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fair-genomes.yml
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fair-genomes.yml
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---
name: FAIR Genomes metadata schema
description: The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare.
version: 1.3
releaseType: SNAPSHOT
date: 2022-02-28
lookupGlobalOptions: lookups/NullFlavors.txt
authors:
- name: K. Joeri van der Velde
email: [email protected]
orcid: 0000-0002-0934-8375
- name: Gurnoor Singh
email: [email protected]
orcid: 0000-0003-1615-4197
- name: Rajaram Kaliyaperumal
email: [email protected]
orcid: 0000-0002-1215-167X
- name: XiaoFeng Liao
email: [email protected]
orcid: 0000-0002-4706-1084
- name: Esther van Enckevort
email: [email protected]
orcid: 0000-0002-2440-3993
- name: Jeroen A.M. Beliën
email: [email protected]
orcid: 0000-0002-7160-5942
- name: Daphne Stemkens
email: [email protected]
orcid: 0000-0003-1301-5204
- name: Peter A.C. 't Hoen
email: [email protected]
orcid: 0000-0003-4450-3112
- name: Mariëlle E. van Gijn
email: [email protected]
orcid: 0000-0002-1073-0539
- name: Morris A. Swertz
email: [email protected]
orcid: 0000-0002-0979-3401
- name: FAIR Genomes Consortium
email:
orcid:
copyright:
holder: University Medical Center Groningen
years: 2019-2021
license:
name: Attribution 4.0 International (CC BY 4.0)
url: https://creativecommons.org/licenses/by/4.0/
technical:
artDecorId: 2.16.840.1.113883.2.4.3.11.60.120
ttlLocation: https://fairgenomes.github.io/fairgenomes-semantic-model/generated/ontology/
gitLocation: https://github.com/fairgenomes/fairgenomes-semantic-model
modules:
- name: Study
description: A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts.
ontology: NCIT:C63536 [http://purl.obolibrary.org/obo/NCIT_C63536]
elements:
- name: Identifier
description: A unique proper name or character sequence that identifies this particular study.
ontology: 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]
values: UniqueID
- name: Name
description: A name that designates this study.
ontology: 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]
values: String
- name: Description
description: A statement or piece of writing that provides details on this study.
ontology: OMIABIS:0000036 [http://purl.obolibrary.org/obo/OMIABIS_0000036]
exactMatch: OBI:0001615 [http://purl.obolibrary.org/obo/OBI_0001615]
broadMatch: SIO:000136 [https://semanticscience.org/resource/SIO_000136]
values: Text
- name: Inclusion criteria
description: The conditions which, if met, make an person eligible for participation in this study.
ontology: OBI:0500027 [http://purl.obolibrary.org/obo/OBI_0500027]
values: LookupMany [lookups/InclusionCriteria.txt], ofType [http://purl.obolibrary.org/obo/OBI_0500027]
- name: Principal investigator
description: The principal investigator or responsible person for this study.
ontology: OMIABIS:0000100 [http://purl.obolibrary.org/obo/OMIABIS_0000100]
broadMatch: SIO:000881 [https://semanticscience.org/resource/SIO_000881], OBI:0000202 [http://purl.obolibrary.org/obo/OBI_0000202]
values: String
- name: Contact information
description: An email address for the purpose of contacting the study contact person.
ontology: OMIABIS:0000035 [http://purl.obolibrary.org/obo/OMIABIS_0000035]
values: String
- 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.
ontology: OBI:0500000 [http://purl.obolibrary.org/obo/OBI_0500000]
values: Text
- name: Start date
description: The date on which this study began.
ontology: 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]
values: Date
- 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.
ontology: 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]
values: Date
# Placeholder: Add many-to-many relation of Study-Personal: ReferenceMany [Personal]
- name: Personal
description: Data, facts or figures about an individual; the set of relevant items would depend on the use case.
ontology: NCIT:C90492 [http://purl.obolibrary.org/obo/NCIT_C90492]
relationWith:
- module: Study
relation: RO:0000056 [http://purl.obolibrary.org/obo/RO_0000056]
elements:
- name: Personal identifier
description: A unique proper name or character sequence that identifies this particular person.
