Beacon Schema

Draft 4

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OntologyTerm

This object describes how to format fields which contain ontology terms. It is not a queryable entity.

id Ontology term ID using CURIE syntax (SO:0001483).

label This is the "preferred label" for this ontology term (SNV).

Datasets

-A common source of a set of variants, either a knowledgebase or a set of individuals-

datasetId alphanumeric value (internal unique identifier) Dataset reference ID

datasetSource categorical value Reference to dataset source, e.g. “DECIPHER”, “DisGenNET”

datasetType categorical value Type of dataset: “case-level” or “variant-level” (aggregated)

Variants Identification

-The minimal set of fixed attributes identifying a variant. These must be convertible to VRS id, or otherwise VRS id must be provided. With the corresponding mapping table in the backend the response can show also the common names or aliases such as “chromosome 9”-

variantId alphanumeric value (internal unique identifier) Variant id

VRSId alphanumeric value Variant identifier in VRS (If this is provided no other fields need to be filled up, otherwise this will be generated from the other fields).

assemblyId categorical value Genomic assembly accession and version. RefSqeq assembly accession (e.g. “GCG 000001405.39”) or the corresponding versioned Genome Reference consortium Human name (e.g. “GRCh38.p13”).

refseqId categorical value Reference sequence. Refseq ID and version for genomic reference sequence in which variant coordinates are given, e.g. “NC 000009” representing human chromosome 9. Alternatively, alternative names, synonymous or aliases e.g. “Chr9” can be provided if assemblyId is also given. For organisms with a single reference sequence genome, the versioned Refseq ID can be provided here as an alternative to the assembly ID and version in assemblyId, e.g. “NC 045512.2” for SARS-CoV2 full-length genome reference sequence.

start numeric value Start position of variant (1-based)

end numeric value End position of variant (1-based)

ref alphanumeric value Reference sequence in start-end coordinates

alt alphanumeric value Alternative sequence in start-end coordinates

variantType OntologyTerm object Type of variant. Value from Sequence Ontology, e.g. “SNV” (SO:0001483), “structural variant” (SO:0001537)

Variants Annotation

-A set of selected variant annotations from annotation tools, that are more or less fixed, related to the genomic region affected by the variant and its molecular consequence, i.e, if it is a protein -coding variant, if non-synonymous, etc-

variantId alphanumeric value Reference to Variant ID in Variant object

variantAlternativeIds (List of) alphanumeric value (s) Cross-referencing ID(s) (CURIE(s)) for

the variant in the original databases or variant-level (aggregated) databases for previously described variants (e.g. clinVarId, ClinGen, COSMIC), e.g. “VCV000055583.1”, “CA003602”

genomicHGVSId alphanumeric value HGVSId descriptor at genomic level (recommended, referred to genome assembly defined in Variant Identification), e.g. “NC 000017.10:g.41199678C>A”

transcriptHGVSIds (List of) alphanumeric value(s) HGVSId descriptor at transcript level: “NC 000023.10(NM 004006.2):c.357+1G

proteinHGVSIds (List of) alphanumeric value(s) HGVSId descriptor(s) at protein level (for protein-altering variants), e.g. “NP 009225.1:p.Glu1817Ter” or “LRG 199p1:p.Val25Gly” (preferred)

genomicRegions (List of) OntologyTerm object(s) Classification(s) of the vari-

ant according to the genomic region affected (all that apply, relative to each feature affected). Value from Ensembl Glossary (ENSGLOSS) Variant consequence ontology (ENSGLOSSARY:00000134,

e.g. “3UTR” (ENSGLOSSARY:0000159), “coding sequence variant” (ENSGLOSSARY:0000159), “upstream gene variant” (ENSGLOSSARY:0000164), “intergenic variant” (ENSGLOSSARY:0000174), “intron variant” (ENSGLOSSARY:0000161), “non-coding transcript variant” (ENSGLOSSARY:0000163)

genomicFeatures Genomic feature(s) affected by the variant. (List of:)

class OntologyTerm object(s) Class of feature affected by the variant. Value from ENSGLOSS Biotype (ENSGLOSSARY:0000025) ontology, e.g. “protein coding gene”, “non-coding RNA”,“long non-coding RNA”

featureId (alphanumeric value) ID /accession/name of feature affected by the variant, matching class, e.g. “TP53”, “GeneID:43740578”

molecularEffects (List of) OntologyTerm object(s) Predicted effect at nucleotide level for protein affecting variants. Value from Sequence ontology (SO) coding sequence variant (SO:0001580) ontology, e.g. “synonymous variant” (SO:0001819), “nonsynonymous variant” (SO:0001992) (and classifications therein, such as “stop gained” (SO:0001587), “missense variant” (SO:0001583), “inframe indel” (SO:0001820))

aminoacidChanges (List of) categorical value(s) Change at aminoacid level for protein affecting

missense variants e.g. “V304*”

