FAIR Genomes metadata schema
type: Ontology
description: The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare.
date: 2025-10-21
version info: 1.3-SNAPSHOT
language: en
rights: This ontology is distributed under a Attribution 4.0 International (CC BY 4.0) License - https://creativecommons.org/licenses/by/4.0/. Copyright: University Medical Center Groningen (2019-2021).
publisher: fairgenomes-semantic-model
license: Attribution 4.0 International (CC BY 4.0)
license document: https://creativecommons.org/licenses/by/4.0/
creator: K. Joeri van der Velde <k.j.van.der.velde@umcg.nl>
creator: https://orcid.org/0000-0002-0934-8375
creator: Gurnoor Singh <gurnoor1990@gmail.com>
creator: https://orcid.org/0000-0003-1615-4197
creator: Rajaram Kaliyaperumal <R.Kaliyaperumal@lumc.nl>
creator: 0000-0002-1215-167X
creator: XiaoFeng Liao <XiaoFeng.Liao@radboudumc.nl>
creator: https://orcid.org/0000-0002-4706-1084
creator: Esther van Enckevort <e.j.van.enckevort@rug.nl>
creator: https://orcid.org/0000-0002-2440-3993
creator: Jeroen A.M. Beliën <jam.belien@amsterdamumc.nl>
creator: https://orcid.org/0000-0002-7160-5942
creator: Daphne Stemkens <d.stemkens@vsop.nl>
creator: https://orcid.org/0000-0003-1301-5204
creator: Peter A.C. 't Hoen <peter-bram.thoen@radboudumc.nl>
creator: https://orcid.org/0000-0003-4450-3112
creator: Mariëlle E. van Gijn <m.e.van.gijn@umcg.nl>
creator: https://orcid.org/0000-0002-1073-0539
creator: Morris A. Swertz <m.a.swertz@umcg.nl>
creator: https://orcid.org/0000-0002-0979-3401
creator: FAIR Genomes Consortium
contributor: fair-genomes-drugs.ttl
contributor: fair-genomes-anatomicfocus.ttl
contributor: fair-genomes-inclusioncriteria.ttl
contributor: fair-genomes-familymembers.ttl
contributor: fair-genomes-imagingdevicesoftwareversion.ttl
contributor: fair-genomes-datausemodifiers.ttl
contributor: fair-genomes-countries.ttl
contributor: fair-genomes-genes.ttl
contributor: fair-genomes-medicalhistory.ttl
contributor: fair-genomes-institutes.ttl
contributor: fair-genomes-genderatbirth.ttl
contributor: fair-genomes-sequencingplatform.ttl
contributor: fair-genomes-sequencinginstrumentmodels.ttl
contributor: fair-genomes-representedby.ttl
contributor: fair-genomes-datausepermissions.ttl
contributor: fair-genomes-dataformats.ttl
contributor: fair-genomes-genomeaccessions.ttl
contributor: fair-genomes-biomarkermolecular.ttl
contributor: fair-genomes-imagetype.ttl
contributor: fair-genomes-treatmentresponse.ttl
contributor: fair-genomes-imagingdevice.ttl
contributor: fair-genomes-dcmitypes.ttl
contributor: fair-genomes-ancestry.ttl
contributor: fair-genomes-inclusionstatus.ttl
contributor: fair-genomes-laterality.ttl
contributor: fair-genomes-pathologicalstate.ttl
contributor: fair-genomes-recontacting.ttl
contributor: fair-genomes-phenotypes.ttl
contributor: fair-genomes-imagingprocedure.ttl
contributor: fair-genomes-biospecimentypes.ttl
contributor: fair-genomes-institutesror.ttl
contributor: fair-genomes-genotypicsex.ttl
contributor: fair-genomes-genderidentity.ttl
contributor: fair-genomes-reasonforimagingprocedure.ttl
contributor: fair-genomes-treatmentsettings.ttl
contributor: fair-genomes-diseases.ttl
contributor: fair-genomes-anatomicalsources.ttl
contributor: fair-genomes-sequencingmethods.ttl
contributor: fair-genomes-storageconditions.ttl
contributor: fair-genomes-ngskits.ttl
contributor: fair-genomes-biomarkertype.ttl
contributor: fair-genomes-analysesperformed.ttl
contributor: fair-genomes-manufacturerofid.ttl
contributor: fair-genomes-modality.ttl

Study
type: Class
description: A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts.