ontology: NCIT:C164337 [http://purl.obolibrary.org/obo/NCIT_C164337]
values: UniqueID
- 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.
ontology: MESH:D005783 [http://purl.bioontology.org/ontology/MESH/D005783]
values: LookupOne [lookups/GenderIdentity.txt], ofType [http://purl.bioontology.org/ontology/MESH/D005783]
- 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.
ontology: GSSO:009418 [http://purl.obolibrary.org/obo/GSSO_009418]
values: LookupOne [lookups/GenderAtBirth.txt], ofType [http://purl.obolibrary.org/obo/GSSO_009418]
- name: Genotypic sex
description: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
ontology: PATO:0020000 [http://purl.obolibrary.org/obo/PATO_0020000]
values: LookupOne [lookups/GenotypicSex.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C168871]
- name: Country of residence
description: Country of residence at enrollment.
ontology: NCIT:C171105 [http://purl.obolibrary.org/obo/NCIT_C171105]
values: LookupOne [lookups/Countries.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0001830]
- name: Ancestry
description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.
ontology: NCIT:C176763 [http://purl.obolibrary.org/obo/NCIT_C176763]
values: LookupMany [lookups/Ancestry.txt], ofType [http://purl.obolibrary.org/obo/HANCESTRO_0004]
- name: Country of birth
description: The country that this person was born in.
ontology: GENEPIO:0001094 [http://purl.obolibrary.org/obo/GENEPIO_0001094]
values: LookupOne [lookups/Countries.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0001830]
- name: Year of birth
description: The year in which this person was born.
ontology: NCIT:C83164 [http://purl.obolibrary.org/obo/NCIT_C83164]
values: Integer
unit: NCIT:C159612 [http://purl.obolibrary.org/obo/NCIT_C159612]
- name: Inclusion status
description: An indicator that provides information on the current health status of this person.
ontology: NCIT:C166244 [http://purl.obolibrary.org/obo/NCIT_C166244]
values: LookupOne [lookups/InclusionStatus.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C19332]
- name: Age at death
description: The age at which death occurred.
ontology: NCIT:C135383 [http://purl.obolibrary.org/obo/NCIT_C135383]
values: Integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
- name: Consanguinity
description: Information on whether the patient is a child from two family members who are second cousins or closer.
ontology: OMIT:0004546 [http://purl.obolibrary.org/obo/OMIT_0004546]
values: Boolean
- 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.
ontology: NCIT:C25412 [http://purl.obolibrary.org/obo/NCIT_C25412]
values: LookupOne [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- 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.
ontology: NCIT:C19012 [http://purl.obolibrary.org/obo/NCIT_C19012]
values: LookupMany [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- name: Participates in study
description: Reference to the study or studies in which this person participates.
ontology: RO:0000056 [http://purl.obolibrary.org/obo/RO_0000056]
values: ReferenceMany [Study]
- name: Leaflet and consent form
description: A document explaining all the relevant information to assist an individual in understanding the expectations and risks in making a decision about a procedure. This document is presented to and signed by the individual or guardian.
ontology: NCIT:C16468 [http://purl.obolibrary.org/obo/NCIT_C16468]
elements:
- name: Leaflet title
description: A title or name given to the leaflet that belongs to this consent form.
ontology: DC:title [http://purl.org/dc/terms/title]
values: String
- name: Leaflet date
description: A point or period of time associated with the publication of this leaflet that belongs to this consent form.
ontology: DC:date [http://purl.org/dc/terms/date]
values: Date
- name: Leaflet version
description: The version, edition, or adaptation of this leaflet that belongs to this consent form.
ontology: DC:hasVersion [http://purl.org/dc/terms/hasVersion]
values: String
- name: Consent form identifier
description: A unique proper name or character sequence that identifies this particular leaflet and consent form combination used in signing individual consent. Using a DOI would be optimal. Using any resolvable URL is suboptimal but still preferable over using a plain text value.
