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"
  • todo: remove OntologyReference?
  • todo: create better protocol editor (mref is confusing)
• 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