Individuals

-A set of characteristics from the individual from whose Biosample the variant is identified, including demographics, diseases and phenotypic features, treatments, medications and exposures (including behavioural and lifestyle) and along with the individual´s age at these events-

individualId alphanumeric value (internal unique identifier) Individual reference ID

datasetId alphanumeric value Reference to dataset ID

taxonId alphanumeric value Taxon ID of Individual, e.g. “9606”

sex OntologyTerm object Sex of Individual. Value from NCIT General Qualifier ontol- ogy (NCIT:C27993): ”UNKNOWN” (not assessed or not available) (NCIT:C17998), ”FEMALE” (NCIT:C46113), ”MALE” (NCIT:C46112) or ”OTHER SEX” (NCIT:C45908)

ethnicity OntologyTerm object Ethnic background of Individual. Value from NCIT Race ontology (NCIT:C17049). e.g. “Latin American” (NCIT:C126531)

geographicOrigin OntologyTerm object Individual’s country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. “United States of America” (GAZ:00002459)

phenotypicFeatures Phenotypic feature(s) observed in the Individual, defined by phenotype, date, type or age of onset and level/ severity. (List of:)

phenotypeId OntologyTerm object Phenotypic feature observed. Value from Human Phenotype Ontology (HPO)

dateOfOnset alphanumeric value (ISO8601 date format) Date of onset/observation of phenotype, e.g. “2010-07-10”

onsetType OntologyTerm object Onset type. Value from HPO Onset ontology (HP:0003674), e.g. “congenital onset” (HP:0003577), “adult onset” (HP:0003581)

ageAtOnset Individual’s age at onset/observation of phenotype

age alphanumeric value (ISO8601 duration format) Age, e.g. “P32Y6M”

ageGroup OntologyTerm object Age group. Value from NCIT Age Group ontology, e.g. ”NCIT:C27954” (Adolescent)

level/severity OntologyTerm object Level/severity when and as applicable to phenotype observed. Value from Human Phenotype Ontology (HPO) Severity ontology (HP:0012824), e.g. “severe” (HP:0012828)

diseases Disease(s) been diagnosed to the Individual, defined by disease ID, date, type or age of onset, stage, level/severity and the presence of family history. (List of:).

diseaseId OntologyTerm object Disease ID. Value from ICD10 disease codes or ontology terms from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. “lactose intolerance” (HP:0004789)

ageOfOnset Individual’s age at onset/ diagnosis of disease

age alphanumeric value (ISO8601 duration format) Age, e.g. “P6M”

ageGroup OntologyTerm object Age group. Value from NCIT Age Group ontology, e.g. “NCIT:C27954” (Adolescent)

dateOfOnset alphanumeric value (ISO8601 date format) Date of onset of disease/ disease symptoms, e.g. “1987-10-25”

onsetType OntologyTerm object Onset type. Value from HPO Onset ontology (HP:0003674), e.g. “congenital onset” (HP:0003577), “adult onset” (HP:0003581)

dateAtDiagnosis alphanumeric value (ISO8601 date format) Date of diagnosis of disease, e.g. “1987-10-28”

stage OntologyTerm object Stage of disease. Value from Ontology for General Medical Science or Disease Stage Qualifier ontology (NCIT:C28108), e.g. “acute onset” (OGMS:0000119)

level/severity OntologyTerm object Level/severity when and as appli- cable to disease course. Value from Human Phenotype Ontology (HPO) Severity ontology (HP:0012824), e.g. “mild” (HP:0012825)

familyHistory boolean Presence of determined or self-reported presence of family history of the disease

treatments Treatment(s) or Medication(s) been prescribed/administered to Individual, defined by treatment ID, date and age of onset, dose, schedule and duration. (List of:)

treatmentId OntologyTerm object Treatment ID. Value from NCIT Drug, Food, Chemical or Biomedical Material, e.g. “COVID-19 Vaccine” (NCIT:C173023)

treatmentRoute OntologyTerm object Route of treatment. Value from NCIT Route of Administration ontology, e.g. “Parenteral Route of Administration” (NCIT:C38291)

