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umdm.yaml
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#//////////////////////////////////////////////////////////////////////////////
# NAME: umdm_emx1.yaml
# AUTHOR: david ruvolo
# CREATED: 2021-11-08
# MODIFIED: 2022-02-23
# PURPOSE: Unified Molgenis Data Model (umdm)
# STATUS: maturing
# COMMENTS: NA
#//////////////////////////////////////////////////////////////////////////////
# define package
name: umdm
label: Unified Molgenis Data Model
description: The Unified Molgenis Data Model (UMDM)
version: 1.1.1
date: 2022-02-17
tags: https://www.w3.org/TR/vocab-dcat-3/#Class:Catalog
# define tags (the rest are added at build time)
tagDefinitions:
- identifier: https://www.w3.org/TR/vocab-dcat-3/#Class:Catalog
label: dcat:catalog
objectIRI: https://www.w3.org/TR/vocab-dcat-3/#Class:Catalog
codeSystem: dcat
relationLabel: isAssociatedWith
relationIRI: http://molgenis.org#isAssociatedWith
- identifier: https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
label: dcat:dataset
objectIRI: https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
codeSystem: dcat
relationLabel: isAssociatedWith
relationIRI: http://molgenis.org#isAssociatedWith
# set attribute level defaults
defaults:
idAttribute: false
dataType: string
nillable: true
lookupAttribute: false
labelAttribute: false
visible: true
# define entities (lookups are defined in umdm_lookups_emx1.yaml)
tables:
# @name umdm_subjects
- name: subjects
label: Subjects
description: Persons who are observed, analyzed, examined, investigated, experimented upon, or/and treated in the course of a particular study
tags: http://purl.obolibrary.org/obo/ExO_0000127, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: subjectID
dataType: string
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
description: An individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: http://purl.obolibrary.org/obo/NCIT_C142495
- name: belongsToFamily
description: A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
tags: http://purl.obolibrary.org/obo/NCIT_C25173
- name: belongsToMother
dataType: xref
refEntity: umdm_subjects
description: A designation that has some relationship to motherhood.
tags: http://purl.obolibrary.org/obo/NCIT_C89336
- name: belongsToFather
dataType: xref
refEntity: umdm_subjects
description: Having to do with the father, coming from the father, or related through the father.
tags: http://purl.obolibrary.org/obo/NCIT_C94324
- name: belongsWithFamilyMembers
dataType: mref
refEntity: umdm_subjects
description: Any individual related biologically or legally to another individual.
tags: http://purl.obolibrary.org/obo/NCIT_C21480
- name: subjectStatus
dataType: xref
refEntity: umdm_lookups_subjectStatus
description: A findings domain that contains general subject characteristics that are evaluated periodically to determine if they have changed.
tags: http://purl.obolibrary.org/obo/NCIT_C117655
- name: dateOfBirth
dataType: date
description: The calendar date on which a person was born.
tags: http://purl.obolibrary.org/obo/NCIT_C68615
- name: yearOfBirth
dataType: int
description: The year in which a person was born.
tags: http://purl.obolibrary.org/obo/NCIT_C83164
- name: dateOfDeath
dataType: date
description: The calendar date of subject's death.
tags: http://purl.obolibrary.org/obo/NCIT_C70810
- name: yearOfDeath
dataType: int
description: The year in which an individual derived.
tags: http://purl.obolibrary.org/obo/NCIT_C156426
- name: ageAtDeath
dataType: decimal
description: The age at which death occurred.
tags: http://purl.obolibrary.org/obo/NCIT_C135383
- name: genderIdentity
dataType: xref
refEntity: umdm_lookups_genderIdentity
description: A person's concept of self as being male and masculine or female and feminine, or ambivalent, based in part on physical characteristics, parental responses, and psychological and social pressures. It is the internal experience of gender role. A person's sense of self as a member of a particular gender.
tags: http://purl.bioontology.org/ontology/MESH/D005783
- name: genderAtBirth
description: Assigned gender is one's gender which was assigned at birth, typically by a medical and/or legal organization, and then later registered with other organizations. Such a designation is typically based off of the superficial appearance of external genitalia present at birth.
