wiki:ObservMeetings/2012_04_03

Minutes OmicsConnect 2012_04_03

Att: Rob, Joeri, Morris

During this meeting the first prototype and experiences loading data were discussed. (source: molgenis_apps/build_omicsconnect.xml)

This resulted in a long list of issues:

References

  • Accession and accession version is confusing
    • Proposed solution: use OntologyTerm? table (or similar) to manage all accessions centrally.
  • PrimaryCitation? -> update label to use not id but something more meaningful (what exactly? pubmedid? nice would be 'Adamusiak et al (2011) Human Mutation)
  • Accession
    • Many items should have accessions / alternateIds + versions
    • Proposal: central Accession table analogous to OntologyTerm? (we could actually used OntologyTerm?????)

Panel

  • DONE: Panel.name -> Panel.identifier
  • DONE: remove Panel.ontologyReference (replaced with panelType)
  • Add user interface to add 'species'
  • DONE: We PanelSources? entity to being able to assemble panels from other panels using some selectionCriteria

Study organization

  • link Contributions <-> Study is missing (as consequence all contributions are shown)
  • Need more types of contribution types/roles
    • multiple roles (author, design, grant holder)
    • multiple affiliations
    • Action:
  • StudyAnalysisMethod? = "protocols during study" or "used protocols"
  • Field 'name' should become 'identifier' (unique)
    • optionally data model can have human readible names
  • Citation.publicationStatus should be xref->OntologyTerm?
  • Experiment.design should be xref->OntologyTerm?
  • DataSet?.protocolParameters
    • Discussion: proposal to remove and instead refer to the Protocol (that has parameters)

Protocols and Measurement

  • Do we really need Measurement? Can we not just use ObservableFeature? directly?
  • Measurement gets lost when adding to subform of Protocol
    • this is the mref issue mentioned above
  • Measurement should not have direct xref to study, because
    • Study uses Protocol (multiple studies may)
    • Protocol uses Measurement (so indirectly the link is there)
  • Protocol.features -> rename to Protocol.parameters as it is confusing
  • Protocol.circumstances -> unclear, remove (people can use parameters instead?)
  • Hotlink
    • Still unclear on how to generalize; for now just apply to Study
  • UsedMarkerset?
    • remove link to Study (because already links to Experiment)
    • Discussion: lookup label is now (Study_name:Experiment_name)

GWAS specific

  • Significances + Frequencies
    • Change superclass (these are NOT ProtocolApplication?)
    • Discussion if we can remove and instead use DataSet?
    • Are these part of a DataSet? i.e. a particular kind of data set?
    • Changer marker to be xref (instead of text)
    • remove odds ration and attr risk
  • PhenotypeProperty? (is confusing compared to Measurement)
    • Property = Measurement?
    • Method = Protocol
    • More discussion needed? Would be nice to merge PhenotypeProperty? with Measurement.
  • Chromosome
    • remove xref to study
    • add 'autosomal'
    • add 'order number'
  • Marker
    • remove 'label'
    • add c.dna and pdna notation?
    • residues and alleleSequence are same thing (remove alleleSequence)
    • validationCode should be xref->OntologyTerm?
    • remove 'added from source build'
    • should alleles be stored elsewhere (see Allele table)?
  • PermittedGenotypes?
    • residue-info
    • what is 'locgroup' (chado heritance)
    • what is 'target' (confusing because we use it in other meaning)

Actions

  • Joeri will add xQTL extensions to OmicsConnnect?
  • [DONE] Morris will add NGS (Genome of NL) extensions to OmicsConnect
  • [Never DONE] Morris will process as far as he can todos from this meeting in the model
  • Rob will integrate citation lookup (of gwascentral curation tool) to OmicsConnect
  • Later: discuss contribution model with Mummy, in particular issue on how to deal with affiliations/roles
  • All: create / get example data!
  • All: create / get example data!
Last modified 12 years ago Last modified on 2012-04-23T08:49:36+02:00