FAIR Genomes metadata schema

Classes

Analysis^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis

is defined by: http://edamontology.org/operation_2945

is in domain of: Abstract data location^dp, Algorithms used^dp, Analysis identifier^dp, Belongs to sequencing^op, Bioinformatic protocol deviation^dp, Bioinformatic protocol used^dp, Data formats stored^op, Physical data location^dp, Reason for bioinformatic protocol deviation^dp, Reference genome used^op, WGS guideline followed^dp

An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output.

Clinical^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical

is defined by: http://purl.obolibrary.org/obo/NCIT_C25398

is in domain of: Age at diagnosis^dp, Age at last screening^dp, Age of onset^dp, Belongs to person^op, Clinical diagnosis^op, Clinical identifier^dp, Consanguinity^dp, Drug regimen^dp, Family members affected^op, Family members sequenced^op, First contact^dp, Functioning^dp, Material used in diagnosis^dp, Medical history^op, Medication^op, Molecular diagnosis gene^op, Molecular diagnosis other^dp, Phenotype^op, Phenotypic data available^op, Unobserved phenotype^op

Findings and circumstances relating to the examination and treatment of a patient.

Individual consent^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent

is defined by: http://purl.obolibrary.org/obo/NCIT_C16735

is in domain of: Allow recontacting^op, Collected by^op, Consent form used^op, Data use modifiers^op, Data use permissions^op, Data use specification^dp, Individual consent identifier^dp, Person consenting^op, Represented by^op, Signing date^dp, Valid from^dp, Valid until^dp

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.

Leaflet and consent form^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form

is defined by: http://purl.obolibrary.org/obo/NCIT_C16468

is in domain of: Consent form accepted date^dp, Consent form creator^op, Consent form identifier^dp, Consent form title^dp, Consent form valid until^dp, Consent form version^dp, Leaflet date^dp, Leaflet title^dp, Leaflet version^dp

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.

Material^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Material

is defined by: http://purl.obolibrary.org/obo/NCIT_C43376

is in domain of: Analyses performed^op, Anatomical source^op, Belongs to diagnosis^op, Biospecimen type^op, Collected from person^op, Derived from^dp, Expiration date^dp, Material identifier^dp, Pathological state^op, Percentage tumor cells^dp, Physical location^dp, Reason for sampling protocol deviation^dp, Registration timestamp^dp, Sampling protocol^dp, Sampling protocol deviation^dp, Sampling timestamp^dp, Storage conditions^op

A natural substance derived from living organisms such as cells, tissues, proteins, and DNA.

Personal^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal

is defined by: http://purl.obolibrary.org/obo/NCIT_C90492

is in domain of: Age at death^dp, Ancestry^op, Country of birth^op, Country of residence^op, Gender at birth^op, Gender identity^op, Genotypic sex^op, Inclusion status^op, Participates in study^op, Personal identifier^dp, Primary affiliated institute^op, Resources in other institutes^op, Year of birth^dp

Data, facts or figures about an individual; the set of relevant items would depend on the use case.

Sample preparation^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation

is defined by: http://purl.obolibrary.org/obo/OBI_0001902

is in domain of: Belongs to material^op, Input amount^dp, Intended insert size^dp, Intended read length^dp, Library preparation kit^op, PCR free^dp, Sampleprep identifier^dp, Target enrichment kit^op, UMIs present^dp

A sample preparation for a nucleic acids sequencing assay.

Sequencing^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing

is defined by: http://edamontology.org/topic_3168

is in domain of: Belongs to sample^op, Median read depth^dp, Observed insert size^dp, Observed read length^dp, Other quality metrics^dp, Percentage Q30^dp, Percentage TR20^dp, Sequencing date^dp, Sequencing identifier^dp, Sequencing instrument model^op, Sequencing method^op, Sequencing platform^op

The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.

