'><text>Mucocutaneous candidiasis</text></comment>
     <comment term='symptom'><text>Malabsorption</text></comment>
     <comment term='symptom'><text>Chronic active hepatitis</text></comment>
 </phenotype>

Attributes

nametypecardinalityvalue
typestringoptionalsymptom | diagnose
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
inheritance_patternVmlInheritancePatternoptional
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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population (VmlPopulation)

Information related to population group the individual belongs to.

Population element has the "type" attribute which indicates the selection criteria of the population, using the values:

The attribute is informative: the actual type of population should be defined in the source ontology (if it is used).

Example:

 <population type="ethnic" term="Caucasian"/>                    

 <population type="ethnic" term="Caucasian"> 
    <evidence_code source="example_ontology_term" accession="abcd" term="ethnicity of mother"/>
 </population>

 <population type="ethnic" term="Asian" > 
    <evidence_code source="example_ontology_term" accession="abcd" term="ethnicity of father"/>
 </population>

 <population type="region" term="Ahvenanmaa" source="ISO 3166"  accession="ISO 3166-2:AX"> 
    <evidence_code term="place of birth"/>
 </population>

Attributes

nametypecardinalityvalue
typestringmandatoryregion | nationality | ethnic | race | organism | group | primary_language | language_family | other | unknown
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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protocol_id (VmlProtocolId)

Cross-reference to a protocol database.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

ref_seq (VmlRefSeq)

Database cross reference for reference sequence.

Can include other database cross-references and annotations.

Use Genbankto source reference sequences.

Example:

 <ref_seq source="genbank" accession="NG_007088.1"/>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
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aliases (VmlRelatedVariants)

Aliases or alternative legacy definitions (names) of the variant.

Element has list of sequence variants (recursive data structure) which can be seen as aliases of the main variant. Typically the variants are annotated against different reference sequences, and/or their name is based on a different naming scheme.

Example:

   <variant>
        <ref_seq source="genbank" accession="NG_001337.2"></ref_seq>
        <name scheme="HGVS">g.22048CG</name>
        <aliases>
            <variant>
                <ref_seq accession="NG_002335.2"/>
                <name>g.1400GC</name>                    
            </variant>
            <variant>
                <ref_seq accession="NG_007072.2"/>
                <name>g.14034GC</name>
            </variant>
            <variant>
                <ref_seq accession="NG_007088.1"/>
                <name>g.28259GC</name>
            </variant>                
        </aliases>

        <db_xref  source="dbsnp" accession="rs13"/>
    </variant>

Elements

nametypecardinalitychoice group
variantVmlVariantone or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

relationship (VmlRelationship)

relationships .. NOT NEEDED

Relationship

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
individualVmlIndividualzero or many
panelVmlPanelzero or many
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

restriction_site (VmlRestrictionSite)

Restriction enzyme site.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

role (VmlRoleType)

Role in a group

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

sample (VmlSample)

Local sample id

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

score (VmlScore)

Score

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
valuestringmandatory
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

seq_region (VmlSeqRegion)

Name of the underlying sequence reqion. Sequence Ontology (SO) terms are used to standardise attributes such as exon, intron, 3' UTR, etc.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
seq_regionVmlSeqRegionzero or many
locationVmlLocationzero or many
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

sequence (VmlSequence)

Reference and variant sequence strings. Accession number of reference sequence is given in ref_seq element (see the variant)

Example:

 <sequence>
     <reference>atttgatcgttc</reference>
     <variant>atttgGtcgttc</variant>
 </sequence>

Elements

nametypecardinalitychoice group
referencestringmandatory
variantstringmandatory
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

sharing_policy (VmlSharingPolicy)

Data sharing policy. Following access policy types are used: closedAccess,embargoedAccess,restrictedAccess and openAccess

Adopted from OpenAIRE specification

Example:

    <sharing_policy type="openAccess">
        <embargo_end_date>2002-12-12</embargo_end_date>
        <use_permission accession="CC0" uri="http://creativecommons.org/publicdomain/zero/1.0/" term="Creative commons"/>
    </sharing_policy>

Attributes

nametypecardinalityvalue
typestringmandatoryclosedAccess | embargoedAccess | restrictedAccess | openAccess

Elements

nametypecardinalitychoice group
embargo_end_dateVmlEmbargo_end_dateoptional
use_permissionVmlUsePermissionoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

source (VmlSource)

Contains information on data source. Typically specifies the source database, although the system, organization, or institution from which data is exported can also be used.

