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unified-schema.yml
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---
name: Unified metadata schema
description: The unified semantic metadata schema to power reuse of NGS data in research and healthcare.
version: 0.1
releaseType: SNAPSHOT
date: 2022-02-23
tags: https://www.w3.org/TR/vocab-dcat-3/#Class:Catalog
lookupGlobalOptions: lookups/NullFlavors.tsv
authors:
- name: David C. Ruvolo
email: d.c.ruvolo@umcg.nl
orcid: 0000-0002-5745-5298
- name: K. Joeri van der Velde
email: k.j.van.der.velde@umcg.nl
orcid: 0000-0002-0934-8375
- name: Morris A. Swertz
email: m.a.swertz@umcg.nl
orcid: 0000-0002-0979-3401
copyright:
holder: University Medical Center Groningen
years: 2022
license:
name: Attribution 4.0 International (CC BY 4.0)
url: https://creativecommons.org/licenses/by/4.0/
technical:
artDecorId: na
ttlLocation: https://fairgenomes.github.io/unified-fg/generated/ontology/
gitLocation: https://github.com/fairgenomes/unified-fg
tables:
- name: Studies
description: A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts.
tags: NCIT:C63536 [http://purl.obolibrary.org/obo/NCIT_C63536]
columns:
- name: Identifier
description: A unique proper name or character sequence that identifies this particular study.
tags: OMIABIS:0000006 [http://purl.obolibrary.org/obo/OMIABIS_0000006]
broadMatch: SIO:000729 [http://semanticscience.org/resource/SIO_000729], IAO:0000577 [http://purl.obolibrary.org/obo/IAO_0000577]
dataType: identifier
example: NEURODB
- name: Name
description: A name that designates this study.
tags: OMIABIS:0000037 [http://purl.obolibrary.org/obo/OMIABIS_0000037]
exactMatch: OBI:0001622 [http://purl.obolibrary.org/obo/OBI_0001622]
broadMatch: SIO:000185 [https://semanticscience.org/resource/SIO_000185]
dataType: string
example: University Hospital Neuro Data Bank
- name: Acronym
description: The non-unique initials or abbreviated name used for identification.
tags: NCIT:C93495 [http://purl.obolibrary.org/obo/NCIT_C93495]
dataType: string
example: NeuroDB
- name: Description
description: A statement or piece of writing that provides details on this study.
tags: OMIABIS:0000036 [http://purl.obolibrary.org/obo/OMIABIS_0000036], NCIT:C142704 [http://purl.obolibrary.org/obo/NCIT_C142704]
exactMatch: OBI:0001615 [http://purl.obolibrary.org/obo/OBI_0001615]
broadMatch: SIO:000136 [https://semanticscience.org/resource/SIO_000136]
dataType: text
example: Biobank of samples collected from patients in the neurology clinic
- name: Inclusion criteria
description: The conditions which, if met, make an person eligible for participation in this study.
tags: OBI:0500027 [http://purl.obolibrary.org/obo/OBI_0500027]
dataType: mref
reference: lookups/InclusionCriteria.tsv
referenceTypeTag: OBI:0500027 [http://purl.obolibrary.org/obo/OBI_0500027]
example: age group inclusion criterion, defined population inclusion criterion, health status inclusion criterion
- name: Principal investigator
description: An investigator who is responsible for all aspects of the conduct of a study.
tags: OMIABIS:0000100 [http://purl.obolibrary.org/obo/OMIABIS_0000100], NCIT:C19924 [http://purl.obolibrary.org/obo/NCIT_C19924]
broadMatch: SIO:000881 [https://semanticscience.org/resource/SIO_000881], OBI:0000202 [http://purl.obolibrary.org/obo/OBI_0000202]
dataType: xref
reference: Person
example: rosemarie.vandale@neurocenter.nl
- name: Contact person
description: Name of study contact.
tags: NCIT:C176373 [http://purl.obolibrary.org/obo/NCIT_C176373]
dataType: xref
reference: Person
example: rosemarie.vandale@neurocenter.nl
#- name: Contact email --> part of Person
# description: An email address for the purpose of contacting the study contact person.
# tags: OMIABIS:0000035 [http://purl.obolibrary.org/obo/OMIABIS_0000035], NCIT:C176375 [http://purl.obolibrary.org/obo/NCIT_C176375]
# dataType: email
- name: Study design
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: OBI:0500000 [http://purl.obolibrary.org/obo/OBI_0500000]
dataType: text
example: "Background: The development of software for use in diagnostic settings is faster than clinical validation and implementation. To enable rapid, large scale validation of diagnostic technologies, it is critical that a comprehensive data bank is established so that these technologies can be validated on a larger scale. Methods/Design: 1000 individuals will be recruited over a five year period at five partnering hospitals. Clinical characteristics and biological materials will be collected once per individual through their regular GP visit."