Study^c back to ToC or Class ToC

IRI: https://w3id.org/fair-genomes/ontology/Study

is defined by: http://purl.obolibrary.org/obo/NCIT_C63536

is in domain of: Completion date^dp, Contact information^dp, Description^dp, Identifier^dp, Inclusion criteria^op, Name^dp, Principal investigator^dp, Start date^dp, Study design^dp

A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts.

Object Properties

Allow recontacting^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Allow_recontacting

is defined by: http://purl.obolibrary.org/obo/NCIT_C25737

has domain: Individual consent^c
has range: n c i t c176244^c

The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances.

Analyses performed^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Analyses_performed

is defined by: http://purl.obolibrary.org/obo/IAO_0000702

has domain: Material^c
has range: topic 3391^c

Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics).

Anatomical source^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Anatomical_source

is defined by: http://purl.obolibrary.org/obo/NCIT_C103264

has domain: Material^c
has range: u b e r o n 0001062^c

Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.

Ancestry^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Ancestry

is defined by: http://purl.obolibrary.org/obo/NCIT_C176763

has domain: Personal^c
has range: h a n c e s t r o 0004^c

Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.

Belongs to diagnosis^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Belongs_to_diagnosis

is defined by: http://semanticscience.org/resource/SIO_000068

has domain: Material^c

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.

Belongs to material^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Belongs_to_material

is defined by: http://purl.obolibrary.org/obo/NCIT_C25683

has domain: Sample preparation^c

Reference to the source material from which this sample was prepared.

Belongs to person^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Belongs_to_person

is defined by: http://purl.obolibrary.org/obo/IAO_0000136

has domain: Clinical^c

Reference to the person whom this clinical information is about.

Belongs to sample^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Belongs_to_sample

is defined by: http://purl.obolibrary.org/obo/NCIT_C25683

has domain: Sequencing^c

Reference to the prepared sample, i.e. the source that was sequenced.

Belongs to sequencing^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Belongs_to_sequencing

is defined by: http://purl.obolibrary.org/obo/NCIT_C25683

has domain: Analysis^c

Reference to the sequencing that was performed, i.e. the source on which this analysis was based.

Biospecimen type^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Biospecimen_type

is defined by: http://purl.obolibrary.org/obo/NCIT_C70713

has domain: Material^c
has range: n c i t c70699^c

The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.

Clinical diagnosis^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Clinical_diagnosis

is defined by: http://purl.obolibrary.org/obo/NCIT_C15607

has domain: Clinical^c
has range: data 3667^c

A diagnosis made from a study of the signs and symptoms of a disease.

Collected by^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Collected_by

is defined by: http://purl.obolibrary.org/obo/NCIT_C45262

has domain: Individual consent^c
has range: s i o 000688^c

Indicates the institute who performed the collection act.

Collected from person^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Collected_from_person

is defined by: http://semanticscience.org/resource/SIO_000244

has domain: Material^c

Reference to the person from whom this material was collected.

Consent form creator^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_creator

is defined by: http://purl.org/dc/terms/creator

has domain: Leaflet and consent form^c
has range: s i o 000688^c

Indicates the authoritative body who brought this consent form into existence.

Consent form used^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Consent_form_used

is defined by: http://purl.obolibrary.org/obo/IAO_0000136

has domain: Individual consent^c

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.

Country of birth^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Country_of_birth

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0001094

has domain: Personal^c
has range: g e n e p i o 0001830^c

The country that this person was born in.

Country of residence^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Country_of_residence

is defined by: http://purl.obolibrary.org/obo/NCIT_C171105

has domain: Personal^c
has range: g e n e p i o 0001830^c

Country of residence at enrollment.

Data formats stored^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Data_formats_stored

is defined by: http://purl.obolibrary.org/obo/NCIT_C142494

has domain: Analysis^c
has range: format 1915^c

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.

Data use modifiers^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_modifiers

is defined by: http://purl.obolibrary.org/obo/DUO_0000017

has domain: Individual consent^c
has range: d u o 0000017^c

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.

Data use permissions^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_permissions

is defined by: http://purl.obolibrary.org/obo/DUO_0000001

has domain: Individual consent^c
has range: d u o 0000001^c

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.