ontology: DC:identifier [http://purl.org/dc/terms/identifier]
values: UniqueID
- name: Consent form title
description: A title or name given to this consent form.
ontology: DC:title [http://purl.org/dc/terms/title]
values: String
- name: Consent form accepted date
description: Date of acceptance of this consent form.
ontology: DC:dateAccepted [http://purl.org/dc/terms/dateAccepted]
values: Date
- name: Consent form valid until
description: End date of the validity of this consent form.
ontology: DC:valid [http://purl.org/dc/terms/valid]
values: Date
- name: Consent form creator
description: Indicates the authoritative body who brought this consent form into existence.
ontology: DC:creator [http://purl.org/dc/terms/creator]
values: LookupMany [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- name: Consent form version
description: The version, edition, or adaptation of this consent form.
ontology: DC:hasVersion [http://purl.org/dc/terms/hasVersion]
values: String
- name: Individual 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.
ontology: NCIT:C16735 [http://purl.obolibrary.org/obo/NCIT_C16735]
relationWith:
- module: Leaflet and consent form
relation: IAO:0021007 [http://purl.obolibrary.org/obo/IAO_0021007]
- module: Personal
relation: ICO:0000005 [http://purl.obolibrary.org/obo/ICO_0000005]
elements:
- name: Individual consent identifier
description: A unique proper name or character sequence that identifies this particular signed individual consent.
ontology: ICO:0000044 [http://purl.obolibrary.org/obo/ICO_0000044]
values: UniqueID
- name: Person consenting
description: Reference to the person (i.e. subject) to whom this individual consent applies.
ontology: IAO:0000136 [http://purl.obolibrary.org/obo/IAO_0000136]
values: ReferenceOne [Personal]
- name: Consent form used
description: Reference to the informed consent form that was signed. Points to a particular instance of leaflet and consent form that usually exists as a record (i.e. a row) within the same database as this individual consent.
ontology: IAO:0000136 [http://purl.obolibrary.org/obo/IAO_0000136]
values: ReferenceOne [Leaflet and consent form]
- name: Collected by
description: Indicates the institute who performed the collection act.
ontology: NCIT:C45262 [http://purl.obolibrary.org/obo/NCIT_C45262]
values: LookupOne [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- name: Signing date
description: A date specification that designates when this individual consent form was signed.
ontology: ICO:0000036 [http://purl.obolibrary.org/obo/ICO_0000036]
values: Date
- name: Valid from
description: Starting date of the validity of this individual consent.
ontology: DC:valid [http://purl.org/dc/terms/valid]
values: Date
- name: Valid until
description: End date of the validity of this individual consent.
ontology: DC:valid [http://purl.org/dc/terms/valid]
values: Date
- name: Represented by
description: An individual who is authorized under applicable State or local law to consent on behalf of a child or incapable person to general medical care including participation in clinical research.
ontology: NCIT:C142600 [http://purl.obolibrary.org/obo/NCIT_C142600]
values: LookupOne_NoGlobals [lookups/RepresentedBy.txt], ofType [http://purl.obolibrary.org/obo/BFO_0000023]
- name: Data use permissions
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.
ontology: DUO:0000001 [http://purl.obolibrary.org/obo/DUO_0000001]
values: LookupOne_NoGlobals [lookups/DataUsePermissions.txt], ofType [http://purl.obolibrary.org/obo/DUO_0000001]
- name: Data use modifiers
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.
ontology: DUO:0000017 [http://purl.obolibrary.org/obo/DUO_0000017]
values: LookupMany_NoGlobals [lookups/DataUseModifiers.txt], ofType [http://purl.obolibrary.org/obo/DUO_0000017]
- name: Data use specification
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.
ontology: SIO:000090 [http://semanticscience.org/resource/SIO_000090]
values: Text
- name: Allow recontacting
description: The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances.
ontology: NCIT:C25737 [http://purl.obolibrary.org/obo/NCIT_C25737]
values: LookupMany_NoGlobals [lookups/Recontacting.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C176244]
- name: Clinical
description: Findings and circumstances relating to the examination and treatment of a patient.