dataType: xref
refEntity: umdm_lookups_genderAtBirth
tags: http://purl.obolibrary.org/obo/GSSO_009418
- name: genotypicSex
dataType: xref
refEntity: umdm_lookups_genotypicSex
description: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
tags: http://purl.obolibrary.org/obo/PATO_0020000
- name: countryOfBirth
description: The country that this person was born in.
dataType: xref
refEntity: umdm_lookups_country
tags: http://purl.obolibrary.org/obo/GENEPIO_0001094
- name: countryOfResidence
description: Country of residence at enrollment.
dataType: xref
refEntity: umdm_lookups_country
tags: http://purl.obolibrary.org/obo/NCIT_C171105
- name: ancestry
dataType: xref
refEntity: umdm_lookups_ancestry
description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.
tags: http://purl.obolibrary.org/obo/NCIT_C176763
- name: affiliation
description: A formal association between entities.
dataType: compound
tags: http://purl.obolibrary.org/obo/NCIT_C25412
- name: primaryOrganization
dataType: xref
refEntity: umdm_organizations
description: The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person.
partOfAttribute: affiliation
tags: http://purl.obolibrary.org/obo/NCIT_C25412
- name: contactPerson
description: A person acting as a channel for communication between groups or on behalf of a group.
partOfAttribute: affiliation
tags: http://purl.obolibrary.org/obo/NCIT_C25461
- name: contactEmail
dataType: email
description: Email address of the contact person or organization
partOfAttribute: affiliation
tags: http://purl.obolibrary.org/obo/MS_1000589
- name: alternativeIdentifiers
description: A backup sequence of characters used to identify an entity.
tags: http://purl.obolibrary.org/obo/NCIT_C90353
- name: firstVisitDate
dataType: date
description: The date for the first patient visit.
tags: http://purl.obolibrary.org/obo/NCIT_C164021
- name: belongsWithTwin
dataType: bool
description: Either of two offspring born from the same pregnancy.
tags: http://purl.obolibrary.org/obo/NCIT_C73427
- name: fetalStatus
dataType: bool
description: Any tissue from a fetus.
tags: http://purl.obolibrary.org/obo/NCIT_C17730
- name: consanguinity
dataType: bool
description: Genetic relatedness between individuals who are descendants of at least one common ancestor.
tags: http://purl.obolibrary.org/obo/NCIT_C71384
- name: belongsToStudy
dataType: mref
refEntity: umdm_studies
description: Reference to the study or studies in which this person participates.
tags: http://purl.obolibrary.org/obo/RO_0000056
- name: belongsToCohort
dataType: mref
refEntity: umdm_cohorts
description: A group of individuals, identified by a common characteristic.
tags: http://purl.obolibrary.org/obo/NCIT_C61512
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_study
- name: studies
label: Studies
description: A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts.
tags: http://purl.obolibrary.org/obo/NCIT_C63536, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: studyID
nillable: false
idAttribute: true
dataType: string
labelAttribute: true
lookupAttribute: true
description: A unique proper name or character sequence that identifies this particular study.
tags: http://purl.obolibrary.org/obo/OMIABIS_0000006
- name: studyAcronym
description: The non-unique initials or abbreviated name used for identification.
tags: http://purl.obolibrary.org/obo/NCIT_C93495
- name: studyName
description: A name that designates this study.
tags: http://purl.obolibrary.org/obo/OMIABIS_0000037
- name: inclusionCriteria
dataType: mref
refEntity: umdm_lookups_inclusionCriteria
description: The conditions which, if met, make an person eligible for participation in this study.
tags: http://purl.obolibrary.org/obo/OBI_0500027
- name: principleInvestigator
description: An investigator who is responsible for all aspects of the conduct of a study.
tags: http://purl.obolibrary.org/obo/NCIT_C19924
- name: contactPerson
description: Name of study contact.
tags: http://purl.obolibrary.org/obo/NCIT_C176373
- name: contactEmail
dataType: email
description: A text string identifier for a location to which e-mail for the study contact can be delivered.
tags: http://purl.obolibrary.org/obo/NCIT_C176375
- name: studyDescription
dataType: text
description: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of this study.
tags: http://purl.obolibrary.org/obo/NCIT_C142704
- name: studyStartDate
dataType: date
description: The date on which this study began.
tags: http://purl.obolibrary.org/obo/NCIT_C69208
- name: studyCompletionDate
dataType: date
description: The date on which the concluding information for this study is completed. Usually, this is when the last subject has a final visit, or the main analysis has finished, or any other protocol-defined completion date.
tags: http://purl.obolibrary.org/obo/NCIT_C142702
- name: currentStudyStatus
dataType: mref
refEntity: umdm_lookups_studyStatus
description: The status of a study or trial.
tags: http://purl.obolibrary.org/obo/NCIT_C171103
- name: numberOfSubjectsEnrolled
dataType: int
description: An integer specifying the quantity of study subjects enrolled in the study at the current time.
tags: http://purl.obolibrary.org/obo/NCIT_C153145
- name: samplesCollected
dataType: int
description: An integer specifying the quantity of samples collected at the current time.
