OmicsConnect wiki

This page reports current issues and plans with omicsconnect, an extension on top of Observ.

NB this document formatted in trac wiki format, so we can include it online. Syntax:

• unsolved issues
• solved issues

  comments

showstoppers

• mrefs master/detail forms don't behave well. Examples:
  • adding new citations for study.
  • adding new measurement to protocol

discussion items

• Phenotype method <-> protocol / measurement
• Who does contribution: Person or an PersonAffiliation??

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
• 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 (?)

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?

checklist of requirements

• study and person should have qualified 'contribution' denoting 'role' in study
• both study and data sets can be submissions (what else?)
• submission can have contributions (== role in submission)
• person can have more than one affiliation, how does that relate to role?
• remove fax and phone
• study design should come from an ontology
• need a way to link panels (e.g. sample panel, assayed panel)
• hotlinks to see only hotlinks related to a specific element, e.g only see experimental specific hotlinks in experiments?

FAQ

Q: Where do I add panel specific information e.g. population information, number of males/females, Geographical location

A: these are a ProtocolApplication? having panel as target

Q: where to add species?

A: species are special kind of ontology term