- name: Start date
description: The date on which this study began.
tags: NCIT:C69208 [http://purl.obolibrary.org/obo/NCIT_C69208]
broadMatch: SIO:000031 [https://semanticscience.org/resource/SIO_000031], IAO:0000582 [http://purl.obolibrary.org/obo/IAO_0000582]
dataType: date
example: 2022-01-01
- name: Completion 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: NCIT:C142702 [http://purl.obolibrary.org/obo/NCIT_C142702]
broadMatch: IAO:0000582 [http://purl.obolibrary.org/obo/IAO_0000582]
relatedMatch: SIO:001083 [https://semanticscience.org/resource/SIO_001083], SIO:001314 [https://semanticscience.org/resource/SIO_001314]
dataType: date
example: 2027-12-31
- name: Current study status
dataType: mref
reference: lookups/StudyStatus.tsv
description: The status of a study or trial.
tags: NCIT:C171103 [http://purl.obolibrary.org/obo/NCIT_C171103]
referenceTypeTag: NCIT:C171103 [http://purl.obolibrary.org/obo/NCIT_C171103]
example: Active Study
- name: Number of subjects enrolled
dataType: integer
description: An integer specifying the quantity of study subjects enrolled in the study at the current time.
tags: NCIT:C153145 [http://purl.obolibrary.org/obo/NCIT_C153145]
example: 112
- name: Numer of samples collected
dataType: integer
description: An integer specifying the quantity of samples collected at the current time.
tags: KISAO:0000326 [http://www.biomodels.net/kisao/KISAO#KISAO_0000326]
example: 72
- name: belongsToDataRelease
dataType: mref
reference: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217]
example: DR01
- name: Person
description: researcher or contactperson involved in the study and/or affliated with organisation
tags: NCIT:C25461 [http://purl.obolibrary.org/obo/NCIT_C25461], NCIT:C25936 [http://purl.obolibrary.org/obo/NCIT_C25936]
columns:
- name: identifier
description: identifier
dataType: identifier
tags: NCIT:C25364 [http://purl.obolibrary.org/obo/NCIT_C25364]
example: rosemarie.vandale@neurocenter.nl
- name: Full Name
description: full name. E.g. Morris Swertz
tags: GSSO:001755 [http://purl.obolibrary.org/obo/GSSO_001755]
example: Rosemarie Vandale
dataType: string
- name: Alternative identifier
description: alternative identifier. E.g. ORCID:1234
tags: NCIT:C90353 [http://purl.obolibrary.org/obo/NCIT_C90353]
example: ORCID:0000-0000-0000-0000
dataType: string
- name: firstName
description: A word or group of words indicating a person's first (personal or given) name
tags: NCIT:C40974 [http://purl.obolibrary.org/obo/NCIT_C40974]
example: Rosemarie
dataType: string
- name: Middle initials
description: middle initiatials. E.g. A.
tags: NCIT:C166237 [http://purl.obolibrary.org/obo/NCIT_C166237]
example: A.
dataType: string
- name: Last name
description: last name. E.g. Swertz
tags: NCIT:C40975 [http://purl.obolibrary.org/obo/NCIT_C40975]
example: Vandale
dataType: string
- name: Email
description: email address. E.g. m.a.swertz@rug.nl
tags: NCIT:C42775 [http://purl.obolibrary.org/obo/NCIT_C42775]
example: rosemarie.vandale@neurocenter.nl
dataType: string
- name: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
columns:
- name: id
dataType: identifier
description: One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing.
tags: NCIT:C25364 [http://purl.obolibrary.org/obo/NCIT_C25364]
example: DR01
- name: name
description: The words or language units by which a thing is known.
tags: NCIT:C42614 [http://purl.obolibrary.org/obo/NCIT_C42614]
dataType: string
example: NeuroDB Data Release 1
- name: description
description: A written or verbal account, representation, statement, or explanation of something.
tags: NCIT:C25365 [http://purl.obolibrary.org/obo/NCIT_C25365]
dataType: text
example: Included patients seen in the clinical between 1 January 2022 and 31 March 2022.
- name: date
description: A date of database submission refers to the moment in time in which some information was submitted/received to a database system.
tags: SIO:001083 [http://semanticscience.org/resource/SIO_001083]
dataType: date
example: 2022-04-01
- name: createdBy
description: Indicates the person or authoritative body who brought the item into existence.
tags: NCIT:C42628 [http://purl.obolibrary.org/obo/NCIT_C42628]
dataType: xref
reference: Person
example: rosemarie.vandale@neurocenter.nl
- name: numberOfEntriesAdded
description: Combined or joined to increase in size or quantity or scope.
tags: NCIT:C45330 [http://purl.obolibrary.org/obo/NCIT_C45330]
dataType: integer
example: 100
# TODO: Should this be an xref to `Organisation` or `Person`?
- name: dataSource
description: The person or authoritative body who provided the information.
tags: NCIT:C16493 [http://purl.obolibrary.org/obo/NCIT_C16493]
dataType: string
example: Bioinformatic database team
- name: releaseComments
description: A notation regarding the decisions, and/or clarification of any information pertaining to data management.