In the LSDB XML format there can be more than one source, so that information on original data providers can be included.

Element is re-used from the LRG specification.

Example:

 <source id="dmudb">   
    <name>DMuDB, NGRL, Manchester</name> 
    <url>http://www.ngrl.org.uk/Manchester/projects/informatics/dmudb</url>  
    <contact>
        <name>Glen Dobson</name>
        <address>NGRL, Genetic Medicine, St Mary's Hospital, Oxford Road, Manchester M13 9WL</address>
        <phone>(+44) 0000 000 0000</phone>
        <fax>(+44) 0000 000 0000</fax>
        <email>example@nnn.nn.nnn</email>
    </contact>
 </source>

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
versionstringoptional
datedateoptional

Elements

nametypecardinalitychoice group
namestringmandatory
urlstringzero or many
contactVmlContactzero or many
acknowledgementVmlAcknowledgementzero or many
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

strain (VmlStrain)

Strain

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

cafe_variome (VmlSubmission)

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
schema_versiondecimaloptional
submissionid_typestringoptional

Elements

nametypecardinalitychoice group
createdstringoptional
sourceVmlSourcezero or many
variantVmlVariantzero or many
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

submitter_id (VmlSubmitterId)

Randomized identifier of individual as used by submitter.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
namestringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

text (VmlText)

text node of type string

Text

Attributes

nametypecardinalityvalue
content_typestringoptional
langstringoptional
encodingstringoptional
[ top ]

tissue (VmlTissue)

Tissue

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

tissue_distribution (VmlTissueDistribution)

Tissue distribution

Controlled vocabulary terms for tissue distribution:

Note: implementation of fixed vocabulary for this element is still pending. See: lsdb-controlled-vocabulary-terms

Example:

 <tissue_distribution term="mosaic"/>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

use_permission (VmlUsePermission)

Licensing information.

Example:

 <use_permission accession="CC0" uri="http://creativecommons.org/publicdomain/zero/1.0/" term="Creative commons"/>

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

value (VmlValue)

A name/value pair can be added to an observation using the value element. E.g. the number of exons, residue, etc.

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory
unitstringoptional
typestringoptionalinteger | float | text | date | datetime
valstringoptional
nvaldoubleoptional

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
valueVmlValuezero or many
choicezero or manyForeign XML nodes
[ top ]

variant (VmlVariant)

Variant. Typically has the following information:

Example:

    <variant diploid_count='1'>
        <gene source='HGNC' accession='AIRE'/>
        <ref_seq source='IDRefSeq' accession='D0003' />
        <name scheme='HGVS'>g.4707AT</name>
        <exon>e1</exon>
        <consequence term='A point mutation in the exon 1 altering initiation codon in HSR domain '/>
        <seq_changes>
            <variant type='RNA'>
                <ref_seq source='IDRefSeq' accession='C0003' />
                <name scheme='HGVS'>r.1au</name>
                <consequence term='predicted to change start codon to position c.268, resulting in a frameshift of translation'/>
                <seq_changes>
                    <variant type='AA'>
                        <ref_seq source='uniprot' accession='O43918' />
                        <name scheme='HGVS'>p.Met1Leu</name>
                    </variant>
                </seq_changes>
            </variant>
        </seq_changes>
    </variant>

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
typestringoptionalDNA | cDNA | RNA | AA
genotypicstringoptionaltrue
subcellular_partstringoptionalnucleus | mitochondrial | chloroplast | other
copy_countfloatoptional

