Submitter comment about the content of whole submission.
This node is populated by submission system since authentication from login is known.
Organization(s) involved into the submission. One organization is the owner of the submission data and is identified by attribute "role"
All data in this submission is requested to be publicly released on or after @release_date
This is set of references to objects submitted to GTR
For a lab, use Org, for a test use Test
Used during submission processing to control what the process type is, e.g. process a new submission (ProcessFile) or
change the status (ChangeStatus) of an existing one.
All action and commands for submitting to GTR are contained in this file
Adding a group of files to the content of particular target archive in given context
Currently not used in GTR processing, but
File attributes - a way to attribute all files under this node to BioProject, BioSample, etc.
Release status, specified by submitter. If not set, it's up to target archive.
Adding a group of data objects, inlined into the submission
Data label the use of which is specific to target database. Same as for AddFiles, but this is inlined data.
Data attributes - a way to attribute all data under this node to BioProject, BioSample, etc.
Release status, specified by submitter. If not set, it's up to target archive.
The ChangeStatus command is applied to Target archive specified by @db and id in the target archive specified by element body
Immediate release
Reference to the existing submission in the case of re-submit.
Common attributes for group of metafiles, data files and inline data.
Target database for the data, e.g. dbGaP, SRA, GEO, etc...
Target database context (if known) for the data, e.g. phs123 for dbGaP study, SRX123 for SRA experiment, etc
Internal tracking information filled up by submission system and needed for internal use by the archives
?? we probably need it on the level og AddFiles or drop it from here completely ..... /mk
?? and if we have response from processing file we need a response (or status notificaiton) from all other actions
?? how it would facrtor in/reflect status incompete web submission
XML is autodected by top-level element and
XML schema reference
This is a data file, the type of which will be determined by GTR.
Path to the file relative from the location of submission XML. Note - at least one of (i) file_path, (ii) file_id or (iii) md5 needs to be present to correctly address the file.
FileTrack file id - unique and more preferred way to address the file. Works for files already in FileTrack.
Purpose of md5 is two-fold: to verify file content or to address the file.
Using of crc32 is infer compare to md5 and expected to be used in internal processing only.
Standard content type - e.g. text/xml, etc.
This is inline data to be embedded into the submission
Internal tracking information filled up by submission system and needed for internal use by the archives
Either XML or base64/plain text data)
A submission requires one laboratory description and at least one test, but it can include many tests.
Optional name of the data object
Data model of the data object
Content type - what is it - XML, text, binary, etc
How data is encoded (or how to decode it) E.g. - plain or base64
Plain text
Base64-encoded binary
Street address: 123 Main St. Suite 104
City: New York
Subdivision of Country(state, province, etc.): New York
Country: USA
Internal tracking information filled up by submission system and needed for internal use by the archives
Full middle name or initials
Contact information if known
Logon name
eRA,pda,NIH,ncbi/ftp-private,.....
Organization for the submission
Full Name
Name abbreviation
Contact(s) with organization when known
Organization type : center, institute, consortium or medical lab
Role of the ogranization in submission - owner of the data or just a participant. It is expected that there is one owner of the submission data.
In case we want to exchange organization list
URL of the organization website.
Db defines the scope of IdTag, which will become local to submission when Db is missing
Named attributes, attached to the file. This way submitter can attribute file to BioProject, BioSample, etc.
Immediate release
Release on or after specific date.
Supported target databases
In the GTR database, these are validated against GTR.dbo.codeVals where type_type = 'check_value'.
In the submission interface, these are often provided as radio button choices.
Type for representing elements that include a descriptive text plus citations.
Citations can be a PubMedID, URL or free text.
There can be any number of citations per element, but only one description.
Type for representing elements that include a descriptive text or URL plus citations.
Citations can be a PubMedID or free text. For this element only a single URL is permitted
There can be any number of citations per element, but only one description.
Type for representing elements that include a descriptive text and/or URL.
Only a single URL and/or Text description should be provided.
Type for representing URL elements, any number of URL's are permitted.
List of lab services currently in GTR.
For Other there is an attribute on the element to populate for the value.
List of suggested titles currently in GTR.
For Other there is an attribute on the element to populate for the value.
Everything related to GTRLab as Organization
Lab Name field, required
Lab Name acronym field, optional, any number can be provided
Institution Name, optional. Lab name may be sufficient for some organizations.