Family members affected^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Family_members_affected

is defined by: http://purl.obolibrary.org/obo/HP_0032320

has domain: Clinical^c
has range: n c i t c71384^c

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).

Family members sequenced^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Family_members_sequenced

is defined by: http://purl.obolibrary.org/obo/NCIT_C79916

has domain: Clinical^c
has range: n c i t c71384^c

Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing.

Gender at birth^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Gender_at_birth

is defined by: http://purl.obolibrary.org/obo/GSSO_009418

has domain: Personal^c
has range: g s s o 009418^c

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.

Gender identity^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Gender_identity

is defined by: http://purl.bioontology.org/ontology/MESH/D005783

has domain: Personal^c
has range: d005783^c

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.

Genotypic sex^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Genotypic_sex

is defined by: http://purl.obolibrary.org/obo/PATO_0020000

has domain: Personal^c
has range: n c i t c168871^c

A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.

Inclusion criteria^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Inclusion_criteria

is defined by: http://purl.obolibrary.org/obo/OBI_0500027

has domain: Study^c
has range: o b i 0500027^c

The conditions which, if met, make an person eligible for participation in this study.

Inclusion status^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Inclusion_status

is defined by: http://purl.obolibrary.org/obo/NCIT_C166244

has domain: Personal^c
has range: n c i t c19332^c

An indicator that provides information on the current health status of this person.

Library preparation kit^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Library_preparation_kit

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0000085

has domain: Sample preparation^c
has range: g e n e p i o 0000081^c

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.

Medical history^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Medical_history

is defined by: http://purl.obolibrary.org/obo/NCIT_C18772

has domain: Clinical^c
has range: s c d o 1000093^c

A record of a person's background regarding health, occurrence of disease events and surgical procedures.

Medication^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Medication

is defined by: http://purl.obolibrary.org/obo/NCIT_C459

has domain: Clinical^c
has range: data 3103^c

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.

Molecular diagnosis gene^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Molecular_diagnosis_gene

is defined by: http://purl.obolibrary.org/obo/NCIT_C20826

has domain: Clinical^c
has range: n c i t c16612^c

Gene affected by pathogenic variation that is causal for disease of the patient.

Participates in study^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Participates_in_study

is defined by: http://purl.obolibrary.org/obo/RO_0000056

has domain: Personal^c

Reference to the study or studies in which this person participates.

Pathological state^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Pathological_state

is defined by: http://purl.obolibrary.org/obo/GO_0001894

has domain: Material^c
has range: n c i t c164617^c

The pathological state of the tissue from which this material was derived.

Person consenting^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Person_consenting

is defined by: http://purl.obolibrary.org/obo/IAO_0000136

has domain: Individual consent^c

Reference to the person (i.e. subject) to whom this individual consent applies.

Phenotype^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Phenotype

is defined by: http://purl.obolibrary.org/obo/NCIT_C16977

has domain: Clinical^c
has range: property: p3841^c

The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.

Phenotypic data available^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Phenotypic_data_available

is defined by: http://purl.obolibrary.org/obo/NCIT_C15783

has domain: Clinical^c
has range: d c m i type^c

Types of phenotypic data collected in a clinical setting that is potentially available upon request.

Primary affiliated institute^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Primary_affiliated_institute

is defined by: http://purl.obolibrary.org/obo/NCIT_C25412

has domain: Personal^c
has range: s i o 000688^c

The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person.

Reference genome used^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Reference_genome_used

is defined by: http://edamontology.org/data_2340

has domain: Analysis^c
has range: data 2787^c

The specific build of the human genome used as reference for sequence alignment and variant calling.

Represented by^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Represented_by

is defined by: http://purl.obolibrary.org/obo/NCIT_C142600

has domain: Individual consent^c
has range: b f o 0000023^c

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.

Resources in other institutes^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Resources_in_other_institutes

is defined by: http://purl.obolibrary.org/obo/NCIT_C19012

has domain: Personal^c
has range: s i o 000688^c

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.