Elements

nametypecardinalitychoice group
geneVmlGenezero or many
ref_seqVmlRefSeqoptional
nameVmlNameoptional
haplotypeVmlHaplotypezero or many
panelVmlPanelzero or many
seq_regionVmlSeqRegionzero or many
variant_typeVmlVariantTypezero or many
variant_classVmlVariantClasszero or many
original_idVmlOriginalIdoptional
exonVmlExonzero or many
sequenceVmlSequenceoptional
genotypeVmlGenotypeoptional
consequenceVmlConsequencezero or many
pathogenicityVmlPathogenicityzero or many
sampleVmlSampleoptional
tissueVmlTissueoptional
variant_detectionVmlVariantDetectionoptional
restriction_siteVmlRestrictionSiteoptional
tissue_distributionVmlTissueDistributionoptional
genetic_originVmlGenetic_originzero or many
frequencyVmlFrequencyzero or many
seq_changesVmlConsequentVariantsoptional
aliasesVmlRelatedVariantsoptional
sourceVmlSourceoptional
locationVmlLocationzero or many
sharing_policyVmlSharingPolicyoptional
creation_dateVmlCreationDateoptional
modification_dateVmlModificationDateoptional
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

variant_class (VmlVariantClass)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

variant_detection (VmlVariantDetection)

Techniques used to detect the variant.

Variant detection method. Element has attributes:

Optional element protocol_id (of type DbXRef) has reference to actual detection protocol.

Controlled vocabulary terms for detection techniques:

Note: implementation of fixed vocabulary for this element is still pending. See: lsdb-controlled-vocabulary-terms

Example:

 <variant_detection template="DNA" technique="DHPLC"/>

Attributes

nametypecardinalityvalue
templatestringmandatoryDNA | RNA | cDNA | AA
techniquestringmandatory

Elements

nametypecardinalitychoice group
protocol_idVmlProtocolIdoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

variant (VmlVariantEvent)

A variant event is a single genomic variation event, co-occurring with the given variant.

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional

Elements

nametypecardinalitychoice group
nameVmlNameoptional
seq_regionVmlSeqRegionzero or many
variant_typeVmlVariantTypezero or many
variant_classVmlVariantClasszero or many
original_idVmlOriginalIdoptional
exonVmlExonzero or many
sequenceVmlSequenceoptional
consequenceVmlConsequencezero or many
pathogenicityVmlPathogenicityzero or many
variant_detectionVmlVariantDetectionoptional
restriction_siteVmlRestrictionSiteoptional
genetic_originVmlGenetic_originzero or many
frequencyVmlFrequencyzero or many
seq_changesVmlConsequentVariantsoptional
aliasesVmlRelatedVariantsoptional
locationVmlLocationzero or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

variant_group (VmlVariantGroup)

Variant group (EXPERIMENTAL)

Attributes

nametypecardinalityvalue
idstringoptional
urianyURIoptional
orientationstringoptionalcis | trans | unknown

Elements

nametypecardinalitychoice group
group_typeVmlGroupTypeoptional
variantVmlVariantone or many
frequencyVmlFrequencyzero or many
pathogenicityVmlPathogenicityzero or many
valueVmlValuezero or many
evidence_codeVmlEvidenceCodezero or many
protocol_idVmlProtocolIdzero or many
observation_dateVmlObservationDateoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

variant_type (VmlVariantType)

Type of variation. SNP, microsatellite... Also sequence alteration terms from SO http://www.sequenceontology.org/browser/current_release/term/SO:0001059

Note: This should not be mixed with classification schemes based on effects of mutations (like missense, alter splicing...) which should go into the consequence element or schemes based on type of underlying sequence (like exon, intron), which should go into seq_region element.

Examples: indel (accession = 1000032) deletion (accession = 0000159) substitution (accession = 1000002) inversion (accession = 1000036)

Attributes

nametypecardinalityvalue
sourcestringoptional
accessionstringoptional
urianyURIoptional
termstringmandatory

Elements

nametypecardinalitychoice group
descriptionstringoptional
db_xrefVmlDbXRefzero or many
commentVmlCommentzero or many
choicezero or manyForeign XML nodes
[ top ]

)