Institution Acronym field, optional, any number can be provided
Department Name, optional.
Must have at least city, state and country of mailing address
Facility contact for the Lab (Facility Phone Number, Facility Fax Number, Facility Email Address fields)
Laboratory Main website URL field
Considering not using an enumerated list here so we can provide either value or db ID
List is captured in LabServiceList complexType. Laboratory Types of Service field
Laboratory Services Order Code field
Laboratory Affiliations field. If provided (field is optional) must provide the lab name for the affiliation, URL is optional.
LABORATORY PARTICIPATION IN EXTERNAL PROGRAMS, STANDARDIZATION PROGRAMS Field.
LABORATORY PARTICIPATION IN EXTERNAL PROGRAMS, DATA EXCHANGE PROGRAMS Field.
GENETESTS LABORATORY ID Field. The is the Lab's public GeneTests ID
Type of Organization, Default should be Laboratory
PERSONNEL INFORMATION section fields. All staff members reported to GTR
LICENSURE AND ACCREDITATION – LABORATORY section.
Includes CLIA certification information, STATE LICENSE infromation, OTHER CERTIFICATIONS/LICENSES. Type indicates which Type of certification
Zero or more per Lab. If there is a CLIA certification other elements are required in XML (documented in other types).
Default values for the lab, optional.
Default values for the lab, optional.
table_id for a database table, for GTR use only.
field_id for table column, for GTR use only
attr type if an attribute table, or list_type if list table, for GTR use only
FACILITY ADDRESS LINE 1 field.
FACILITY ADDRESS LINE 2 field.
FACILITY ADDRESS OTHER field.
FACILITY CITY field.
FACILITY STATE/PROVINCE. state_id is for GTR use only.
FACILITY POSTAL CODE field.
FACILITY COUNTRY field. country_id is for GTR use only.
FACILITY ADDRESS CAN BE MADE PUBLIC field.
Includes PERSON PUBLIC PHONE NUMBER, PERSON PUBLIC FAX NUMBER, PERSON PUBLIC EMAIL ADDRESS, PERSON CONTACT PUBLIC COMMENT fields
Includes PERSON PRIVATE PHONE NUMBER, PERSON PRIVATE FAX NUMBER, PERSON PRIVATE EMAIL ADDRESS fields
PERSON TITLE field.
gtr_identifiers attribute is for GTR use only
PERSON DATABASE PERMISSIONS field.
PRIMARY LABORATORY CONTACT field.
LABORATORY DIRECTOR field.
DISPLAY PERSON ON GTR WEBSITE field.
PERSON NAME/FIRST NAME field.
PERSON NAME/LAST NAME field.
PERSON NAME/MIDDLE INITIAL field.
PERSON ID field. Only used for bulk submissions.
PERSON ACADEMIC DEGREE(S) field. Capturing ID from db qualification table.
There is not an option for other, or if a degree should be displayed.
PERSON GENETIC CERTIFICATIONS and PERSON OTHER CERTIFICATIONS fields.
There is not an option for other, or if a certification should be displayed.
PERSON PUBLICALLY DISPLAYED CREDENTIALS fields.
There is not an option for other, or if a certification should be displayed.
ID here should be the id for the most specific information supplied (SubSpecialty if selected, else specialty, else board.
Should include either Type or TypeID, type is the value of the certification type, typeID is the db ID for GTR use.
The gtr_identifier is the id for the certification in the qualification table.
Can provide Name or the DegreeID.
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 its own.
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.
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.
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.
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 type is used to support providing a string for TestService
or an integer (NCBI use primarily)
List of test services currently in GTR.
For the value Other please populate the optional attribute named other with the value.
This type is used to support providing a string for TestSddService
or an integer (NCBI use primarily)
List of test additional services currently in GTR.
These are the only permitted values currently. They are included on the lab comparison page grid.
This type is used to support providing a string for Specimen
or an integer (NCBI use primarily)
List of specimens currently in GTR.
For Other there is an attribute on the element to populate for the value.
List of Type of test currently in GTR.
These are the only options currently for GTR.
WHAT THE TEST MEASURES field, list of allowed values, also in ClinVar section, consider which we need
List of options for who can order a test currently in GTR.
These are the only options currently for GTR.
List of test purpose optoins currently in GTR.
These are the only options currently for GTR.