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_consent
- name: consent
label: Consent
description: Consent given by a patient to a surgical or medical procedure or participation in a study, examination or analysis after achieving an understanding of the relevant medical facts and the risks involved.
tags: http://purl.obolibrary.org/obo/NCIT_C16735, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: consentID
idAttribute: true
nillable: false
description: A unique proper name or character sequence that identifies this particular signed individual consent.
tags: http://purl.obolibrary.org/obo/ICO_0000044
- name: belongsToSubject
dataType: xref
refEntity: umdm_subjects
description: An individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: http://purl.obolibrary.org/obo/NCIT_C142495
- name: collectedBy
description: Indicates the person, group, or institution who performed the collection act.
tags: http://purl.obolibrary.org/obo/NCIT_C45262
- name: signingDate
dataType: date
description: A date specification that designates when this individual consent form was signed.
tags: http://purl.obolibrary.org/obo/ICO_0000036
- name: validUntil
dataType: date
description: End date of the validity of this individual consent.
tags: http://purl.org/dc/terms/valid
- name: consentWithdrawn
dataType: bool
description: An indication that the consent to participate in the study or one or more segments of the study has been revoked.
tags: http://purl.obolibrary.org/obo/NCIT_C176342
- name: dataUsePermission
dataType: mref
refEntity: umdm_lookups_dataUsePermissions
description: A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be used.
tags: http://purl.obolibrary.org/obo/DUO_0000001
- name: dataUseModifiers
dataType: mref
refEntity: umdm_lookups_dataUseModifiers
description: Data use modifiers indicate additional conditions for use. For instance, a dataset is restricted to investigations into specific diseases or performed at specific geographical locations.
tags: http://purl.obolibrary.org/obo/DUO_0000017
- name: dataUseSpecification
dataType: text
description: Further specification of applied data use permissions and modifiers. For example, a list of countries in case of geographic restrictions or a list of diseases when restricted to disease-specific research.
tags: http://semanticscience.org/resource/SIO_000090
- name: allowIncidentalFindingRecontact
dataType: bool
description: A planned process for a subject agrees not to be informed about any incidental finding.
tags: http://purl.obolibrary.org/obo/ICO_0000178
- name: allowMatchmaker
dataType: bool
description: Permission is given for MatchMaking
- name: allowRecontacting
dataType: bool
description: The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances.
tags: http://purl.obolibrary.org/obo/NCIT_C25737
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_clinical
- name: clinical
label: Clinical
description: Findings and circumstances relating to the examination and treatment of a patient.
tags: http://purl.obolibrary.org/obo/NCIT_C25398, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: clinicalID
idAttribute: true
description: A unique proper name or character sequence that identifies this particular clinical examination.
tags: http://purl.obolibrary.org/obo/NCIT_C87853
- name: belongsToSubject
dataType: xref
refEntity: umdm_subjects
description: An individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: http://purl.obolibrary.org/obo/NCIT_C142495
- name: affectedStatus
dataType: bool
description: Individuals in a pedigree who exhibit the specific phenotype under study.
tags: http://purl.obolibrary.org/obo/NCIT_C64917
- name: dateOfDiagnosis
dataType: date
description: The date on which a diagnosis of disease was made.
tags: http://purl.obolibrary.org/obo/NCIT_C164339
- name: ageAtDiagnosis
dataType: decimal
description: The age (in years), measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease.
tags: http://purl.bioontology.org/ontology/SNOMEDCT/423493009
- name: ageOfOnset
dataType: decimal
description: Age (in years) of onset of clinical manifestations related to the disease of the patient.
tags: http://www.orpha.net/ORDO/Orphanet_C023
- name: observedPhenotype
dataType: mref
refEntity: umdm_lookups_phenotype
description: The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.