Sequencing instrument model^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_instrument_model

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0001921

has domain: Sequencing^c
has range: g e n e p i o 0001921^c

The used product name and model number of a manufacturer's genomic (dna) sequencer.

Sequencing method^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_method

is defined by: http://purl.obolibrary.org/obo/FIX_0000704

has domain: Sequencing^c
has range: n c i t c17565^c

Method used to determine the order of bases in a nucleic acid sequence.

Sequencing platform^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_platform

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0000071

has domain: Sequencing^c
has range: g e n e p i o 0000071^c

The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).

Storage conditions^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Storage_conditions

is defined by: http://purl.obolibrary.org/obo/NCIT_C96145

has domain: Material^c
has range: n c i t c96145^c

The conditions under which this biological material was stored.

Target enrichment kit^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Target_enrichment_kit

is defined by: http://purl.obolibrary.org/obo/NCIT_C154307

has domain: Sample preparation^c
has range: g e n e p i o 0000081^c

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.

Unobserved phenotype^op back to ToC or Object Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Unobserved_phenotype

is defined by: http://purl.bioontology.org/ontology/HL7/C0442737

has domain: Clinical^c
has range: property: p3841^c

Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.

Data Properties

Abstract data location^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Abstract_data_location

is defined by: http://purl.obolibrary.org/obo/NCIT_C142494

has domain: Analysis^c

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).

Age at death^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Age_at_death

is defined by: http://purl.obolibrary.org/obo/NCIT_C135383

has domain: Personal^c

The age at which death occurred.

Age at diagnosis^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Age_at_diagnosis

is defined by: http://purl.bioontology.org/ontology/SNOMEDCT/423493009

has domain: Clinical^c

The age, measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease.

Age at last screening^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Age_at_last_screening

is defined by: http://purl.obolibrary.org/obo/NCIT_C81258

has domain: Clinical^c

Age of the patient at the moment of the most recent screening.

Age of onset^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Age_of_onset

is defined by: http://www.orpha.net/ORDO/Orphanet_C023

has domain: Clinical^c

Age of onset of clinical manifestations related to the disease of the patient.

Algorithms used^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Algorithms_used

is defined by: http://purl.obolibrary.org/obo/NCIT_C16275

has domain: Analysis^c

Any used problem-solving procedures implemented in software to be executed by a computer.

Analysis identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Analysis_identifier

is defined by: http://purl.allotrope.org/ontologies/result#AFR_0001979

has domain: Analysis^c

A unique proper name or character sequence that identifies this particular analysis.

Bioinformatic protocol deviation^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Bioinformatic_protocol_deviation

is defined by: http://purl.obolibrary.org/obo/NCIT_C50996

has domain: Analysis^c

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.

Bioinformatic protocol used^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Bioinformatic_protocol_used

is defined by: http://edamontology.org/data_2531

has domain: Analysis^c

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.

Clinical identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Clinical_identifier

is defined by: http://purl.obolibrary.org/obo/NCIT_C87853

has domain: Clinical^c

A unique proper name or character sequence that identifies this particular clinical examination.

Completion date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Completion_date

is defined by: http://purl.obolibrary.org/obo/NCIT_C142702

has domain: Study^c

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.

Consanguinity^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Consanguinity

is defined by: http://purl.obolibrary.org/obo/GSSO_007578

has domain: Clinical^c

Information on whether the patient is a child from two family members who are second cousins or closer.

Consent form accepted date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_accepted_date

is defined by: http://purl.org/dc/terms/dateAccepted

has domain: Leaflet and consent form^c

Date of acceptance of this consent form.

Consent form identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_identifier

is defined by: http://purl.org/dc/terms/identifier

has domain: Leaflet and consent form^c

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.

Consent form title^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_title

is defined by: http://purl.org/dc/terms/title

has domain: Leaflet and consent form^c

A title or name given to this consent form.

