If you have any question about this xsd, please contact us. (clinvar@ncbi.nlm.nih.gov). The database ID will be captured as attribute when a submission is updating a record with an identifier. Temporary unique ID, used for submission processing. For internal use only. Contact info - an address with email Account - a person with logon Contact information if known. This usage is required when logging in via NCBI's submission system. Logon name eRA,pda,NIH,ncbi/ftp-private,..... XRefs are used to represent references to data from external databases. These are stored in the ClinVar database to represent objects like GeneIDs in Gene or MIM numbers in OMIM, and are flexible enough to be used broadly. The db is the database name used for the external reference (e.g. 'Gene' or 'OMIM') and the ID is that database identifier (e.g. the GeneID or MIM number). The type is optional and should be used if there are multiple types of identifiers from a database. For example, from OMIM we may get both MIM numbers and identifiers for allelic variants; those should be specified as the type for the XRef. Expect ID to not be provided only if this is used for submitting a URL on it's own. XSD does not permit choice for attributes so validation of these will need to be in another layer (XSLT) A free text comment to submit data (public) or to provide explanations for internal use. The name or id of comment_type in clinvar This is for internal use only. Citations provide the identifers or descriptions of a publication that supports a data element. The citation can be any of (1) the combination of a data source and the identifier used by that source (e.g. PubMed and PubMed UID), (2) a URL, or (3) a text title. Will be set to 'general' on submission processing if not provided. The attribute is a general element to represent a defined set of data qualified by an enumerated set of types. For each attribute element, the value will be a character string and is optional. Source shall be used to store identifiers for supplied data from source other than the submitter (e.g. SequenceOntology). The data submitted where Type="variation" shall be validated against sequence_alternation in Sequence Ontology http://www.sequenceontology.org/. This is to be a generic version of AttributeType and should be used with extension when it is used to specify Type and its enumerations. Structure to describe the name, version, and use of code used in a particular method. Structure to describe attributes of any family data in an observation. If the details of the number of families and the de-identified pedigree id are not available, use FamilyHistory to describe what type of family data is available. Can also be used to report 'Yes' or 'No' if there are no more details. The attribute set groups an attribute and citations for that attribute. We allow citations for each attribute. Used generically to define the attributes of sets of data (such as sets of conditions or phenotypes, or sets of variations) or their relationships (measure-target). The attribute is a general element to represent a defined set of data qualified by an enumerated set of types. For each decimal attribute element, the value will be a decimal and is optional. Source shall be used to store identifiers for supplied data from source other than the submitter (e.g. SequenceOntology). This is a generic version for decimal attributes and should be used with extension when it is used to specify Type and its enumerations. The integerValue attribute type is retained as an option because the generic structure of this element could support a decimal value being submitted with some qualifying integer value as well. Details of a method used to generate variant calls or predict/report functional consequence. The name of the platform should represent a sequencer or an array, e.g. sequencing or array , e.g. capillary, 454, Helicos, Solexa, SOLiD. This structure should also be used if the method is 'Curation'. Free text to enrich the description of the method and to provide information not captured in specific fields. Use this when this attribute is not a generic attribute of this method but rather an attribute specific this method in conjuction with this observation An example is a method used to validate the the variant call; the AttributeType would be MethodResult, and value is one of pass/fail/inconclusive Another example is indication TestingLaboratory and interpretation made by the testing lab; use AttributeType TestingLaboratory, and put name of the lab as value, and This is an AttributeSet, there will be 1 attribute supported by optional citations, xrefs and comment. There must be at least one ObservedData Set, but can be any number. For each ObservedData set the Attribute will be either decimal or string depending on type. The value will be stored here, but decimals will be entered to the database as a string. Documents in what populations or samples an allele or genotype has been observed relative to the described trait. Summary observations can be registered per submitted assertion, grouped by common citation, study type, origin, ethnicity, tissue, cell line, and species data. Not all options are valid per study type, but these will not be validated in the xsd. Each ClinVar