ontology: NCIT:C25398 [http://purl.obolibrary.org/obo/NCIT_C25398]
relationWith:
- module: Personal
relation: SIO:000332 [http://semanticscience.org/resource/SIO_000332]
elements:
- name: Clinical identifier
description: A unique proper name or character sequence that identifies this particular clinical examination.
ontology: NCIT:C87853 [http://purl.obolibrary.org/obo/NCIT_C87853]
values: UniqueID
- name: Belongs to person
description: Reference to the person whom this clinical information is about.
ontology: IAO:0000136 [http://purl.obolibrary.org/obo/IAO_0000136]
values: ReferenceOne [Personal]
- name: Phenotype
description: The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.
ontology: NCIT:C16977 [http://purl.obolibrary.org/obo/NCIT_C16977]
values: LookupMany [lookups/Phenotypes.txt], ofType [https://www.wikidata.org/wiki/Property:P3841]
- name: Unobserved phenotype
description: Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.
ontology: HL7:C0442737 [http://purl.bioontology.org/ontology/HL7/C0442737]
values: LookupMany [lookups/Phenotypes.txt], ofType [https://www.wikidata.org/wiki/Property:P3841]
- name: Phenotypic data available
description: Types of phenotypic data collected in a clinical setting that is potentially available upon request.
ontology: NCIT:C15783 [http://purl.obolibrary.org/obo/NCIT_C15783]
values: LookupMany [lookups/DCMITypes.txt], ofType [http://purl.org/dc/terms/DCMIType]
- name: Clinical diagnosis
description: A diagnosis made from a study of the signs and symptoms of a disease.
ontology: NCIT:C15607 [http://purl.obolibrary.org/obo/NCIT_C15607]
values: LookupMany [lookups/Diseases.txt], ofType [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).
- name: Molecular diagnosis gene
description: Gene affected by pathogenic variation that is causal for disease of the patient.
ontology: NCIT:C20826 [http://purl.obolibrary.org/obo/NCIT_C20826]
values: LookupMany [lookups/Genes.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C16612]
- name: Molecular diagnosis other
description: Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.
ontology: NCIT:C20826 [http://purl.obolibrary.org/obo/NCIT_C20826]
values: Text
- name: Age at diagnosis
description: The age, measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease.
ontology: SNOMEDCT:423493009 [http://purl.bioontology.org/ontology/SNOMEDCT/423493009]
values: Integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
- name: Age at last screening
description: Age of the patient at the moment of the most recent screening.
ontology: NCIT:C81258 [http://purl.obolibrary.org/obo/NCIT_C81258]
values: Integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
- 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.
ontology: NCIT:C459 [http://purl.obolibrary.org/obo/NCIT_C459]
values: LookupMany [lookups/Drugs.txt], ofType [http://edamontology.org/data_3103]
- 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.
ontology: NCIT:C142516 [http://purl.obolibrary.org/obo/NCIT_C142516]
values: Text
- 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).
ontology: HP:0032320 [http://purl.obolibrary.org/obo/HP_0032320]
values: LookupMany [lookups/FamilyMembers.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C71384]
- name: Family members sequenced
description: Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing.
ontology: NCIT:C79916 [http://purl.obolibrary.org/obo/NCIT_C79916]
values: LookupMany [lookups/FamilyMembers.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C71384]
- name: Medical history
description: A record of a person's background regarding health, occurrence of disease events and surgical procedures.
ontology: NCIT:C18772 [http://purl.obolibrary.org/obo/NCIT_C18772]
values: LookupMany [lookups/MedicalHistory.txt], ofType [http://scdontology.h3abionet.org/ontology/SCDO_1000093]
- name: Age of onset
description: Age of onset of clinical manifestations related to the disease of the patient.
ontology: Orphanet:C023 [http://www.orpha.net/ORDO/Orphanet_C023]
values: Integer
unit: UO:0000036 [http://purl.obolibrary.org/obo/UO_0000036]
- name: First contact
description: First contact of the patient with a specialised center in context of disease or study inclusion.