TreatmentStartDate alphanumeric value (ISO8601 duration format) Date of the beginning of treatment

TreatmentEndDate alphanumeric value (ISO8601 duration format) Date of the end of treatment

ageAtTreatment Individual’s age at the beginning of treatment

age alphanumeric value (ISO8601 duration format) Age

ageGroup OntologyTerm object Age group. Value from NCIT Age Group ontology, e.g. “Adolescent” (NCIT:C27954)

treatmentDose Treatment dose

doseValue numeric value Quantity value of Dose

doseUnits OntologyTerm object Treatment dose units. Value from Units of measurement Ontology (UO)

schedule OntologyTerm object Treatment schedule. Value from NCIT Schedule Frequency ontology, e.g “weekly” (NCIT:C67069)

duration alphanumeric value (ISO8601 duration format) Treatment duration

interventions Intervention(s) been practiced on Individual, defined by intervention ID), date and age at intervention (List of:)

interventionId OntologyTerm object Intervention ID. Value from Medical Action Ontology or code from OPCS Classifications of Interventions and Procedures.

modifier Modifier of the intervention. Value from TBD.

interventionDate alphanumeric value (ISO8601 date format) Date of intervention

ageAtIntervention Individual’s age at the date of intervention, as age or age range

age alphanumeric value (ISO8601 duration format) Age

ageGroup OntologyTerm object Age group value, from NCIT Age Group ontology, e.g. “NCIT:C27954” (Adolescent)

measures Measures(s) been taken from Individual, defined by measure ID, date and/or age at measurement, unit and value. (List of:)

measureId OntologyTerm object Measure ID. Value from Clinical Measurement ontology (CMO), e.g. “waist circumference” (CMO:0000242)

measureQuantity

measureValue numeric value Quantity value of measurement, e.g. 90

measureUnit OntologyTerm object Measure units. Value from Units of Measurement Ontology (UO), e.g. “centimeter” (UO:0000015)

modifier Modifier of the measurement. Value from TBD.

measureDate alphanumeric value (ISO8601 date format) Date of measurement

ageAtMeasure Individual’s age at the date of measurement, as age or age range

age alphanumeric value (ISO8601 duration format) Age

ageGroup OntologyTerm object Age group value, from NCIT Age Group ontology, e.g. “NCIT:C27954” (Adolescent)

exposures Exposures(s) occurred to or practiced (lifestyle, behavioural exposures) by Individual, defined by exposure ID, date and age at exposure, dose, schedule and duration. (List of:)

exposureId OntologyTerm object Intervention ID. Value from Environment Exposure Ontology.

exposureDose Exposure dose

doseValue numeric value Quantity value of exposure, e.g. 1

doseUnit OntologyTerm object Exposure units. Value from Units of Measurement Ontology (UO), e.g. “becquerel” (UO:0000132)

modifier Modifier of the exposure. Value from TBD. e.g frequency

exposureDate alphanumeric value (ISO8601 duration format) Date of exposure

ageAtExposure Individual’s age at the date of exposure, as age or age range

age alphanumeric value (ISO8601 duration format) Age

ageGroup OntologyTerm object Age group value, from NCIT Age Group ontology, e.g. “NCIT:C27954” (Adolescent)

exposureDuration alphanumeric value (ISO8601 duration format) Exposure duration, e.g.“P3Y6M4DT12H30M5S”

pedigrees Pedigree(s) to which the Individual belongs. (List of:)

pedigreeId alphanumeric value Reference to pedigree ID (internal unique identifier)

pedigreeDisease OntologyTerm object Disease ID. Value from ICD10 disease codes or disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. “lactose intolerance” (HP:0004789)

pedigreeRole OntologyTerm object Pedigree role, defined as relation- ship to proband. Value from Family member ontology (NCIT:C41256), e.g. “proband” (NCIT:C64435), “identical twin” (NCIT:C73429), “mother” (NCIT:C25189)

affectedStatus OntologyTerm object Health status of Individual regarding the pedigree disease. Value from HPO Health Status ontology (HP:0032319)

numOfSubjects numeric value Number of subjects in pedigree

Biosamples

-A set of characteristics from the Biosample where the variant is identified, including anatomical origin, obtention procedure and the age of the individual at sample collection-

biosampleId alphanumeric value (internal unique identifier) Biosample reference ID