Identifier
type: DatatypeProperty
domain: Study
description: A unique proper name or character sequence that identifies this particular study.

Name
type: DatatypeProperty
domain: Study
description: A name that designates this study.

Description
type: DatatypeProperty
domain: Study
description: A statement or piece of writing that provides details on this study.

Inclusion criteria
type: ObjectProperty
domain: Study
description: The conditions which, if met, make an person eligible for participation in this study.
range: OBI_0500027

Principal investigator
type: DatatypeProperty
domain: Study
description: The principal investigator or responsible person for this study.

Contact information
type: DatatypeProperty
domain: Study
description: An email address for the purpose of contacting the study contact person.

Study design
type: DatatypeProperty
domain: Study
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.

Start date
type: DatatypeProperty
domain: Study
description: The date on which this study began.

Completion date
type: DatatypeProperty
domain: Study
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.

Personal
type: Class
description: Data, facts or figures about an individual; the set of relevant items would depend on the use case.
RO_0000056: Study

Personal identifier
type: DatatypeProperty
domain: Personal
description: A unique proper name or character sequence that identifies this particular person.

Gender identity
type: ObjectProperty
domain: Personal
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.
range: D005783

Gender at birth
type: ObjectProperty
domain: Personal
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.
range: GSSO_009418

Genotypic sex
type: ObjectProperty
domain: Personal
description: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
range: NCIT C168871

Country of residence
type: ObjectProperty
domain: Personal
description: Country of residence at enrollment.
range: GENEPIO_0001830

Ancestry
type: ObjectProperty
domain: Personal
description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data.
range: HANCESTRO_0004

Country of birth
type: ObjectProperty
domain: Personal
description: The country that this person was born in.
range: GENEPIO_0001830

Year of birth
type: DatatypeProperty
SIO_000074: NCIT C159612
domain: Personal
description: The year in which this person was born.

Inclusion status
type: ObjectProperty
domain: Personal
description: An indicator that provides information on the current health status of this person.
range: NCIT C19332

Age at death
type: DatatypeProperty
SIO_000074: UO_0000036
domain: Personal
description: The age at which death occurred.

Consanguinity
type: DatatypeProperty
domain: Personal
description: Information on whether the patient is a child from two family members who are second cousins or closer.

Primary affiliated institute
type: ObjectProperty
domain: Personal
description: The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person.
range: SIO_000688

Resources in other institutes
type: ObjectProperty
domain: Personal
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.
range: SIO_000688

Participates in study
type: ObjectProperty
domain: Personal
description: Reference to the study or studies in which this person participates.

Leaflet and consent form
type: Class
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.

Leaflet title
type: DatatypeProperty
domain: Leaflet and consent form
description: A title or name given to the leaflet that belongs to this consent form.

Leaflet date
type: DatatypeProperty
domain: Leaflet and consent form
description: A point or period of time associated with the publication of this leaflet that belongs to this consent form.

Leaflet version
type: DatatypeProperty
domain: Leaflet and consent form
description: The version, edition, or adaptation of this leaflet that belongs to this consent form.

Consent form identifier
type: DatatypeProperty
domain: Leaflet and consent form
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.

Consent form title
type: DatatypeProperty
domain: Leaflet and consent form
description: A title or name given to this consent form.

Consent form accepted date
type: DatatypeProperty
domain: Leaflet and consent form
description: Date of acceptance of this consent form.

Consent form valid until
type: DatatypeProperty
domain: Leaflet and consent form
description: End date of the validity of this consent form.

Consent form creator
type: ObjectProperty
domain: Leaflet and consent form
description: Indicates the authoritative body who brought this consent form into existence.
range: SIO_000688

Consent form version
type: DatatypeProperty
domain: Leaflet and consent form
description: The version, edition, or adaptation of this consent form.

Individual consent
type: Class
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.
IAO_0021007: Leaflet and consent form
ICO_0000005: Personal

Individual consent identifier
type: DatatypeProperty
domain: Individual consent
description: A unique proper name or character sequence that identifies this particular signed individual consent.

Person consenting
type: ObjectProperty
domain: Individual consent
description: Reference to the person (i.e. subject) to whom this individual consent applies.