ontology: LOINC:MTHU048806 [http://purl.bioontology.org/ontology/LNC/MTHU048806]
values: Date
- name: Functioning
description: Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF).
ontology: NCIT:C21007 [http://purl.obolibrary.org/obo/NCIT_C21007]
values: Text
- name: Material used in diagnosis
description: This diagnosis c.q. clinical examination is based on one or more sampled materials.
ontology: SIO:000641 [http://semanticscience.org/resource/SIO_000641]
values: String #Placeholder. This field should be proper ReferenceMany to Material, but this is technically problematic due to circular dependencies.]
# values: ReferenceMany [Material]
- name: Material
description: A natural substance derived from living organisms such as cells, tissues, proteins, and DNA.
ontology: NCIT:C43376 [http://purl.obolibrary.org/obo/NCIT_C43376]
relationWith:
- module: Personal
relation: HSO:0000242 [http://purl.obolibrary.org/obo/HSO_0000242]
elements:
- name: Material identifier
description: A unique proper name or character sequence that identifies this particular material.
ontology: NCIT:C93400 [http://purl.obolibrary.org/obo/NCIT_C93400]
values: UniqueID
- name: Collected from person
description: Reference to the person from whom this material was collected.
ontology: SIO:000244 [http://semanticscience.org/resource/SIO_000244]
values: ReferenceOne [Personal]
- 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.
ontology: SIO:000068 [http://semanticscience.org/resource/SIO_000068]
values: ReferenceMany [Clinical]
- name: Sampling timestamp
description: Date and time at which this material was collected.
ontology: EFO:0000689 [http://www.ebi.ac.uk/efo/EFO_0000689]
values: DateTime
- name: Registration timestamp
description: Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.
ontology: NCIT:C25646 [http://purl.obolibrary.org/obo/NCIT_C25646]
values: DateTime
- name: Sampling protocol
description: The procedure whereby this material was sampled for an analysis.
ontology: EFO:0005518 [http://www.ebi.ac.uk/efo/EFO_0005518]
values: Text
- name: Sampling protocol deviation
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.
ontology: NCIT:C50996 [http://purl.obolibrary.org/obo/NCIT_C50996]
values: String
- name: Reason for sampling protocol deviation
description: The rationale for why a deviation from the sampling protocol has occurred.
ontology: NCIT:C93529 [http://purl.obolibrary.org/obo/NCIT_C93529]
values: String
- name: Biospecimen type
description: The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.
ontology: NCIT:C70713 [http://purl.obolibrary.org/obo/NCIT_C70713]
values: LookupOne [lookups/BiospecimenTypes.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C70699]
- name: Anatomical source
description: Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.
ontology: NCIT:C103264 [http://purl.obolibrary.org/obo/NCIT_C103264]
values: LookupOne [lookups/AnatomicalSources.txt], ofType [http://purl.obolibrary.org/obo/UBERON_0001062]
- name: Pathological state
description: The pathological state of the tissue from which this material was derived.
ontology: NCIT:C28257 [http://purl.obolibrary.org/obo/NCIT_C28257]
values: LookupOne [lookups/PathologicalState.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C164617]
- name: Storage conditions
description: The conditions under which this biological material was stored.
ontology: NCIT:C96145 [http://purl.obolibrary.org/obo/NCIT_C96145]
values: LookupOne [lookups/StorageConditions.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C96145]
- name: Expiration date
description: The date beyond which this material is no longer regarded as fit for use.
ontology: NCIT:C164516 [http://purl.obolibrary.org/obo/NCIT_C164516]
values: Date
- name: Percentage tumor cells
description: The percentage of tumor cells compared to total cells present in this material.
ontology: NCIT:C127771 [http://purl.obolibrary.org/obo/NCIT_C127771]
values: Decimal
- 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).
ontology: GAZ:00000448 [http://purl.obolibrary.org/obo/GAZ_00000448]
values: String
- name: Analyses performed
description: Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics).
ontology: IAO:0000702 [http://purl.obolibrary.org/obo/IAO_0000702]
values: LookupMany [lookups/AnalysesPerformed.txt], ofType [http://edamontology.org/topic_3391]
- name: Derived from
description: Indicate if this material was produced from or related to another.
ontology: NCIT:C28355 [http://purl.obolibrary.org/obo/NCIT_C28355]
values: String #[WORK IN PROGRESS. This field should be proper ReferenceOne to Material, but this is technically problematic due to circular dependencies.]