tags: NCIT:C115505 [http://purl.obolibrary.org/obo/NCIT_C115505]
dataType: text
example:
- name: Subjects
description: Persons who are observed, analyzed, examined, investigated, experimented upon, or/and treated in the course of a particular study.
tags: NCIT:C90492 [http://purl.obolibrary.org/obo/NCIT_C90492], ExO:0000127 [http://purl.obolibrary.org/obo/ExO_0000127], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
relationWith:
- table: Studies
relation: RO:0000056 [http://purl.obolibrary.org/obo/RO_0000056]
columns:
- name: Identifier
description: A unique proper name or character sequence that identifies this particular individual who is the subject of personal data, persons to whom data refers, and from whom data are collected, processed, and stored.
tags: NCIT:C164337 [http://purl.obolibrary.org/obo/NCIT_C164337], NCIT:C142495 [http://purl.obolibrary.org/obo/NCIT_C142495]
dataType: identifier
example: P00001
- name: Alternative identifiers
description: A backup sequence of characters used to identify an entity.
tags: NCIT:C90353 [http://purl.obolibrary.org/obo/NCIT_C90353]
dataType: string
example:
- name: Gender identity
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. For practical reasons the lookups are limited to first and second-level entries, but can be expanded when needed. Note that 'Gender at birth', 'Genotypic sex' and any (gender-related) hormone therapies in 'Medication' are usually medically more relevant than this term.
tags: MESH:D005783 [http://purl.bioontology.org/ontology/MESH/D005783]
dataType: xref
reference: lookups/GenderIdentity.tsv
referenceTypeTag: MESH:D005783 [http://purl.bioontology.org/ontology/MESH/D005783]
example: female gender identity
- name: Gender at birth
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.
tags: GSSO:009418 [http://purl.obolibrary.org/obo/GSSO_009418]
dataType: xref
reference: lookups/GenderAtBirth.tsv
referenceTypeTag: GSSO:009418 [http://purl.obolibrary.org/obo/GSSO_009418]
example: assigned female at birth
- name: Genotypic sex
description: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
tags: PATO:0020000 [http://purl.obolibrary.org/obo/PATO_0020000]
dataType: xref
reference: lookups/GenotypicSex.tsv
referenceTypeTag: NCIT:C168871 [http://purl.obolibrary.org/obo/NCIT_C168871]
example: XX Genotype
- name: Country of residence
description: Country of residence at enrollment.
tags: NCIT:C171105 [http://purl.obolibrary.org/obo/NCIT_C171105]
dataType: xref
reference: lookups/Countries.tsv
referenceTypeTag: GENEPIO:0001830 [http://purl.obolibrary.org/obo/GENEPIO_0001830]
example: Netherlands (the)
- name: Ancestry
description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.
tags: NCIT:C176763 [http://purl.obolibrary.org/obo/NCIT_C176763]
dataType: xref
reference: lookups/Ancestry.tsv
referenceTypeTag: HANCESTRO:0004 [http://purl.obolibrary.org/obo/HANCESTRO_0004]
example: Dutch
- name: Country of birth
description: The country that this person was born in.
tags: GENEPIO:0001094 [http://purl.obolibrary.org/obo/GENEPIO_0001094]
dataType: xref
reference: lookups/Countries.tsv
referenceTypeTag: GENEPIO:0001830 [http://purl.obolibrary.org/obo/GENEPIO_0001830]
example: Netherlands (the)
- name: Year of birth
description: The year in which this person was born.
tags: NCIT:C83164 [http://purl.obolibrary.org/obo/NCIT_C83164]
dataType: integer
unit: NCIT:C159612 [http://purl.obolibrary.org/obo/NCIT_C159612]
example: 1970
- name: Date of birth
dataType: date
description: The calendar date on which a person was born.
tags: NCIT:C68615 [http://purl.obolibrary.org/obo/NCIT_C68615]
example: 1970-01-01
- name: Inclusion status
description: A findings domain that contains general subject characteristics that are evaluated periodically to determine if they have changed.
#description: An indicator that provides information on the current health status of this person.
tags: NCIT:C166244 [http://purl.obolibrary.org/obo/NCIT_C166244], NCIT:C117655 [http://purl.obolibrary.org/obo/NCIT_C117655]
dataType: xref
reference: lookups/InclusionStatus.tsv
referenceTypeTag: NCIT:C19332 [http://purl.obolibrary.org/obo/NCIT_C19332]
example: Alive
- name: Age at death
description: The age at which death occurred.
tags: NCIT:C135383 [http://purl.obolibrary.org/obo/NCIT_C135383]
dataType: integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
example:
- name: Date of death
dataType: date
description: The calendar date of subject's death.
tags: NCIT:C70810 [http://purl.obolibrary.org/obo/NCIT_C70810]
example:
- name: Year of death
dataType: integer
description: The year in which an individual derived.