Consent form used
type: ObjectProperty
domain: Individual consent
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.

Collected by
type: ObjectProperty
domain: Individual consent
description: Indicates the institute who performed the collection act.
range: SIO_000688

Signing date
type: DatatypeProperty
domain: Individual consent
description: A date specification that designates when this individual consent form was signed.

Valid from
type: DatatypeProperty
domain: Individual consent
description: Starting date of the validity of this individual consent.

Valid until
type: DatatypeProperty
domain: Individual consent
description: End date of the validity of this individual consent.

Represented by
type: ObjectProperty
domain: Individual consent
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.
range: BFO_0000023

Data use permissions
type: ObjectProperty
domain: Individual consent
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.
range: DUO_0000001

Data use modifiers
type: ObjectProperty
domain: Individual consent
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.
range: DUO_0000017

Data use specification
type: DatatypeProperty
domain: Individual consent
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.

Allow recontacting
type: ObjectProperty
domain: Individual consent
description: The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances.
range: NCIT C176244

Clinical
type: Class
description: Findings and circumstances relating to the examination and treatment of a patient.
SIO_000332: Personal

Clinical identifier
type: DatatypeProperty
domain: Clinical
description: A unique proper name or character sequence that identifies this particular clinical examination.

Belongs to person
type: ObjectProperty
domain: Clinical
description: Reference to the person whom this clinical information is about.

Phenotype
type: ObjectProperty
domain: Clinical
description: The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease.
range: Property:P3841

Unobserved phenotype
type: ObjectProperty
domain: Clinical
description: Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance.
range: Property:P3841

Phenotypic data available
type: ObjectProperty
domain: Clinical
description: Types of phenotypic data collected in a clinical setting that is potentially available upon request.
range: DCMIType

Clinical diagnosis
type: ObjectProperty
domain: Clinical
description: A diagnosis made from a study of the signs and symptoms of a disease.
range: data 3667

Molecular diagnosis gene
type: ObjectProperty
domain: Clinical
description: Gene affected by pathogenic variation that is causal for disease of the patient.
range: NCIT C16612

Molecular diagnosis other
type: DatatypeProperty
domain: Clinical
description: Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.

Age at diagnosis
type: DatatypeProperty
SIO_000074: UO_0000036
domain: Clinical
description: The age, measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease.

Age at last screening
type: DatatypeProperty
SIO_000074: UO_0000036
domain: Clinical
description: Age of the patient at the moment of the most recent screening.

Medication
type: ObjectProperty
domain: Clinical
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.
range: data 3103

Drug regimen
type: DatatypeProperty
domain: Clinical
description: The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.

Family members affected
type: ObjectProperty
domain: Clinical
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).
range: NCIT C71384

Family members sequenced
type: ObjectProperty
domain: Clinical
description: Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing.
range: NCIT C71384

Medical history
type: ObjectProperty
domain: Clinical
description: A record of a person's background regarding health, occurrence of disease events and surgical procedures.
range: SCDO_1000093

Age of onset
type: DatatypeProperty
SIO_000074: UO_0000036
domain: Clinical
description: Age of onset of clinical manifestations related to the disease of the patient.

First contact
type: DatatypeProperty
domain: Clinical
description: First contact of the patient with a specialised center in context of disease or study inclusion.

Functioning
type: DatatypeProperty
domain: Clinical
description: Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF).

Material used in diagnosis
type: DatatypeProperty
domain: Clinical
description: This diagnosis c.q. clinical examination is based on one or more sampled materials.

Material
type: Class
description: A natural substance derived from living organisms such as cells, tissues, proteins, and DNA.
HSO_0000242: Personal

Material identifier
type: DatatypeProperty
domain: Material
description: A unique proper name or character sequence that identifies this particular material.

Collected from person
type: ObjectProperty
domain: Material
description: Reference to the person from whom this material was collected.

Belongs to diagnosis
type: ObjectProperty
domain: Material
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.

Sampling timestamp
type: DatatypeProperty
domain: Material
description: Date and time at which this material was collected.

Registration timestamp
type: DatatypeProperty
domain: Material
description: Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.

Sampling protocol
type: DatatypeProperty
domain: Material
description: The procedure whereby this material was sampled for an analysis.