tags: http://purl.obolibrary.org/obo/NCIT_C16977
- name: unobservedPhenotype
dataType: mref
refEntity: umdm_lookups_phenotype
description: Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.
tags: http://purl.bioontology.org/ontology/HL7/C0442737
- name: provisionalPhenotype
dataType: mref
refEntity: umdm_lookups_phenotype
description: The test or procedure was successfully performed, but the results are borderline and can neither be declared positive / negative nor detected / not detected according to the current established criteria.
tags: http://purl.bioontology.org/ontology/HL7/C0332241
- name: clinicalDiagnosis
dataType: mref
refEntity: umdm_lookups_diseases
description: A diagnosis made from a study of the signs and symptoms of a disease.
tags: http://purl.obolibrary.org/obo/NCIT_C15607
- name: molecularDiagnosis
dataType: mref
refEntity: umdm_lookups_molecularDiagnosis
description: Gene affected by pathogenic variation that is causal for disease of the patient.
tags: http://purl.obolibrary.org/obo/NCIT_C20826
- name: molecularDiagnosisOther
dataType: text
description: Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.
tags: http://purl.obolibrary.org/obo/NCIT_C20826
- name: statusOfDiagnosis
dataType: xref
refEntity: umdm_lookups_diagnosisConfirmationStatuses
description: A condition or state at a particular time.
tags: http://purl.obolibrary.org/obo/NCIT_C25688
- name: dateDiagnosisConfirmed
dataType: date
description: The particular day, month and year an event has happened or will happen.
tags: http://purl.obolibrary.org/obo/NCIT_C25164
- name: belongsToSample
dataType: mref
refEntity: umdm_samples
description: Name or other identifier of an entry from a biosample database.
tags: http://edamontology.org/data_3273
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_samples
# @references http://purl.obolibrary.org/obo/SCDO_0002829
- name: samples
label: Samples
description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a material) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
tags: http://purl.obolibrary.org/obo/SCDO_0002829, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: sampleID
idAttribute: true
nillable: false
description: Name or other identifier of an entry from a biosample database.
tags: http://edamontology.org/data_3273
- name: belongsToSubject
dataType: xref
refEntity: umdm_subjects
description: An individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: http://purl.obolibrary.org/obo/NCIT_C142495
- name: belongsToRequest
description: A sequence of letters, numbers, or other characters that specifically identifies a particular order.
tags: http://purl.obolibrary.org/obo/NCIT_C164567
- name: dateOfRequest
dataType: date
description: The date on which the activity or entity was ordered.
tags: http://purl.obolibrary.org/obo/NCIT_C164566
- name: reasonForSampling
dataType: mref
refEntity: umdm_lookups_samplingReason
description: The explanation for why a test, measurement, or assessment is executed.
tags: http://purl.obolibrary.org/obo/NCIT_C171003
- name: samplingDate
dataType: date
description: The date that a sample was collected or obtained.
tags: http://purl.obolibrary.org/obo/NCIT_C164024
- name: samplingTimestamp
dataType: datetime
description: Date and time at which this material was collected.
tags: http://www.ebi.ac.uk/efo/EFO_0000689
- name: samplingProtocol
dataType: mref
refEntity: umdm_samplingProtocols
description: The procedure whereby this material was sampled for an analysis.
tags: http://www.ebi.ac.uk/efo/EFO_0005518
- name: samplingProtocolDeviation
dataType: text
description: A variation from processes or procedures defined in the sampling protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor.
tags: http://purl.obolibrary.org/obo/NCIT_C50996
- name: reasonForSamplingProtocolDeviation
dataType: text
description: The rationale for why a deviation from the sampling protocol has occurred.
tags: http://purl.obolibrary.org/obo/NCIT_C93529
- name: biospecimenType
dataType: xref
refEntity: umdm_lookups_biospecimenType
description: The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.
tags: http://purl.obolibrary.org/obo/NCIT_C70713
- name: anatomicalSource
dataType: xref
refEntity: umdm_lookups_anatomicalSource
description: Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.
tags: http://purl.obolibrary.org/obo/NCIT_C103264
- name: pathologicalState
dataType: xref
refEntity: umdm_lookups_pathologicalState
description: The pathological state of the tissue from which this material was derived.
