Object Properties
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Allow_recontacting
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C25737
The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances.
IRI: https://w3id.org/fair-genomes/ontology/Material_Analyses_performed
- is defined by
- http://purl.obolibrary.org/obo/IAO_0000702
Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics).
IRI: https://w3id.org/fair-genomes/ontology/Material_Anatomical_source
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C103264
- has domain
- Materialc
- has range
- u b e r o n 0001062c
Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Ancestry
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C176763
- has domain
- Personalc
- has range
- h a n c e s t r o 0004c
Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.
IRI: https://w3id.org/fair-genomes/ontology/Material_Belongs_to_diagnosis
- is defined by
- http://semanticscience.org/resource/SIO_000068
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.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Belongs_to_sequencing
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C25683
Reference to the sequencing that was performed, i.e. the source on which this analysis was based.
IRI: https://w3id.org/fair-genomes/ontology/Material_Biospecimen_type
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C70713
- has domain
- Materialc
- has range
- n c i t c70699c
The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_creator
- is defined by
- http://purl.org/dc/terms/creator
Indicates the authoritative body who brought this consent form into existence.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Consent_form_used
- is defined by
- http://purl.obolibrary.org/obo/IAO_0000136
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.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Data_formats_stored
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C142494
- has domain
- Analysisc
- has range
- format 1915c
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.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_modifiers
- is defined by
- http://purl.obolibrary.org/obo/DUO_0000017
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.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_permissions
- is defined by
- http://purl.obolibrary.org/obo/DUO_0000001
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Family_members_affected
- is defined by
- http://purl.obolibrary.org/obo/HP_0032320
- has domain
- Clinicalc
- has range
- n c i t c71384c
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).
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Family_members_sequenced
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C79916
- has domain
- Clinicalc
- has range
- n c i t c71384c
Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Gender_at_birth
- is defined by
- http://purl.obolibrary.org/obo/GSSO_009418
- has domain
- Personalc
- has range
- g s s o 009418c
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.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Gender_identity
- is defined by
- http://purl.bioontology.org/ontology/MESH/D005783
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.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Genotypic_sex
- is defined by
- http://purl.obolibrary.org/obo/PATO_0020000
- has domain
- Personalc
- has range
- n c i t c168871c
A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
IRI: https://w3id.org/fair-genomes/ontology/Study_Inclusion_criteria
- is defined by
- http://purl.obolibrary.org/obo/OBI_0500027
- has domain
- Studyc
- has range
- o b i 0500027c
The conditions which, if met, make an person eligible for participation in this study.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Library_preparation_kit
- is defined by
- http://purl.obolibrary.org/obo/GENEPIO_0000085
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Medical_history
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C18772
- has domain
- Clinicalc
- has range
- s c d o 1000093c
A record of a person's background regarding health, occurrence of disease events and surgical procedures.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Medication
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C459
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Molecular_diagnosis_gene
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C20826
- has domain
- Clinicalc
- has range
- n c i t c16612c
Gene affected by pathogenic variation that is causal for disease of the patient.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Person_consenting
- is defined by
- http://purl.obolibrary.org/obo/IAO_0000136
Reference to the person (i.e. subject) to whom this individual consent applies.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Phenotype
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C16977
- has domain
- Clinicalc
- has range
- property: p3841c
The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Phenotypic_data_available
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C15783
- has domain
- Clinicalc
- has range
- d c m i typec
Types of phenotypic data collected in a clinical setting that is potentially available upon request.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Primary_affiliated_institute
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C25412
- has domain
- Personalc
- has range
- s i o 000688c
The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Reference_genome_used
- is defined by
- http://edamontology.org/data_2340
The specific build of the human genome used as reference for sequence alignment and variant calling.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Represented_by
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C142600
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.
IRI: https://w3id.org/fair-genomes/ontology/Personal_Resources_in_other_institutes
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C19012
- has domain
- Personalc
- has range
- s i o 000688c
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.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_platform
- is defined by
- http://purl.obolibrary.org/obo/GENEPIO_0000071
- has domain
- Sequencingc
- has range
- g e n e p i o 0000071c
The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Target_enrichment_kit
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C154307
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Unobserved_phenotype
- is defined by
- http://purl.bioontology.org/ontology/HL7/C0442737
- has domain
- Clinicalc
- has range
- property: p3841c
Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.
Data Properties
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Abstract_data_location
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C142494
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).
