wanted entities

Domain model:

observation

• Characteristic: 'is a' or 'has a' statements about an object
• ObservableFeature?: characteristic observed (is/has) or question asked (what is?)
  • Measurement: feature defined by description, unit, dataType, permittedValue
  • PermittedValue?: a categorical value state for Measurement
• ObservationTarget?: target of observation
  • Individual: ObservationTarget? consisting of one individual
  • Panel: ObservationTarget? consisting of group of individuals
• Protocol: procedure of observation on a defined set of features
  • discussion: many-to-many OR xref relation with Feature?
  • see PhenotypeMethod? discussion
• ProtocolApplication?: one bundle of values for exactly one target
  • xref to ObservationTarget? (e.g. Individual, but also SNP)
  • xref to Protocol
  • discussion: xref to DataSet??
• Observation: value relation between ProtocolApplication? and ObservableFeature?
  • xref to ProtocolApplication?
  • xref to ObservableFeature?
  • (no xref to Target, this is via ProtocolApplication?)

organization

• Study: a bundle of experiments typically published in a paper
  • discussion: bundle of Experiment, i.e. StudyElement??
• Experiment: a story of experimental objectives and outcomes
  • discussion: refers to dataSets?
• DataSet?: a group of ProtocolApplication?
  • discussion: homogeneous (i.e. using one protocol only?)
• SelectionCriteria?: conditions of relationship between Panel
  • xref to Source and Target panel
  • has: number of individuals, details
  • discussion: how to formalize

attribution

• Contact: an entity having contact details such as address
• Person: to refer to natural actors in the process
• Organization: organization actor, Can this also be a used when we need to acknowledge a funder?
• PersonAffiliation?: association between individual and Organization
• Submission: the event of data contribution
  • dicussion: what are Submissable items? I.e. can have Contribution
• Contribution: metadata describing Role of Person in a Study (?)
• Licences: Can we use CC licences, attach to Study Details or Data sets?

references

• Hotlinks: hyperlinks to external? Or internal?
• Citation: literature reference
  • discussion: what entities can have references?
• OntologyReference?: reference to coding lists
  • Species: reference to species definitions
• AlternateIds?: alternative identifiers
• FeatureAnnotion?: qualitative association between Feature and OntologyTerm?
  • has 'exactmatch' and 'description'

genome

• SequenceCharacteristic?
  • Marker: genomic variable site
  • Allele: alternative alleles of marker
  • Genotype: valid genotypes for a marker
• SequenceRelation?

gwas central specific

• FrequencyCluster?
  • can be modelled as Protocol?
• GenotypeFrequency?
  • can be modelled as Protocol?
• AlleleFrequency?
  • can be modelled as Protocol?
• SamplePanel?
  • is a Panel with panelType=SamplePanel??
  • is a Panel with panelType=AssayedPanel??
• UsedMarkerset?
  • can be modelled as Protocol? or DataSet??
• EffectSize?
  • can be modelled as Protocol?