Sampling protocol deviation
type: DatatypeProperty
domain: Material
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.

Reason for sampling protocol deviation
type: DatatypeProperty
domain: Material
description: The rationale for why a deviation from the sampling protocol has occurred.

Biospecimen type
type: ObjectProperty
domain: Material
description: The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes.
range: NCIT C70699

Anatomical source
type: ObjectProperty
domain: Material
description: Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken.
range: UBERON_0001062

Pathological state
type: ObjectProperty
domain: Material
description: The pathological state of the tissue from which this material was derived.
range: NCIT C164617

Storage conditions
type: ObjectProperty
domain: Material
description: The conditions under which this biological material was stored.
range: NCIT C96145

Expiration date
type: DatatypeProperty
domain: Material
description: The date beyond which this material is no longer regarded as fit for use.

Percentage tumor cells
type: DatatypeProperty
domain: Material
description: The percentage of tumor cells compared to total cells present in this material.

Physical location
type: DatatypeProperty
domain: Material
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).

Analyses performed
type: ObjectProperty
domain: Material
description: Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics).
range: topic 3391

Derived from
type: DatatypeProperty
domain: Material
description: Indicate if this material was produced from or related to another.

Fixed Block
type: Class
description: Refers to preserved specimens embedded in support material. These are typically cut into thin slices for microscopic examination, with or without an enhancement such as staining.
HSO_0000242: Personal

Block identifier
type: DatatypeProperty
domain: Fixed Block
description: A unique proper name or character sequence that identifies this fixed block.

Sample preparation
type: Class
description: A sample preparation for a nucleic acids sequencing assay.
NCIT C179746: Material

Sampleprep identifier
type: DatatypeProperty
domain: Sample preparation
description: A unique proper name or character sequence that identifies this particular sample preparation.

Belongs to material
type: ObjectProperty
domain: Sample preparation
description: Reference to the source material from which this sample was prepared.

Input amount
type: DatatypeProperty
SIO_000074: UO_0000024
domain: Sample preparation
description: Amount of input material in nanogram (ng).

Library preparation kit
type: ObjectProperty
domain: Sample preparation
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.
range: GENEPIO_0000081

PCR free
type: DatatypeProperty
domain: Sample preparation
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.

Target enrichment kit
type: ObjectProperty
domain: Sample preparation
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.
range: GENEPIO_0000081

UMIs present
type: DatatypeProperty
domain: Sample preparation
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.

Intended insert size
type: DatatypeProperty
domain: Sample preparation
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.

Intended read length
type: DatatypeProperty
domain: Sample preparation
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.

Sequencing
type: Class
description: The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
SIO_001220: Sample preparation

Sequencing identifier
type: DatatypeProperty
domain: Sequencing
description: A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay.

Belongs to sample preparation
type: ObjectProperty
domain: Sequencing
description: Reference to the prepared sample, i.e. the source that was sequenced.

Sequencing date
type: DatatypeProperty
domain: Sequencing
description: Date on which this sequencing assay was performed.

Sequencing platform
type: ObjectProperty
domain: Sequencing
description: The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).
range: GENEPIO_0000071

Sequencing instrument model
type: ObjectProperty
domain: Sequencing
description: The used product name and model number of a manufacturer's genomic (dna) sequencer.
range: GENEPIO_0001921

Sequencing method
type: ObjectProperty
domain: Sequencing
description: Method used to determine the order of bases in a nucleic acid sequence.
range: NCIT C17565

Median read depth
type: DatatypeProperty
domain: Sequencing
description: The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.

Observed read length
type: DatatypeProperty
domain: Sequencing
description: The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.

Observed insert size
type: DatatypeProperty
domain: Sequencing
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.

Percentage Q30
type: DatatypeProperty
domain: Sequencing
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.

Percentage TR20
type: DatatypeProperty
domain: Sequencing
description: Percentage of the target sequence on which 20 or more unique reads were successfully mapped.

Other quality metrics
type: DatatypeProperty
domain: Sequencing
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.

Analysis
type: Class
description: An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output.
SIO_000253: Sequencing

Analysis identifier
type: DatatypeProperty
domain: Analysis
description: A unique proper name or character sequence that identifies this particular analysis.