individualId Reference to Individual ID

description free text Any relevant info about the biosample that does not fit in any field in the schema

biosampleStatus OntologyTerm object Classification of biosample based on their

role in study. Value from Experimental Factor Ontology (EFO) Material Sample ontology (OBI:0000747) Classification of the sample in ”abnormal sample ”(EFO:0009655) or ”reference sample” (EFO:0009654)

collectionDate alphanumeric value (ISO8601 date format) Date of biosample collection, e.g. “2019-12-01’”

subjectAgeAtCollection alphanumeric value (ISO8601 duration format) Individual’s age at the time of biosample collection, e.g. “P72Y6M19D”

sampleOriginDescriptors Descriptor(s) of origin of biosample. (List of:)

sampleOriginType OntologyTerm object Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology, e.g. “specimen from organism” (OBI:0001479), “xenograft” (OBI:0100058), “cell cul-

ture” (OBI:0001876), “cell specimen” (OBI:0001468), “environmental swab specimen” (OBI:0002613)

sampleOriginDetail OntologyTerm object Specific instance of sample origin matching the category set in sampleOriginType. Value from Uber-anatomy ontology (UBERON) or BRENDA tissue / enzyme source (BTO), Ontology for Biomedical Investi- gations (OBI) or Cell Line Ontology (CLO), e.g. “cerebellar vermis” (UBERON:0004720), “HEK-293T cell” (BTO:0002181), “nasopharyngeal swab specimen” (OBI:0002606), “cere- brospinal fluid specimen” (OBI:0002502)

obtentionProcedure OntologyTerm object Ontology ID from NCI Thesaurus (NCIT) Intervention or Procedure (NCIT:C25218) ontology. e.g. “biopsy” (NCIT:C15189)

cancerFeatures Values specifying cancer-specific features, including progression and tumor grade

tumorProgression OntologyTerm object Descriptor of tumor progression. Value from Neoplasm by Special Category ontology (NCIT:C7062). Tumor progression category indicating primary, metastatic or recurrent progression e.g.“Primary Malignant Neo- plasm” (NCIT:C84509)

tumorGrade OntologyTerm object Tumor grading. Value from Tumor Grading Characteristic ontology (Mondo Disease Ontology MONDO:0024488), e.g. “Grade 3” (MONDO:0024493)

Experiments

-A set of parameters describing the sequencing experiment carried on the Biosample and leading to the variant identification-

experimentId alphanumeric value (internal unique identifier) Run reference ID

biosampleId alphanumeric value Reference to Biosample ID

experimentDate alphanumeric value (ISO8601 date format) Date at which run was performed , e.g. “2019-12-28”

librarySource categorical value Sequencing library source, e.g. “Metagenomic”, “Viral RNA”

libraryStrategy categorical value Sequencing library strategy, e.g. “WGS”

librarySelection categorical value Selection method for sequencing library preparation, e.g. “RANDOM”, “RT-PCR”

libraryLayout categorical value Sequencing library layout, e.g. “PAIRED”, “SINGLE”

platform categorical value Sequencing technology, e.g. “Illumina”, “Oxford Nanopore Technologies”

platformModel categorical value Sequencing platform model, e.g. “Illumina MiSeq”, “GridION”

Analyses

-A set of parameters describing the bioinformatic analysis carried on the sequencing raw data from the Experiment leading to the variant identification-

analysisId alphanumeric value (internal unique identifier) Analysis reference ID

experimentId alphanumeric value Reference to Experiment ID

analysisDate alphanumeric value (ISO8601 date format) Date at which analysis was performed, e.g. “2020-01-10”

pipelineName categorical value Analysis pipeline and version, e.g., “Isaac Whole Genome Sequencing; version 3.0.0.0”

pipelineRef url Link to Analysis pipeline resource

aligner categorical value Mapping/Alignment software e.g. “bwa-0.7.8”

variantCaller categorical value Variant calling software/ pipeline, e.g. “GATK4.0”

Variants Finding

-A set of parameters describing the findings associated to the variant identification in the study-

variantId alphanumeric value Reference to Variant ID

analysisId alphanumeric value Reference to Analysis ID

biosampleId alphanumeric value Reference to Biosample ID

variantFrequency numeric value Variant/allele frequency in biosample, when applicable (tumors and other complex samples)

zigosity OntologyTerm object Zigosity in which variant is present in the sample, when applicable (diploid organisms)