submission is a single asserted relationship. There must be at least 1 in a set, but there may be many. Record status is optional, because if not supplied it defaults to current. A release status can be applied to each assertion in the submission. When not provided, the value is set to 'public'. This value has precedence over that in ClinvarSubmissionSet. Each assertion of the relationship between a set of variations and a set of phenotype measures is assigned an accession in ClinVar. The prefix for the an external submitter's accession is SCV (submitted ClinVar); assertions curated by NCBI staff are assigned a private NCV accession (such as gene-disease relationship reported in the literature. The aggregate of submissions for the same assertion is assigned an RCV accession (aka reference ClinVar) If this accession replaces another, the other does not need to be submitted explictitly but can be listed here and clinvar will do the merge on the database side. ClinVar uses the term measure to indicate what is measured (sequence variation, expression, protein electrophoretic mobility, etc.) to assess the asserted relationship to the phenotype or condition (trait). Measures of the same type can be grouped into sets; this is useful when, for example, a combination of alleles defines a 'diagnosis' name; or a local haplotype needs to be defined. All measures in a measure-set will have the asserted relationship to all traits in the trait set described here. The measures and traits for this assertion are described below, this element describes only the attributes of the assertion itself. The measure set describes the set of measures (analytes, genes, variants, etc.) indicated for this assertion. If variants, should represent data from one chromosome (in cis) Container for 2 MeasureSets, one for each allele The trait set describes the set of traits (phenotypes, conditions, etc.) indicated for this assertion. private comment or public comment; expect at most one of each, but not controlled explicitly in the XSD. Structure to report the organization and person requesting that one or more accessions they submitted be deleted. The accessions must be listed, and either the reason for each accession being deleted, or a general reason to be applied to all that are listed. Because the data about the submission must already be in the database, the source of the request can be simple and processed only by OrgID and PersonID The reason reported at this level will be applied to each accession being deleted. MeasureTrait type is the assertion relationship stored in the clinvar.measure_target table. This represents a single asserted relationship which will be assigned an accession of the type SCV, RCV or NCV. relat_type in measure_target XRef type to identify the source of this assertion. In the database this will be used as the source for the data in the ClinvarSubmission XML. This is optional becuase not all sources have an ID specific to the assertion. When there is no ID the extrn_src is calculated from the submitter information. The name or id of measureset_type in clinvar Measure is used to represent the sequence or analyte being measured to evaluate a relationship to the trait. This can be a gene, a variation, a protein, etc. The measure must be unambiguously defined. That definition may be supplied either by a unique name or symbol or expression, a sequence location, or an identifier in a public database such as a GeneID or an HGNC id. The name or id of measure_type in clinvar The name or id of measure_attr_type in clinvar An AttributeSet is used to represent a single attribute which will have just one attribute value but can have many citations or xrefs. Multiple attributes are represented by multiple attribute sets. MeasureRelationship is used to represent relationships to genes or other objects. The name or id of measure_attr_type in clinvar The name or id of measure_set_attr_type in clinvar The name or id of trait_set_type in clinvar To assert that an allele is thought to be benign, without enumerating disorders for which it is benign, please submit the trait name 'not specified' The name or id of trait_set_type in clinvar Represent the value for the test indication as a name of a trait. The name or id of tset_attr_type in clinvar The name or id of trait_type in clinvar The name or id of trait_attr_type in clinvar TraitRelationship is used to represent relationships among traits. In the relational model, this is captured in the tset and tsubset tables. The type of relationship is captured in TraitRelationshipType. This is to be used within co-occurrence set Age can be a single value or a range, defined by the use of type. Denominator, total individuals included in this observation set. Denominator, total males included in this observation set. Denominator, total females included in this observation set. Denominator, total number chromosomes tested. Gender should be used ONLY if explicit values are not available for number of males or females, and there is a need to indicate that the genders in the sample are known. this refers to the variant being asserted's zygosity Review status is used to summarize the level of support for the interpretation of clinical significance based on submissions to ClinVar. 