List of PT providers currently in GTR.
For Other there is an attribute on the element to populate for the value.
List of Clinical Utility categories currently in GTR.
For Other there is an attribute on the element to populate for the value.
List of test development options currently in GTR.
These are the only values currently in GTR.
List of FDA cateogry options currently in GTR.
These are the only values currently in GTR.
List of FDA review item options currently in GTR.
These are the only values currently in GTR.
List of FDA status options currently in GTR.
These are the only values currently in GTR.
DESCRIPTION OF THE TARGET POPULATION field.
LABORATORY TEST NAME field
LABORATORY TEST SHORT NAME field
MANUFACTURER TEST NAME field. TestID is an internal GTR database identifier.
OTHER NAMES field, specify type of other name.
LABORATORY UNIQUE CODE field, required for bulk upload, unique code the lab uses to identify the test to help with data exchange.
If provided (field is optional), a name for the service must be provided, order code is optional. The name of the service
should be selected from TestServiceList. If Other is chosen, the value for other must be provided as an attribute.
The optional integer value is for internal use.
TEST-SPECIFIC LABORATORY SERVICES field.
Allowed values are defined in TestServiceList
TEST-SPECIFIC LABORATORY SERVICE ORDER CODE field
If provided (field is optional), a name for the service must be provided, order code is optional
TEST-SPECIFIC LABORATORY ADDITIONAL SERVICES field.
Values in TestAddServiceList, or, for internal processing, an integer id.
TEST-SPECIFIC LABORATORY ADDITIONAL SERVICES ORDER CODE field.
HOW TO ORDER field. URL and/or text can be provided.
SPECIMEN SOURCE field
TEST-SPECIFIC CONTACT PERSON field.
Specify person_id with attribute if known, if not then use firstname/lastname for person
Expect the name to be unique for the lab. Identify the person_id from people with org_person connections to the lab
TEST-SPECIFIC CONTACT POLICY field.
INFORMED CONSENT REQUIRED field.
GENETIC COUNSELING REQUIRED PRE-TEST field.
GENETIC COUNSELING REQUIRED POST-TEST field.
TESTING STRATEGY field.
LABORATORY TEST ORDER CODE field.
LOINC CODES field (one text field, can include multiple codes).
TEST CODES field, URL at the labs website with information on test codes (e.g. CPT codes)
URL FOR THE TEST field.
TEST PERFORMED IN-HOUSE field.
TEST PERFORMED IN-HOUSE field. Optional supporting text.
TEST ORDERABLE BY field. Values in OrderableByList, or, for internal use, an integer identifier.
SAMPLE NEGATIVE REPORT field. The file name of the sample report.
SAMPLE POSITIVE REPORT field. The file name of the sample report.
WHAT IS THE PROTOCOL FOR INTERPRETING A VARIATION AS A VUS? field.
WHAT SOFTWARE IS USED TO INTERPRET NOVEL VARIATIONS? field.
WHAT IS THE LABORATORY’S POLICY ON REPORTING NOVEL VARIATIONS? field.
From GTR Field Definitions: ARE FAMILY MEMBERS WHO HAVE DEFINED CLINICAL STATUS RECRUITED TO ASSESS SIGNIFICANCE OF VUS WITHOUT CHARGE?
SAMPLE VUS REPORT field. The path to the file of the sample report.
From the Field Definitions: WILL THE LABORATORY RE-CONTACT THE ORDERING PHYSICIAN IF VARIANT INTERPRETATION CHANGES?
IS RESEARCH ALLOWED ON THE SAMPLE AFTER CLINICAL TESTING IS COMPLETE? field
PURPOSE OF THE TEST field. Values in TestPurposeList or, for internal use, an integer id.
CLINICAL OR RESEARCH TEST field. Values in TestTypeList, for internal use, an integer id.
Free text about this test. Please use only for information that cannot be
represented more explicity.
For the method section either the value or db ID (val_type) can be provided at each level.