tags: NCIT:C156426 [http://purl.obolibrary.org/obo/NCIT_C156426]
example:
- name: Primary affiliated institute
description: The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person.
tags: NCIT:C25412 [http://purl.obolibrary.org/obo/NCIT_C25412]
dataType: xref
reference: lookups/Institutes.tsv
referenceTypeTag: SIO:000688 [http://semanticscience.org/resource/SIO_000688]
example: Universitair Medisch Centrum Groningen (UMCG)
- name: Affiliated institute contact person
description: A person acting as a channel for communication between groups or on behalf of a group.
tags: NCIT:C25461 [http://purl.obolibrary.org/obo/NCIT_C25461]
dataType: xref
reference: Person
example: rosemarie.vandale@neurocenter.nl
# - name: Affiliated institute contact email --> part of Person
# dataType: email
# description: Email address of the contact person or organization
# tags: MS:1000589 [http://purl.obolibrary.org/obo/MS_1000589]
- name: Resources in other institutes
description: Material or data related to this person that is not captured by this system though known to be available in other institutes such as biobanks or hospitals.
tags: NCIT:C19012 [http://purl.obolibrary.org/obo/NCIT_C19012]
dataType: mref
reference: lookups/Institutes.tsv
referenceTypeTag: SIO:000688 [http://semanticscience.org/resource/SIO_000688]
example: Martini Ziekenhuis, Groningen
- name: Participates in study
description: Reference to the study or studies in which this person participates.
tags: RO:0000056 [http://purl.obolibrary.org/obo/RO_0000056]
dataType: mref
reference: Studies
example: NEURODB
- name: Belongs to family
description: A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
tags: NCIT:C25173 [http://purl.obolibrary.org/obo/NCIT_C25173]
dataType: string
example: F1000
- name: Belongs to mother
dataType: xref
reference: Subjects
description: A designation that has some relationship to motherhood.
tags: NCIT:C89336 [http://purl.obolibrary.org/obo/NCIT_C89336]
example: P00002
- name: Belongs to father
dataType: xref
reference: Subjects
description: Having to do with the father, coming from the father, or related through the father.
tags: NCIT:C94324 [http://purl.obolibrary.org/obo/NCIT_C94324]
example: P00003
- name: Belongs with family members
dataType: mref
reference: Subjects
description: Any individual related biologically or legally to another individual.
tags: NCIT:C21480 [http://purl.obolibrary.org/obo/NCIT_C21480]
example: P00002,P00003,P00004
- name: Belongs with twin
dataType: bool
description: Either of two offspring born from the same pregnancy.
tags: NCIT:C73427 [http://purl.obolibrary.org/obo/NCIT_C73427]
example: false
- name: First visit date
dataType: date
description: The date for the first patient visit.
tags: NCIT:C164021 [http://purl.obolibrary.org/obo/NCIT_C164021]
example: 2022-01-03
- name: Fetal status
dataType: bool
description: Any tissue from a fetus.
tags: NCIT:C17730 [http://purl.obolibrary.org/obo/NCIT_C17730]
example: false
- name: Consanguinity
dataType: bool
description: Information on whether the patient is a child from two family members who are second cousins or closer.
#description: Genetic relatedness between individuals who are descendants of at least one common ancestor.
tags: OMIT:0004546 [http://purl.obolibrary.org/obo/OMIT_0004546], SNOMED:842009 [http://snomed.info/id/842009]
# old tags, dont fit well: http://purl.obolibrary.org/obo/NCIT_C71384, GSSO:007578 [http://purl.obolibrary.org/obo/GSSO_007578]
example: false
- name: Part of data release
dataType: mref
reference: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217]
example: DR01
- name: Belongs to cohort
dataType: mref
reference: Cohorts
description: A group of individuals, identified by a common characteristic.
tags: NCIT:C61512 [http://purl.obolibrary.org/obo/NCIT_C61512]
example:
- name: Clinical
description: Findings and circumstances relating to the examination and treatment of a patient.
tags: NCIT:C25398 [http://purl.obolibrary.org/obo/NCIT_C25398], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
relationWith:
- table: Personal
relation: SIO:000332 [http://semanticscience.org/resource/SIO_000332]
columns:
- name: Identifier
description: A unique proper name or character sequence that identifies this particular clinical examination.
tags: NCIT:C87853 [http://purl.obolibrary.org/obo/NCIT_C87853]
dataType: identifier
example: DX36310
- name: Belongs to subject
dataType: xref
reference: Subjects
#description: Reference to the person whom this clinical information is about.
