wiki:ObservMeetings/2012_04_03

Version 1 (modified by Morris Swertz, 13 years ago) (diff)

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Minutes OmicsConnect 2012_04_03

Att: Rob, Joeri, Morris

During the meeting the first prototype and experiences loading data were discussed. This resulted in a long list of issues:

  • Attach existing mrefs via subform

    now, if you have an mref from parent->subform and you [add new] the new entity is not shown because the mref is parentform is not updated

  • mref nulls are not checked
  • DataSource? on chromosome is used to define what genome build the chromosome is in.
  • HotLink? mechanism needs more work (parked for now)
  • We want example data sets for:
    • gwas (SNV, CNV)
    • pheno
    • exome (Rob has example paper for that)
    • protocols
  • We urgently need a TableView?
    • A new module therefore will be created by Joris (other project)
  • StudyAnalysis?

part 1

  • 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)
  • Panel.name -> Panel.identifier
  • remove Panel.ontologyReference
  • We would really like a way to create more filtered OntologyReferences?. Ideally these would be like 'saved filters' as users may have multiple ways to choose their ontology terms.
  • Add user interface to add 'species'
  • We need to link Panel -> other Panel (as subform of Panel) to being able to assemble panels from other panels using some SelectionCriteria?
  • 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:

part 2

  • StudyAnalysisMethod? = "protocols during study" or "used protocols"
  • Field 'name' should become 'identifier' (unique)
    • optionally data model can have human readible names
  • 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)
  • 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)
  • 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)

part 3

  • 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'
  • Accession
    • Many items should have accessions / alternateIds + versions
    • Proposal: central Accession table analogous to OntologyTerm? (we could actually used OntologyTerm?????)
  • 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?
  • Morris will add NGS (Genome of NL) extensions to OmicsConnect
  • 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