tags: http://purl.obolibrary.org/obo/GO_0001894
- name: biospecimenUsability
dataType: bool
description: An indication as to whether a biospecimen is suitable for testing purposes.
tags: http://purl.obolibrary.org/obo/NCIT_C171004
- name: alternativeIdentifiers
description: A backup sequence of characters used to identify an entity.
tags: http://purl.obolibrary.org/obo/NCIT_C90353
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_samplePreparation
- name: samplePreparation
label: Sample Preparation
description: A sample preparation for a nucleic acids sequencing assay.
tags: http://purl.obolibrary.org/obo/OBI_0001902, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: sampleID
idAttribute: true
nillable: false
description: A unique proper name or character sequence that identifies this particular sample preparation.
tags: http://purl.obolibrary.org/obo/NCIT_C132299
- name: belongsToSample
dataType: xref
refEntity: umdm_samples
description: Name or other identifier of an entry from a biosample database.
tags: http://purl.obolibrary.org/obo/NCIT_C93400
- name: belongsToLabProcedure
dataType: xref
refEntity: umdm_labProcedures
description: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
tags: http://purl.obolibrary.org/obo/NCIT_C25294
- name: belongsToRequest
description: A sequence of letters, numbers, or other characters that specifically identifies a particular order.
tags: http://purl.obolibrary.org/obo/NCIT_C164567
- name: inputAmount
dataType: int
description: Amount of input material in nanogram (ng).
tags: http://purl.allotrope.org/ontologies/role#AFRL_0000010
- name: libraryPreparationKit
dataType: xref
refEntity: umdm_lookups_ngsKits
description: Pre-filled, ready-to-use reagent cartridges intented to improve chemistry, cluster density and read length as well as improve quality (Q) scores for this sample. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications.
tags: http://purl.obolibrary.org/obo/GENEPIO_0000085
- name: pcrFree
dataType: bool
description: Indicates whether a polymerase chain reaction (PCR) was used to prepare this sample. PCR is a method for amplifying a DNA base sequence using multiple rounds of heat denaturation of the DNA and annealing of oligonucleotide primers complementary to flanking regions in the presence of a heat-stable polymerase.
tags: http://purl.obolibrary.org/obo/NCIT_C17003
- name: targetEnrichmentKit
dataType: xref
refEntity: umdm_lookups_ngsKits
description: Indicates which target enrichment kit was used to prepare this sample. Target enrichment is a pre-sequencing DNA preparation step where DNA sequences are either directly amplified (amplicon or multiplex PCR-based) or captured (hybrid capture-based) in order to only focus on specific regions of a genome or DNA sample.
tags: http://purl.obolibrary.org/obo/NCIT_C154307
- name: umisPresent
dataType: bool
description: Indicates whether any unique molecular identifiers (UMIs) are present. An UMI barcode is a short nucleotide sequence that is used to identify reads originating from an individual mRNA molecule.
tags: http://www.ebi.ac.uk/efo/EFO_0010199
- name: intendedInsertSize
dataType: int
description: In paired-end sequencing, the DNA between the adapter sequences is the insert. The length of this sequence is known as the insert size, not to be confused with the inner distance between reads. So, fragment length equals read adapter length (2x) plus insert size, and insert size equals read lenght (2x) plus inner distance.
tags: https://w3id.org/fair-genomes/resource/FG_0000001
- name: intendedReadLength
dataType: int
description: The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.
tags: http://purl.obolibrary.org/obo/NCIT_C153362
- name: barcode
description: A machine-readable representation of information in a visual format on a surface.
tags: http://purl.obolibrary.org/obo/NCIT_C43361
- name: belongsToBatch
description: A quantity of people or things treated or regarded as a group, especially when subdivided from a larger group.
tags: http://purl.obolibrary.org/obo/NCIT_C67073
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_sequencing
- name: sequencing
label: Sequencing
description: The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
tags: http://edamontology.org/topic_3168, https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset
columns:
- name: sequencingID
idAttribute: true
nillable: false
lookupAttribute: true
labelAttribute: true
description: A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.
tags: http://purl.obolibrary.org/obo/NCIT_C171337
- name: belongsToLabProcedure
dataType: xref
refEntity: umdm_labProcedures
description: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
tags: http://purl.obolibrary.org/obo/NCIT_C25294
- name: belongsToSamplePreparation
dataType: xref
refEntity: umdm_samplePreparation
description: A unique proper name or character sequence that identifies this particular sample preparation.