Value from the Zigosity Ontology (GENO:0000133), e.g. “heterozygous” (GENO:0000135)

alleleOrigin OntologyTerm object Allele origin of variant in sample. Value from the Variant Origin (SO:0001762), e.g. “somatic variant”, “germline variant”, “de novo variant”.

phenotypicEffects Effect(s) of variant on phenotype, as determined in the study. (List of:)

phenotypeId OntologyTerm object Descriptor of phenotype found associated to variant in the present study. Value from Human Phenotype Ontology (HPO)

phenotypeEffect OntologyTerm object Phenotypic effect classification determined in the present study. Value from Sequence types and features ontology (SO) variant phenotype (SO:0001769), e.g. “quantitative variant” (SO:0001774)

evidenceType OntologyTerm object Type of evidence supporting variant-phenotype association from the Evidence & Conclusion Ontology (ECO), e.g. “experimental evidence”

clinicalRelevances Effect(s) of variant on disease, as determined in the study. (List of:)

diseaseId OntologyTerm object Descriptor of disease associated. Value from ICD10 disease codes or ontology terms from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. “lactose intolerance” (HP:0004789)

clinicalEffect OntologyTerm object Clinical effect classification. Value from Sequence types and features ontology (SO) variant phenotype (SO:0001769), e.g. “disease causing variant” (SO:0001772)

evidenceType OntologyTerm object Type of evidence supporting variant- disease association from the Evidence & Conclusion Ontology (ECO), e.g. “experimental evidence”

qualityParameters:

vcfQual numeric value Value from VCF column “QUAL”. Set to -1 if not present.

vcfPass boolean Value from the VCF column “FILTER”. Zero (0) for all values that are not equal to ‘PASS’ and one (1) for those equal to ‘PASS’.

vcfDP numeric value Value for the alleles (ref + alt) read depth coming from the field “DP” on VCF’ samples columns (i.e., each sample will have one DP value). Note that this field is not mandatory and will be set to -1 if not present.

Variants Evidence

-(For variant-level datasets, where the variant information comes from Knowledgebases or other evidence sources as opposed to a Biosample). A set of parameters describing the knowledge about the variant and its provenance-

variantId alphanumeric value Reference to Variant ID

datasetId alphanumeric value Reference to dataset ID source of variant interpretation

phenotypicEffects Annotated effect(s) of variant on any phenotypic feature other than a disease. (List of:)

phenotypeId OntologyTerm object Descriptor of phenotype associated. Value from Human Phenotype Ontology (HPO)

phenotypeEffect OntologyTerm object Phenotypic effect classification. Value from Sequence types and features ontology (SO) variant phenotype (SO:0001769), e.g. “benign variant” (SO:0001770)

alleleOrigin (List of) OntologyTerm object(s) Annotation(s) on allele origins in which the variant has been found in association to phenotype. Value(s) from Se- quence types and features ontology (SO) variant origin (SO:0001762) ontology, e.g. “somatic variant” (SO:0001777), “germline variant” (SO:0001778), “de novo variant” (SO:0001781)

references (List of) publication identifier(s) Reference(s) to publication(s) describing association, as PMID(s), e.g. “PMID:17024373”

clinicalRelevances Annotated effect(s) of variant on disease. (List of:)

diseaseId OntologyTerm object Disease. Value from ICD10 disease codes or ontology terms from disease ontologies such as HPO, OMIM, Orphanet, MONDO. e.g. “lactose intolerance” (ICD10CM:E73)

clinicalEffect OntologyTerm object Clinical effect classification. Value from Sequence types and features ontology (SO) variant phenotype (SO:0001769), e.g. “disease associated variant” (SO:0001771)

alleleOrigin (List of) OntologyTerm object(s) Annotation(s) on allele origins in which the variant has been in association to condition. Value(s) from Sequence types and features ontology (SO) variant origin (SO:0001762) ontology, e.g. “somatic variant” (SO:0001777), “germline variant” (SO:0001778), “de novo variant” (SO:0001781)

references (List of) publication identifier(s) Reference(s) to publication(s) describing association, as PMID(s), e.g. “PMID:19793655”

Interactors

-A set of characteristics describing an organism/agent whose phenotypic data is collected in association with the Individual, but which is not the sequenced/genotyped Individual itself. This block accounts for the ’extended phenotype’ of variants in organisms/agents other than the one harboring them-

interactorId alphanumeric value (internal unique identifier) Interactor organism/ agent reference ID (external accession or internal ID)

relationType OntologyTerm object Type of relation with Individual. Value from Infectious disease Ontology(IDO), e.g. “host” (IDO:0000531), “commensal” (IDO:0000525), “infectious agent” (IDO:0000596)

