Daphne Stemkens <d.stemkens@vsop.nl> Esther van Enckevort <e.j.van.enckevort@rug.nl> FAIR Genomes Consortium Gurnoor Singh <gurnoor1990@gmail.com> Jeroen A.M. Beliën <jam.belien@amsterdamumc.nl> K. Joeri van der Velde <k.j.van.der.velde@umcg.nl> Mariëlle E. van Gijn <m.e.van.gijn@umcg.nl> Morris A. Swertz <m.a.swertz@umcg.nl> Peter A.C. 't Hoen <peter-bram.thoen@radboudumc.nl> Rajaram Kaliyaperumal <R.Kaliyaperumal@lumc.nl> XiaoFeng Liao <XiaoFeng.Liao@radboudumc.nl> 2022-02-28 The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. en 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). FAIR Genomes metadata schema Attribution 4.0 International (CC BY 4.0) 1.2-Minor Reference to the sequencing that was performed, i.e. the source on which this analysis was based. Belongs to sequencing Reference to the person whom this clinical information is about. Belongs to person 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. Consent form used Reference to the person (i.e. subject) to whom this individual consent applies. Person consenting 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 diagnosis Reference to the person from whom this material was collected. Collected from person Reference to the study or studies in which this person participates. Participates in study Reference to the source material from which this sample was prepared. Belongs to material Reference to the prepared sample, i.e. the source that was sequenced. Belongs to sample 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). Abstract data location Any used problem-solving procedures implemented in software to be executed by a computer. Algorithms used A unique proper name or character sequence that identifies this particular analysis. Analysis identifier 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 deviation 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 used 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 data location The rationale for why a deviation from the bioinformatic protocol has occurred. Reason for bioinformatic protocol deviation 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. WGS guideline followed The age, measured from some defined time point (e.g. birth) at which a patient is diagnosed with a disease. Age at diagnosis Age of the patient at the moment of the most recent screening. Age at last screening Age of onset of clinical manifestations related to the disease of the patient. Age of onset A unique proper name or character sequence that identifies this particular clinical examination. Clinical identifier Information on whether the patient is a child from two family members who are second cousins or closer. Consanguinity The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration. Drug regimen First contact of the patient with a specialised center in context of disease or study inclusion. First contact Patient's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF). Functioning This diagnosis c.q. clinical examination is based on one or more sampled materials. Material used in diagnosis Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved. Molecular diagnosis other 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. Data use specification A unique proper name or character sequence that identifies this particular signed individual consent. Individual consent identifier A date specification that designates when this individual consent form was signed. Signing date Starting date of the validity of this individual consent. Valid from End date of the validity of this individual consent. Valid until Date of acceptance of this consent form. Consent form accepted date 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 identifier A title or name given to this consent form. Consent form title End date of the validity of this consent form. Consent form valid until The version, edition, or adaptation of this consent form. Consent form version A point or period of time associated with the publication of this leaflet that belongs to this consent form. Leaflet date A title or name given to the leaflet that belongs to this consent form. Leaflet title The version, edition, or adaptation of this leaflet that belongs to this consent form. Leaflet version Indicate if this material was produced from or related to another. Derived from The date beyond which this material is no longer regarded as fit for use. Expiration date A unique proper name or character sequence that identifies this particular material. Material identifier The percentage of tumor cells compared to total cells present in this material. Percentage tumor cells 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). Physical location The rationale for why a deviation from the sampling protocol has occurred. Reason for sampling protocol deviation Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled. Registration timestamp The procedure whereby this material was sampled for an analysis. Sampling protocol 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 protocol deviation Date and time at which this material was collected. Sampling timestamp The age at which death occurred. Age at death A unique proper name or character sequence that identifies this particular person. Personal identifier The year in which this person was born. Year of birth Amount of input material in nanogram (ng). Input amount 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 insert size The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process. Intended read length 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. PCR free A unique proper name or character sequence that identifies this particular sample preparation. Sampleprep identifier 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. UMIs present The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced. Median read depth 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. Observed insert size The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process. Observed read length 