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: NCIT:C142495 [http://purl.obolibrary.org/obo/NCIT_C142495], IAO:0000136 [http://purl.obolibrary.org/obo/IAO_0000136]
example: P00001
- name: Affected status
dataType: bool
description: Individuals in a pedigree who exhibit the specific phenotype under study.
tags: NCIT:C64917 http://purl.obolibrary.org/obo/NCIT_C64917
example: false
- name: Date of diagnosis
dataType: date
description: The date on which a diagnosis of disease was made.
tags: NCIT:C164339 [http://purl.obolibrary.org/obo/NCIT_C164339]
example: 2022-01-05
- name: Age at diagnosis
dataType: integer
description: The age (in years), measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease.
tags: SNOMEDCT:423493009 [http://purl.bioontology.org/ontology/SNOMEDCT/423493009]
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
example: 53
- name: Age of onset
dataType: integer
description: Age (in years) of onset of clinical manifestations related to the disease of the patient.
tags: Orphanet:C023 [http://www.orpha.net/ORDO/Orphanet_C023]
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
example: 52
- name: Age at last screening
description: Age of the patient at the moment of the most recent screening.
tags: NCIT:C81258 [http://purl.obolibrary.org/obo/NCIT_C81258]
dataType: integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
example: 52
- name: Observed phenotype
dataType: mref
reference: lookups/Phenotypes.tsv
referenceTypeTag: Wikidata:P3841 [https://www.wikidata.org/wiki/Property:P3841]
description: The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.
tags: NCIT:C16977 [http://purl.obolibrary.org/obo/NCIT_C16977]
example: Schizophrenia
- name: Unobserved phenotype
dataType: mref
reference: lookups/Phenotypes.tsv
referenceTypeTag: Wikidata:P3841 [https://www.wikidata.org/wiki/Property:P3841]
description: Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.
tags: HL7:C0442737 [http://purl.bioontology.org/ontology/HL7/C0442737]
example:
- name: Provisional phenotype
dataType: mref
reference: lookups/Phenotypes.tsv
referenceTypeTag: Wikidata:P3841 [https://www.wikidata.org/wiki/Property:P3841]
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: HL7:C0332241 [http://purl.bioontology.org/ontology/HL7/C0332241]
example: Myopia
- name: Clinical diagnosis
dataType: mref
reference: lookups/Diseases.tsv
referenceTypeTag: EDAM:data_3667 [http://edamontology.org/data_3667] #Note that lookup type EDAM:data_2800 would best match the default Orpha codes, but EDAM:data_3667 was chosen to allow alternative disease coding systems (e.g. ICD or SNOMED).
description: A diagnosis made from a study of the signs and symptoms of a disease.
tags: NCIT:C15607 [http://purl.obolibrary.org/obo/NCIT_C15607]
example: "NON RARE IN EUROPE: Schizophrenia"
- name: Molecular diagnosis gene
dataType: mref
reference: lookups/Genes.tsv
referenceTypeTag: NCIT:C16612 [http://purl.obolibrary.org/obo/NCIT_C16612]
description: Gene affected by pathogenic variation that is causal for disease of the patient.
tags: NCIT:C20826 [http://purl.obolibrary.org/obo/NCIT_C20826]
example:
- name: Molecular diagnosis other
dataType: text
description: Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.
tags: NCIT:C20826 [http://purl.obolibrary.org/obo/NCIT_C20826]
example:
- name: Medication
description: A drug product that contains one or more active and/or inactive ingredients used by the patient intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.
tags: NCIT:C459 [http://purl.obolibrary.org/obo/NCIT_C459]
dataType: mref
reference: lookups/Drugs.tsv
referenceTypeTag: EDAM:data_3103 [http://edamontology.org/data_3103]
example:
- name: Drug regimen
description: The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.
tags: NCIT:C142516 [http://purl.obolibrary.org/obo/NCIT_C142516]
dataType: text
example: No medications perscribed
- name: Medical history
description: A record of a person's background regarding health, occurrence of disease events and surgical procedures.
tags: NCIT:C18772 [http://purl.obolibrary.org/obo/NCIT_C18772]
dataType: mref
reference: lookups/MedicalHistory.tsv
referenceTypeTag: SCDO:1000093 [http://scdontology.h3abionet.org/ontology/SCDO_1000093]
example:
- name: Phenotypic data available
description: Types of phenotypic data collected in a clinical setting that is potentially available upon request.
tags: NCIT:C15783 [http://purl.obolibrary.org/obo/NCIT_C15783]
dataType: mref
reference: lookups/DCMITypes.tsv
referenceTypeTag: DC:DCMIType [http://purl.org/dc/terms/DCMIType]
example: Dataset
- name: Status of diagnosis
dataType: xref
reference: lookups/DiagnosisConfirmationStatus.tsv
referenceTypeTag: NCIT:C48655 [http://purl.obolibrary.org/obo/NCIT_C48655]
description: A condition or state at a particular time.
tags: NCIT:C25688 [http://purl.obolibrary.org/obo/NCIT_C25688]
example: Confirmed
- name: First contact
description: First contact of the patient with a specialised center in context of disease or study inclusion.
tags: LOINC:MTHU048806 [http://purl.bioontology.org/ontology/LNC/MTHU048806]
dataType: date
example: 2022-01-03
- name: Date diagnosis confirmed
dataType: date
description: The particular day, month and year an event has happened or will happen.