Belongs to sequencing
type: ObjectProperty
domain: Analysis
description: Reference to the sequencing that was performed, i.e. the source on which this analysis was based.

Physical data location
type: DatatypeProperty
domain: Analysis
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).

Abstract data location
type: DatatypeProperty
domain: Analysis
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).

Data formats stored
type: ObjectProperty
domain: Analysis
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.
range: format 1915

Algorithms used
type: DatatypeProperty
domain: Analysis
description: Any used problem-solving procedures implemented in software to be executed by a computer.

Reference genome used
type: ObjectProperty
domain: Analysis
description: The specific build of the human genome used as reference for sequence alignment and variant calling.
range: data 2787

Bioinformatic protocol used
type: DatatypeProperty
domain: Analysis
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.

Bioinformatic protocol deviation
type: DatatypeProperty
domain: Analysis
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.

Reason for bioinformatic protocol deviation
type: DatatypeProperty
domain: Analysis
description: The rationale for why a deviation from the bioinformatic protocol has occurred.

WGS guideline followed
type: DatatypeProperty
domain: Analysis
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.

HMD Submission
type: Class
description: A class specific for the 1+MG GDI project containing items for metadata submission.

Submitter Role
type: DatatypeProperty
domain: HMD Submission
description: Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI).

Data Center
type: DatatypeProperty
domain: HMD Submission
description: Refers to the Department in charge of Data Production and/ or analysis

Clinical Center
type: DatatypeProperty
domain: HMD Submission
description: Refers to the Clinical Department in charge of the patient.

Institution Clinical
type: ObjectProperty
domain: HMD Submission
description: Identifies the Institution/s involved.
range: SIO_000688

Institution Data Center
type: ObjectProperty
domain: HMD Submission
description: Identifies the Institution/s involved.
range: SIO_000688

Publication description
type: DatatypeProperty
domain: HMD Submission
description: Linked to the instance of publication_doi; should provide a human-readably description of the publication.

Collection
type: DatatypeProperty
domain: HMD Submission
description: Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.

Research Consortia
type: DatatypeProperty
domain: HMD Submission
description: Identifies Research Consortia Involved.

Treatment
type: Class
description: An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.

Dose Units
type: DatatypeProperty
domain: Treatment
description: Indicates the total dose given in units (e.g. of Gray (Gy) when radiation, Millimeters/24hours for medication)

Setting
type: ObjectProperty
domain: Treatment
description: Indicate the treatment setting, which describes the treatment's purpose in relation to the primary treatment.
range: NCIT C124308

Response to Treatment
type: ObjectProperty
domain: Treatment
description: The patients' response to the applied treatment regimen.
range: http://purl.bioontology.org/ontology/SNOMEDCT/182985004

Biomarker
type: Class
description: TODO

Type
type: ObjectProperty
domain: Biomarker
description: What type is the biomarker classified as.
range: NCIT C164707

Subtype_Molecular
type: ObjectProperty
domain: Biomarker
description: Subtype of the molecular biomarker.
range: FG_0000766

Imaging Study
type: Class
description: The Study IE defines the characteristics of a medical Study performed on a Patient. A Study is a collection of one or more Series of medical images, presentation states, and/or SR documents that are logically related for the purpose of diagnosing a Patient. Each Study is associated with exactly one Patient. A Study may include Composite Instances that are created by a single modality, multiple modalities or by multiple devices of the same modality. The Study IE is modality independent.
RO_0000056: Patient

Imaging Study identifier
type: DatatypeProperty
domain: Imaging Study
description: The user- or equipment-generated identifier of an instance of a DICOM study entity.

Belongs to person
type: ObjectProperty
domain: Imaging Study
description: Reference to the person whom this imaging study is about.

Imaging Technique (Modality)
type: ObjectProperty
domain: Imaging Study
description: Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy.
range: NCIT C17369

Body Region
type: ObjectProperty
domain: Imaging Study
description: Named areas of the body.
range: http://snomed.info/id/52530000

Imaging Procedure
type: ObjectProperty
domain: Imaging Study
description: An imaging procedure as defined by SNOMED CT, representing a specific diagnostic or acquisition procedure (e.g., 'CT of breast', 'MRI of head', or 'Whole Slide Imaging'), rather than the general modality or technique alone. The general modality or technique (e.g., 'CT', 'MR', 'SM') is captured separately in the 'Imaging Technique' field.
range: http://snomed.info/id/15220000

Reason for Imaging Procedure
type: ObjectProperty
domain: Imaging Study
description: The clinical or research rationale for performing the imaging procedure. This field captures why the procedure was indicated for the patient, such as screening, diagnosis, treatment planning, or research purposes. It should express the intent or medical reason, not the technical details of the procedure itself.
range: http://snomed.info/id/138875005

Study Start Date
type: DatatypeProperty
domain: Imaging Study
description: The date on which a study began.