Consent form valid until^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_valid_until

is defined by: http://purl.org/dc/terms/valid

has domain: Leaflet and consent form^c

End date of the validity of this consent form.

Consent form version^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_version

is defined by: http://purl.org/dc/terms/hasVersion

has domain: Leaflet and consent form^c

The version, edition, or adaptation of this consent form.

Contact information^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Contact_information

is defined by: http://purl.obolibrary.org/obo/OMIABIS_0000035

has domain: Study^c

An email address for the purpose of contacting the study contact person.

Data use specification^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_specification

is defined by: http://semanticscience.org/resource/SIO_000090

has domain: Individual consent^c

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.

Derived from^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Derived_from

is defined by: http://purl.obolibrary.org/obo/NCIT_C28355

has domain: Material^c

Indicate if this material was produced from or related to another.

Description^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Description

is defined by: http://purl.obolibrary.org/obo/OMIABIS_0000036

has domain: Study^c

A statement or piece of writing that provides details on this study.

Drug regimen^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Drug_regimen

is defined by: http://purl.obolibrary.org/obo/NCIT_C142516

has domain: Clinical^c

The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.

Expiration date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Expiration_date

is defined by: http://purl.obolibrary.org/obo/NCIT_C164516

has domain: Material^c

The date beyond which this material is no longer regarded as fit for use.

First contact^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_First_contact

is defined by: http://purl.bioontology.org/ontology/LNC/MTHU048806

has domain: Clinical^c

First contact of the patient with a specialised center in context of disease or study inclusion.

Functioning^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Functioning

is defined by: http://purl.obolibrary.org/obo/NCIT_C21007

has domain: Clinical^c

Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF).

Identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Identifier

is defined by: http://purl.obolibrary.org/obo/OMIABIS_0000006

has domain: Study^c

A unique proper name or character sequence that identifies this particular study.

Individual consent identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Individual_consent_identifier

is defined by: http://purl.obolibrary.org/obo/ICO_0000044

has domain: Individual consent^c

A unique proper name or character sequence that identifies this particular signed individual consent.

Input amount^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Input_amount

is defined by: http://purl.allotrope.org/ontologies/role#AFRL_0000010

has domain: Sample preparation^c

Amount of input material in nanogram (ng).

Intended insert size^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Intended_insert_size

is defined by: https://w3id.org/fair-genomes/resource/FG_0000001

has domain: Sample preparation^c

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.

Intended read length^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Intended_read_length

is defined by: http://purl.obolibrary.org/obo/NCIT_C153362

has domain: Sample preparation^c

The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.

Leaflet date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_date

is defined by: http://purl.org/dc/terms/date

has domain: Leaflet and consent form^c

A point or period of time associated with the publication of this leaflet that belongs to this consent form.

Leaflet title^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_title

is defined by: http://purl.org/dc/terms/title

has domain: Leaflet and consent form^c

A title or name given to the leaflet that belongs to this consent form.

Leaflet version^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_version

is defined by: http://purl.org/dc/terms/hasVersion

has domain: Leaflet and consent form^c

The version, edition, or adaptation of this leaflet that belongs to this consent form.

Material identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Material_identifier

is defined by: http://purl.obolibrary.org/obo/NCIT_C93400

has domain: Material^c

A unique proper name or character sequence that identifies this particular material.

Material used in diagnosis^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Material_used_in_diagnosis

is defined by: http://semanticscience.org/resource/SIO_000641

has domain: Clinical^c

This diagnosis c.q. clinical examination is based on one or more sampled materials.

Median read depth^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Median_read_depth

is defined by: http://purl.obolibrary.org/obo/NCIT_C155320

has domain: Sequencing^c

The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.

Molecular diagnosis other^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Clinical_Molecular_diagnosis_other

is defined by: http://purl.obolibrary.org/obo/NCIT_C20826

has domain: Clinical^c

Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.

Name^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Name

is defined by: http://purl.obolibrary.org/obo/OMIABIS_0000037

has domain: Study^c

A name that designates this study.