tags: NCIT:C25164 [http://purl.obolibrary.org/obo/NCIT_C25164]
example: 2022-01-05
- name: Family members affected
description: Family members related by descent rather than by marriage or law who were diagnosed with the same condition as the individual who is the primary focus of investigation (i.e. the proband).
tags: HP:0032320 [http://purl.obolibrary.org/obo/HP_0032320]
dataType: mref
reference: lookups/FamilyMembers.tsv
referenceTypeTag: NCIT:C71384 [http://purl.obolibrary.org/obo/NCIT_C71384]
example: Biological Father
- name: Family members sequenced
description: Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing.
tags: NCIT:C79916 [http://purl.obolibrary.org/obo/NCIT_C79916]
dataType: mref
reference: lookups/FamilyMembers.tsv
referenceTypeTag: NCIT:C71384 [http://purl.obolibrary.org/obo/NCIT_C71384]
example: Biological Father,Full Brother,Full Sister
- name: Functioning
description: Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF).
tags: NCIT:C21007 [http://purl.obolibrary.org/obo/NCIT_C21007]
dataType: text
example:
- name: Material used in diagnosis
description: This diagnosis c.q. clinical examination is based on one or more sampled materials.
tags: SIO:000641 [http://semanticscience.org/resource/SIO_000641]
dataType: string #Placeholder. This field should be proper MREF to Material, but this is technically problematic due to circular dependencies.]
# - 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: Part of data release
dataType: mref
reference: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217]
example: DR01
- name: Materials
description: A natural substance derived from living organisms such as cells, tissues, proteins, and DNA.
tags: NCIT:C43376 [http://purl.obolibrary.org/obo/NCIT_C43376], SCDO:0002829 [http://purl.obolibrary.org/obo/SCDO_0002829], NCIT:C13236 [http://purl.obolibrary.org/obo/NCIT_C13236], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
relationWith:
- table: Personal
relation: HSO:0000242 [http://purl.obolibrary.org/obo/HSO_0000242]
columns:
- name: Identifier
description: Name or other identifier of an entry from a biosample database.
#description: A unique proper name or character sequence that identifies this particular material.
tags: EDAM:data_3273 [http://edamontology.org/data_3273], NCIT:C93400 [http://purl.obolibrary.org/obo/NCIT_C93400]
dataType: identifier
example: M28139
- name: Alternative identifiers
description: A backup sequence of characters used to identify an entity.
tags: NCIT:C90353 [http://purl.obolibrary.org/obo/NCIT_C90353]
dataType: string
example:
- name: Collected from subject
dataType: xref
reference: Subjects
description: Reference to the subject from whom this material was collected.
#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: SIO:000244 [http://semanticscience.org/resource/SIO_000244], NCIT:C142495 [http://purl.obolibrary.org/obo/NCIT_C142495]
example: P00001
- name: Belongs to request
description: A sequence of letters, numbers, or other characters that specifically identifies a particular order.
tags: NCIT:C164567 [http://purl.obolibrary.org/obo/NCIT_C164567]
dataType: string
example: REQ693264
- name: Belongs to diagnosis
description: Reference to a diagnosis c.q. clinical examination of which this material may be a part of. There can be multiple diagnoses when a non-tumor material is reused as reference.
tags: SIO:000068 [http://semanticscience.org/resource/SIO_000068]
dataType: mref
reference: Clinical
example: DX36310
- name: Date of request
dataType: date
description: The date on which the activity or entity was ordered.
tags: NCIT:C164566 [http://purl.obolibrary.org/obo/NCIT_C164566]
example: 2022-01-03
- name: Reason for sampling
dataType: mref
reference: lookups/samplingReason.tsv
referenceTypeTag: NCIT:C171003 [http://purl.obolibrary.org/obo/NCIT_C171003]
description: The explanation for why a test, measurement, or assessment is executed.
tags: NCIT:C171003 [http://purl.obolibrary.org/obo/NCIT_C171003]
example: Diagnostic
- name: Sampling date
dataType: date
description: The date that a sample was collected or obtained.
tags: NCIT:C164024 [http://purl.obolibrary.org/obo/NCIT_C164024]
example: 2022-01-04
- name: Sampling timestamp
dataType: datetime
description: Date and time at which this material was collected.
tags: EFO:0000689 [http://www.ebi.ac.uk/efo/EFO_0000689]
example: 2022-01-04
- name: Registration timestamp
description: Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.
tags: NCIT:C25646 [http://purl.obolibrary.org/obo/NCIT_C25646]
dataType: datetime
example: 2022-01-04T07:16:04Z
- name: Sampling protocol text
description: The procedure whereby this material was sampled for an analysis.
tags: EFO:0005518 [http://www.ebi.ac.uk/efo/EFO_0005518]
dataType: text
example:
- name: Sampling protocol reference
dataType: mref
reference: Sampling protocols
description: The procedure whereby this material was sampled for an analysis.