'reviewed by professional society' includes practice guidelines. 'DateLastEvaluated' is the date the significance was last evaluated; it may differ from the submission date. A trait set allows the submitter to provide one or more traits, either characterizing the assertion (//ClinvarSubmission/TraitSet) or the set of findings (clinical features) characteristic of an observation (//ObservedIn/TraitSet). Unless the type is TraitChoice, a submission of multiple values is asssumed to represent all values were always observed, i.e. asserted to be Pathogenic for the co-occurence of Disease A and Disease B. If a variant is identified to be Pathogenic for Disease A and also Pathogeneic for Disease B, these should be submitted as distinct ClinvarSubmissions, not as one ClinvarSubmission with a multi-member TraitSet. If, however, data are not currently available to represent distinct submissions, the TraitChoice can be used to indicate an assertion is about any one of the Traits in the TraitSet. The name or id of measureset_type in clinvar This is used to identify the one individual or process that is the submitter of record, in contrast to the many who contributed to the submission. The latter are reported under submitter. The person submitting the data. Internally, represented in the entered_by fields. used in submissions via submit.ncbi.nlm.nih.gov to identify the submitte Need to be able to identify the organization or extrn_src for who is making this assertion Names and addresses of an organization. Representation of staff in the organization For Type use 'primary' if this is the primary organization that should get attribution for the submission; use 'secondary' if this is an additional organization that should get attribution; use 'behalf' if this is an organization that is submitting on behalf of another and should not get attribution for the submission Not required, name may be sufficient for some organizations. To be used if an organization is part of a larger institution. Must have at least city,state and country of mailing address The number and name of the street or avenue. Official(not personal) contact for the organization List of states is in db. List of countries is in db. Needs to be on the list. You have to provide between one and two contacts per Personnel. If you provide two, one has to be PublicContact and the other PrivateContact. Both may contain the same contact information (i.e., email, phone, etc.), however. In that case, the PublicContact will have precedence will provide a list of suggested titles. List is in the TitleList type. If the submitter has an ID in another system. May want to think about how we do this. Perhaps boolean values for all permission options, for now will leave as text and can have 1 to many Need the full controlled list of titles here. Need the full controlled list of certifications here and include an other. Need the full controlled list of degrees here and include an other. Need the full controlled list of credentials here and include an other. The SubmissionSet is a set of asserted relationships. Within ClinVar this may be the set of assertions that constitute the accession (prefix RCV) assigned to independent assertions (accession prefix SCV). For testing laboratories, this may be a test panel. If the set represents a reference accession (RCV) there can be be only 1 for the SubmissionSet. If the Set is a test panel, the Set can consist of any mixture of RCV and SCV assertions. If an SCV is known to be a member of an RCV, only the RCV should be included in the submission. The set can also be used to submit a set of assertions from a source that are not part of a single accession, but a collection of SCV's from a laboratory. This data structure is consistent with the Genetic Testing Registry (GTR) and is used to describe the organization submitting data. This may be an LSDB, a testing laboratory, etc. Use submitter if there is more than one person or group to be acknowledged for generating the content of the submission. In other words, use submitter to document persons and organizations not documented under Submitter of Record. A title is recommended to describe the asserted relationship. This is the primary condition/phenotype/trait for the submission. If there are multiple assertions that all are for the same trait, the trait can be defined once here. If there are multiple, they must be submitted in the TraitSet section. Comment intended for internal use only; not part of the public display. When a citation is submitted at this level, the citation will be added to the display of each Measure Trait, TraitSet, and MeasureSet A release status can be applied the set of submissions, or to each submission. When not provided, the value is set to 'public'. If some assertions need to have a value different from the complete set, the value of ReleaseStatus at the ClinvarSubmission level has precedence. date of submission This attribute should be used if the the submission set has public data associated with the set, such as a citation or an accession. The set_key facilitates tracking of a batch of records as a unit, and is particularly important if a submitter provides multiple submissions sets that need to be processed as discrete sets.