Observed insert size^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Observed_insert_size

is defined by: https://w3id.org/fair-genomes/resource/FG_0000002

has domain: Sequencing^c

Observed read length^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Observed_read_length

is defined by: http://purl.obolibrary.org/obo/NCIT_C153362

has domain: Sequencing^c

The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.

Other quality metrics^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Other_quality_metrics

is defined by: http://edamontology.org/data_3914

has domain: Sequencing^c

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.

PCR free^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_PCR_free

is defined by: http://purl.obolibrary.org/obo/NCIT_C17003

has domain: Sample preparation^c

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.

Percentage Q30^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Percentage_Q30

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0000089

has domain: Sequencing^c

Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.

Percentage TR20^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Percentage_TR20

is defined by: https://w3id.org/fair-genomes/resource/FG_0000003

has domain: Sequencing^c

Percentage of the target sequence on which 20 or more unique reads were successfully mapped.

Percentage tumor cells^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Percentage_tumor_cells

is defined by: http://purl.obolibrary.org/obo/NCIT_C127771

has domain: Material^c

The percentage of tumor cells compared to total cells present in this material.

Personal identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Personal_identifier

is defined by: http://purl.obolibrary.org/obo/NCIT_C164337

has domain: Personal^c

A unique proper name or character sequence that identifies this particular person.

Physical data location^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Physical_data_location

is defined by: http://purl.obolibrary.org/obo/GAZ_00000448

has domain: Analysis^c

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).

Physical location^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Physical_location

is defined by: http://purl.obolibrary.org/obo/GAZ_00000448

has domain: Material^c

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).

Principal investigator^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Principal_investigator

is defined by: http://purl.obolibrary.org/obo/OMIABIS_0000100

has domain: Study^c

The principal investigator or responsible person for this study.

Reason for bioinformatic protocol deviation^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_Reason_for_bioinformatic_protocol_deviation

is defined by: http://purl.obolibrary.org/obo/NCIT_C93529

has domain: Analysis^c

The rationale for why a deviation from the bioinformatic protocol has occurred.

Reason for sampling protocol deviation^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Reason_for_sampling_protocol_deviation

is defined by: http://purl.obolibrary.org/obo/NCIT_C93529

has domain: Material^c

The rationale for why a deviation from the sampling protocol has occurred.

Registration timestamp^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Registration_timestamp

is defined by: http://purl.obolibrary.org/obo/NCIT_C25646

has domain: Material^c

Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.

Sampleprep identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Sampleprep_identifier

is defined by: http://purl.obolibrary.org/obo/NCIT_C132299

has domain: Sample preparation^c

A unique proper name or character sequence that identifies this particular sample preparation.

Sampling protocol^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Sampling_protocol

is defined by: http://www.ebi.ac.uk/efo/EFO_0005518

has domain: Material^c

The procedure whereby this material was sampled for an analysis.

Sampling protocol deviation^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Sampling_protocol_deviation

is defined by: http://purl.obolibrary.org/obo/NCIT_C50996

has domain: Material^c

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.

Sampling timestamp^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Material_Sampling_timestamp

is defined by: http://www.ebi.ac.uk/efo/EFO_0000689

has domain: Material^c

Date and time at which this material was collected.

Sequencing date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_date

is defined by: http://purl.obolibrary.org/obo/GENEPIO_0000069

has domain: Sequencing^c

Date on which this sequencing assay was performed.

Sequencing identifier^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_identifier

is defined by: http://purl.obolibrary.org/obo/NCIT_C171337

has domain: Sequencing^c

A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.

Signing date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Signing_date

is defined by: http://purl.obolibrary.org/obo/ICO_0000036

has domain: Individual consent^c

A date specification that designates when this individual consent form was signed.

Start date^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Start_date

is defined by: http://purl.obolibrary.org/obo/NCIT_C69208

has domain: Study^c

The date on which this study began.

Study design^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Study_Study_design

is defined by: http://purl.obolibrary.org/obo/OBI_0500000

has domain: Study^c

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.