tags: EFO:0005518 [http://www.ebi.ac.uk/efo/EFO_0005518]
example: SP026
- name: Sampling protocol deviation
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: NCIT:C50996 [http://purl.obolibrary.org/obo/NCIT_C50996]
example: No sampling protocol deviations occurred
- name: Reason for sampling protocol deviation
dataType: text
description: The rationale for why a deviation from the sampling protocol has occurred.
tags: NCIT:C93529 [http://purl.obolibrary.org/obo/NCIT_C93529]
example:
- name: Biospecimen type
description: The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.
tags: NCIT:C70713 [http://purl.obolibrary.org/obo/NCIT_C70713]
dataType: xref
reference: lookups/BiospecimenTypes.tsv
referenceTypeTag: NCIT:C70699 [http://purl.obolibrary.org/obo/NCIT_C70699]
example: Whole Blood
- name: Anatomical source
dataType: xref
reference: lookups/AnatomicalSources.tsv
referenceTypeTag: UBERON:0001062 [http://purl.obolibrary.org/obo/UBERON_0001062]
description: Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.
tags: NCIT:C103264 [http://purl.obolibrary.org/obo/NCIT_C103264]
example: principal vein of forelimb
- name: Pathological state
dataType: xref
reference: lookups/PathologicalState.tsv
referenceTypeTag: NCIT:C164617 [http://purl.obolibrary.org/obo/NCIT_C164617]
description: The pathological state of the tissue from which this material was derived.
tags: GO:0001894 [http://purl.obolibrary.org/obo/GO_0001894]
example: Normal
- name: Biospecimen usability
dataType: bool
description: An indication as to whether a biospecimen is suitable for testing purposes.
tags: NCIT:C171004 [http://purl.obolibrary.org/obo/NCIT_C171004]
example: true
- name: Storage conditions
description: The conditions under which this biological material was stored.
tags: NCIT:C96145 [http://purl.obolibrary.org/obo/NCIT_C96145]
dataType: xref
reference: lookups/StorageConditions.tsv
referenceTypeTag: NCIT:C96145 [http://purl.obolibrary.org/obo/NCIT_C96145]
example: "PP tube ≥5mL (-85) to (-60)°C"
- name: Expiration date
description: The date beyond which this material is no longer regarded as fit for use.
tags: NCIT:C164516 [http://purl.obolibrary.org/obo/NCIT_C164516]
dataType: date
example: 2026-08-07
- name: Percentage tumor cells
description: The percentage of tumor cells compared to total cells present in this material.
tags: NCIT:C127771 [http://purl.obolibrary.org/obo/NCIT_C127771]
dataType: decimal
example:
- name: Physical location
description: A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).
tags: GAZ:00000448 [http://purl.obolibrary.org/obo/GAZ_00000448]
dataType: string
example: "NeuroDB; Freezer-position: 0819-3500; Biomedical Services Department"
- name: Analyses performed
description: Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics).
tags: IAO:0000702 [http://purl.obolibrary.org/obo/IAO_0000702]
dataType: mref
reference: lookups/AnalysesPerformed.tsv
referenceTypeTag: EDAM:topic_3391 [http://edamontology.org/topic_3391]
example: Genomics
- name: Derived from
description: Indicate if this material was produced from or related to another.
tags: NCIT:C28355 [http://purl.obolibrary.org/obo/NCIT_C28355]
dataType: string #[WORK IN PROGRESS. This field should be proper xref to Material, but this is technically problematic due to circular dependencies.]
- name: Part of data release
dataType: mref
reference: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217]
example: DR1
- name: Sampling protocols
description: Describes the procedure whereby biological samples for an experiment are sourced.
tags: EFO:0005518 [http://www.ebi.ac.uk/efo/EFO_0005518], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
columns:
- name: Identifier
dataType: identifier
description: One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing.
tags: NCIT:C25364 [http://purl.obolibrary.org/obo/NCIT_C25364]
example: SP026
- name: Name
dataType: string
description: The words or language units by which a thing is known.
tags: NCIT:C42614 [http://purl.obolibrary.org/obo/NCIT_C42614]
example: Neuro Data Bank Sampling Protocol
- name: Description
dataType: text
description: A written or verbal account, representation, statement, or explanation of something.
tags: NCIT:C25365 [http://purl.obolibrary.org/obo/NCIT_C25365]
example: Sampling procedures and methods for the Neuro data bank
- name: Version
dataType: string
description: A form or variant of a type or original; one of a sequence of copies of a program, each incorporating new modifications.
tags: NCIT:C25714 [http://purl.obolibrary.org/obo/NCIT_C25714]
example: 1.1.0
- name: IRI
dataType: hyperlink
description: A unique symbol that establishes identity of the resource.
tags: NCIT:C165071 [http://purl.obolibrary.org/obo/NCIT_C165071]
example: https://github.com/fairgenomes
- name: NGS sample preparations
description: A sample preparation for a nucleic acids sequencing assay.