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. Other quality metrics 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 Q30 Percentage of the target sequence on which 20 or more unique reads were successfully mapped. Percentage TR20 Date on which this sequencing assay was performed. Sequencing date A unique proper name or character sequence that identifies this particular nucleic acid sequencing assay. Sequencing identifier 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. Completion date An email address for the purpose of contacting the study contact person. Contact information A statement or piece of writing that provides details on this study. Description A unique proper name or character sequence that identifies this particular study. Identifier A name that designates this study. Name The principal investigator or responsible person for this study. Principal investigator The date on which this study began. Start date 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. Study design Analysis An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. Analysis Clinical Findings and circumstances relating to the examination and treatment of a patient. Clinical Individual_consent 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. Individual consent Leaflet_and_consent_form 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 and consent form Material A natural substance derived from living organisms such as cells, tissues, proteins, and DNA. Material Personal Data, facts or figures about an individual; the set of relevant items would depend on the use case. Personal Sample_preparation A sample preparation for a nucleic acids sequencing assay. Sample preparation Sequencing The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. Sequencing Study A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts. Study 1.2-Minor Daphne Stemkens <d.stemkens@vsop.nl> Esther van Enckevort <e.j.van.enckevort@rug.nl> FAIR Genomes Consortium Gurnoor Singh <gurnoor1990@gmail.com> Jeroen A.M. Beliën <jam.belien@amsterdamumc.nl> K. Joeri van der Velde <k.j.van.der.velde@umcg.nl> Mariëlle E. van Gijn <m.e.van.gijn@umcg.nl> Morris A. Swertz <m.a.swertz@umcg.nl> Peter A.C. 't Hoen <peter-bram.thoen@radboudumc.nl> Rajaram Kaliyaperumal <R.Kaliyaperumal@lumc.nl> XiaoFeng Liao <XiaoFeng.Liao@radboudumc.nl> 2022-02-28 The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. en 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). FAIR Genomes metadata schema Attribution 4.0 International (CC BY 4.0) 1.2-Minor 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 formats stored The specific build of the human genome used as reference for sequence alignment and variant calling. Reference genome used A diagnosis made from a study of the signs and symptoms of a disease. Clinical diagnosis 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 affected Family members related by descent rather than by marriage or law who were also tested by next-generation sequencing. Family members sequenced A record of a person's background regarding health, occurrence of disease events and surgical procedures. Medical history 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. Medication Gene affected by pathogenic variation that is causal for disease of the patient. Molecular diagnosis gene The outward appearance of the individual. In medical context, these are often the symptoms caused by a disease. Phenotype Types of phenotypic data collected in a clinical setting that is potentially available upon request. Phenotypic data available Phenotypes or symptoms that were looked for but not observed, which may help in differential diagnosis or establish incomplete penetrance. Unobserved phenotype The procedure of recontacting the patient for specified reasons. This means the patient agrees to be re-identifiable under those circumstances. Allow recontacting Indicates the institute who performed the collection act. Collected by 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 modifiers 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. Data use permissions 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. Represented by Indicates the authoritative body who brought this consent form into existence. Consent form creator Reports the existence of any analyses performed on this material other than genomics (e.g. transcriptomics, metabolomics, proteomics). Analyses performed Biological entity that constitutes the structural organization of an individual member of a biological species from which this material was taken. Anatomical source The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. Biospecimen type The pathological state of the tissue from which this material was derived. Pathological state The conditions under which this biological material was stored. Storage conditions Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data. Ancestry The country that this person was born in. Country of birth Country of residence at enrollment. Country of residence 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 at birth 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. Gender identity A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. Genotypic sex An indicator that provides information on the current health status of this person. Inclusion status The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of this person. Primary affiliated institute 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. Resources in other institutes 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. Library preparation kit 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. Target enrichment kit The used product name and model number of a manufacturer's genomic (dna) sequencer. Sequencing instrument model Method used to determine the order of bases in a nucleic acid sequence. Sequencing method The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment). Sequencing platform The conditions which, if met, make an person eligible for participation in this study. Inclusion criteria