UMIs present^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_UMIs_present

is defined by: http://www.ebi.ac.uk/efo/EFO_0010199

has domain: Sample preparation^c

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.

Valid from^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Valid_from

is defined by: http://purl.org/dc/terms/valid

has domain: Individual consent^c

Starting date of the validity of this individual consent.

Valid until^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Valid_until

is defined by: http://purl.org/dc/terms/valid

has domain: Individual consent^c

End date of the validity of this individual consent.

WGS guideline followed^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Analysis_WGS_guideline_followed

is defined by: http://purl.obolibrary.org/obo/NCIT_C17564

has domain: Analysis^c

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.

Year of birth^dp back to ToC or Data Property ToC

IRI: https://w3id.org/fair-genomes/ontology/Personal_Year_of_birth

is defined by: http://purl.obolibrary.org/obo/NCIT_C83164

has domain: Personal^c

The year in which this person was born.

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni .

FAIR Genomes metadata schema

Table of Content

Introduction

Classes

Analysisc back to ToC or Class ToC

Clinicalc back to ToC or Class ToC

Individual consentc back to ToC or Class ToC

Leaflet and consent formc back to ToC or Class ToC

Materialc back to ToC or Class ToC

Personalc back to ToC or Class ToC

Sample preparationc back to ToC or Class ToC

Sequencingc back to ToC or Class ToC

Studyc back to ToC or Class ToC

Object Properties

Allow recontactingop back to ToC or Object Property ToC

Analyses performedop back to ToC or Object Property ToC

Anatomical sourceop back to ToC or Object Property ToC

Ancestryop back to ToC or Object Property ToC

Belongs to diagnosisop back to ToC or Object Property ToC

Belongs to materialop back to ToC or Object Property ToC

Belongs to personop back to ToC or Object Property ToC

Belongs to sampleop back to ToC or Object Property ToC

Belongs to sequencingop back to ToC or Object Property ToC

Biospecimen typeop back to ToC or Object Property ToC

Clinical diagnosisop back to ToC or Object Property ToC

Collected byop back to ToC or Object Property ToC

Collected from personop back to ToC or Object Property ToC

Consent form creatorop back to ToC or Object Property ToC

Consent form usedop back to ToC or Object Property ToC

Country of birthop back to ToC or Object Property ToC

Country of residenceop back to ToC or Object Property ToC

Data formats storedop back to ToC or Object Property ToC

Data use modifiersop back to ToC or Object Property ToC

Data use permissionsop back to ToC or Object Property ToC

Family members affectedop back to ToC or Object Property ToC

Family members sequencedop back to ToC or Object Property ToC

Gender at birthop back to ToC or Object Property ToC

Gender identityop back to ToC or Object Property ToC

Genotypic sexop back to ToC or Object Property ToC

Inclusion criteriaop back to ToC or Object Property ToC

Inclusion statusop back to ToC or Object Property ToC

Library preparation kitop back to ToC or Object Property ToC

Medical historyop back to ToC or Object Property ToC

Medicationop back to ToC or Object Property ToC

Molecular diagnosis geneop back to ToC or Object Property ToC

Participates in studyop back to ToC or Object Property ToC

Pathological stateop back to ToC or Object Property ToC

Person consentingop back to ToC or Object Property ToC

Phenotypeop back to ToC or Object Property ToC

Phenotypic data availableop back to ToC or Object Property ToC

Primary affiliated instituteop back to ToC or Object Property ToC

Reference genome usedop back to ToC or Object Property ToC

Represented byop back to ToC or Object Property ToC

Resources in other institutesop back to ToC or Object Property ToC

Sequencing instrument modelop back to ToC or Object Property ToC

Sequencing methodop back to ToC or Object Property ToC

Sequencing platformop back to ToC or Object Property ToC

Storage conditionsop back to ToC or Object Property ToC

Target enrichment kitop back to ToC or Object Property ToC

Unobserved phenotypeop back to ToC or Object Property ToC