HIGHER LEVEL METHOD CATEGORY field, Value in attribute, restricted list of values
METHOD CATEGORY field, Value in attribute, restricted list of values
TEST METHODOLOGY field, Value in attribute, restricted list of values, can suggest values (OtherValue attribute)
INSTRUMENT(S) USED DURING TESTING field, restricted list of values, can suggest values (OtherValue attribute)
PLATFORMS field, need list of allowed values
DESCRIPTION OF TEST PROCEDURE/PROTOCOL field
CONFIRMATION OF TEST RESULTS field
EXON(S) BEING TESTED: TEXT FIELD – MANUAL ENTRY OR POSSIBLY PICK LIST – OPTIONAL
ANALYTICAL VALIDITY field
ASSAY LIMITATIONS field
From the Field Definitions: METHOD USED FOR PROFICIENCY TESTING field. Allowed values are defined in ProficiencyMethodList or,
for internal use, an integer id.
PT PROVIDER field. Allowed values in TestPTProviderList or,
for internal use, an integer id.
CAP TEST LIST field
DESCRIPTION OF PROFICIENCY TESTING METHOD field
INTERNAL TEST VALIDATION METHOD DESCRIPTION field
CLINICAL VALIDITY field
PROFICIENCY TESTING PERFORMED ON THIS TEST field
CLINICAL UTILITY field
Allowed values in ClinicalUtilityTypeList or,
for internal use, an integer id.
FDA CATEGORY DESIGNATION field
If there is a set for regulatory clearance, category must be provided, all other fields are optional.
FDA REVIEW OF field
FDA REGULATORY STATUS field
FDA APPLICATION # field
Also automatically provide the URL for FDA APPROVAL DOCUMENTS.
FDA APPROVAL DOCUMENTS field: will calculate url based on application number
FDA APPROVAL DOCUMENTS field: Can provide file rather than using automatically provided URL
Will not include a list here as the list will change often
currently only have NYSCLEP and ISO and other. Will add others to list in db as needed
used for status primarily of NYCLEP, will not keep controlled list here but in db since it may changes
The internal id assigned to a laboratory by NCBI. Used only in NCBI's submission processing.
GTR ACCESSION ID field. Assigned by NCBI. Do not need to provide
GTR ACCESSION ID (AUTO ASSIGNED BY NCBI WITH VERSIONING) field. Assigned by NCBI. Should not be provdied, will automatically assign a version.
Not in the GTR fields doc, used for migration from GeneTests.
Need the full controlled list here.
Condition for test fields.
CONDITION FOR WHICH TEST IS OFFERED, where Type = 'preferred', should be from posted list of disorder names
LAB-DISPLAYED CONDITION NAME, where Type = 'lab preferred'.
Additional information about the condition is in the TraitSet in ClinVarAssertionType
Will be used when ClinVar reports its identifiers.
Each ClinVar submission is a single asserted relationship from a submitter about the relationship between a[set of] measure(s) (gene or allele) and a [set of] trait(s) (phenotype). 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.
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)
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.
The trait set describes the set of traits (phenotypes,
conditions, etc.) indicated for this assertion.
private comment
Structure to describe attributes of any family data in an observation
this refers to the variant being asserted's zygosity
This is to be used within co-occurrence set
MeasureTrait type is the assertion relationship stored in the
clinvar.measure_target table. This represents a single asserted relationship which
maybe an 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 the types of measure data being included in this set.
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 other measures via mset and msubset tables. The
relat_type in msubset should be the Type attribute
here.
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
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 relat_type in tsubset is the Type attribute
here.
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.
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).
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.
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.
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.
Structure to describe the name, version, and use of code used in a
particular method.
database ID will be captured as attributes when data is pulled from the database.
database ID will be captured as attributes when data is pulled from the database. May be extended (accessions,date,etc) when needed
This XML should represent a single test in GTR.
For TextCitationsList there is not a required description field. There will be an additional drop down list in the element that may be selected in place of a description
required for bulk upload
This should be the person_id and person_id must be represented in the lab section
ARE FAMILY MEMBERS WHO HAVE DEFINED CLINICAL STATUS RECRUITED TO ASSESS SIGNIFICANCE OF VUS WITHOUT CHARGE?
Will the Laboratory Re-contact the Ordering Physician if Variant Interpretation Changes?
Is research allowed on the sample after clinical testing is complete?
Information on Measure in clinvar will be in ClinVar
XML, there is a CVID attribute to indicate the clinvar record
used for status primarily of NYCLEP, will not keep controlled list here but in db since it may change.
Retaining this as a placeholder for possible export of database identifiers from ClinVar.
Should conform to variation-ref.phenotype.clinical-significance
need to make this a controlled list and include other attributes if type = sequence