# values: ReferenceOne [Material]
- name: Sample preparation
description: A sample preparation for a nucleic acids sequencing assay.
ontology: OBI:0001902 [http://purl.obolibrary.org/obo/OBI_0001902]
relationWith:
- module: Material
relation: NCIT:C179746 [http://purl.obolibrary.org/obo/NCIT_C179746]
elements:
- name: Sampleprep identifier
description: A unique proper name or character sequence that identifies this particular sample preparation.
ontology: NCIT:C132299 [http://purl.obolibrary.org/obo/NCIT_C132299]
values: UniqueID
- name: Belongs to material
description: Reference to the source material from which this sample was prepared.
ontology: NCIT:C25683 [http://purl.obolibrary.org/obo/NCIT_C25683]
values: ReferenceOne [Material]
- name: Input amount
description: Amount of input material in nanogram (ng).
ontology: AFRL:0000010 [http://purl.allotrope.org/ontologies/role#AFRL_0000010]
values: Integer
unit: UO:0000024 [http://purl.obolibrary.org/obo/UO_0000024]
- name: Library preparation kit
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.
ontology: GENEPIO:0000085 [http://purl.obolibrary.org/obo/GENEPIO_0000085]
values: LookupOne [lookups/NGSKits.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0000081]
- name: PCR free
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.
ontology: NCIT:C17003 [http://purl.obolibrary.org/obo/NCIT_C17003]
values: Boolean
- name: Target enrichment kit
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.
ontology: NCIT:C154307 [http://purl.obolibrary.org/obo/NCIT_C154307]
values: LookupOne [lookups/NGSKits.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0000081]
- name: UMIs present
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.
ontology: EFO:0010199 [http://www.ebi.ac.uk/efo/EFO_0010199]
values: Boolean
- name: Intended insert size
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.
ontology: FG:0000001 [https://w3id.org/fair-genomes/resource/FG_0000001]
values: Integer
- name: Intended read length
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.
ontology: NCIT:C153362 [http://purl.obolibrary.org/obo/NCIT_C153362]
values: Integer
- name: Sequencing
description: The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
ontology: EDAM:topic_3168 [http://edamontology.org/topic_3168]
relationWith:
- module: Sample preparation
relation: SIO:001220 [http://semanticscience.org/resource/SIO_001220]
elements:
- name: Sequencing identifier
description: A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.
ontology: NCIT:C171337 [http://purl.obolibrary.org/obo/NCIT_C171337]
values: UniqueID
- name: Belongs to sample preparation
description: Reference to the prepared sample, i.e. the source that was sequenced.
ontology: NCIT:C25683 [http://purl.obolibrary.org/obo/NCIT_C25683]
values: ReferenceOne [Sample preparation]
- name: Sequencing date
description: Date on which this sequencing assay was performed.
ontology: GENEPIO:0000069 [http://purl.obolibrary.org/obo/GENEPIO_0000069]
values: Date
- name: Sequencing platform
description: The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).
ontology: GENEPIO:0000071 [http://purl.obolibrary.org/obo/GENEPIO_0000071]
values: LookupOne [lookups/SequencingPlatform.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0000071]
- name: Sequencing instrument model
description: The used product name and model number of a manufacturer's genomic (dna) sequencer.
ontology: GENEPIO:0001921 [http://purl.obolibrary.org/obo/GENEPIO_0001921]
values: LookupOne [lookups/SequencingInstrumentModels.txt], ofType [http://purl.obolibrary.org/obo/GENEPIO_0001921]
- name: Sequencing method
description: Method used to determine the order of bases in a nucleic acid sequence.