DICOM Series Count
type: DatatypeProperty
domain: Imaging Study
description: The number of DICOM series.

DICOM Images Count
type: DatatypeProperty
domain: Imaging Study
description: The number of DICOM instances in the imaging study.

Affiliated Institution
type: ObjectProperty
domain: Imaging Study
description: The organisation or institution responsible for performing the imaging study.
range: SIO_000688

Imaging Series
type: Class
description: A distinct logical set used to group composite instances. All instances within a Series are of the same modality, in the same Frame of Reference (if any), and created by the same equipment.
SIO_000068: Imaging Study

Series Instance UID
type: DatatypeProperty
domain: Imaging Series
description: A unique identifier for series of images.

Belongs to Imaging Study
type: ObjectProperty
domain: Imaging Series
description: Reference to the parent imaging study of which this series is a part, linking the series to the overall study context.

DICOM Images Count
type: DatatypeProperty
domain: Imaging Series
description: The number of DICOM instances in the imaging study.

Imaging Technique (Modality)
type: ObjectProperty
domain: Imaging Series
description: Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy.
range: NCIT C17369

Imaging Procedure
type: ObjectProperty
domain: Imaging Series
description: An imaging procedure as defined by SNOMED CT, representing a specific diagnostic or acquisition procedure (e.g., 'CT of breast', 'MRI of head', or 'Whole Slide Imaging'), rather than the general modality or technique alone. The general modality or technique (e.g., 'CT', 'MR', 'SM') is captured separately in the 'Imaging Technique' field.
range: http://snomed.info/id/15220000

Series Start Date
type: DatatypeProperty
domain: Imaging Series
description: The date when this imaging series started within the parent study.

Body Region
type: ObjectProperty
domain: Imaging Series
description: Named areas of the body.
range: http://snomed.info/id/52530000

Laterality
type: ObjectProperty
domain: Imaging Series
description: Indicates the side of the body examined within the imaging series. This field specifies whether the imaging procedure focused on the right side, left side, both sides, or an unpaired (midline) structure.
range: http://snomed.info/id/106233006

Imaging Device
type: ObjectProperty
domain: Imaging Series
description: A device for producing a representation or picture, usually of a part of the body, to aid in diagnosis and evaluation.
range: http://snomed.info/id/314789007

Manufacturer of Imaging Device
type: ObjectProperty
domain: Imaging Series
description: The company or organization that produces or supplies an imaging device, such as MRI, CT, X-ray, ultrasound, or whole-slide scanners, used to generate visual representations of anatomical structures or tissue samples for diagnostic, research, or clinical evaluation purposes.
range: OBI_0000835

Software Version
type: ObjectProperty
domain: Imaging Series
description: A form or variant of software; one of a sequence of copies of a software program, each incorporating new modifications.
range: http://snomed.info/id/706687001

Image Instance
type: Class
description: Any record of an imaging event whether physical or electronic.
SIO_000068: Imaging Study
SIO_000068: Imaging Series

Image Instance Identifier
type: DatatypeProperty
domain: Image Instance
description: A sequence of letters, numbers, or other characters that specifically identifies a particular image.

Belongs to Imaging Study
type: ObjectProperty
domain: Image Instance
description: Reference to the parent imaging study of which this image is a part, linking the series to the overall study context.

Belongs to Imaging Series
type: ObjectProperty
domain: Image Instance
description: Reference to the parent imaging series of which this image is a part, linking the series to the overall study context.

Image Instance Date
type: DatatypeProperty
domain: Image Instance
description: The date when this image was generated.

Image Type
type: ObjectProperty
domain: Image Instance
description: Indicates the characteristics and derivation of the image, e.g., whether it is a primary acquisition or a derived image.
range: http://snomed.info/id/363679005