[... ] All the rest of objects from Individual

Cohorts (link to Cohort schema doc)

-A set of characteristics describing a cohort, that is defined as a set of individuals that can belong to one or more Datasets-

cohortType categorical value Cohort type by its definition. One of: ´study-defined´, ´beacon-defined´ or ´user-defined´. If a cohort is declared ´study-defined´ or ´beacon-defined´, criteria are to be entered in cohortInclusionCriteria; if a cohort is declared ‘user-defined’ cohortInclusionCriteria will be automatically populated from the parameters used to perform the query.

cohortId alphanumeric value (internal unique identifier) Cohort identifier. For ´study-defined´ or ´beacon-defined´cohorts this field is set by the implementer. For ´user-defined´ this unique identifier could be generated upon the query that defined the cohort, but could be later edited by the user

cohortName alphanumeric value Cohort name. For ´user-defined´ this field could be generated upon the query, e.g. a value that is a concatenation or some representation of the user query

cohortInclusionCriteria Inclusion criteria. For ´beacon-defined´cohorts, cohorts matching the whole dataset will not apply criteria for if cohorts are subsets of Datasets the criteria used to defined them can be added in these fields). (List of:)

cohortLocations (List of) OntologyTerm object(s) Geographic location(s) in cohort inclusion criteria

cohortGenders (List of) OntologyTerm object(s) Gender(s) in cohort inclusion criteria

cohortEthnicities (List of) OntologyTerm object(s) Ethnicity(ies) in cohort criteria

cohortDiseases (List of) OntologyTerm object(s) Disease(s) in cohort inclusion criteria

cohortPhenotypicFeatures (List of) OntologyTerm object(s) Phenotypic feature(s) in in cohort inclusion criteria

cohortAgeRange Individual age range in cohort inclusion criteria

start alphanumeric value (ISO8601 duration format) Min age accepted in cohort criteria

end alphanumeric value (ISO8601 duration format) Max age accepted in cohort criteria

cohortExclusionCriteria Exclusion criteria. Same structure as cohortInclusionCriteria

cohortLicense TBD

cohortRight TBD

cohortContact TBD

cohortSize integer Count of unique Individuals in cohort (individuals meeting criteria for ´user-defined´ cohorts). If not previously known, it could be calculated by counting the individuals in the cohort.

cohortDataTypes Data types available from the Cohort. (List of:)

dataType OntologyTerm object Data types included in cohort (GECKO, e.g. Genomic data (GECKO:0000032), Clinical Measurements (CMO:0000000), Lifestyle (GECKO:0000067), etc.

num paired to id field, number of individuals with this data type in the cohort

collectionEvents Collection events/ data points (List of:)

collectionEvent

eventNum numeric value Cardinality of the collection event/data point in a series

eventDate ISO8601 date and time format date of collection event/data point.

eventTimeline Aggregated information of dates of visit/diagnostic/inclusion in study obtained from individual level info in database. Will coincide with collection event date for multi-time

start alphanumeric value (ISO8601 date format) Earliest date of event

end alphanumeric value (ISO8601 date format) Latest date of event

eventSize numeric value Count of individuals in cohort at data point (for ´user-defined´ cohorts, this is individuals meeting criteria) obtained from individual level info in database.

eventCases numeric value count of cases

eventControls numeric value Count of controls

eventLocations Aggregated information of geographic location obtained from individual level info in database.

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]

eventGenders (Aggregated information of gender(s) obtained from individual level info in database.

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]

eventEthnicities Aggregated information of ethnicity obtained from individual level info in database.

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]

eventAgeRange Individual age range, obtained from individual level info in database

start: alphanumeric value (ISO8601 duration format) Min age in collection event

end alphanumeric value (ISO8601 duration format) Max age in collection event

eventDiseases Aggregated information of disease/condition(s) obtained from individual level info in database.

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]

eventPhenotypes (GECKO disease or disorder: MONDO:0000001) Aggregated information of phenotype(s) obtained from individual level info in database.

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]

eventDataTypes (List of:) Aggregated data type information available for each cohort data type as declared in cohort_data types, and obtained from individual level info

availability boolean Data availability

availabilityCount numeric value Count of individuals with data available

distribution (List of:) [unique values in field, count]