ontology: FIX:0000704 [http://purl.obolibrary.org/obo/FIX_0000704]
values: LookupOne [lookups/SequencingMethods.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C17565]
- name: Median read depth
description: The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.
ontology: NCIT:C155320 [http://purl.obolibrary.org/obo/NCIT_C155320]
values: Integer
- name: Observed read length
description: The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.
ontology: NCIT:C153362 [http://purl.obolibrary.org/obo/NCIT_C153362]
values: Integer
- name: Observed insert size
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.
ontology: FG:0000002 [https://w3id.org/fair-genomes/resource/FG_0000002]
values: Integer
- name: Percentage Q30
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.
ontology: GENEPIO:0000089 [http://purl.obolibrary.org/obo/GENEPIO_0000089]
values: Decimal
- name: Percentage TR20
description: Percentage of the target sequence on which 20 or more unique reads were successfully mapped.
ontology: FG:0000003 [https://w3id.org/fair-genomes/resource/FG_0000003]
values: Decimal
- name: Other quality metrics
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.
ontology: EDAM:data_3914 [http://edamontology.org/data_3914]
values: Text
- name: Analysis
description: An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output.
ontology: EDAM:operation_2945 [http://edamontology.org/operation_2945]
relationWith:
- module: Sequencing
relation: SIO:000253 [http://semanticscience.org/resource/SIO_000253]
elements:
- name: Analysis identifier
description: A unique proper name or character sequence that identifies this particular analysis.
ontology: AFR:0001979 [http://purl.allotrope.org/ontologies/result#AFR_0001979]
values: UniqueID
- name: Belongs to sequencing
description: Reference to the sequencing that was performed, i.e. the source on which this analysis was based.
ontology: NCIT:C25683 [http://purl.obolibrary.org/obo/NCIT_C25683]
values: ReferenceOne [Sequencing]
- name: Physical data location
description: A place on the Earth where the data is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which computer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).
ontology: GAZ:00000448 [http://purl.obolibrary.org/obo/GAZ_00000448]
values: String
- name: Abstract data location
description: The file location of the data, or a copy of the data, on an electronically accessible device for preservation (either in plain-text or encrypted format).
ontology: NCIT:C142494 [http://purl.obolibrary.org/obo/NCIT_C142494]
values: String
- name: Data formats stored
description: Which data file formats (i.e. defined ways or layouts of representing and structuring data in a computer file, blob, string, message, or elsewhere) are stored and potentially available.
ontology: NCIT:C142494 [http://purl.obolibrary.org/obo/NCIT_C142494]
values: LookupMany [lookups/DataFormats.txt], ofType [http://edamontology.org/format_1915]
- name: Algorithms used
description: Any used problem-solving procedures implemented in software to be executed by a computer.
ontology: NCIT:C16275 [http://purl.obolibrary.org/obo/NCIT_C16275]
values: Text
- name: Reference genome used
description: The specific build of the human genome used as reference for sequence alignment and variant calling.
ontology: EDAM:data_2340 [http://edamontology.org/data_2340]
values: LookupOne [lookups/GenomeAccessions.txt], ofType [http://edamontology.org/data_2787]
- name: Bioinformatic protocol used
description: A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.
ontology: EDAM:data_2531 [http://edamontology.org/data_2531]
values: Text
- name: Bioinformatic protocol deviation
description: A variation from processes or procedures defined in the bioinformatic 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.
ontology: NCIT:C50996 [http://purl.obolibrary.org/obo/NCIT_C50996]
values: String
- name: Reason for bioinformatic protocol deviation
description: The rationale for why a deviation from the bioinformatic protocol has occurred.
ontology: NCIT:C93529 [http://purl.obolibrary.org/obo/NCIT_C93529]
values: String
- name: WGS guideline followed
description: Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels.
ontology: NCIT:C17564 [http://purl.obolibrary.org/obo/NCIT_C17564]
values: String