tags: http://purl.obolibrary.org/obo/NCIT_C132299
- name: reasonForSequencing
dataType: xref
refEntity: umdm_lookups_samplingReason
description: A rationale for executing a plan of action.
tags: http://purl.obolibrary.org/obo/NCIT_C69216
- name: sequencingDate
dataType: date
description: Date on which this sequencing assay was performed.
tags: http://purl.obolibrary.org/obo/GENEPIO_0000069
- name: sequencingFacilityOrganization
dataType: xref
refEntity: umdm_organizations
description: An organization that provides sequence determination service
tags: http://purl.obolibrary.org/obo/OBI_0001891
- name: sequencingPlatform
dataType: xref
refEntity: umdm_lookups_sequencingPlatform
description: The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).
tags: http://purl.obolibrary.org/obo/GENEPIO_0000071
- name: sequencingInstrumentModel
dataType: xref
refEntity: umdm_lookups_sequencingInstrumentModels
description: The used product name and model number of a manufacturer's genomic (dna) sequencer.
tags: http://purl.obolibrary.org/obo/GENEPIO_0001921
- name: sequencingMethod
dataType: xref
refEntity: umdm_lookups_sequencingMethods
description: Method used to determine the order of bases in a nucleic acid sequence.
tags: http://purl.obolibrary.org/obo/FIX_0000704
- name: averageReadDepth
dataType: int
description: The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.
tags: http://purl.obolibrary.org/obo/NCIT_C155320
- name: observedReadLength
dataType: int
description: The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.
tags: http://purl.obolibrary.org/obo/NCIT_C153362
- name: observedInsertSize
dataType: int
description: In paired-end sequencing, the DNA between the adapter sequences is the insert. The length of this sequence is known as the insert size, not to be confused with the inner distance between reads. So, fragment length equals read adapter length (2x) plus insert size, and insert size equals read lenght (2x) plus inner distance.
tags: https://w3id.org/fair-genomes/resource/FG_0000002
- name: percentageQ30
dataType: decimal
description: Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.
tags: http://purl.obolibrary.org/obo/GENEPIO_0000089
- name: percentageTR20
dataType: decimal
description: Percentage of the target sequence on which 20 or more unique reads were successfully mapped.
tags: https://w3id.org/fair-genomes/resource/FG_0000003
- name: otherQualityMetrics
dataType: text
description: Other NGS quality control metrics, including but not limited to (i) sequencer metrics such as yield, error rate, density (K/mm2), cluster PF (%) and phas/prephas (%), (ii) alignment metrics such as QM insert size, GC content, QM duplicated reads (%), QM error rate, uniformity/evenness of coverage and maternal cell contamination, and (iii) variant call metrics such as number of SNVs/CNVs/SVs called, number of missense/nonsense variants, common variants (%), unique variants (%), gender match and trio inheritance check.
tags: http://edamontology.org/data_3914
- name: referenceGenomeUsed
dataType: xref
refEntity: umdm_lookups_genomeAccessions
description: The specific build of the human genome used as reference for sequence alignment and variant calling.
tags: http://edamontology.org/data_2340
- name: belongsToDataRelease
dataType: mref
refEntity: umdm_releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: http://purl.obolibrary.org/obo/NCIT_C172217
- name: recordMetadata
dataType: compound
description: metadata is data that provides information about data.
tags: http://semanticscience.org/resource/SIO_001330
- name: comments
dataType: text
description: A written explanation, observation or criticism added to textual material.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C25393
- name: dateRecordCreated
nillable: false
dataType: datetime
description: The date on which the activity or entity is created.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C164483
- name: recordCreatedBy
nillable: false
description: Indicates the person or authoritative body who brought the item into existence.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C42628
- name: dateRecordUpdated
dataType: datetime
description: The date (and time) on which report was updated after it had been submitted.
partOfAttribute: recordMetadata
tags: http://purl.obolibrary.org/obo/NCIT_C93629
- name: wasUpdatedBy
description: An entity which is updated by another entity or an agent.
partOfAttribute: recordMetadata
tags: https://w3id.org/reproduceme#wasUpdatedBy
#////////////////////////////////////////////////////////////////////////////
# @name umdm_files
- name: files
label: Files