tags: OBI:0001902 [http://purl.obolibrary.org/obo/OBI_0001902], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
relationWith:
- table: Materials
relation: NCIT:C179746 [http://purl.obolibrary.org/obo/NCIT_C179746]
columns:
- name: Identifier
description: A unique proper name or character sequence that identifies this particular sample preparation.
tags: NCIT:C132299 [http://purl.obolibrary.org/obo/NCIT_C132299]
dataType: identifier
example: MP2364
- name: Belongs to materials
dataType: xref
reference: Materials
#description: Name or other identifier of an entry from a biosample database.
description: Reference to the source material from which this sample was prepared.
tags: NCIT:C93400 [http://purl.obolibrary.org/obo/NCIT_C93400], NCIT:C25683 [http://purl.obolibrary.org/obo/NCIT_C25683]
example: M28139
- name: Belongs to lab procedure
dataType: xref
reference: Laboratory Procedures
description: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
tags: NCIT:C25294 [http://purl.obolibrary.org/obo/NCIT_C25294]
example: LP2558
profile: COSAS
- name: Belongs to request
description: A sequence of letters, numbers, or other characters that specifically identifies a particular order.
tags: NCIT:C164567 [http://purl.obolibrary.org/obo/NCIT_C164567]
dataType: string
example: REQ693264
profile: COSAS
- name: Input amount
dataType: integer
description: Amount of input material in nanogram (ng).
tags: AFRL:0000010 [http://purl.allotrope.org/ontologies/role#AFRL_0000010]
unit: UO:0000024 [http://purl.obolibrary.org/obo/UO_0000024]
example: 200
profile: FAIR Genomes
- name: Library preparation kit
dataType: xref
reference: lookups/NGSKits.tsv
referenceTypeTag: GENEPIO:0000081 [http://purl.obolibrary.org/obo/GENEPIO_0000081]
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: GENEPIO:0000085 [http://purl.obolibrary.org/obo/GENEPIO_0000085]
example: Illumina TruSeq DNA PCR-Free
profile: FAIR Genomes, COSAS
- name: PCR free
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: NCIT:C17003 [http://purl.obolibrary.org/obo/NCIT_C17003]
example: true
profile: FAIR Genomes, COSAS
- name: Target enrichment kit
dataType: xref
reference: lookups/NGSKits.tsv
referenceTypeTag: GENEPIO:0000081 [http://purl.obolibrary.org/obo/GENEPIO_0000081]
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: NCIT:C154307 [http://purl.obolibrary.org/obo/NCIT_C154307]
- name: UMIs present
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: EFO:0010199 [http://www.ebi.ac.uk/efo/EFO_0010199]
example: true
- name: Intended insert size
dataType: integer
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: FG:0000001 [https://w3id.org/fair-genomes/resource/FG_0000001]
- name: Intended read length
dataType: integer
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: NCIT:C153362 [http://purl.obolibrary.org/obo/NCIT_C153362]
- name: Barcode
description: A machine-readable representation of information in a visual format on a surface.
dataType: string
tags: NCIT:C43361 [http://purl.obolibrary.org/obo/NCIT_C43361]
example: B357913884948
- name: Belongs to batch
description: A quantity of people or things treated or regarded as a group, especially when subdivided from a larger group.
tags: NCIT:C67073 [http://purl.obolibrary.org/obo/NCIT_C67073]
dataType: string
example: B-165
- name: Part of data release
dataType: mref
reference: Data releases
description: The act of making data or other structured information accessible to the public or to the user group of a database.
tags: NCIT:C172217 [http://purl.obolibrary.org/obo/NCIT_C172217]
example: DR01
- name: Laboratory Procedures
description: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
tags: NCIT:C25294 [http://purl.obolibrary.org/obo/NCIT_C25294], dcat:Dataset [https://www.w3.org/TR/vocab-dcat-3/#Property:catalog_dataset]
columns:
- name: Code
dataType: identifier
description: A character or string that represents the short code name of the laboratory test.
tags: NCIT:C83322 [http://purl.obolibrary.org/obo/NCIT_C83322]
example: LP2558
- name: Test
description: A character or string that represents the full name of the laboratory assessment.
tags: NCIT:C117142 [http://purl.obolibrary.org/obo/NCIT_C117142]
dataType: string
example: Neuro WES
- name: Description
dataType: text
description: A written or verbal account, representation, statement, or explanation of something
tags: NCIT:C25365 [http://purl.obolibrary.org/obo/NCIT_C25365]
example:
- name: Category
description: A classification of the laboratory test.
tags: NCIT:C83017 [http://purl.obolibrary.org/obo/NCIT_C83017]
dataType: string
example: Neurological
- name: Subcategory
description: A sub-division of the laboratory test classification.
tags: NCIT:C83142 [http://purl.obolibrary.org/obo/NCIT_C83142]
dataType: string
example:
- name: Gene list
dataType: text
description: A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
tags: OBI:0000118 [http://purl.obolibrary.org/obo/OBI_0000118]
example:
- name: Sequencing runs
description: The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.