== 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