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Age_of_onset
- is defined by
- http://www.orpha.net/ORDO/Orphanet_C023
Age of onset of clinical manifestations related to the disease of the patient.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Algorithms_used
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C16275
Any used problem-solving procedures implemented in software to be executed by a computer.
Bioinformatic protocol deviationdp 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
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 useddp 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
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Clinical_identifier
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C87853
A unique proper name or character sequence that identifies this particular clinical examination.
IRI: https://w3id.org/fair-genomes/ontology/Study_Completion_date
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C142702
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Consanguinity
- is defined by
- http://purl.obolibrary.org/obo/GSSO_007578
Information on whether the patient is a child from two family members who are second cousins or closer.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_identifier
- is defined by
- http://purl.org/dc/terms/identifier
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.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_title
- is defined by
- http://purl.org/dc/terms/title
A title or name given to this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_valid_until
- is defined by
- http://purl.org/dc/terms/valid
End date of the validity of this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Consent_form_version
- is defined by
- http://purl.org/dc/terms/hasVersion
The version, edition, or adaptation of this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Data_use_specification
- is defined by
- http://semanticscience.org/resource/SIO_000090
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.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Drug_regimen
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C142516
The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Functioning
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C21007
Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF).
Individual consent identifierdp 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
A unique proper name or character sequence that identifies this particular signed individual consent.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Intended_insert_size
- is defined by
- https://w3id.org/fair-genomes/resource/FG_0000001
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.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Intended_read_length
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C153362
The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_date
- is defined by
- http://purl.org/dc/terms/date
A point or period of time associated with the publication of this leaflet that belongs to this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_title
- is defined by
- http://purl.org/dc/terms/title
A title or name given to the leaflet that belongs to this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Leaflet_and_consent_form_Leaflet_version
- is defined by
- http://purl.org/dc/terms/hasVersion
The version, edition, or adaptation of this leaflet that belongs to this consent form.
IRI: https://w3id.org/fair-genomes/ontology/Material_Material_identifier
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C93400
A unique proper name or character sequence that identifies this particular material.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Median_read_depth
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C155320
The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.
IRI: https://w3id.org/fair-genomes/ontology/Clinical_Molecular_diagnosis_other
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C20826
Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Observed_insert_size
- is defined by
- https://w3id.org/fair-genomes/resource/FG_0000002
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.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Observed_read_length
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C153362
The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Other_quality_metrics
- is defined by
- http://edamontology.org/data_3914
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.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_PCR_free
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C17003
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.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Percentage_Q30
- is defined by
- http://purl.obolibrary.org/obo/GENEPIO_0000089
Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_Physical_data_location
- is defined by
- http://purl.obolibrary.org/obo/GAZ_00000448
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).
IRI: https://w3id.org/fair-genomes/ontology/Material_Physical_location
- is defined by
- http://purl.obolibrary.org/obo/GAZ_00000448
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).
IRI: https://w3id.org/fair-genomes/ontology/Material_Registration_timestamp
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C25646
Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_Sampleprep_identifier
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C132299
A unique proper name or character sequence that identifies this particular sample preparation.
IRI: https://w3id.org/fair-genomes/ontology/Material_Sampling_protocol
- is defined by
- http://www.ebi.ac.uk/efo/EFO_0005518
The procedure whereby this material was sampled for an analysis.
Sampling protocol deviationdp 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
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.
IRI: https://w3id.org/fair-genomes/ontology/Sequencing_Sequencing_identifier
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C171337
A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Signing_date
- is defined by
- http://purl.obolibrary.org/obo/ICO_0000036
A date specification that designates when this individual consent form was signed.
IRI: https://w3id.org/fair-genomes/ontology/Study_Study_design
- is defined by
- http://purl.obolibrary.org/obo/OBI_0500000
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.
IRI: https://w3id.org/fair-genomes/ontology/Sample_preparation_UMIs_present
- is defined by
- http://www.ebi.ac.uk/efo/EFO_0010199
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.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Valid_from
- is defined by
- http://purl.org/dc/terms/valid
Starting date of the validity of this individual consent.
IRI: https://w3id.org/fair-genomes/ontology/Individual_consent_Valid_until
- is defined by
- http://purl.org/dc/terms/valid
End date of the validity of this individual consent.
IRI: https://w3id.org/fair-genomes/ontology/Analysis_WGS_guideline_followed
- is defined by
- http://purl.obolibrary.org/obo/NCIT_C17564
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.
This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni
.